Barry Pogson

Deconvoluting apocarotenoid‐mediated retrograde signaling networks regulating plastid translation and leaf development

Publisher: Wiley

Date: 03-2021

DOI: 10.1111/TPJ.15134

A mutation in the purine biosynthetic enzyme ATASE2 impacts high light signalling and acclimation responses in green and chlorotic sectors of Arabidopsis leaves

Publisher: CSIRO Publishing

Date: 2011

DOI: 10.1071/FP10218

Abstract: In this report, we investigate the altered APX2 expression 13 (alx13) mutation of Arabidopsis thaliana, a mutation in glutamine phosphoribosyl pyrophosphate amidotransferase 2 (ATASE2), the primary isoform of the enzyme mediating the first committed step of purine biosynthesis. Light-dependent leaf variegation was exhibited by alx13 plants, with partial shading of alx13 rosettes revealing that the development of chlorosis in emerging leaves is influenced by the growth irradiance of established leaves. Chlorotic sectors arose from emerging green alx13 leaves during a phase of rapid cell ision and expansion, which shows that each new cell’s fate is independent of its progenitor. In conjunction with the variegated phenotype, alx13 plants showed altered high light stress responses, including changed expression of genes encoding proteins with antioxidative functions, impaired anthocyanin production and over-accumulation of reactive oxygen species. These characteristics were observed in both photosynthetically-normal green tissues and chlorotic tissues. Chlorotic tissues of alx13 leaves accumulated mRNAs of nuclear-encoded photosynthesis genes that are repressed in other variegated mutants of Arabidopsis. Thus, defective purine biosynthesis impairs chloroplast biogenesis in a light-dependent manner and alters the induction of high light stress pathways and nuclear-encoded photosynthesis genes.

Evolutionary Conservation of ABA Signaling for Stomatal Closure

Publisher: Oxford University Press (OUP)

Date: 23-02-2017

DOI: 10.1104/PP.16.01848

Genomic analysis of focal nodular hyperplasia with associated hepatocellular carcinoma unveils its malignant potential: a case report

Publisher: Springer Science and Business Media LLC

Date: 03-02-2022

DOI: 10.1038/S43856-022-00074-Y

Abstract: Focal nodular hyperplasia (FNH) is typically considered a benign tumor of the liver without malignant potential. The co-occurrence of FNH and hepatocellular carcinoma (HCC) has been reported in rare cases. In this study we sought to investigate the clonal relationship between these lesions in a patient with FNH-HCC co-occurrence. A 74-year-old female patient underwent liver tumor resection. The resected nodule was subjected to histologic analyses using hematoxylin and eosin stain and immunohistochemistry. DNA extracted from microdissected FNH and HCC regions was subjected to whole exome sequencing. Clonality analysis were performed using PyClone. Histologic analysis reveals that the nodule consists of an FNH and two adjoining HCC components with distinct histopathological features. Immunophenotypic characterization and genomic analyses suggest that the FNH is clonally related to the HCC components, and is composed of multiple clones at diagnosis, that are likely to have progressed to HCC through clonal selection and/or the acquisition of additional genetic events. To the best of our knowledge, our work is the first study showing a clonal relationship between FNH and HCC. We show that FNH may possess the capability to undergo malignant transformation and to progress to HCC in very rare cases.

The nucleotidase/phosphatase SAL1 is a negative regulator of drought tolerance in Arabidopsis

Publisher: Wiley

Date: 04-2009

DOI: 10.1111/J.1365-313X.2008.03780.X

Chloroplast function and ion regulation in plants growing on saline soils: lessons from halophytes

Publisher: Oxford University Press (OUP)

Date: 02-05-2017

DOI: 10.1093/JXB/ERX142

Abstract: Salt stress impacts multiple aspects of plant metabolism and physiology. For instance it inhibits photosynthesis through stomatal limitation, causes excessive accumulation of sodium and chloride in chloroplasts, and disturbs chloroplast potassium homeostasis. Most research on salt stress has focused primarily on cytosolic ion homeostasis with few studies of how salt stress affects chloroplast ion homeostasis. This review asks the question whether membrane-transport processes and ionic relations are differentially regulated between glycophyte and halophyte chloroplasts and whether this contributes to the superior salt tolerance of halophytes. The available literature indicates that halophytes can overcome stomatal limitation by switching to CO2 concentrating mechanisms and increasing the number of chloroplasts per cell under saline conditions. Furthermore, salt entry into the chloroplast stroma may be critical for grana formation and photosystem II activity in halophytes but not in glycophytes. Salt also inhibits some stromal enzymes (e.g. fructose-1,6-bisphosphatase) to a lesser extent in halophyte species. Halophytes accumulate more chloride in chloroplasts than glycophytes and appear to use sodium in functional roles. We propose the molecular identities of candidate transporters that move sodium, chloride and potassium across chloroplast membranes and discuss how their operation may regulate photochemistry and photosystem I and II activity in chloroplasts.

Remodeled Respiration in ndufs4 with Low Phosphorylation Efficiency Suppresses Arabidopsis Germination and Growth and Alters Control of Metabolism at Night

Publisher: Oxford University Press (OUP)

Date: 12-08-2009

DOI: 10.1104/PP.109.141770

Abstract: Respiratory oxidative phosphorylation is a cornerstone of cellular metabolism in aerobic multicellular organisms. The efficiency of this process is generally assumed to be maximized, but the presence of dynamically regulated nonphosphorylating bypasses implies that plants can alter phosphorylation efficiency and can benefit from lowered energy generation during respiration under certain conditions. We characterized an Arabidopsis (Arabidopsis thaliana) mutant, ndufs4 (for NADH dehydrogenase [ubiquinone] fragment S subunit 4), lacking complex I of the respiratory chain, which has constitutively lowered phosphorylation efficiency. Through analysis of the changes to mitochondrial function as well as whole cell transcripts and metabolites, we provide insights into how cellular metabolism flexibly adapts to reduced phosphorylation efficiency and why this state may benefit the plant by providing moderate stress tolerance. We show that removal of the single protein subunit NDUFS4 prevents assembly of complex I and removes its function from mitochondria without pleiotropic effects on other respiratory components. However, the lack of complex I promotes broad changes in the nuclear transcriptome governing growth and photosynthetic function. We observed increases in organic acid and amino acid pools in the mutant, especially at night, concomitant with alteration of the adenylate content. While germination is delayed, this can be rescued by application of gibberellic acid, and root growth assays of seedlings show enhanced tolerance to cold, mild salt, and osmotic stress. We discuss these observations in the light of recent data on the knockout of nonphosphorylating respiratory bypass enzymes that show opposite changes in metabolites and stress sensitivity. Our data suggest that the absence of complex I alters the adenylate control of cellular metabolism.

Pileup mitigation at CMS in 13 TeV data

Publisher: IOP Publishing

Date: 15-09-2020

DOI: 10.1088/1748-0221/15/09/P09018

Suppression of glucan, water dikinase in the endosperm alters wheat grain properties, germination and coleoptile growth

Publisher: Wiley

Date: 18-05-2016

DOI: 10.1111/PBI.12394

Abstract: Starch phosphate ester content is known to alter the physicochemical properties of starch, including its susceptibility to degradation. Previous work producing wheat (Triticum aestivum) with down-regulated glucan, water dikinase, the primary gene responsible for addition of phosphate groups to starch, in a grain-specific manner found unexpected phenotypic alteration in grain and growth. Here, we report on further characterization of these lines focussing on mature grain and early growth. We find that coleoptile length has been increased in these transgenic lines independently of grain size increases. No changes in starch degradation rates during germination could be identified, or any major alteration in soluble sugar levels that may explain the coleoptile growth modification. We identify some alteration in hormones in the tissues in question. Mature grain size is examined, as is Hardness Index and starch conformation. We find no evidence that the increased growth of coleoptiles in these lines is connected to starch conformation or degradation or soluble sugar content and suggest these findings provide a novel means of increasing coleoptile growth and early seedling establishment in cereal crop species.

Impact of chloroplastic- and extracellular-sourced ROS on high light-responsive gene expression in Arabidopsis

Publisher: Oxford University Press (OUP)

Date: 22-01-2008

DOI: 10.1093/JXB/ERM289

Abstract: The expression of 28 high light (HL)-responsive genes of Arabidopsis was analysed in response to environmental and physiological factors known to influence the expression of the HL-responsive gene, ASCORBATE PEROXIDASE2 (APX2). Most (81%) of the HL-responsive genes, including APX2, required photosynthetic electron transport for their expression, and were responsive to abscisic acid (ABA 68%), strengthening the impression that these two signals are crucial in the expression of HL-responsive genes. Further, from the use of mutants altered in reactive oxygen species (ROS) metabolism, it was shown that 61% of these genes, including APX2, may be responsive to chloroplast-sourced ROS. In contrast, apoplastic lasma membrane-sourced H2O2, in part directed by the respiratory burst NADPH oxidases AtrbohD and AtrbohF, was shown to be important only for APX2 expression. APX2 expression in leaves is limited to bundle sheath parenchyma however, for the other genes in this study, information on their tissue specificity of expression is sparse. An analysis of expression in petioles, enriched for bundle sheath tissue compared with distal leaf blade, in HL and control leaves showed that 25% of them had >10-fold higher expression in the petiole than in the leaf blade. However, this did not mean that these petiole expression genes followed a pattern of regulation observed for APX2.

A GDSL Esterase/Lipase Catalyzes the Esterification of Lutein in Bread Wheat

Publisher: Oxford University Press (OUP)

Date: 10-2019

DOI: 10.1105/TPC.19.00272

Alternative splicing, activation of cryptic exons and amino acid substitutions in carotenoid biosynthetic genes are associated with lutein accumulation in wheat endosperm

Publisher: Springer Science and Business Media LLC

Date: 28-03-2009

DOI: 10.1007/S10142-009-0121-3

Abstract: Endosperm carotenoid content in wheat is a primary determinant of flour colour and this affects both the nutritional value of the grain and its utility for different applications. Utilising wheat rice synteny two genes, epsilon-cyclase (epsilon-LCY) and phytoene synthase (Psy-A1), were identified as candidate genes for two of the QTL affecting lutein content in wheat endosperm. Analysis of the sequence changes in epsilon-LCY and Psy-A1 revealed possible causal mechanisms for both QTL. A point mutation in epsilon-LCY results in the substitution of a conserved amino acid in the high lutein allele. This substitution has been observed in high lutein-accumulating species from the Gentiales order. In Psy-A1, a sequence duplication at the end of exon 2 creates a new splice site and causes alternative splicing of the transcript and activation of a cryptic exon, resulting in four different transcripts: a wild-type transcript, two transcripts with early terminations and a transcript that would produce an in-frame, albeit longer protein. Only the wild-type splice variant produced an enzymatically active protein and its mRNA abundance was reduced by titration with the other splice variants. This reduction in wild-type mRNA is argued to result in a reduction in PSY protein and thus carotenoid content in wheat.

Postharvest Senescence of Vegetables and its Regulation

Publisher: Elsevier

Date: 2004

DOI: 10.1016/B978-012520915-1/50025-4

Probing functional and optical cross-sections of PSII in leaves during state transitions using fast repetition rate light induced fluorescence transients

Publisher: CSIRO Publishing

Date: 2019

DOI: 10.1071/FP18054

Abstract: Plants adjust the relative sizes of PSII and PSI antennae in response to the spectral composition of weak light favouring either photosystem by processes known as state transitions (ST), attributed to a discrete antenna migration involving phosphorylation of light-harvesting chlorophyll-protein complexes in PSII. Here for the first time we monitored the extent and dynamics of ST in leaves from estimates of optical absorption cross-section (relative PSII antenna size aPSII). These estimates were obtained from in situ measurements of functional absorption cross-section (σPSII) and maximum photochemical efficiency of PSII (φPSII) i.e. aPSII = σPSII/φPSII (Kolber et al. 1998) and other parameters from a light induced fluorescence transient (LIFT) device (Osmond et al. 2017). The fast repetition rate (FRR) QA flash protocol of this instrument monitors chlorophyll fluorescence yields with reduced QA irrespective of the redox state of plastoquinone (PQ), as well as during strong ~1 s white light pulses that fully reduce the PQ pool. Fitting this transient with the FRR model monitors kinetics of PSII → PQ, PQ → PSI, and the redox state of the PQ pool in the ‘PQ pool control loop’ that underpins ST, with a time resolution of a few seconds. All LIFT/FRR criteria confirmed the absence of ST in antenna mutant chlorina-f2 of barley and asLhcb2–12 of Arabidopsis, as well as STN7 kinase mutants stn7 and stn7/8. In contrast, wild-type barley and Arabidopsis genotypes Col, npq1, npq4, OEpsbs, pgr5 bkg and pgr5, showed normal ST. However, the extent of ST (and by implication the size of the phosphorylated LHCII pool participating in ST) deduced from changes in aʹPSII and other parameters with reduced QA range up to 35%. Estimates from strong WL pulses in the same assay were only ~10%. The larger estimates of ST from the QA flash are discussed in the context of contemporary dynamic structural models of ST involving formation and participation of PSII and PSI megacomplexes in an ‘energetically connected lake’ of phosphorylated LHCII trimers (Grieco et al. 2015). Despite the absence of ST, asLhcb2-12 displays normal wild-type modulation of electron transport rate (ETR) and the PQ pool during ST assays, reflecting compensatory changes in antenna LHCIIs in this genotype. Impaired LHCII phosphorylation in stn7 and stn7/8 accelerates ETR from PSII →PQ, over-reducing the PQ pool and abolishing the yield difference between the QA flash and WL pulse, with implications for photochemical and thermal phases of the O-J-I-P transient.

Measurement of the Y(1S) pair production cross section and search for resonances decaying to Y(1S)μ+μ− in proton-proton collisions at

Publisher: Elsevier BV

Date: 09-2020

DOI: 10.1016/J.PHYSLETB.2020.135578

Isolation of the plant cytosolic fraction for proteomic analysis

Publisher: Humana Press

Date: 22-08-2014

DOI: 10.1007/978-1-62703-631-3_31

Abstract: The cytosol is the fluid portion of the cell that is not partitioned by membranes. It contains a highly erse collection of substances and is central to many essential cellular processes ranging from signal transduction, metabolite production and transport, protein biosynthesis and degradation to stress response and defense. Despite its importance, only a few proteomic studies have been performed on the plant cytosol. This is largely due to difficulties in isolating relatively pure s les from plant material free of disrupted organelle material. In this chapter we outline methods for isolating the cytosolic fraction from Arabidopsis cell cultures and seedlings and provide guidance on assessing purity for analysis by mass spectrometry.

Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation

Publisher: Cold Spring Harbor Laboratory

Date: 10-06-2022

DOI: 10.1101/2022.06.10.495589

Abstract: Transcript stability is an important determinant of its abundance and, consequently, translation. However, it is unclear the extent to which it is modulated between environmental conditions. We previously hypothesised that recovery-induced transcript destabilisation facilitated a phenomenon of rapid recovery gene down-regulation (RRGD) in Arabidopsis thaliana following stress, based on mathematical calculations to account for ongoing transcription. Here, we test this hypothesis, and investigate processes regulating transcript abundance and fate, by quantifying changes in transcription, stability, and translation before, during, and after light stress. We adapt syringe infiltration to apply a transcriptional inhibitor to soil-grown plants in combination with stress. Compared to measurements in juvenile plants and cell culture, we find reduced stability in a range of transcripts. We also observe transcript destabilisation during light stress, followed by stabilisation upon recovery. Alongside fast transcriptional shut-off in recovery, this destabilisation appears to facilitate RRGD. Translation was dynamic over the course of light stress and recovery, with substantial transcript-specific increases in ribosome-association, independent of changes in total transcript abundance, observed after 30 minutes of light stress. Taken together, we provide evidence for the combinatorial regulation of transcription, stability, and translation that occurs to facilitate responses to light stress and recovery.

Uncoupling High Light Responses from Singlet Oxygen Retrograde Signaling and Spatial-Temporal Systemic Acquired Acclimation

Publisher: Oxford University Press (OUP)

Date: 10-06-2016

DOI: 10.1104/PP.16.00404

Global changes in gene expression in response to high light in Arabidopsis

Publisher: Oxford University Press (OUP)

Date: 11-2002

DOI: 10.1104/PP.005595

Abstract: A range of environmental conditions can lead to oxidative stress thus, a prompt and effective response to oxidative stress is crucial for the survival of plants. Microarray and northern-blot analyses were performed toward the identification of the factors and signaling pathways that enable plants to limit oxidative damage caused by exposure to high light (HL). Arabidopsis plants grown under moderate light (100 μmol m−2 s−1) were exposed to HL (1,000 μmol m−2 s−1) for 1 h. The microarray analyses revealed that exposure of Arabidopsis to HL caused an increase in known antioxidant genes, as well as several unknown genes. Some of these unknown genes had homologies to possible regulatory genes and metabolic enzymes. Furthermore, it was found that a range of chaperones were up-regulated in the HL treatment and that this induction was specifically due to the HL stress. The temporal expression under HL and different oxidative stress conditions of a subset of HL-responsive genes was confirmed via northern-blot analysis. Results from the arrays were also compared with publicly available microarray data sets from a range of different stress conditions at the Arabidopsis Functional Genomics Consortium. This cross comparison enabled the identification of genes that may be induced by changes in redox poise. Finally, to determine if the genes that were differentially expressed by HL stress were under similar transcriptional control, we analyzed the promoter sequences for the presence of common motifs.

