ORCID Profile
0000-0003-0832-0829
Current Organisations
United Institute of Informatics Problems
,
Australian Research Council
,
Centre for Tropical Crops and Biocommodities, QUT
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Publisher: Proceedings of the National Academy of Sciences
Date: 11-09-2007
Abstract: In plants, silencing of mRNA can be transmitted from cell to cell and also over longer distances from roots to shoots. To investigate the long-distance mechanism, WT and mutant shoots were grafted onto roots silenced for an mRNA. We show that three genes involved in a chromatin silencing pathway, NRPD1a encoding RNA polymerase IVa, RNA-dependent RNA polymerase 2 ( RDR2 ), and DICER-like 3 ( DCL3 ), are required for reception of long-distance mRNA silencing in the shoot. A mutant representing a fourth gene in the pathway, argonaute4 ( ago4 ), was also partially compromised in the reception of silencing. This pathway produces 24-nt siRNAs and resulted in decapped RNA, a known substrate for lification of dsRNA by RDR6. Activation of silencing in grafted shoots depended on RDR6, but no 24-nt siRNAs were detected in mutant rdr6 shoots, indicating that RDR6 also plays a role in initial signal perception. After lification of decapped transcripts, DCL4 and DCL2 act hierarchically as they do in antiviral resistance to produce 21- and 22-nt siRNAs, respectively, and these guide mRNA degradation. Several dcl genotypes were also tested for their capacity to transmit the mobile silencing signal from the rootstock. dcl1–8 and a dcl2 dcl3 dcl4 triple mutant are compromised in micro-RNA and siRNA biogenesis, respectively, but were unaffected in signal transmission.
Publisher: Annual Reviews
Date: 25-08-2018
DOI: 10.1146/ANNUREV-PHYTO-080417-050141
Abstract: A decade ago, the value of Nicotiana benthamiana as a tool for plant molecular biologists was beginning to be appreciated. Scientists were using it to study plant-microbe and protein-protein interactions, and it was the species of choice with which to activate plasmid-encoded viruses, screen for gene functions with virus-induced gene silencing (VIGS), and transiently express genes by leaf agroinfiltration. However, little information about the species’ origin, ersity, genetics, and genomics was available, and biologists were asking the question of whether N. benthamiana is a second fiddle or virtuoso. In this review, we look at the increased knowledge about the species and its applications over the past decade. Although N. benthamiana may still be the sidekick to Arabidopsis, it shines ever more brightly with realized and yet-to-be-exploited potential.
Publisher: CSIRO Publishing
Date: 23-07-2021
DOI: 10.1071/SB20025
Abstract: Nicotiana is found predominantly in the Americas and Australia, but also has representatives in Africa and the Pacific Islands. All native Australian Nicotiana species belong to section Suaveolentes. The number of species in this section is uncertain and subject to revision. An ex le of this uncertainty is the taxonomic status of a South Australian Nicotiana accession colloquially termed ‘Corunna’. Here, we report sequences for nuclear and plastid markers for N. sp. Corunna (D.E.Symon 17088) and accessions of two other Australian species, N. burbidgeae and N. benthamiana. Phylogenetic comparison of these sequences with those of other members of Nicotiana places all three taxa in N. section Suaveolentes and shows that ‘Corunna’ represents a distinct phylogenetic lineage in a well supported clade along with N. goodspeedii, N. maritima, N. lexicaulis and N. suaveolentes. Phenetic analysis of floral characters also supports recognition of N. sp. Corunna (D.E.Symon 17088) as a distinct species, which we describe here as Nicotiana paulineana Newbigin & P.M.Waterh., sp. nov. The enlarged molecular dataset described here contributes to a better understanding of taxonomic relationships within the section.
Publisher: Springer Science and Business Media LLC
Date: 02-11-2015
Abstract: A single lineage of Nicotiana benthamiana is widely used as a model plant(1) and has been instrumental in making revolutionary discoveries about RNA interference (RNAi), viral defence and vaccine production. It is peerless in its susceptibility to viruses and its amenability in transiently expressing transgenes(2,3). These unparalleled characteristics have been associated both positively and negatively with