More than meets the eye: From carotenoid biosynthesis, to new insights into apocarotenoid signaling

Publisher: Elsevier BV

Date: 10-2015

DOI: 10.1016/J.PBI.2015.06.020

Abstract: Carotenoids are a class of isoprenoids synthesized almost exclusively in plants involved in a myriad of roles including the provision of flower and fruit pigmentation for the attraction of pollinators and seed dispersing organisms. While carotenoids are essential throughout plant development, they are also extremely important in human diets providing necessary nutrition and aiding in the prevention of various cancers, age-related diseases and macular degeneration. Utilization of multiple plant models systems (i.e. Arabidopsis maize and tomato) has provided a comprehensive framework detailing the regulation of carotenogenesis throughout plant development covering all levels of genetic regulation from epigenetic to post-translational modifications. That said, the understanding of how carotenoids self-regulate remains fragmented. Recent reports demonstrate the potential influence of carotenoid-cleavage products (apocarotenoids) as signaling molecules regulating carotenoid biosynthesis in addition to various aspects of plants development (i.e. leaf and root development). This review highlights recent advances in carotenogenic regulation and insights into potential roles of novel apocarotenoids in plants.

Canopy conundrums: Building on the Biosphere 2 experience to scale measurements of inner and outer canopy photoprotection from the leaf to the landscape

Publisher: CSIRO Publishing

Date: 2012

DOI: 10.1071/FP11255

Abstract: Recognising that plant leaves are the fundamental productive units of terrestrial vegetation and the complexity of different environments in which they must function, this review considers a few of the ways in which these functions may be measured and potentially scaled to the canopy. Although canopy photosynthetic productivity is clearly the sum of all leaves in the canopy, we focus on the quest for ‘economical insights’ from measurements that might facilitate integration of leaf photosynthetic activities into canopy performance, to better inform modelling based on the ‘insights of economics’. It is focussed on the reversible downregulation of photosynthetic efficiency in response to light environment and stress and summarises various xanthophyll-independent and dependent forms of photoprotection within the inner and outer canopy of woody plants. Two main themes are developed. First, we review experiments showing the retention of leaves that grow old in the shade may involve more than the ‘payback times’ required to recover the costs of their construction and maintenance. In some cases at least, retention of these leaves may reflect selection for distinctive properties that contribute to canopy photosynthesis through utilisation of sun flecks or provide ‘back up’ capacity following damage to the outer canopy. Second, we report experiments offering hope that remote sensing of photosynthetic properties in the outer canopy (using chlorophyll fluorescence and spectral reflectance technologies) may overcome problems of access and provide integrated measurements of these properties in the canopy as a whole. Finding appropriate tools to scale photosynthesis from the leaf to the landscape still presents a challenge but this synthesis identifies some measurements and criteria in the laboratory and the field that improve our understanding of inner and outer canopy processes.

A rapid, non-invasive procedure for quantitative assessment of drought survival using chlorophyll fluorescence

Publisher: Springer Science and Business Media LLC

Date: 11-11-2008

DOI: 10.1186/1746-4811-4-27

Abstract: Analysis of survival is commonly used as a means of comparing the performance of plant lines under drought. However, the assessment of plant water status during such studies typically involves detachment to estimate water shock, imprecise methods of estimation or invasive measurements such as osmotic adjustment that influence or annul further evaluation of a specimen's response to drought. This article presents a procedure for rapid, inexpensive and non-invasive assessment of the survival of soil-grown plants during drought treatment. The changes in major photosynthetic parameters during increasing water deficit were monitored via chlorophyll fluorescence imaging and the selection of the maximum efficiency of photosystem II (F v /F m ) parameter as the most straightforward and practical means of monitoring survival is described. The veracity of this technique is validated through application to a variety of Arabidopsis thaliana ecotypes and mutant lines with altered tolerance to drought or reduced photosynthetic efficiencies. The method presented here allows the acquisition of quantitative numerical estimates of Arabidopsis drought survival times that are amenable to statistical analysis. Furthermore, the required measurements can be obtained quickly and non-invasively using inexpensive equipment and with minimal expertise in chlorophyll fluorometry. This technique enables the rapid assessment and comparison of the relative viability of germplasm during drought, and may complement detailed physiological and water relations studies.

Enhancing crop yields through improvements in the efficiency of photosynthesis and respiration

Publisher: Wiley

Date: 17-11-2023

DOI: 10.1111/NPH.18545

Abstract: The rate with which crop yields per hectare increase each year is plateauing at the same time that human population growth and other factors increase food demand. Increasing yield potential () of crops is vital to address these challenges. In this review, we explore a component of that has yet to be optimised – that being improvements in the efficiency with which light energy is converted into biomass () via modifications to CO 2 fixed per unit quantum of light ( α ), efficiency of respiratory ATP production () and efficiency of ATP use (). For α , targets include changes in photoprotective machinery, ribulose bisphosphate carboxylase/oxygenase kinetics and photorespiratory pathways. There is also potential for to be increased via targeted changes to the expression of the alternative oxidase and mitochondrial uncoupling pathways. Similarly, there are possibilities to improve via changes to the ATP costs of phloem loading, nutrient uptake, futile cycles and/or protein/membrane turnover. Recently developed high‐throughput measurements of respiration can serve as a proxy for the cumulative energy cost of these processes. There are thus exciting opportunities to use our growing knowledge of factors influencing the efficiency of photosynthesis and respiration to create a step‐change in yield potential of globally important crops.

A mutation affecting ASCORBATE PEROXIDASE 2 gene expression reveals a link between responses to high light and drought tolerance

Publisher: Wiley

Date: 02-2006

DOI: 10.1111/J.1365-3040.2005.01419.X

Abstract: Molecular analyses of plants have revealed a number of genes whose expression changes in response to high light (HL), including the H2O2 scavenger, ASCORBATE PEROXIDASE 2 (APX2). We carried out a screen in Arabidopsis thaliana for lesions that alter HL-induced expression of APX2 to identify components in abiotic stress signalling pathways. High light was used as it can be instantaneously applied or removed and accurately measured. We identified a number of alx mutations causing altered APX2 expression. Here we describe the gain-of-function mutant, alx8, which has constitutively higher APX2 expression and higher levels of foliar abscisic acid (ABA) than wild type. In fact, exogenous ABA increased APX2 expression and the APX2 promoter contains ABA response elements. Furthermore, we have shown that HL stress increases ABA in wild-type plants, implicating ABA in the regulation of HL-inducible genes. The alx8 mutant is drought tolerant, exhibits improved water-use efficiency and a number of drought-tolerance genes are upregulated. Additionally, alx8 demonstrates the complexity of ABA-dependent and ABA-independent transcriptional networks as some components in both pathways are upregulated in alx8. This study provides evidence for common steps in drought and HL stress response pathways.

Functional Analysis of the b and e Lycopene Cyclase Enzymes of Arabidopsis Reveals a Mechanism for Control of Cyclic Carotenoid Formation

Publisher: JSTOR

Date: 09-1996

DOI: 10.2307/3870254

Subset of heat-shock transcription factors required for the early response of Arabidopsis to excess light

Publisher: Proceedings of the National Academy of Sciences

Date: 05-08-2013

DOI: 10.1073/PNAS.1311632110

Abstract: Sunlight provides energy for photosynthesis and is essential for nearly all life on earth. However, too much or too little light or rapidly fluctuating light conditions cause stress to plants. Rapid changes in the amount of light are perceived as a change in the reduced/oxidized (redox) state of photosynthetic electron transport components in chloroplasts. However, how this generates a signal that is relayed to changes in nuclear gene expression is not well understood. We modified redox state in the reference plant, Arabidopsis thaliana , using either excess light or low light plus the herbicide DBMIB (2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone), a well-known inhibitor of photosynthetic electron transport. Modification of redox state caused a change in expression of a common set of about 750 genes, many of which are known stress-responsive genes. Among the most highly enriched promoter elements in the induced gene set were heat-shock elements (HSEs), known motifs that change gene expression in response to high temperature in many systems. We show that HSEs from the promoter of the ASCORBATE PEROXIDASE 2 ( APX2 ) gene were necessary and sufficient for APX2 expression in conditions of excess light, or under low light plus the herbicide. We tested APX2 expression phenotypes in overexpression and loss-of-function mutants of 15 Arabidopsis A-type heat-shock transcription factors (HSFs), and identified HSFA1D, HSFA2, and HSFA3 as key factors regulating APX2 expression in erse stress conditions. Excess light regulates both the subcellular location of HSFA1D and its biochemical properties, making it a key early component of the excess light stress network of plants.

A transparent iron-incorporated nickel hydroxide electrocatalyst for efficient water oxidation

Publisher: Royal Society of Chemistry (RSC)

Date: 2023

DOI: 10.1039/D3SE00527E

Abstract: Transparent electrocatalysts were developed by a facile solution-based method. The highly transparent iron-incorporated nickel hydroxide (FeNi-10) oxygen evolution electrode exhibited low overpotential compared to the benchmark electrocatalyst.

Carotenoid Metabolism in Plants

Publisher: Elsevier BV

Date: 2015

DOI: 10.1016/J.MOLP.2014.12.007

Abstract: Carotenoids are mostly C40 terpenoids, a class of hydrocarbons that participate in various biological processes in plants, such as photosynthesis, photomorphogenesis, photoprotection, and development. Carotenoids also serve as precursors for two plant hormones and a erse set of apocarotenoids. They are colorants and critical components of the human diet as antioxidants and provitamin A. In this review, we summarize current knowledge of the genes and enzymes involved in carotenoid metabolism and describe recent progress in understanding the regulatory mechanisms underlying carotenoid accumulation. The importance of the specific location of carotenoid enzyme metabolons and plastid types as well as of carotenoid-derived signals is discussed.

Sensing and signaling of oxidative stress in chloroplasts by inactivation of the SAL1 phosphoadenosine phosphatase

Publisher: Proceedings of the National Academy of Sciences

Date: 18-07-2016

DOI: 10.1073/PNAS.1604936113

Abstract: Management of oxidative stress in plant chloroplasts involves signaling pathways to the nucleus that trigger stress response mechanisms. Yet, how oxidative stress is initially sensed in the chloroplast to activate accumulation of a stress signal remains enigmatic. We show that inactivation of a phosphatase, SAL1, by oxidative stress in chloroplasts controls accumulation of its substrate, as a plant stress signal. This regulatory mechanism is highly conserved across the plant kingdom and confers a second function to this metabolic enzyme as an oxidative stress sensor.

Regulation of lutein biosynthesis and prolamellar body formation in Arabidopsis

Publisher: CSIRO Publishing

Date: 2007

DOI: 10.1071/FP07034

Abstract: Carotenoids are critical for photosynthetic function in chloroplasts, and are essential for the formation of the prolamellar body in the etioplasts of dark-grown (etiolated) seedlings. They are also precursors for plant hormones in both types of plastids. Lutein is one of the most abundant carotenoids found in both plastids. In this study we examine the regulation of lutein biosynthesis and investigate the effect of perturbing carotenoid biosynthesis on the formation of the lattice-like membranous structure of etioplasts, the prolamellar body (PLB). Analysis of mRNA abundance in wildtype and lutein-deficient mutants, lut2 and ccr2, in response to light transitions and herbicide treatments demonstrated that the mRNA abundance of the carotenoid isomerase (CRTISO) and epsilon-cyclase (ϵLCY) can be rate limiting steps in lutein biosynthesis. We show that accumulation of tetra-cis-lycopene and all-trans-lycopene correlates with the abundance of mRNA of several carotenoid biosynthetic genes. Herbicide treatments that inhibit carotenoid biosynthetic enzymes in wildtype and ccr2 etiolated seedlings were used to demonstrate that the loss of the PLB in ccr2 mutants is a result of perturbations in carotenoid accumulation, not indirect secondary effects, as PLB formation could be restored in ccr2 mutants treated with norflurazon.

Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics

Publisher: American Association for the Advancement of Science (AAAS)

Date: 05-02-2016

DOI: 10.1126/SCIADV.1501340

Abstract: Have plants learned to forget stress? This review proposes benefits to forgetfulness and finds key roles for RNA turnover.

A foliar pigment-based bioassay for interrogating chloroplast signalling revealed that carotenoid isomerisation regulates chlorophyll abundance

Publisher: Springer Science and Business Media LLC

Date: 17-02-2022

DOI: 10.1186/S13007-022-00847-5

Abstract: Some plastid-derived metabolites can control nuclear gene expression, chloroplast biogenesis, and chlorophyll biosynthesis. For ex le, norflurazon (NFZ) induced inhibition of carotenoid biosynthesis in leaves elicits a protoporphyrin IX (Mg-ProtoIX) retrograde signal that controls chlorophyll biosynthesis and chloroplast development. Carotenoid cleavage products, known as apocarotenoids, also regulate plastid development. The key steps in carotenoid biosynthesis or catabolism that can regulate chlorophyll biosynthesis in leaf tissues remain unclear. Here, we established a foliar pigment-based bioassay using Arabidopsis rosette leaves to investigate plastid signalling processes in young expanding leaves comprising rapidly iding and expanding cells containing active chloroplast biogenesis. We demonstrate that environmental treatments (extended darkness and cold exposure) as well as chemical (norflurazon NFZ) inhibition of carotenoid biosynthesis, reduce chlorophyll levels in young, but not older leaves of Arabidopsis . Mutants with disrupted xanthophyll accumulation, apocarotenoid phytohormone biosynthesis (abscisic acid and strigolactone), or enzymatic carotenoid cleavage, did not alter chlorophyll levels in young or old leaves. However, perturbations in acyclic cis -carotene biosynthesis revealed that disruption of CAROTENOID ISOMERASE (CRTISO), but not ZETA-CAROTENE ISOMERASE (Z-ISO) activity, reduced chlorophyll levels in young leaves of Arabidopsis plants. NFZ-induced inhibition of PHYTOENE DESATURASE (PDS) activity caused higher phytoene accumulation in younger crtiso leaves compared to WT indicating a continued substrate supply from the methylerythritol 4-phosphate (MEP) pathway. The Arabidopsis foliar pigment-based bioassay can be used to differentiate signalling events elicited by environmental change, chemical treatment, and/or genetic perturbation, and determine how they control chloroplast biogenesis and chlorophyll biosynthesis. Genetic perturbations that impaired xanthophyll biosynthesis and/or carotenoid catabolism did not affect chlorophyll biosynthesis. The lack of CAROTENOID ISOMERISATION reduced chlorophyll accumulation, but not phytoene biosynthesis in young leaves of Arabidopsis plants growing under a long photoperiod. Findings generated using the newly customised foliar pigment-based bioassay implicate that carotenoid isomerase activity and NFZ-induced inhibition of PDS activity elicit different signalling pathways to control chlorophyll homeostasis in young leaves of Arabidopsis .

Acis-carotene derived apocarotenoid regulates etioplast and chloroplast development

Publisher: Cold Spring Harbor Laboratory

Date: 23-01-2019

DOI: 10.1101/528331

Abstract: Carotenoids are core plastid components, yet a regulatory function during plastid biogenesis remains enigmatic. A unique carotenoid biosynthesis mutant, carotenoid chloroplast regulation 2 ( ccr2 ), that has no prolamellar body (PLB) and normal PROTOCHLOROPHYLLIDE OXIDOREDUCTASE (POR) levels, was used to demonstrate a regulatory function for carotenoids under varied dark-light regimes. A forward genetics approach revealed how an epistatic interaction between a (-carotene isomerase mutant ( ziso-155 ) and ccr2 blocked the biosynthesis of specific cis -carotenes and restored PLB formation in etioplasts. We attributed this to a novel apocarotenoid signal, as chemical inhibition of carotenoid cleavage dioxygenase activity restored PLB formation in ccr2 etioplasts during skotomorphogenesis. The apocarotenoid acted in parallel to the transcriptional repressor of photomorphogenesis, DEETIOLATED1 (DET1), to post-transcriptionally regulate PROTOCHLOROPHYLLIDE OXIDOREDUCTASE (POR), PHYTOCHROME INTERACTING FACTOR3 (PIF3) and ELONGATED HYPOCOTYL5 (HY5) protein levels. The apocarotenoid signal and det1 complemented each other to restore POR levels and PLB formation, thereby controlling plastid development. Carotenoids are not just required as core components for plastid biogenesis, they can be cleaved into an apocarotenoid signal that regulates etioplast and chloroplast development during extended periods of darkness.

Interferon lambda 4 impairs hepatitis C viral antigen presentation and attenuates T cell responses

Publisher: Springer Science and Business Media LLC

Date: 12-08-2021

DOI: 10.1038/S41467-021-25218-X

Abstract: Genetic variants of the interferon lambda ( IFNL ) gene locus are strongly associated with spontaneous and IFN treatment-induced clearance of hepatitis C virus (HCV) infections. In iduals with the ancestral IFNL4-dG allele are not able to clear HCV in the acute phase and have more than a 90% probability to develop chronic hepatitis C (CHC). Paradoxically, the IFNL4-dG allele encodes a fully functional IFNλ4 protein with antiviral activity against HCV. Here we describe an effect of IFNλ4 on HCV antigen presentation. Only minor amounts of IFNλ4 are secreted, because the protein is largely retained in the endoplasmic reticulum (ER) where it induces ER stress. Stressed cells are significantly weaker activators of HCV specific CD8 + T cells than unstressed cells. This is not due to reduced MHC I surface presentation or extracellular IFNλ4 effects, since T cell responses are restored by exogenous loading of MHC with HCV antigens. Rather, IFNλ4 induced ER stress impairs HCV antigen processing and/or loading onto the MHC I complex. Our results provide a potential explanation for the IFNλ4–HCV paradox.

Do multiple forms of tomato fruit endopolygalacturonase exist in situ?

Publisher: Elsevier BV

Date: 07-1993

DOI: 10.1016/0925-5214(93)90023-V

5585542 DNA sequences encoding at least part of the tomato enzyme endopolygalacturonase PG1 beta-subunit

Publisher: Elsevier BV

Date: 1997

DOI: 10.1016/S0734-9750(97)87651-3

The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress

Publisher: Oxford University Press (OUP)

Date: 06-10-2017

DOI: 10.1104/PP.17.00744

Exploring the Function-Location Nexus: Using Multiple Lines of Evidence in Defining the Subcellular Location of Plant Proteins

Publisher: Oxford University Press (OUP)

Date: 06-2009

DOI: 10.1105/TPC.109.066019

Epigenetic priming in chronic liver disease impacts the transcriptional and genetic landscapes of hepatocellular carcinoma

Publisher: Wiley

Date: 29-12-2021

DOI: 10.1002/1878-0261.13154

Abstract: Hepatocellular carcinomas (HCCs) usually arise from chronic liver disease (CLD). Precancerous cells in chronically inflamed environments may be ‘epigenetically primed’, sensitising them to oncogenic transformation. We investigated whether epigenetic priming in CLD may affect HCC outcomes by influencing the genomic and transcriptomic landscapes of HCC. Analysis of DNA methylation arrays from 10 paired CLD‐HCC identified 339 shared dysregulated CpG sites and 18 shared differentially methylated regions compared with healthy livers. These regions were associated with dysregulated expression of genes with relevance in HCC, including ubiquitin D ( UBD ), cytochrome P450 family 2 subfamily C member 19 ( CYP2C19 ) and O ‐6‐methylguanine‐DNA methyltransferase ( MGMT ). Methylation changes were recapitulated in an independent cohort of nine paired CLD‐HCC. High CLD methylation score, defined using the 124 dysregulated CpGs in CLD and HCC in both cohorts, was associated with poor survival, increased somatic genetic alterations and TP53 mutations in two independent HCC cohorts. Oncogenic transcriptional and methylation dysregulation is evident in CLD and compounded in HCC. Epigenetic priming in CLD sculpts the transcriptional landscape of HCC and creates an environment favouring the acquisition of genetic alterations, suggesting that the extent of epigenetic priming in CLD could influence disease outcome.

Arabidopsis tRNA Adenosine Deaminase Arginine Edits the Wobble Nucleotide of Chloroplast tRNA(Arg)(ACG) and Is Essential for Efficient Chloroplast Translation

Publisher: Oxford University Press (OUP)

Date: 07-2009

DOI: 10.1105/TPC.109.066654

Abstract: RNA editing changes the coding/decoding information relayed by transcripts via nucleotide insertion, deletion, or conversion. Editing of tRNA anticodons by deamination of adenine to inosine is used both by eukaryotes and prokaryotes to expand the decoding capacity of in idual tRNAs. This limits the number of tRNA species required for codon-anticodon recognition. We have identified the Arabidopsis thaliana gene that codes for tRNA adenosine deaminase arginine (TADA), a chloroplast tRNA editing protein specifically required for deamination of chloroplast (cp)-tRNAArg(ACG) to cp-tRNAArg(ICG). Land plant TADAs have a C-terminal domain similar in sequence and predicted structure to prokaryotic tRNA deaminases and also have very long N-terminal extensions of unknown origin and function. Biochemical and mutant complementation studies showed that the C-terminal domain is sufficient for cognate tRNA deamination both in vitro and in planta. Disruption of TADA has profound effects on chloroplast translation efficiency, leading to reduced yields of chloroplast-encoded proteins and impaired photosynthetic function. By contrast, chloroplast transcripts accumulate to levels significantly above those of wild-type plants. Nevertheless, absence of cp-tRNAArg(ICG) is compatible with plant survival, implying that two out of three CGN codon recognition occurs in chloroplasts, though this mechanism is less efficient than wobble pairing.

The Arabidopsis SAL1-PAP Pathway: A Case Study for Integrating Chloroplast Retrograde, Light and Hormonal Signaling in Modulating Plant Growth and Development?

Publisher: Frontiers Media SA

Date: 08-08-2018

DOI: 10.3389/FPLS.2018.01171

Phosphoprotein enriched in diabetes (PED/PEA15) promotes migration in hepatocellular carcinoma and confers resistance to sorafenib

Publisher: Springer Science and Business Media LLC

Date: 26-10-2017

DOI: 10.1038/CDDIS.2017.512

Abstract: Hepatocellular carcinoma (HCC) is the third-leading cause of cancer-related death with limited treatment options and frequent resistance to sorafenib, the only drug currently approved for first-line therapy. Therefore, better understanding of HCC tumor biology and its resistance to treatment is urgently needed. Here, we analyzed the role of phosphoprotein enriched in diabetes (PED) in HCC. PED has been shown to regulate cell proliferation, apoptosis and migration in several types of cancer. However, its function in HCC has not been addressed yet. Our study revealed that both transcript and protein levels of PED were significantly high in HCC compared with non-tumoral tissue. Clinico-pathological correlation revealed that PED high HCCs showed an enrichment of gene signatures associated with metastasis and poor prognosis. Further, we observed that PED overexpression elevated the migration potential and PED silencing the decreased migration potential in liver cancer cell lines without effecting cell proliferation. Interestingly, we found that PED expression was regulated by a hepatocyte specific nuclear factor, HNF4 α . A reduction of HNF4 α induced an increase in PED expression and consequently, promoted cell migration in vitro . Finally, PED reduced the antitumoral effect of sorafenib by inhibiting caspase-3/7 activity. In conclusion, our data suggest that PED has a prominent role in HCC biology. It acts particularly on promoting cell migration and confers resistance to sorafenib treatment. PED may be a novel target for HCC therapy and serve as a predictive marker for treatment response against sorafenib.

The protein histidine phosphatase LHPP is a tumour suppressor

Publisher: Springer Science and Business Media LLC

Date: 03-2018

DOI: 10.1038/NATURE26140

Addressing Research Bottlenecks to Crop Productivity

Publisher: Elsevier BV

Date: 06-2021

DOI: 10.1016/J.TPLANTS.2021.03.011

On the Occurrence and Structure of Subunits of Endopolygalacturonase Isoforms in Mature-Green and Ripening Tomato Fruits

Publisher: CSIRO Publishing

Date: 1991

DOI: 10.1071/PP9910065

Abstract: Endopolygalacturonase [poly(1,4-α-galacturonide) glycanohydrolase EC 3.2.1.151 occurs in tomato fruit in three molecular forms- PG1, PG2A, PG2B. Trace amounts of PG1, 1-10 pkat g-1 are shown to occur in mature-green fruit as compared to 17 nkat in ripe fruit. As polygalacturonase activity increases through ripening, the percentage of the activity due to PG1 decreases progressively from 100 to less than 20. On fully or partly demethylated substrates, PG1 is more active than PG2 when the ionic strength is that expected in the tissue apoplast. A method for purifying PGI from ripe fruit is described. PG1 preparations contain polypeptides of Mr 45, 43 and 38 thousand. The Mr 43 thousand and 45 thousand components correspond in size to PG2A and PG2B and are detected by antisera raised against PG2A. The M, 38 thousand polypeptide is immunologically distinct. From carbohydrate and amino acid analyses, this polypeptide appears to contain 2870 carbohydrate as glucosamine, mannose, xylose and fucose attached to a polypeptide of estimated Mr 28 342 that is rich in tyrosine and glycine. A method for purifying the subunits of PG1 by cation exchange chromatography in 6 M urea is described. PG2A and PG2B were separated by column chromatography and shown to have identical N-terminal sequences, and serine at the C-terminus. PG2A and PG2B are confirmed as two glycoforms of the one polypeptide. The possibility that PGl consists of populations of molecules containing either PG2A or PG2B coupled with the Mr 38 thousand polypeptide is discussed.

Photoprotection of residual functional photosystem II units that survive illumination in the absence of repair, and their critical role in subsequent recovery

Publisher: Wiley

Date: 11-2006

DOI: 10.1111/J.1399-3054.2006.00754.X

Synthesis and Function of Apocarotenoid Signals in Plants

Publisher: Elsevier BV

Date: 09-2016

DOI: 10.1016/J.TPLANTS.2016.06.001

Abstract: In plants, carotenoids are essential for photosynthesis and photoprotection. However, carotenoids are not the end products of the pathway apocarotenoids are produced by carotenoid cleavage dioxygenases (CCDs) or non-enzymatic processes. Apocarotenoids are more soluble or volatile than carotenoids but they are not simply breakdown products, as there can be modifications post-cleavage and their functions include hormones, volatiles, and signals. Evidence is emerging for a class of apocarotenoids, here referred to as apocarotenoid signals (ACSs), that have regulatory roles throughout plant development beyond those ascribed to abscisic acid (ABA) and strigolactone (SL). In this context we review studies of carotenoid feedback regulation, chloroplast biogenesis, stress signaling, and leaf and root development providing evidence that apocarotenoids may fine-tune plant development and responses to environmental stimuli.

An Overview of Chloroplast Biogenesis and Development

Publisher: Springer New York

Date: 2014

DOI: 10.1007/978-1-4939-1136-3_4

Inflorescence stem grafting made easy in Arabidopsis

Publisher: Springer Science and Business Media LLC

Date: 12-2012

DOI: 10.1186/1746-4811-8-50

Abstract: Plant grafting techniques have deepened our understanding of the signals facilitating communication between the root and shoot, as well as between shoot and reproductive organs. Transmissible signalling molecules can include hormones, peptides, proteins and metabolites: some of which travel long distances to communicate stress, nutrient status, disease and developmental events. While hypocotyl micrografting techniques have been successfully established for Arabidopsis to explore root to shoot communications, inflorescence grafting in Arabidopsis has not been exploited to the same extent. Two different strategies (horizontal and wedge-style inflorescence grafting) have been developed to explore long distance signalling between the shoot and reproductive organs. We developed a robust wedge-cleft grafting method, with success rates greater than 87%, by developing better tissue contact between the stems from the inflorescence scion and rootstock. We describe how to perform a successful inflorescence stem graft that allows for reproducible translocation experiments into the physiological, developmental and molecular aspects of long distance signalling events that promote reproduction. Wedge grafts of the Arabidopsis inflorescence stem were supported with silicone tubing and further sealed with parafilm to maintain the vascular flow of nutrients to the shoot and reproductive tissues. Nearly all (87%) grafted plants formed a strong union between the scion and rootstock. The success of grafting was scored using an inflorescence growth assay based upon the growth of primary stem. Repeated pruning produced new cauline tissues, healthy flowers and reproductive siliques, which indicates a healthy flow of nutrients from the rootstock. Removal of the silicone tubing showed a tightly fused wedge graft junction with callus proliferation. Histological staining of sections through the graft junction demonstrated the differentiation of newly formed vascular connections, parenchyma tissue and lignin accumulation, supporting the presumed success of the graft union between two sections of the primary inflorescence stem. We describe a simple and reliable method for grafting sections of an Arabidopsis inflorescence stem. This step-by-step protocol facilitates laboratories without grafting experience to further explore the molecular and chemical signalling which coordinates communications between the shoot and reproductive tissues.

LATS1 but not LATS2 represses autophagy by a kinase-independent scaffold function

Publisher: Springer Science and Business Media LLC

Date: 17-12-2019

DOI: 10.1038/S41467-019-13591-7

Abstract: Autophagy perturbation represents an emerging therapeutic strategy in cancer. Although LATS1 and LATS2 kinases, core components of the mammalian Hippo pathway, have been shown to exert tumor suppressive activities, here we report a pro-survival role of LATS1 but not LATS2 in hepatocellular carcinoma (HCC) cells. Specifically, LATS1 restricts lethal autophagy in HCC cells induced by sorafenib, the standard of care for advanced HCC patients. Notably, autophagy regulation by LATS1 is independent of its kinase activity. Instead, LATS1 stabilizes the autophagy core-machinery component Beclin-1 by promoting K27-linked ubiquitination at lysine residues K32 and K263 on Beclin-1. Consequently, ubiquitination of Beclin-1 negatively regulates autophagy by promoting inactive dimer formation of Beclin-1. Our study highlights a functional ersity between LATS1 and LATS2, and uncovers a scaffolding role of LATS1 in mediating a cross-talk between the Hippo signaling pathway and autophagy.

Biosynthesis and regulation of carotenoids in plants - Micronutrients, vitamins and health benefits

Publisher: Springer Berlin Heidelberg

Date: 2010

DOI: 10.1007/978-3-642-04670-4_7

TraitCapture: genomic and environment modelling of plant phenomic data

Publisher: Elsevier BV

Date: 04-2014

DOI: 10.1016/J.PBI.2014.02.002

Abstract: Agriculture requires a second green revolution to provide increased food, fodder, fiber, fuel and soil fertility for a growing population while being more resilient to extreme weather on finite land, water, and nutrient resources. Advances in phenomics, genomics and environmental control/sensing can now be used to directly select yield and resilience traits from large collections of germplasm if software can integrate among the technologies. Traits could be Captured throughout development and across environments from multi-dimensional phenotypes, by applying Genome Wide Association Studies (GWAS) to identify causal genes and background variation and functional structural plant models (FSPMs) to predict plant growth and reproduction in target environments. TraitCapture should be applicable to both controlled and field environments and would allow breeders to simulate regional variety trials to pre-select for increased productivity under challenging environments.

Nucleotide Sequence of a cDNA Clone Encoding 1-Aminocyclopropane-1-Carboxylic Acid Synthase from Broccoli

Publisher: Oxford University Press (OUP)

Date: 06-1995

DOI: 10.1104/PP.108.2.857

Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis

Publisher: Oxford University Press (OUP)

Date: 08-10-2010

DOI: 10.1093/JXB/ERP296

Development of strategies for genetic manipulation and fine-tuning of a chloroplast retrograde signal 3′-phosphoadenosine 5′-phosphate

Publisher: Wiley

Date: 2018

DOI: 10.1002/PLD3.31

Abstract: Homeostasis of metabolism and regulation of stress‐signaling pathways are important for plant growth. The metabolite 3′‐phosphoadenosine‐5′‐phosphate (PAP) plays dual roles as a chloroplast retrograde signal during drought and high light stress, as well as a toxic by‐product of secondary sulfur metabolism, and thus, its levels are regulated by the chloroplastic phosphatase, SAL1. Constitutive PAP accumulation in sal1 mutants improves drought tolerance but can impair growth and alter rosette morphology. Therefore, it is of interest to derive strategies to enable controlled and targeted PAP manipulation that could enhance drought tolerance while minimizing the negative effects on plant growth. We systematically tested the potential and efficiency of multiple established transgenic manipulation tools in altering PAP levels in Arabidopsis. Dexamethasone (dex)‐inducible silencing of SAL1 via hpRNAi [pOpOff: SAL1 hpRNAi] yielded reduction in SAL1 transcript and protein levels, yet failed to significantly induce PAP accumulation. Surprisingly, this was not due to insufficient silencing of the inducible system, as constitutive silencing using a strong promoter to drive hpRNAi and amiRNA targeting the SAL1 transcript also failed to increase PAP content or induce a sal1 ‐like plant morphology despite significantly reducing the SAL1 transcript levels. In contrast, using dex‐inducible expression of SAL1 cDNA to complement an Arabidopsis sal1 mutant successfully modulated PAP levels and restored rosette growth in a dosage‐dependent manner. Results from this inducible complementation system indicate that plants with intermediate PAP levels could have improved rosette growth without compromising its drought tolerance. Additionally, preliminary evidence suggests that SAL1 cDNA driven by promoters of genes expressed specifically during early developmental stages such as ABA‐Insensitive 3 ( ABI3 ) could be another potential strategy for studying and optimizing PAP levels and drought tolerance while alleviating the negative impact of PAP on plant growth in sal1 . Thus, we have identified ways that can allow future dissection into multiple aspects of stress and developmental regulation mediated by this chloroplast signal.

Glucose-induced expression of carotenoid biosynthesis genes in the dark is mediated by cytosolic pH in the cyanobacterium Synechocystis sp PCC 6803

Publisher: Elsevier BV

Date: 06-2004

DOI: 10.1074/JBC.M402541200

Excess light priming in Arabidopsis thaliana genotypes with altered DNA methylomes

Publisher: Cold Spring Harbor Laboratory

Date: 27-11-2018

DOI: 10.1101/475798

Abstract: Plants must continuously react to the ever-fluctuating nature of their environment. Repeated exposure to stressful conditions can lead to priming, whereby prior encounters heighten a plant’s ability to respond to future events. A clear ex le of priming is provided by the model plant Arabidopsis thaliana (Arabidopsis), in which photosynthetic and photoprotective responses are enhanced following recurring light stress. While there are various post-translational mechanisms underpinning photoprotection, an unresolved question is the relative importance of transcriptional changes towards stress priming and, consequently, the potential contribution from DNA methylation – a heritable chemical modification of DNA capable of influencing gene expression. Here, we systematically investigate the potential molecular underpinnings of physiological priming against recurring excess-light (EL), specifically DNA methylation and transcriptional regulation: the latter having not been examined with respect to EL priming. The capacity for physiological priming of photosynthetic and photoprotective parameters following a recurring EL treatment was not impaired in Arabidopsis mutants with perturbed establishment, maintenance, or removal of DNA methylation. Importantly, no differences in development or basal photoprotective capacity were identified in the mutants that may confound the above result. Little evidence for a causal transcriptional component of physiological priming was identified in fact, most alterations in primed plants presented as a transcriptional ‘d ening’ in response to an additional EL exposure, likely a consequence of physiological priming. However, a set of transcripts uniquely regulated in primed plants provide preliminary evidence for a novel transcriptional component of recurring EL priming, independent of physiological changes. Thus, we propose that physiological priming of recurring EL in Arabidopsis occurs independently of DNA methylation and that the majority of the associated transcriptional alterations are a consequence, not cause, of this physiological priming. Photoprotection and priming against recurring excess light is functional despite impaired maintenance of the DNA methylome.

Learning the Languages of the Chloroplast: Retrograde Signaling and Beyond

Publisher: Annual Reviews

Date: 29-04-2016

DOI: 10.1146/ANNUREV-ARPLANT-043015-111854

Abstract: The chloroplast can act as an environmental sensor, communicating with the cell during biogenesis and operation to change the expression of thousands of proteins. This process, termed retrograde signaling, regulates expression in response to developmental cues and stresses that affect photosynthesis and yield. Recent advances have identified many signals and pathways—including carotenoid derivatives, isoprenes, phosphoadenosines, tetrapyrroles, and heme, together with reactive oxygen species and proteins—that build a communication network to regulate gene expression, RNA turnover, and splicing. However, retrograde signaling pathways have been viewed largely as a means of bilateral communication between organelles and nuclei, ignoring their potential to interact with hormone signaling and the cell as a whole to regulate plant form and function. Here, we discuss new findings on the processes by which organelle communication is initiated, transmitted, and perceived, not only to regulate chloroplastic processes but also to intersect with cellular signaling and alter physiological responses.

Nucleotide Sequence of a cDNA Clone from Broccoli with High Identity with the PSST Subunit of NADH:Ubiquinone Oxidoreductase

Publisher: Oxford University Press (OUP)

Date: 06-1995

DOI: 10.1104/PP.108.2.859

Histone Acetylation, VERNALIZATION INSENSITIVE 3 , FLOWERING LOCUS C , and the Vernalization Response

Publisher: Elsevier BV

Date: 07-2009

DOI: 10.1093/MP/SSP021

Abstract: The quantitative induction of VIN3 by low temperatures is required for PRC2 repression of FLC and promotion of flowering (vernalization) in Arabidopsis. Histone acetylation, a chromatin modification commonly associated with gene transcription, increased on VIN3 chromatin in two spatially and temporally distinct phases in response to low temperatures. During short-term cold exposure, histone H3 acetylation at the transcription start site rapidly increased, implying that it is required for VIN3 induction. Subsequent changes in histone H3 and H4 acetylation occurred following continued VIN3 transcription during prolonged cold exposure. Members of the SAGA-like transcriptional adaptor complex, including the histone acetyltransferase GCN5, which induces expression of the cold acclimation pathway genes, do not regulate VIN3 induction during cold exposure, indicating that the cold acclimation pathway and the cold-induction of VIN3 are regulated by different transcriptional mechanisms. Mutations in the other 11 histone acetyltransferase genes did not affect VIN3 induction. However, nicotinamide, a histone deacetylase inhibitor, induced VIN3 and altered histone acetylation at the VIN3 locus. VIN3 induction was proportional to the length of nicotinamide treatment, which was associated with an early-flowering phenotype and repression of FLC. However, unlike vernalization, the repression of FLC was independent of VIN3 activity. Nicotinamide treatment did not cause a change in the expression of any genes in the autonomous pathway or members of the PRC2 complex, the well characterized repressors of FLC. Our data suggest that FLC is repressed via a novel pathway involving the SIR2 class of histone deacetylases.

The SCO2 protein disulphide isomerase is required for thylakoid biogenesis and interacts with LHCB1 chlorophyll a/b binding proteins which affects chlorophyll biosynthesis in Arabidopsis seedlings.

Publisher: Wiley

Date: 02-12-2012

DOI: 10.1111/J.1365-313X.2011.04833.X

The Transcription Factor MYB29 Is a Regulator of ALTERNATIVE OXIDASE1a

Publisher: Oxford University Press (OUP)

Date: 06-02-2017

DOI: 10.1104/PP.16.01494

Immunofluorescence localization of ?-amylase in the scutellum, germ aleurone and ?normal? aleurone of germinated barley grains

Publisher: Springer Science and Business Media LLC

Date: 06-1989

DOI: 10.1007/BF01403450

The Cytoskeleton and the Peroxisomal-Targeted SNOWY COTYLEDON3 Protein Are Required for Chloroplast Development in Arabidopsis

Publisher: Oxford University Press (OUP)

Date: 10-2010

DOI: 10.1105/TPC.110.074781

Abstract: Here, we describe the snowy cotyledon3 (sco3-1) mutation, which impairs chloroplast and etioplast development in Arabidopsis thaliana seedlings. SCO3 is a member of a largely uncharacterized protein family unique to the plant kingdom. The sco3-1 mutation alters chloroplast morphology and development, reduces chlorophyll accumulation, impairs thylakoid formation and photosynthesis in seedlings, and results in photoinhibition under extreme CO2 concentrations in mature leaves. There are no readily apparent changes to chloroplast biology, such as transcription or assembly that explain the disruption to chloroplast biogenesis. Indeed, SCO3 is actually targeted to another organelle, specifically to the periphery of peroxisomes. However, impaired chloroplast development cannot be attributed to perturbed peroxisomal metabolic processes involving germination, fatty acid β-oxidation or photorespiration, though there are so far undescribed changes in low and high CO2 sensitivity in seedlings and young true leaves. Many of the chloroplasts are bilobed, and some have persistent membranous extensions that encircle other cellular components. Significantly, there are changes to the cytoskeleton in sco3-1, and microtubule inhibitors have similar effects on chloroplast biogenesis as sco3-1 does. The localization of SCO3 to the periphery of the peroxisomes was shown to be dependent on a functional microtubule cytoskeleton. Therefore, the microtubule and peroxisome-associated SCO3 protein is required for chloroplast development, and sco3-1, along with microtubule inhibitors, demonstrates an unexpected role for the cytoskeleton and peroxisomes in chloroplast biogenesis.

Photoprotection in a zeaxanthin- and lutein-deficient double mutant of Arabidopsis

Publisher: Springer Science and Business Media LLC

Date: 2001

DOI: 10.1023/A:1010661102365

Genetic manipulation of carotenoid biosynthesis and photoprotection

Publisher: The Royal Society

Date: 29-10-2000

DOI: 10.1098/RSTB.2000.0701

Abstract: There are multiple complementary and redundant mechanisms to provide protection against photooxidative damage, including non–photochemical quenching (NPQ). NPQ dissipates excess excitation energy as heat by using xanthophylls in combination with changes to the light–harvesting complex (LHC) antenna. The xanthophylls are oxygenated carotenoids that in addition to contributing to NPQ can quench singlet or triplet chlorophyll and are necessary for the assembly and stability of the antenna. We have genetically manipulated the expression of the ε–cyclase and β–carotene hydroxylase carotenoid biosynthetic enzymes in Arabidopsis thaliana . The ε–cyclase overexpression confirmed that lut2 (lutein deficient) is a mutation in the ε–cyclase gene and demonstrated that lutein content can be altered at the level of mRNA abundance with levels ranging from 0 to 180% of wild–type. Also, it is clear that lutein affects the induction and extent of NPQ. The deleterious effects of lutein deficiency on NPQ in Arabidopsis and Chlamydomonas are additive, no matter what the genetic background, whether npq1 (zeaxanthin deficient), aba1 or antisense β–hydroxylase (xanthophyll cycle pool decreased). Additionally, increasing lutein content causes a marginal, but significant, increase in the rate of induction of NPQ despite a reduction in the xanthophyll cycle pool size.

Antisense inhibition of the beta-carotene hydroxylase enzyme in Arabidopsis and the implications for carotenoid accumulation, photoprotection and antenna assembly

Publisher: Springer Science and Business Media LLC

Date: 2001

DOI: 10.1023/A:1010669404183

Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model

Publisher: Public Library of Science (PLoS)

Date: 06-09-2022

DOI: 10.1371/JOURNAL.PCBI.1009767

Abstract: Comprehensive molecular characterization of cancer subtypes is essential for predicting clinical outcomes and searching for personalized treatments. We present bnClustOmics, a statistical model and computational tool for multi-omics unsupervised clustering, which serves a dual purpose: Clustering patient s les based on a Bayesian network mixture model and learning the networks of omics variables representing these clusters. The discovered networks encode interactions among all omics variables and provide a molecular characterization of each patient subgroup. We conducted simulation studies that demonstrated the advantages of our approach compared to other clustering methods in the case where the generative model is a mixture of Bayesian networks. We applied bnClustOmics to a hepatocellular carcinoma (HCC) dataset comprising genome (mutation and copy number), transcriptome, proteome, and phosphoproteome data. We identified three main HCC subtypes together with molecular characteristics, some of which are associated with survival even when adjusting for the clinical stage. Cluster-specific networks shed light on the links between genotypes and molecular phenotypes of s les within their respective clusters and suggest targets for personalized treatments.

Autophagy promotes photomorphogenesis during seedling development in Arabidopsis in carbon limiting conditions

Publisher: Cold Spring Harbor Laboratory

Date: 25-03-2021

DOI: 10.1101/2021.03.25.437007

Abstract: Autophagy is a conserved catabolic process that plays an essential role under nutrient starvation condition and influences different developmental processes. We observed that seedlings of autophagy mutants ( atg2 , atg5 , atg7, and atg9 ) germinated in the dark showed delayed chloroplast development following illumination. The delayed chloroplast development was characterized by a decrease in photosynthetic and chlorophyll biosynthetic proteins, lower chlorophyll content, reduced chloroplast size, and increased levels of proteins involved in lipid biosynthesis. Confirming the biological impact of these differences, photosynthetic performance was impaired in autophagy mutants 12h post illumination. We investigated if the delayed chloroplast development could be explained by lower lipid import to the chloroplast or lower triglyceride (TAG) turnover. We observed that the limitations in the chloroplast lipid import imposed by trigalactosyldiacylglycerol1 are unlikely to explain the delay in photomorphogenesis. However, we found that lower TAG mobility in the triacylglycerol lipase mutant sugardependent1 significantly affected photomorphogenesis. Moreover, we showed that lower levels of carbon resources exacerbated the delay in photomorphogenesis whereas higher levels of carbon resources had an opposite effect. This work provides evidence that autophagic process operate during de-etiolation in a manner that contributes to photomorphogenesis through increasing lipid turnover to physically or energetically sustain photomorphogenesis.

A cis-carotene derived apocarotenoid regulates etioplast and chloroplast development

Publisher: eLife Sciences Publications, Ltd

Date: 31-01-2020

DOI: 10.7554/ELIFE.45310

Abstract: Carotenoids are a core plastid component and yet their regulatory function during plastid biogenesis remains enigmatic. A unique carotenoid biosynthesis mutant, carotenoid chloroplast regulation 2 ( ccr2 ), that has no prolamellar body (PLB) and normal PROTOCHLOROPHYLLIDE OXIDOREDUCTASE (POR) levels, was used to demonstrate a regulatory function for carotenoids and their derivatives under varied dark-light regimes. A forward genetics approach revealed how an epistatic interaction between a ζ-carotene isomerase mutant ( ziso-155 ) and ccr2 blocked the biosynthesis of specific cis -carotenes and restored PLB formation in etioplasts. We attributed this to a novel apocarotenoid retrograde signal, as chemical inhibition of carotenoid cleavage dioxygenase activity restored PLB formation in ccr2 etioplasts during skotomorphogenesis. The apocarotenoid acted in parallel to the repressor of photomorphogenesis, DEETIOLATED1 (DET1), to transcriptionally regulate PROTOCHLOROPHYLLIDE OXIDOREDUCTASE (POR), PHYTOCHROME INTERACTING FACTOR3 (PIF3) and ELONGATED HYPOCOTYL5 (HY5). The unknown apocarotenoid signal restored POR protein levels and PLB formation in det1 , thereby controlling plastid development.

Autophagy promotes photomorphogenesis during seedling development in Arabidopsis in carbon limiting conditions

Publisher: Wiley

Date: 21-08-2021

DOI: 10.1111/TPJ.15452

Abstract: Autophagy is a conserved catabolic process that plays an essential role under nutrient starvation conditions and influences different developmental processes. We observed that seedlings of autophagy mutants ( atg2 , atg5 , atg7 , and atg9 ) germinated in the dark showed delayed chloroplast development following illumination. The delayed chloroplast development was characterized by a decrease in photosynthetic and chlorophyll biosynthetic proteins, lower chlorophyll content, reduced chloroplast size, and increased levels of proteins involved in lipid biosynthesis. Confirming the biological impact of these differences, photosynthetic performance was impaired in autophagy mutants 12 h post‐illumination. We observed that while gene expression for photosynthetic machinery during de‐etiolation was largely unaffected in atg mutants, several genes involved in photosystem assembly were transcriptionally downregulated. We also investigated if the delayed chloroplast development could be explained by lower lipid import to the chloroplast or lower triglyceride (TAG) turnover. We observed that the limitations in the chloroplast lipid import imposed by trigalactosyldiacylglycerol1 are unlikely to explain the delay in chloroplast development. However, we found that lower TAG mobility in the triacylglycerol lipase mutant sugardependent1 significantly affected de‐etiolation. Moreover, we showed that lower levels of carbon resources exacerbated the slow greening phenotype whereas higher levels of carbon resources had an opposite effect. This work suggests a lack of autophagy machinery limits chloroplast development during de‐etiolation, and this is exacerbated by limited lipid turnover (lipophagy) that physically or energetically restrains chloroplast development.

De novo synthesis and degradation of Lx and V cycle pigments during shade and sun acclimation in avocado leaves

Publisher: Oxford University Press (OUP)

Date: 05-12-2009

DOI: 10.1104/PP.108.131417

Identification of the carotenoid isomerase provides insight into carotenoid biosynthesis, prolamellar body formation, and photomorphogenesis

Publisher: Oxford University Press (OUP)

Date: 02-2002

DOI: 10.1105/TPC.010302

Abstract: Carotenoids are essential photoprotective and antioxidant pigments synthesized by all photosynthetic organisms. Most carotenoid biosynthetic enzymes were thought to have evolved independently in bacteria and plants. For ex le, in bacteria, a single enzyme (CrtI) catalyzes the four desaturations leading from the colorless compound phytoene to the red compound lycopene, whereas plants require two desaturases (phytoene and zeta-carotene desaturases) that are unrelated to the bacterial enzyme. We have demonstrated that carotenoid desaturation in plants requires a third distinct enzyme activity, the carotenoid isomerase (CRTISO), which, unlike phytoene and zeta-carotene desaturases, apparently arose from a progenitor bacterial desaturase. The Arabidopsis CRTISO locus was identified by the partial inhibition of lutein synthesis in light-grown tissue and the accumulation of poly-cis-carotene precursors in dark-grown tissue of crtISO mutants. After positional cloning, enzymatic analysis of CRTISO expressed in Escherichia coli confirmed that the enzyme catalyzes the isomerization of poly-cis-carotenoids to all-trans-carotenoids. Etioplasts of dark-grown crtISO mutants accumulate acyclic poly-cis-carotenoids in place of cyclic all-trans-xanthophylls and also lack prolamellar bodies (PLBs), the lattice of tubular membranes that defines an etioplast. This demonstrates a requirement for carotenoid biosynthesis to form the PLB. The absence of PLBs in crtISO mutants demonstrates a function for this unique structure and carotenoids in facilitating chloroplast development during the first critical days of seedling germination and photomorphogenesis.

A Novel Proteinase, SNOWY COTYLEDON4, Is Required for Photosynthetic Acclimation to Higher Light Intensities in Arabidopsis  

Publisher: Oxford University Press (OUP)

Date: 12-08-2013

DOI: 10.1104/PP.113.216036

Abstract: Excess light can have a negative impact on photosynthesis thus, plants have evolved many different ways to adapt to different light conditions to both optimize energy use and avoid damage caused by excess light. Analysis of the Arabidopsis (Arabidopsis thaliana) mutant snowy cotyledon4 (sco4) revealed a mutation in a chloroplast-targeted protein that shares limited homology with CaaX-type endopeptidases. The SCO4 protein possesses an important function in photosynthesis and development, with point mutations rendering the seedlings and adult plants susceptible to photooxidative stress. The sco4 mutation impairs the acclimation of chloroplasts and their photosystems to excess light, evidenced in a reduction in photosystem I function, decreased linear electron transfer, yet increased nonphotochemical quenching. SCO4 is localized to the chloroplasts, which suggests the existence of an unreported type of protein modification within this organelle. Phylogenetic and yeast complementation analyses of SCO4-like proteins reveal that SCO4 is a member of an unknown group of higher plant-specific proteinases quite distinct from the well-described CaaX-type endopeptidases RAS Converting Enzyme1 (RCE1) and zinc metallopeptidase STE24 and lacks canonical CaaX activity. Therefore, we hypothesize that SCO4 is a novel endopeptidase required for critical protein modifications within chloroplasts, influencing the function of proteins involved in photosynthesis required for tolerance to excess light.

Occurrence of the lutein-epoxide cycle in mistletoes of the Loranthaceae and Viscaceae

Publisher: Springer Science and Business Media LLC

Date: 10-2003

DOI: 10.1007/S00425-003-1059-7

Abstract: The lutein-epoxide cycle (Lx cycle) is an auxiliary xanthophyll cycle known to operate only in some higher-plant species. It occurs in parallel with the common violaxanthin cycle (V cycle) and involves the same epoxidation and de-epoxidation reactions as in the V cycle. In this study, the occurrence of the Lx cycle was investigated in the two major families of mistletoe, the Loranthaceae and the Viscaceae. In an attempt to find the limiting factor(s) for the occurrence of the Lx cycle, pigment profiles of mistletoes with and without the Lx cycle were compared. The availability of lutein as a substrate for the zeaxanthin epoxidase appeared not to be critical. This was supported by the absence of the Lx cycle in the transgenic Arabidopsis plant lutOE, in which synthesis of lutein was increased at the expense of V by overexpression of epsilon-cyclase, a key enzyme for lutein synthesis. Furthermore, analysis of pigment distribution within the mistletoe thylakoids excluded the possibility of different localizations for the Lx- and V-cycle pigments. From these findings, together with previous reports on the substrate specificity of the two enzymes in the V cycle, we propose that mutation to zeaxanthin epoxidase could have resulted in altered regulation and/or substrate specificity of the enzyme that gave rise to the parallel operation of two xanthophyll cycles in some plants. The distribution pattern of Lx in the mistletoe phylogeny inferred from 18S rRNA gene sequences also suggested that the occurrence of the Lx cycle is determined genetically. Possible molecular evolutionary processes that may have led to the operation of the Lx cycle in some mistletoes are discussed.

Systemic and Intracellular Responses to Photooxidative Stress in Arabidopsis

Publisher: Oxford University Press (OUP)

Date: 12-2007

DOI: 10.1105/TPC.106.045898

Abstract: As the sun tracks daily through the sky from east to west, different parts of the canopy are exposed to high light (HL). The extent of and mechanisms by which a systemic acquired acclimation (SAA) response might preacclimate shaded leaves that will be subsequently exposed to full sunlight is largely undefined. We investigated the role of an Arabidopsis thaliana zinc finger transcription factor, ZAT10, in SAA. ZAT10 overexpression resulted in enhanced tolerance to photoinhibitory light and exogenous H2O2, increased expression of antioxidative genes whose products are targeted to multiple subcellular compartments. Partial HL exposure of a leaf or leaves rapidly induced ZAT10 mRNA in distal, shaded photosynthetic tissues, including the floral stem, cauline leaves, and rosette, but not in roots. Fully 86% of fivefold HL-upregulated and 71% of HL-downregulated genes were induced and repressed, respectively, in distal, shaded leaves. Between 15 and 23% of genes whose expression changed in the HL and/or distal tissues were coexpressed in the ZAT10 overexpression plants, implicating ZAT10 in modulating the expression of SAA-regulated genes. The SAA response was detectable in plants with mutations in abscisic acid, methyl jasmonate, or salicylic acid synthesis or perception, and systemic H2O2 diffusion was not detected. Hence, SAA is distinct from pathogen-stimulated systemic acquired resistance and apparently involves a novel signal or combination of signals that preacclimate photosynthetic tissues to HL.

A comparison of the EU regulatory approach to directed mutagenesis with that of other jurisdictions, consequences for international trade and potential steps forward

Publisher: Wiley

Date: 16-01-2019

DOI: 10.1111/NPH.15627

Abstract: A special regulatory regime applies to products of recombinant nucleic acid modifications. A ruling from the European Court of Justice has interpreted this regulatory regime in a way that it also applies to emerging mutagenesis techniques. Elsewhere regulatory progress is also ongoing. In 2015, Argentina launched a regulatory framework, followed by Chile in 2017 and recently Brazil and Colombia. In March 2018, the USDA announced that it will not regulate genome-edited plants differently if they could have also been developed through traditional breeding. Canada has an altogether different approach with their Plants with Novel Traits regulations. Australia is currently reviewing its Gene Technology Act. This article illustrates the deviation of the European Union's (EU's) approach from the one of most of the other countries studied here. Whereas the EU does not implement a case-by-case approach, this approach is taken by several other jurisdictions. Also, the EU court ruling adheres to a process-based approach while most other countries have a stronger emphasis on the regulation of the resulting product. It is concluded that, unless a functioning identity preservation system for products of directed mutagenesis can be established, the deviation results in a risk of asynchronous approvals and disruptions in international trade.

Chrophyll biosynthesis. Expression of a second Chl I gene of magnesium chelatase in Arabidopsis supports only limited chlorophyll synthesis

Publisher: Oxford University Press (OUP)

Date: 02-2002

DOI: 10.1104/PP.010625

Abstract: Magnesium (Mg) chelatase is a heterotrimeric enzyme complex that catalyzes a key regulatory and enzymatic reaction in chlorophyll biosynthesis, the insertion of Mg2+ into protoporphyrin IX. Studies of the enzyme complex reconstituted in vitro have shown that all three of its subunits, CHL I, CHL D, and CHL H, are required for enzymatic activity. However, a new T-DNA knockout mutant of the chlorina locus, ch42-3 (Chl I), in Arabidopsis is still able to accumulate some chlorophyll despite the absence of Chl I mRNA and protein. In barley (Hordeum vulgare), CHL I is encoded by a single gene. We have identified an open reading frame that apparently encodes a second Chl Igene, Chl I2. Chl I1 and Chl I2 mRNA accumulate to similar levels in wild type, yet CHL I2 protein is not detectable in wild type or ch42-3, although the protein is translated and stromally processed as shown by in vivo pulse labeling and in vitro chloroplast imports. It is surprising that CHL D accumulates to wild-type levels in ch42-3, which is in contrast to reports that CHL D is unstable in CHL I-deficient backgrounds of barley. Our results show that limited Mg chelatase activity and CHL D accumulation can occur without detectable CHL I, despite its obligate requirement in vitro and its proposed chaperone-like stabilization and activation of CHL D. Thus, the unusual post-translational regulation of the CHL I2 protein provides an opportunity to study the different steps involved in stabilization and activation of the heterotrimeric Mg chelatase in vivo.

Reducing PSY activity fine tunes threshold levels of acis-carotene-derived signal that regulates the PIF3/HY5 module and plastid biogenesis

Publisher: Cold Spring Harbor Laboratory

Date: 30-06-2023

DOI: 10.1101/2023.06.29.546996

Abstract: PHYTOENE SYNTHASE (PSY) is a rate-limiting enzyme catalysing the first committed step of carotenoid biosynthesis, and changes in PSY gene expression and/or protein activity alter carotenoid composition and plastid differentiation in plants. Here we identified four genetic variants of PSY ( psy −4 , psy −90 , psy −130 and psy −145 ) using a forward genetics approach that rescued leaf virescence phenotypes displayed by the Arabidopsis CAROTENOID ISOMERASE (CRTISO) mutant ccr2 ( carotenoid and chloroplast regulation 2 ) when grown under a shorter photoperiod. The four non-lethal mutations affected alternative splicing, enzyme-substrate interactions, and PSY:ORANGE multi-enzyme complex binding, constituting the dynamic posttranscriptional fine-tuning of PSY levels and activity without changing localization to the stroma and protothylakoid membranes. psy genetic variants did not alter overall total xanthophyll or cis-carotene accumulation in ccr2 yet reduced specific acyclic linear cis -carotenes linked to the biosynthesis of a yet-to-be-identified apocarotenoid signal. ccr2 psy variants modulated the ratio of PHYTOCHROME-INTERACTING FACTOR 3/ELONGATED HYPOCOTYL 5 (PIF3/HY5), displayed a normal PLB formation in etioplasts, and chlorophyll accumulation during seedling photomorphogenesis. Thus, suppressing PSY activity and impairing PSY:ORANGE protein interactions reveals how threshold specific cis -carotene levels can be fine-tuned through holoenzyme-metabolon interactions to control plastid development. Manipulation of the PHYTOENE SYNTHASE catalytic activity in concert with its regulatory protein, ORANGE, reduces threshold levels of acyclic linear cis -carotenes that signal control over plastid biogenesis in dark and light grown Arabidopsis seedlings

Author response: A chloroplast retrograde signal, 3’-phosphoadenosine 5’-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination

Publisher: eLife Sciences Publications, Ltd

Date: 11-03-2017

DOI: 10.7554/ELIFE.23361.026

Genetic suppression of plant development and chloroplast biogenesis via the Snowy Cotyledon 3 and Phytochrome B pathways

Publisher: CSIRO Publishing

Date: 2015

DOI: 10.1071/FP15026

Abstract: Plant development is regulated by external and internal factors such as light and chloroplast development. A revertant of the Arabidopsis thaliana (L.) Heyhn. chloroplast biogenesis mutant snowy cotyledon 3 (sco3–1) was isolated partially recovering the impaired chloroplast phenotype. The mutation was identified in the Phytochrome B (PhyB) gene and is a result of an amino acid change within the PAS repeat domain required for light-induced nuclear localisation. An independent phyB-9 mutation was crossed into sco3–1 mutants, resulting in the same partial reversion of sco3–1. Further analysis demonstrated that SCO3 and PhyB influence the greening process of seedlings and rosette leaves, embryogenesis, rosette formation and flowering. Interestingly, the functions of these proteins are interwoven in various ways, suggesting a complex genetic interaction. Whole-transcriptome profiling of sco3–1phyB-9 indicated that a completely distinct set of genes was differentially regulated in the double mutant compared with the single sco3–1 or phyB-9 mutants. Thus, we hypothesise that PhyB and SCO3 genetically suppress each other in plant and chloroplast development.

Transcriptional control of SET DOMAIN GROUP 8 and CAROTENOID ISOMERASE during Arabidopsis development.

Publisher: Elsevier BV

Date: 2010

DOI: 10.1093/MP/SSP092

Abstract: Carotenoids are pigments required for photosynthesis, photoprotection and the production of carotenoid-derived hormones such as ABA and strigolactones. The carotenoid biosynthetic pathway bifurcates after lycopene to produce epsilon- and beta-carotenoids and this branch is critical for determining carotenoid composition. Here, we show how the branch point can be regulated by the chromatin-modifying histone methyltransferase, Set Domain Group 8 (SDG8) targeting the carotenoid isomerase (CRTISO). SDG8 is required to maintain permissive expression of CRTISO during seedling development, in leaves, shoot apex, and some floral organs. The CRTISO and SDG8 promoters show overlapping tissue-specific patterns of reporter gene activity. Interestingly, CRTISO showed atypical reporter gene expression in terms of greater variability between different lines compared to the Cauliflower Mosaic Virus 35S promoter (CaMV35s) and epsilonLCY promoters, potentially due to chromosomal position effects. Regulation of the CRTISO promoter was dependent in part upon the presence or absence of SDG8. Knockouts of SDG8 (carotenoid and chloroplast regulation (ccr1)) and CRTISO (ccr2) result in altered carotenoid composition and this could be restored in ccr2 using the CaMV35s or CRTISO promoters. In contrast, varying degrees of GUS expression and carotenoid complementation by CRTISO overexpression using CaMV35S or CRTISO promoters in the ccr1 background demonstrated that both the CRTISO promoter and open reading frame are necessary for SDG8-mediated expression of CRTISO.

Observation of the Bs

Publisher: American Physical Society (APS)

Date: 07-10-2020

DOI: 10.1103/PHYSREVLETT.125.152001

Comparative proteomics of high light stress in the model alga Chlamydomonas reinhardtii

Publisher: Wiley

Date: 08-2006

DOI: 10.1002/PMIC.200500907

Abstract: High light (HL) stress adversely affects growth, productivity and viability of photosynthetic organisms. The green alga Chlamydomonas reinhardtii is a model system to study photosynthesis and light stress. Comparative proteomics of wild-type and two very high light (VHL)-resistant mutants, VHL(R)-S4 and VHL(R)-S9, revealed complex alterations in response to excess light. A two-dimensional reference map of the soluble subproteome was constructed representing about 1500 proteins. A total of 83 proteins from various metabolic pathways were identified by peptide mass fingerprinting. Quantitative comparisons of 444 proteins showed 105 significantly changed proteins between wild type and mutants under different light conditions. Commonly, more proteins were decreased than increased, but different proteins were affected in each genotype. Proteins uniquely altered in either VHL(R) mutant may be involved in VHL resistance. Such candidate proteins similarly altered without light stress, thus possibly contributing to "pre-adaptation" of mutants to VHL, included decreased levels of a DEAD box RNA helicase (VHL(R)-S4) and NAB1 and RB38 proteins (VHL(R)-S9), and increased levels of an oxygen evolving enhancer 1 (OEE1) isoform and an unknown protein (VHL(R)-S4). Changes from increased levels in HL to decreased levels in excess light, included OEE1 (VHL(R)-S9) or the reverse change for NAB1, RB38, beta-carbonic anhydrase and an ABC transporter-like protein (VHL(R)-S4).

Source to sink: regulation of carotenoid biosynthesis in plants

Publisher: Elsevier BV

Date: 05-2010

DOI: 10.1016/J.TPLANTS.2010.02.003

Abstract: Carotenoids are a erse group of colourful pigments naturally found in plants, algae, fungi and bacteria. They play essential roles in development, photosynthesis, root-mycorrhizal interactions and the production of phytohormones, such as abscisic acid and strigolactone. Carotenoid biosynthesis is regulated throughout the life cycle of a plant with dynamic changes in composition matched to prevailing developmental requirements and in response to external environmental stimuli. There are key regulatory nodes in the pathway that control the flux of metabolites into the pathway and alter flux through the pathway. The molecular nature of the mechanisms regulating carotenoid biosynthesis, including evidence for metabolite feedback, transcription and epigenetic control as well as their accumulation, storage and degradation will be the focus of this review.

Genetic dissection of chloroplast biogenesis and development: An overview

Publisher: Oxford University Press (OUP)

Date: 17-02-2011

DOI: 10.1104/PP.110.170365

A Novel fry1 Allele Reveals the Existence of a Mutant Phenotype Unrelated to 5′->3′ Exoribonuclease (XRN) Activities in Arabidopsis thaliana Roots

Publisher: Public Library of Science (PLoS)

Date: 03-02-2011

DOI: 10.1371/JOURNAL.PONE.0016724

Decreased photochemical efficiency of photosystem II following sunlight exposure of shade-grown leaves of avocado: Because of, or in spite of, two kinetically distinct xanthophyll cycles?

Publisher: Oxford University Press (OUP)

Date: 04-12-2013

DOI: 10.1104/PP.112.209692

Abstract: This study resolved correlations between changes in xanthophyll pigments and photosynthetic properties in attached and detached shade-grown avocado (Persea americana) leaves upon sun exposure. Lutein epoxide (Lx) was deepoxidized to lutein (L), increasing the total pool by ƊL over 5 h, whereas violaxanthin (V) conversion to antheraxanthin (A) and zeaxanthin (Z) ceased after 1 h. During subsequent dark or shade recovery, de novo synthesis of L and Z continued, followed by epoxidation of A and Z but not of L. Light-saturated nonphotochemical quenching (NPQ) was strongly and linearly correlated with decreasing [Lx] and increasing [∆L] but showed a biphasic correlation with declining [V] and increasing [A+Z] separated when V deepoxidation ceased. When considering [ƊL+∆Z], the monophasic linear correlation was restored. Photochemical efficiency of photosystem II (PSII) and photosystem (PSI deduced from the delivery of electrons to PSI in saturating single-turnover flashes) showed a strong correlation in their continuous decline in sunlight and an increase in NPQ capacity. This decrease was also reflected in the initial reduction of the slope of photosynthetic electron transport versus photon flux density. Generally longer, stronger sun exposures enhanced declines in both slope and maximum photosynthetic electron transport rates as well as photochemical efficiency of PSII and PSII/PSI more severely and prevented full recovery. Interestingly, increased NPQ capacity was accompanied by slower relaxation. This was more prominent in detached leaves with closed stomata, indicating that photorespiratory recycling of CO2 provided little photoprotection to avocado shade leaves. Sun exposure of these shade leaves initiates a continuum of photoprotection, beyond full engagement of the Lx and V cycle in the antenna, but ultimately photoinactivated PSII reaction centers.

Ethylene Responses in Rice Roots and Coleoptiles Are Differentially Regulated by a Carotenoid Isomerase-Mediated Abscisic Acid Pathway

Publisher: Oxford University Press (OUP)

Date: 04-2015

DOI: 10.1105/TPC.15.00080

Abstract: Ethylene and abscisic acid (ABA) act synergistically or antagonistically to regulate plant growth and development. ABA is derived from the carotenoid biosynthesis pathway. Here, we analyzed the interplay among ethylene, carotenoid biogenesis, and ABA in rice (Oryza sativa) using the rice ethylene response mutant mhz5, which displays a reduced ethylene response in roots but an enhanced ethylene response in coleoptiles. We found that MHZ5 encodes a carotenoid isomerase and that the mutation in mhz5 blocks carotenoid biosynthesis, reduces ABA accumulation, and promotes ethylene production in etiolated seedlings. ABA can largely rescue the ethylene response of the mhz5 mutant. Ethylene induces MHZ5 expression, the production of neoxanthin, an ABA biosynthesis precursor, and ABA accumulation in roots. MHZ5 overexpression results in enhanced ethylene sensitivity in roots and reduced ethylene sensitivity in coleoptiles. Mutation or overexpression of MHZ5 also alters the expression of ethylene-responsive genes. Genetic studies revealed that the MHZ5-mediated ABA pathway acts downstream of ethylene signaling to inhibit root growth. The MHZ5-mediated ABA pathway likely acts upstream but negatively regulates ethylene signaling to control coleoptile growth. Our study reveals novel interactions among ethylene, carotenogenesis, and ABA and provides insight into improvements in agronomic traits and adaptive growth through the manipulation of these pathways in rice.

5585542 DNA sequences encoding at least part of the tomato enzyme endopolygalacturonase PG1 beta-subunit

Publisher: Elsevier BV

Date: 1997

DOI: 10.1016/S0734-9750(97)87491-5

Insights into chloroplast biogenesis and development

Publisher: Elsevier BV

Date: 09-2015

DOI: 10.1016/J.BBABIO.2015.02.003

Abstract: In recent years many advances have been made to obtain insight into chloroplast biogenesis and development. In plants several plastids types exist such as the proplastid (which is the progenitor of all plastids), leucoplasts (group of colourless plastids important for storage including elaioplasts (lipids), amyloplasts (starch) or proteinoplasts (proteins)), chromoplasts (yellow to orange-coloured due to carotenoids, in flowers or in old leaves as gerontoplasts), and the green chloroplasts. Chloroplasts are indispensable for plant development not only by performing photosynthesis and thus rendering the plant photoautotrophic, but also for biochemical processes (which in some instances can also take place in other plastids types), such as the synthesis of pigments, lipids, and plant hormones and sensing environmental stimuli. Although we understand many aspects of these processes there are gaps in our understanding of the establishment of functional chloroplasts and their regulation. Why is that so? Even though chloroplast function is comparable in all plants and most of the algae, ferns and moss, detailed analyses have revealed many differences, specifically with respect to its biogenesis. As an update to our prior review on the genetic analysis of chloroplast biogenesis and development [1] herein we will focus on recent advances in Angiosperms (monocotyledonous and dicotyledonous plants) that provide novel insights and highlight the challenges and prospects for unravelling the regulation of chloroplast biogenesis specifically during the establishment of the young plants. This article is part of a Special Issue entitled: Chloroplast Biogenesis.

A simple chlorophyll fluorescence parameter that correlates with the rate coefficient of photoinactivation of Photosystem II

Publisher: Springer Science and Business Media LLC

Date: 06-2005

DOI: 10.1007/S11120-004-6430-4

Abstract: A method of partitioning the energy in a mixed population of active and photoinactivated Photosystem II (PS II) complexes based on chlorophyll fluorescence measurements is presented. There are four energy fluxes, each with its quantum efficiency: a flux associated with photochemical electron flow in active PS II reaction centres (JPS II), thermal dissipation in photoinactivated, non-functional PS IIs (JNF), light-regulated thermal dissipation in active PS IIs (JNPQ) and a combined flux of fluorescence and constitutive, light-independent thermal dissipation (Jf,D). The four quantum efficiencies add up to 1.0, without the need to introduce an 'excess' term E, which in other studies has been claimed to be linearly correlated with the rate coefficient of photoinactivation of PS II (kpi). We examined the correlation of kpi with various fluxes, and found that the combined flux (JNPQ + Jf,D= Jpi) is as well correlated with kpi as is E. This combined flux arises from Fs/Fm ', the ratio of steady-state to maximum fluorescence during illumination, which represents the quantum efficiency of combined non-photochemical dissipation pathways in active PS IIs. Since Fs/Fm ' or its equivalent, Jpi, is a likely source of events leading to photoinactivation of PS II, we conclude that Fs/Fm ' is a simple predictor of kpi.

Systemic and Local Responses to Repeated HL Stress-Induced Retrograde Signaling in Arabidopsis.

Publisher: Frontiers Media SA

Date: 2012

DOI: 10.3389/FPLS.2012.00303

Enzymes degraded under high light maintain proteostasis by transcriptional regulation in Arabidopsis

Publisher: Cold Spring Harbor Laboratory

Date: 03-10-2021

DOI: 10.1101/2021.10.03.462903

Abstract: Photo-inhibitory high light stress in Arabidopsis leads to increases in markers of protein degradation and transcriptional upregulation of proteases and proteolytic machinery, but proteostasis is largely maintained. We find significant increases in the in vivo degradation rate for specific molecular chaperones, nitrate reductase, glyceraldehyde-3 phosphate dehydrogenase, and phosphoglycerate kinase and other plastid, mitochondrial, peroxisomal, and cytosolic enzymes involved in redox shuttles. Coupled analysis of protein degradation rates, mRNA levels, and protein abundance reveal that 57% of the nuclear-encoded enzymes with higher degradation rates also had high light-induced transcriptional responses to maintain proteostasis. In contrast, plastid-encoded proteins with enhanced degradation rates showed decreased transcript abundances and must maintain protein abundance by other processes. This analysis reveals a light-induced transcriptional program for nuclear-encoded genes, beyond the regulation of PSII D1 subunit and the function of PSII, to replace key protein degradation targets in plants and ensure proteostasis under high light stress.

Regulation of Carotenoid Composition and Shoot Branching inArabidopsisby a Chromatin Modifying Histone Methyltransferase, SDG8

Publisher: Oxford University Press (OUP)

Date: 2009

DOI: 10.1105/TPC.108.063131

Abstract: Carotenoid pigments are critical for plant survival, and carotenoid composition is tuned to the developmental stage, tissue, and to environmental stimuli. We report the cloning of the CAROTENOID CHLOROPLAST REGULATORY1 (CCR1) gene. The ccr1 mutant has increased shoot branching and altered carotenoid composition, namely, reduced lutein in leaves and accumulation of cis-carotenes in dark-grown seedlings. The CCR1 gene was previously isolated as EARLY FLOWERING IN SHORT DAYS and encodes a histone methyltransferase (SET DOMAIN GROUP 8) that methylates histone H3 on Lys 4 and/or 36 (H3K4 and H3K36). ccr1 plants show reduced trimethyl-H3K4 and increased dimethyl-H3K4 surrounding the CAROTENOID ISOMERASE (CRTISO) translation start site, which correlates with low levels of CRTISO mRNA. Microarrays of ccr1 revealed the downregulation of 85 genes, including CRTISO and genes associated with signaling and development, and upregulation of just 28 genes. The reduction in CRTISO transcript abundance explains the altered carotenoid profile. The changes in shoot branching are additive with more axillary branching mutants, but the altered carotenoid profile may partially affect shoot branching, potentially by perturbed biosynthesis of the carotenoid substrates of strigolactones. These results are consistent with SDG8 regulating shoot meristem activity and carotenoid biosynthesis by modifying the chromatin surrounding key genes, including CRTISO. Thus, the level of lutein, the most abundant carotenoid in higher plants that is critical for photosynthesis and photoprotection, appears to be regulated by a chromatin modifying enzyme in Arabidopsis thaliana.

Reconstruction of signal amplitudes in the CMS electromagnetic calorimeter in the presence of overlapping proton-proton interactions

Publisher: IOP Publishing

Date: 10-2020

DOI: 10.1088/1748-0221/15/10/P10002

Accumulation of the ?-subunit of polygalacturonase 1 in normal and mutant tomato fruit

Publisher: Springer Science and Business Media LLC

Date: 07-1993

DOI: 10.1007/BF00240897

Reconsidering the nature and mode of action of metabolite retrograde signals from the chloroplast

Publisher: Frontiers Media SA

Date: 2013

DOI: 10.3389/FPLS.2012.00300

Genomic breeding for food, environment and livelihoods

Publisher: Springer Science and Business Media LLC

Date: 14-03-2015

DOI: 10.1007/S12571-015-0431-3

Signaling from the Endoplasmic Reticulum Activates Brassinosteroid Signaling and Promotes Acclimation to Stress in Arabidopsis

Publisher: American Association for the Advancement of Science (AAAS)

Date: 28-09-2010

DOI: 10.1126/SCISIGNAL.2001140

Abstract: BR signaling may integrate stress responses and growth processes to optimize growth under challenging environmental conditions.

Lutein from Deepoxidation of Lutein Epoxide Replaces Zeaxanthin to Sustain an Enhanced Capacity for Nonphotochemical Chlorophyll Fluorescence Quenching in Avocado Shade Leaves in the Dark

Publisher: Oxford University Press (OUP)

Date: 22-03-2011

DOI: 10.1104/PP.111.173369

Abstract: Leaves of avocado (Persea americana) that develop and persist in deep shade canopies have very low rates of photosynthesis but contain high concentrations of lutein epoxide (Lx) that are partially deepoxidized to lutein (L) after 1 h of exposure to 120 to 350 μmol photons m−2 s−1, increasing the total L pool by 5% to 10% (ƊL). Deepoxidation of Lx to L was near stoichiometric and similar in kinetics to deepoxidation of violaxanthin (V) to antheraxanthin (A) and zeaxanthin (Z). Although the V pool was restored by epoxidation of A and Z overnight, the Lx pool was not. Depending on leaf age and pretreatment, the pool of ƊL persisted for up to 72 h in the dark. Metabolism of ƊL did not involve epoxidation to Lx. These contrasting kinetics enabled us to differentiate three states of the capacity for nonphotochemical chlorophyll fluorescence quenching (NPQ) in attached and detached leaves: ƊpH dependent (NPQƊpH) before deepoxidation after deepoxidation in the presence of ƊL, A, and Z (NPQƊLAZ) and after epoxidation of A+Z but with residual ƊL (NPQƊL). The capacity of both NPQƊLAZ and NPQƊL was similar and 45% larger than NPQƊpH, but dark relaxation of NPQƊLAZ was slower. The enhanced capacity for NPQ was lost after metabolism of ƊL. The near equivalence of NPQƊLAZ and NPQƊL provides compelling evidence that the small dynamic pool ƊL replaces A+Z in avocado to “lock in” enhanced NPQ. The results are discussed in relation to data obtained with other Lx-rich species and in mutants of Arabidopsis (Arabidopsis thaliana) with increased L pools.

Molecular and physiological responses during thermal acclimation of leaf photosynthesis and respiration in rice.

Publisher: Wiley

Date: 10-01-2020

DOI: 10.1111/PCE.13706

Abstract: To further our understanding of how sustained changes in temperature affect the carbon economy of rice (Oryza sativa), hydroponically grown plants of the IR64 cultivar were developed at 30°C/25°C (day/night) before being shifted to 25/20°C or 40/35°C. Leaf messenger RNA and protein abundance, sugar and starch concentrations, and gas-exchange and elongation rates were measured on preexisting leaves (PE) already developed at 30/25°C or leaves newly developed (ND) subsequent to temperature transfer. Following a shift in growth temperature, there was a transient adjustment in metabolic gene transcript abundance of PE leaves before homoeostasis was reached within 24 hr, aligning with R

An Uncharacterized Apocarotenoid-Derived Signal Generated in ζ-Carotene Desaturase Mutants Regulates Leaf Development and the Expression of Chloroplast and Nuclear Genes inArabidopsis   

Publisher: Oxford University Press (OUP)

Date: 06-2014

DOI: 10.1105/TPC.114.123349

Abstract: In addition to acting as photoprotective compounds, carotenoids also serve as precursors in the biosynthesis of several phytohormones and proposed regulatory signals. Here, we report a signaling process derived from carotenoids that regulates early chloroplast and leaf development. Biosynthesis of the signal depends on ζ-carotene desaturase activity encoded by the ζ-CAROTENE DESATURASE (ZDS)/CHLOROPLAST BIOGENESIS5 (CLB5) gene in Arabidopsis thaliana. Unlike other carotenoid-deficient plants, zds/clb5 mutant alleles display profound alterations in leaf morphology and cellular differentiation as well as altered expression of many plastid- and nucleus-encoded genes. The leaf developmental phenotypes and gene expression alterations of zds/clb5/spc1 de181 plants are rescued by inhibitors or mutations of phytoene desaturase, demonstrating that phytofluene and/or ζ-carotene are substrates for an unidentified signaling molecule. Our work further demonstrates that this signal is an apocarotenoid whose synthesis requires the activity of the carotenoid cleavage dioxygenase CCD4.

Diagnostic Targeted Sequencing Panel for Hepatocellular Carcinoma Genomic Screening

Publisher: Elsevier BV

Date: 11-2018

DOI: 10.1016/J.JMOLDX.2018.07.003

Abstract: Commercially available targeted panels miss genomic regions frequently altered in hepatocellular carcinoma (HCC). We sought to design and benchmark a sequencing assay for genomic screening of HCC. We designed an AmpliSeq custom panel targeting all exons of 33 protein-coding and two long noncoding RNA genes frequently mutated in HCC, TERT promoter, and nine genes with frequent copy number alterations. By using this panel, the profiling of DNA from fresh-frozen (n = 10, 1495×) and/or formalin-fixed, paraffin-embedded (FFPE) tumors with low-input DNA (n = 36, 530×) from 39 HCCs identified at least one somatic mutation in 90% of the cases. Median of 2.5 (range, 0 to 74) and 3 (range, 0 to 76) mutations were identified in fresh-frozen and FFPE tumors, respectively. Benchmarked against the mutations identified from Illumina whole-exome sequencing (WES) of the corresponding fresh-frozen tumors (105×), 98% (61 of 62) and 100% (104 of 104) of the mutations from WES were detected in the 10 fresh-frozen tumors and the 36 FFPE tumors, respectively, using the HCC panel. In addition, 18 and 70 somatic mutations in coding and noncoding genes, respectively, not found by WES were identified by using our HCC panel. Copy number alterations between WES and our HCC panel showed an overall concordance of 86%. In conclusion, we established a cost-effective assay for the detection of genomic alterations in HCC.

A Mak-like kinase is a repressor of GAMYB in barley aleurone

Publisher: Wiley

Date: 02-2003

DOI: 10.1046/J.1365-313X.2003.01663.X

Abstract: GAMYB is a gibberellin (GA)-regulated activator of hydrolase gene expression in the aleurone layer of germinating cereal grains. Although it is clear that GAMYB expression is regulated by GA, more remains to be understood about how this transcription factor operates within the GA-response pathway. In order to isolate new components from the GA-response pathway, barley aleurone libraries were screened for GAMYB-binding proteins using a recently developed yeast two-hybrid system, which is compatible with the use of transcription factors as baits. We isolated a new member of the emerging Mak-subgroup of cdc2- and MAP kinase-related protein kinases. We have termed this GAMYB-binding protein KGM (for kinase associated with GAMYB). Transient expression of KGM specifically repressed alpha-amylase promoter activity at the level of GAMYB function but a mutation designed to de-stabilise the activation loop of KGM alleviated this repression. We propose that KGM is a negative regulator of GAMYB function in aleurone that may prevent precocious hydrolase gene expression.

Predicting dark respiration rates of wheat leaves from hyperspectral reflectance

Publisher: Wiley

Date: 28-03-2019

DOI: 10.1111/PCE.13544

Abstract: Greater availability of leaf dark respiration (R

From ecophysiology to phenomics: some implications of photoprotection and shade-sun acclimation in situ for dynamics of thylakoids in vitro

Publisher: The Royal Society

Date: 19-12-2012

DOI: 10.1098/RSTB.2012.0072

Abstract: Half a century of research into the physiology and biochemistry of sun–shade acclimation in erse plants has provided reality checks for contemporary understanding of thylakoid membrane dynamics. This paper reviews recent insights into photosynthetic efficiency and photoprotection from studies of two xanthophyll cycles in old shade leaves from the inner canopy of the tropical trees Inga sapindoides and Persea americana (avocado). It then presents new physiological data from avocado on the time frames of the slow coordinated photosynthetic development of sink leaves in sunlight and on the slow renovation of photosynthetic properties in old leaves during sun to shade and shade to sun acclimation. In so doing, it grapples with issues in vivo that seem relevant to our increasingly sophisticated understanding of Δ pH-dependent, xanthophyll-pigment-stabilized non-photochemical quenching in the antenna of PSII in thylakoid membranes in vitro .

Improved survival of very high light and oxidative stress is conferred by spontaneous gain-of-function mutations in Chlamydomonas

Publisher: Elsevier BV

Date: 08-2005

DOI: 10.1016/J.BBABIO.2005.05.012

Abstract: Investigations into high light and oxidative stress in photosynthetic organisms have focussed primarily on genetic impairment of different photoprotective functions. There are few reports of "gain-of-function" mutations that provide enhanced resistance to high light and/or oxidative stress without reduced productivity. We have isolated at least four such very high light resistant (VHL(R)) mutations in the green alga, Chlamydomonas reinhardtii, that permit near maximal growth rates at light intensities lethal to wild type. This resistance is not due to an alteration in electron transport rate or quantity and functionality of the two photosystems that could have enhanced photochemical quenching. Nor is it due to reduced excitation pressure by downregulation of the light harvesting antennae or increased nonphotochemical quenching. In fact, photosynthetic activity is unaffected in more than 30 VHL(R) isolates. Instead, the basis of the VHL(R) phenotype is a combination of traits, which appears to be dominated by enhanced capacity to tolerate reactive oxygen species generated by excess light, methylviologen, rose bengal or hydrogen peroxide. This is further evidenced in lower levels of ROS after exposure to very high light in the VHL(R)-S9 mutant. Additionally, the VHL(R) phenotype is associated with increased zeaxanthin accumulation, maintenance of fast synthesis and degradation rates of the D1 protein, and sustained balanced electron flow into and out of PSI under very high light. We conclude that the VHL(R) mutations arose from a selection pressure that favors changes to the regulatory system(s) that coordinates several photoprotective processes amongst which repair of PSII and enhanced detoxification of reactive oxygen species play seminal roles.

Plastid signalling to the nucleus and beyond

Publisher: Elsevier BV

Date: 11-2008

DOI: 10.1016/J.TPLANTS.2008.08.008

Abstract: Communication between the compartments or organelles of cells is essential for plant growth and development. There is an emerging understanding of signals generated within energy-transducing organelles, such as chloroplasts and mitochondria, and the nuclear genes that respond to them, a process known as retrograde signalling. A recent series of unconnected breakthroughs have given scientists a glimpse inside the 'black box' of organellar signalling thanks to the identification of some of the factors involved in generating and propagating signals to the nucleus and, in some instances, systemically throughout photosynthetic tissues. This review will focus on recent developments in our understanding of retrograde and systemic signals generated by organelles, with an emphasis on chloroplasts.

Cell-specialized chloroplast signaling orchestrates photosynthetic and extracellular reactive oxygen species for stress responses

Publisher: Cold Spring Harbor Laboratory

Date: 03-08-2023

DOI: 10.1101/2023.08.02.551742

Abstract: Cellular responses to abiotic stress involve multiple secondary messengers including reactive oxygen species (ROS), Ca 2+ , phytohormones such as abscisic acid (ABA) and chloroplast-to-nucleus retrograde signals such as 3’-phosphoadenosine 5’-phosphate (PAP). Mechanism(s) by which these messengers, produced in different subcellular compartments, intersect for cell regulation remain enigmatic. Here we demonstrate a mechanistic link enabling ABA and the chloroplast retrograde signal PAP to coordinate both chloroplast and plasma membrane ROS production. In whole leaves, PAP alters various ROS-related processes including plasmodesmal permeability as well as responses to ozone and the bacterial elicitor flg22, but largely quenches ROS during oxidative stress. Conversely, in guard cells, both PAP and ABA induce a ROS burst in both chloroplasts via photosynthetic electron transport, and the apoplast via the RESPIRATORY BURST OXIDASE HOMOLOG (RBOH). Both subcellular ROS sources were necessary for ABA- and PAP-mediated stomatal closure. However, PAP signaling erges from ABA by activating RBOHD, instead of RBOHF, for apoplastic ROS production. We identify calcium-dependent protein kinases (CPKs) transcriptionally induced by PAP as the post-translational activators of RBOHD-mediated ROS production. CPK13, CPK32, and CPK34 concurrently activate RBOHD and the slow anion channel SLAC1 by phosphorylating two Serine (S) residues, including S120 which is also targeted by the core ABA signaling kinase OPEN STOMATA 1 (OST1). Consequently, overexpressing the PAP-induced CPKs rescues stomatal closure in ost1. Our data identify chloroplasts, as sources and mediators of ROS and retrograde signals such PAP, to be critical environmental sensors and focal node in the multifaceted cellular stress response network. The chloroplast is an important node to coordinate multiple plant signaling pathways in response to stresses such as drought. However, how does it function in specialized cells for which carbon fixation is secondary? Here we show that the chloroplast retrograde signal 3’-phosphoadenosine 5’-phosphate (PAP) plays multiple roles in reactive oxygen species (ROS) signaling and homeostasis. While PAP suppresses ROS in photosynthetic tissue, surprisingly PAP induces ROS in chloroplasts and extracellular space of guard cells to induce stomatal closure. We decipher how PAP-induced proteins activate both extracellular ROS production and anion channels for stomatal closure, thus providing a mechanism by which chloroplasts provide a strategic complement to canonical hormonal pathways in regulating plant physiological responses in specialized cells.

Periodic root branching in Arabidopsis requires synthesis of an uncharacterized carotenoid derivative

Publisher: Proceedings of the National Academy of Sciences

Date: 17-03-2014

DOI: 10.1073/PNAS.1403016111

Abstract: A fundamental question in developmental biology is how patterns are established in space and time. In plants, key differences in root system architecture are attributed to the spatial distribution pattern of lateral roots (LRs), yet how the pattern of LRs is established is only beginning to be understood. We demonstrate that the establishment of sites competent to form LRs roots requires carotenoid biosynthesis. Furthermore, our results implicate an uncharacterized carotenoid-derived molecule that functions non–cell-autonomously, specifically in LR formation. The results of this study reveal novel aspects of carotenoid biology and expand the roles of carotenoid-derived molecules into root developmental patterning.

Molecular characterization and transcriptome analysis of orange head Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Publisher: Springer Science and Business Media LLC

Date: 17-02-2015

DOI: 10.1007/S00425-015-2262-Z

Abstract: The orange head phenotype of Br - or resulted from a large insertion in carotenoid isomerase (BrCRTISO) . Comparative transcriptome analysis revealed that the mutation affected the expression of abundant transcription factor genes. A new orange trait-specific marker was developed for marker-assisted breeding. Orange head leaves are a desirable quality trait for Chinese cabbage. Our previous fine mapping identified BrCRTISO as the Br-or candidate gene for the orange Chinese cabbage mutant. Here, we examined the BrCRTISO gene from white and orange head Chinese cabbage. While BrCRTISO from the white control plant was able to complement the Arabidopsis Atcrtiso mutant phenotype, Brcrtiso with a large insertion from the orange head Chinese cabbage failed to rescue the Arabidopsis mutant phenotype. The results show that Brcrtiso was non-functional, concomitant with the accumulation of prolycopene in Br-or to yield orange head. Comparative transcriptome analysis by RNA-seq identified 372 differentially expressed genes between the control and Br-or mutant using two near-isogenic lines with white and orange inner leaves. The mutation in BrCRTISO specifically affected many genes in the functional groups involved in RNA, protein, transport, and signaling. Particularly, expressions of many transcription factor genes were dramatically altered in Br-or, suggesting a potential role of BrCRTISO or carotenoid metabolites in affecting transcription. A novel co-dominant gene-specific marker was developed that co-segregated with orange color phenotype and would be useful for marker-assisted selection with enhanced selection efficiency. Our study provides new insights into understanding of the molecular basis of Br-or in mediating head leaf color and depicts a global view of the effect of BrCRTISO on cellular processes in plant. It also provides a molecular tool to accelerate breeding new Chinese cabbage cultivars with unique health quality and visual appearance.

Altered xanthophyll compositions adversely affect chlorophyll accumulation and nonphotochemical quenching in Arabidopsis mutants

Publisher: Proceedings of the National Academy of Sciences

Date: 27-10-1998

DOI: 10.1073/PNAS.95.22.13324

Abstract: Collectively, the xanthophyll class of carotenoids perform a variety of critical roles in light harvesting antenna assembly and function. The xanthophyll composition of higher plant photosystems (lutein, violaxanthin, and neoxanthin) is remarkably conserved, suggesting important functional roles for each. We have taken a molecular genetic approach in Arabidopsis toward defining the respective roles of in idual xanthophylls in vivo by using a series of mutant lines that selectively eliminate and substitute a range of xanthophylls . The mutations, lut1 and lut2 ( lut = lutein deficient), disrupt lutein biosynthesis. In lut2, lutein is replaced mainly by a stoichiometric increase in violaxanthin and antheraxanthin. A third mutant, aba1, accumulates normal levels of lutein and substitutes zeaxanthin for violaxanthin and neoxanthin. The lut2aba1 double mutant completely lacks lutein, violaxanthin, and neoxanthin and instead accumulates zeaxanthin. All mutants were viable in soil and had chlorophyll a / b ratios ranging from 2.9 to 3.5 and near wild-type rates of photosynthesis. However, mutants accumulating zeaxanthin exhibited a delayed greening virescent phenotype, which was most severe and often lethal when zeaxanthin was the only xanthophyll present. Chlorophyll fluorescence quenching kinetics indicated that both zeaxanthin and lutein contribute to nonphotochemical quenching specifically, lutein contributes, directly or indirectly, to the rapid rise of nonphotochemical quenching. The results suggest that the normal complement of xanthophylls, while not essential, is required for optimal assembly and function of the light harvesting antenna in higher plants.

The multiple roles of light-harvesting chlorophyll a/b-protein complexes define structure and optimize function of Arabidopsis chloroplasts: A study using two chlorophyll b-less mutants

Publisher: Elsevier BV

Date: 08-2009

DOI: 10.1016/J.BBABIO.2009.04.009

Abstract: The multiple roles of light-harvesting chlorophyll a/b-protein complexes in the structure and function of Arabidopsis chloroplasts were investigated using two chlorophyll b-less mutants grown under metal halide l s with a significant far-red component. In ch1-3, all six light-harvesting proteins of photosystem (PS) II were greatly decreased in ch1-3lhcb5, Lhcb5 was completely absent while the other five proteins were further decreased. The thylakoids of ch1-3 were less negatively-charged than the wild type, and those of ch1-3lhcb5 were even less so. Despite the expected weaker electrostatic repulsion, however, thylakoids in leaves of the mutants were not well stacked, an effect we attribute to lower van der Waals attraction, lower electrostatic attraction between opposite charges, and the absence or instability of PSII supercomplexes and peripheral light-harvesting trimers. The quantum yield of oxygen evolution in leaves decreased from 0.109 (wild type) to 0.087 (ch1-3) and 0.081 (ch1-3lhcb5) O(2) (photon absorbed)(-1) we attribute this decrease to an excessive spillover from PSII to PSI, a limited PSII antenna, and increased light-independent thermal dissipation in PSII in the mutants. Destabilization of the donor side of PSII, indicated by slower electron donation to the redox-active tyrosine Y(Z)(*) in ch1-3, probably enhanced PSII susceptibility to photoinactivation, increased the non-functional PSII complexes in vivo, and further inactivated PSII complexes in vitro. The evolution of chlorophyll b-containing chloroplasts seems to fine-tune oxygenic photosynthesis.

Quantification of cyclic electron flow around Photosystem I in spinach leaves during photosynthetic induction

Publisher: Springer Science and Business Media LLC

Date: 09-01-2007

DOI: 10.1007/S11120-006-9127-Z

Abstract: The variation of the rate of cyclic electron transport around Photosystem I (PS I) during photosynthetic induction was investigated by illuminating dark-adapted spinach leaf discs with red + far-red actinic light for a varied duration, followed by abruptly turning off the light. The post-illumination re-reduction kinetics of P700+, the oxidized form of the photoactive chlorophyll of the reaction centre of PS I (normalized to the total P700 content), was well described by the sum of three negative exponential terms. The analysis gave a light-induced total electron flux from which the linear electron flux through PS II and PS I could be subtracted, yielding a cyclic electron flux. Our results show that the cyclic electron flux was small in the very early phase of photosynthetic induction, rose to a maximum at about 30 s of illumination, and declined subsequently to <10% of the total electron flux in the steady state. Further, this cyclic electron flow, largely responsible for the fast and intermediate exponential decays, was sensitive to 3-(3,4-dichlorophenyl)-1,1-dimethyl urea, suggesting an important role of redox poising of the cyclic components for optimal function. Significantly, our results demonstrate that analysis of the post-illumination re-reduction kinetics of P700+ allows the quantification of the cyclic electron flux in intact leaves by a relatively straightforward method.

Long-term trends in intrinsic water-use efficiency and growth of subtropical Pinus tabulaeformis Carr. and Pinus taiwanensis Hayata in central China

Publisher: Springer Science and Business Media LLC

Date: 18-03-2014

DOI: 10.1007/S11368-014-0878-4

RNA polymerase II read-through promotes expression of neighboring genes in SAL1-PAP-XRN retrograde signaling

Publisher: Oxford University Press (OUP)

Date: 09-10-2018

DOI: 10.1104/PP.18.00758

Remodeled Respiration in ndufs4 with Low Phosphorylation Efficiency Suppresses Arabidopsis Germination and Growth and Alters Control of Metabolism at Night (vol 151, 603, 2009)

Publisher: Oxford University Press (OUP)

Date: 12-2009

DOI: 10.1104/PP.109.900310

Volatile apocarotenoid discovery and quantification in Arabidopsis thaliana: optimized sensitive analysis via HS-SPME-GC/MS

Publisher: Springer Science and Business Media LLC

Date: 05-2019

DOI: 10.1007/S11306-019-1529-Y

Abstract: In the field of carotenoid metabolism researchers' focus has been directed recently toward the discovery and quantification of carotenoid cleavage products (i.e. apocarotenoids, excluding the well-studied carotenoid-derived hormones abscisic acid and strigolactones), due to their emerging roles as putative signaling molecules. Gas chromatography mass spectrometry (GC/MS) and s le preparation via headspace solid phase micro-extraction (HS-SPME) are widely used analytical techniques for broad untargeted metabolomics studies and until now, no optimized quantitative targeted HS-SPME-GC/MS method has been developed specifically for volatile apocarotenoids (VAs) in planta. Optimization and subsequent validation of the HS-SPME technique for extracting and quantifying volatile apocarotenoids in planta. Factors considered during method optimization were HS-SPME parameters vial storage conditions different adsorbent SPME fibre coating chemistries plant tissue matrix effects and fresh tissues to be analyzed. Mean linear regression in planta calibration correlation coefficients (R An optimized HS-SPME-GC/MS method for VA detection and quantification was validated in vitro and in planta: based on biological replicates and stringent QA/QC approaches, thereby providing robust detection and quantification of VAs across a broad range of Arabidopsis tissues, fifteen of which were identified for the first time in Arabidopsis.

The global plant council: Increasing the impact of plant research to meet global challenges

Publisher: Springer Science and Business Media LLC

Date: 16-09-2012

DOI: 10.1007/S12374-012-0901-5

Relative functional and optical absorption cross-sections of PSII and other photosynthetic parameters monitored in situ, at a distance with a time resolution of a few seconds, using a prototype light

Publisher: CSIRO Publishing

Date: 2017

DOI: 10.1071/FP17024

Abstract: The prototype light-induced fluorescence transient (LIFT) instrument provides continuous, minimally intrusive, high time resolution (~2 s) assessment of photosynthetic performance in terrestrial plants from up to 2 m. It induces a chlorophyll fluorescence transient by a series of short flashes in a saturation sequence (180 ~1μs flashlets in μs) to achieve near-full reduction of the primary acceptor QA, followed by a relaxation sequence (RQA 90 flashlets at exponentially increasing intervals over ~30 ms) to observe kinetics of QA re-oxidation. When fitted by the fast repetition rate (FRR) model (Kolber et al. 1998) the QA flash of LIFT/FRR gives smaller values for FmQA from dark adapted leaves than FmPAM from pulse litude modulated (PAM) assays. The ratio FmQA/FmPAM resembles the ratio of fluorescence yield at the J/P phases of the classical O-J-I-P transient and we conclude that the difference simply is due to the levels of PQ pool reduction induced by the two techniques. In a strong PAM-analogous WL pulse in the dark monitored by the QA flash of LIFT/FRR φPSIIWL ≈ φPSIIPAM. The QA flash also tracks PQ pool reduction as well as the associated responses of ETR QA → PQ and PQ → PSI, the relative functional (σPSII) and optical absorption (aPSII) cross-sections of PSII in situ with a time resolution of ~2 s as they relax after the pulse. It is impractical to deliver strong WL pulses at a distance in the field but a longer PQ flash from LIFT/FRR also achieves full reduction of PQ pool and delivers φPSIIPQ ≈ φPSIIPAM to obtain PAM-equivalent estimates of ETR and NPQ at a distance. In situ values of σPSII and aPSII from the QA flash with smaller antenna barley (chlorina-f2) and Arabidopsis mutants (asLhcb2–12, ch1–3 Lhcb5) are proportionally similar to those previously reported from in vitro assays. These direct measurements are further validated by changes in antenna size in response to growth irradiance. We illustrate how the QA flash facilitates our understanding of photosynthetic regulation during sun flecks in natural environments at a distance, with a time resolution of a few seconds.

LETM Proteins Play a Role in the Accumulation of Mitochondrially Encoded Proteins in Arabidopsis thaliana and AtLETM2 Displays Parent of Origin Effects

Publisher: Elsevier BV

Date: 12-2012

DOI: 10.1074/JBC.M112.383836

Potential implications for epigenetic regulation of carotenoid biosynthesis during root and shoot development

Publisher: Informa UK Limited

Date: 04-2009

DOI: 10.4161/PSB.4.4.8193

Morphine-pathway block in top1 poppies

Publisher: Springer Science and Business Media LLC

Date: 09-2004

DOI: 10.1038/431413A

Convergence of mitochondrial and chloroplastic ANAC017/PAP-dependent retrograde signalling pathways and suppression of programmed cell death

Publisher: Springer Science and Business Media LLC

Date: 12-05-2017

DOI: 10.1038/CDD.2017.68

Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development

Publisher: Public Library of Science (PLoS)

Date: 29-07-2013

DOI: 10.1371/JOURNAL.PONE.0070069

Chloroplast-to-nucleus communication

Publisher: Informa UK Limited

Date: 12-2010

DOI: 10.4161/PSB.5.12.13758

Evidence for a SAL1-PAP Chloroplast Retrograde Pathway That Functions in Drought and High Light Signaling in Arabidopsis      

Publisher: Oxford University Press (OUP)

Date: 11-2011

DOI: 10.1105/TPC.111.091033

Abstract: Compartmentation of the eukaryotic cell requires a complex set of subcellular messages, including multiple retrograde signals from the chloroplast and mitochondria to the nucleus, to regulate gene expression. Here, we propose that one such signal is a phosphonucleotide (3′-phosphoadenosine 5′-phosphate [PAP]), which accumulates in Arabidopsis thaliana in response to drought and high light (HL) stress and that the enzyme SAL1 regulates its levels by dephosphorylating PAP to AMP. SAL1 accumulates in chloroplasts and mitochondria but not in the cytosol. sal1 mutants accumulate 20-fold more PAP without a marked change in inositol phosphate levels, demonstrating that PAP is a primary in vivo substrate. Significantly, transgenic targeting of SAL1 to either the nucleus or chloroplast of sal1 mutants lowers the total PAP levels and expression of the HL-inducible ASCORBATE PEROXIDASE2 gene. This indicates that PAP must be able to move between cellular compartments. The mode of action for PAP could be inhibition of 5′ to 3′ exoribonucleases (XRNs), as SAL1 and the nuclear XRNs modulate the expression of a similar subset of HL and drought-inducible genes, sal1 mutants accumulate XRN substrates, and PAP can inhibit yeast (Saccharomyces cerevisiae) XRNs. We propose a SAL1-PAP retrograde pathway that can alter nuclear gene expression during HL and drought stress.

Differential Expression of Two 1-Aminocyclopropane-1-Carboxylic Acid Oxidase Genes in Broccoli after Harvest

Publisher: Oxford University Press (OUP)

Date: 06-0270

DOI: 10.1104/PP.108.2.651

Abstract: Broccoli (Brassica oleracea L.) floral tissues rapidly differentiate and grow before harvest and then senesce rapidly after harvest. Associated with this postharvest deterioration is an increase in ethylene production by florets. Two cDNA clones having high nucleotide identity to sequences encoding 1-amino-cyclopropane-1-carboxylic acid (ACC) oxidase were isolated from senescing florets. The cDNAs, ACC Ox1 and ACC Ox2, apparently encode mRNAs from different genes. ACC Ox1 transcripts were found at low levels in whole florets at the time of harvest and increased markedly in abundance after harvest. ACC Ox1 transcript abundance also increased in sepals after harvest and in excised yellowing leaves. Transcripts corresponding to ACC Ox2 were found exclusively within the reproductive structures. These ACC Ox2 transcripts were absent at harvest but started to increase in abundance within 2 h of harvest and then accumulated to high levels. Hormone treatment did not alter the abundance of ACC Ox1 transcripts, whereas ACC Ox2 transcripts increased in abundance after treatment with abscisic acid and propylene. Wounding did not affect the levels of ACC Ox1 or Ox2 transcripts after harvest. At harvest, in idual broccoli florets were closed and remained unpollinated. We propose a model whereby the rapid increase in ACC Ox1 and Ox2 transcript abundance after harvest contributes to increased ethylene production by florets. This ethylene may regulate aspects of postharvest senescence, in particular chlorophyll loss.

A chloroplast retrograde signal, 3’phosphoadenosine 5’-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination

Publisher: eLife Sciences Publications, Ltd

Date: 21-03-2017

DOI: 10.7554/ELIFE.23361

Abstract: Organelle-nuclear retrograde signaling regulates gene expression, but its roles in specialized cells and integration with hormonal signaling remain enigmatic. Here we show that the SAL1-PAP (3′-phosphoadenosine 5′- phosphate) retrograde pathway interacts with abscisic acid (ABA) signaling to regulate stomatal closure and seed germination in Arabidopsis. Genetically or exogenously manipulating PAP bypasses the canonical signaling components ABA Insensitive 1 (ABI1) and Open Stomata 1 (OST1) priming an alternative pathway that restores ABA-responsive gene expression, ROS bursts, ion channel function, stomatal closure and drought tolerance in ost1-2. PAP also inhibits wild type and abi1-1 seed germination by enhancing ABA sensitivity. PAP-XRN signaling interacts with ABA, ROS and Ca2+ up-regulating multiple ABA signaling components, including lowly-expressed Calcium Dependent Protein Kinases (CDPKs) capable of activating the anion channel SLAC1. Thus, PAP exhibits many secondary messenger attributes and exemplifies how retrograde signals can have broader roles in hormone signaling, allowing chloroplasts to fine-tune physiological responses.

Arabidopsis carotenoid mutants demonstrate that lutein is not essential for photosynthesis in higher plants.

Publisher: Oxford University Press (OUP)

Date: 09-1996

DOI: 10.1105/TPC.8.9.1627

A chromatin modifying enzyme, SDG8, is involved in morphological, gene expression, and epigenetic responses to mechanical stimulation

Publisher: Frontiers Media SA

Date: 21-10-2014

DOI: 10.3389/FPLS.2014.00533

VERNALIZATION INSENSITIVE 3(VIN3) is required for the response ofArabidopsis thalianaseedlings exposed to low oxygen conditions

Publisher: Wiley

Date: 08-2009

DOI: 10.1111/J.1365-313X.2009.03891.X

Distributed control of plant-wide chemical processes with uncertain time-delays

Publisher: Elsevier BV

Date: 12-2012

DOI: 10.1016/J.CES.2012.08.045

Prospects for Carotenoid Biofortification Targeting Retention and Catabolism

Publisher: Elsevier BV

Date: 05-2020

DOI: 10.1016/J.TPLANTS.2019.12.021

Abstract: Due to the ongoing prevalence of vitamin A deficiency (VAD) in developing countries there has been a large effort towards increasing the carotenoid content of staple foods via biofortification. Common strategies used for carotenoid biofortification include altering flux through the biosynthesis pathway to direct synthesis to a specific product, generally β-carotene, or via increasing the expression of genes early in the carotenoid biosynthesis pathway. Recently, carotenoid biofortification strategies are turning towards increasing the retention of carotenoids in plant tissues either via altering sequestration within the cell or via downregulating enzymes known to cause degradation of carotenoids. To date, little attention has focused on increasing the stability of carotenoids, which may be a promising method of increasing carotenoid content in staple foods.

Characterization of a cDNA encoding the protein moiety of a putative arabinogalactan protein from Lycopersicon esculentum

Publisher: Springer Science and Business Media LLC

Date: 05-1995

DOI: 10.1007/BF00020254

Carotenoid accumulation and function in seeds and non-green tissues

Publisher: Wiley

Date: 03-2006

DOI: 10.1111/J.1365-3040.2005.01492.X

Abstract: Carotenoids are plant pigments that function as antioxidants, hormone precursors, colourants and essential components of the photosynthetic apparatus. Carotenoids accumulate in nearly all types of plastids, not just the chloroplast, and are thus found in most plant organs and tissues, albeit at trace levels in some tissues. In this review we summarise the current knowledge of the carotenoid content of non-green plastids and discuss what is known about the regulation of their biosynthesis in roots, fruits, flowers, tubers and seeds. The emphasis is on food crops as carotenoids are essential components of human diets, primarily as some are precursors of vitamin A. The low carotenoid content of many staple foods, such as cereals, can exacerbate dietary deficiencies. The World Health Organisation has estimated that more than 100 million children are vitamin A-deficient and up to 500,000 of these children become blind each year. Many of these children die within 12 months of going blind. Thus, understanding the regulation of carotenoid accumulation in food crops, especially tubers and cereals, should facilitate improvements to nutritional value with potentially significant health benefits.

Immunolocalisation of pectinases in tomato fruit

Publisher: Informa UK Limited

Date: 04-1992

DOI: 10.1080/01140671.1992.10421907

Potential abiotic stress targets for modern genetic manipulation

Publisher: Oxford University Press (OUP)

Date: 15-11-2023

DOI: 10.1093/PLCELL/KOAC327

Abstract: Research into crop yield and resilience has underpinned global food security, evident in yields tripling in the past 5 decades. The challenges that global agriculture now faces are not just to feed 10+ billion people within a generation, but to do so under a harsher, more variable, and less predictable climate, and in many cases with less water, more expensive inputs, and declining soil quality. The challenges of climate change are not simply to breed for a “hotter drier climate,” but to enable resilience to floods and droughts and frosts and heat waves, possibly even within a single growing season. How well we prepare for the coming decades of climate variability will depend on our ability to modify current practices, innovate with novel breeding methods, and communicate and work with farming communities to ensure viability and profitability. Here we define how future climates will impact farming systems and growing seasons, thereby identifying the traits and practices needed and including exemplars being implemented and developed. Critically, this review will also consider societal perspectives and public engagement about emerging technologies for climate resilience, with participatory approaches presented as the best approach.

Vitamin synthesis in plants: Tocopherols and carotenoids

Publisher: Annual Reviews

Date: 06-2006

DOI: 10.1146/ANNUREV.ARPLANT.56.032604.144301

Abstract: Carotenoids and tocopherols are the two most abundant groups of lipid-soluble antioxidants in chloroplasts. In addition to their many functional roles in photosynthetic organisms, these compounds are also essential components of animal diets, including humans. During the past decade, a near complete set of genes required for the synthesis of both classes of compounds in photosynthetic tissues has been identified, primarily as a result of molecular genetic and biochemical genomics-based approaches in the model organisms Arabidopsis thaliana and Synechocystis sp. PCC6803. Mutant analysis and transgenic studies in these and other systems have provided important insight into the regulation, activities, integration, and evolution of in idual enzymes and are already providing a knowledge base for breeding and transgenic approaches to modify the types and levels of these important compounds in agricultural crops.

Observation of the Production of Three Massive Gauge Bosons at s=

Publisher: American Physical Society (APS)

Date: 05-10-2020

DOI: 10.1103/PHYSREVLETT.125.151802

Balancing metabolites in drought: the sulfur assimilation conundrum

Publisher: Elsevier BV

Date: 2013

DOI: 10.1016/J.TPLANTS.2012.07.005

Abstract: A key plant response to drought is the accumulation of specific sets of metabolites that act as osmoprotectants, osmolytes, antioxidants, and/or stress signals. An emerging question is: how do plants regulate metabolism to balance the 'competing interests' between metabolites during stress? Recent research connects primary sulfur metabolism (e.g., sulfate transport in the vasculature, its assimilation in leaves, and the recycling of sulfur-containing compounds) with the drought stress response. In this review, we highlight key steps in sulfur metabolism that play significant roles in drought stress signaling and responses. We propose that a complex balancing act is required to coordinate primary and secondary sulfur metabolism during the drought stress response in plants.

Enzymes degraded under high light maintain proteostasis by transcriptional regulation in Arabidopsis

Publisher: Proceedings of the National Academy of Sciences

Date: 12-05-2022

DOI: 10.1073/PNAS.2121362119

Abstract: Photoinhibitory high light stress in plants leads to increases in markers of protein degradation and transcriptional up-regulation of proteases and proteolytic machinery, but protein homeostasis (proteostasis) of most enzymes is largely maintained under high light, so we know little about the metabolic consequences of it beyond photosystem damage. We developed a technique to look for rapid protein turnover events in response to high light through 13 C partial labeling and detailed peptide mass spectrometry. This analysis reveals a light-induced transcriptional program for nuclear-encoded genes, beyond the regulation of photosystem II, to replace key protein degradation targets in plants and ensure proteostasis under high light stress.

The Plant CellIntroduces Breakthrough Reports: A New Forum for Cutting-Edge Plant Research

Publisher: Oxford University Press (OUP)

Date: 20-10-2015

DOI: 10.1105/TPC.15.00862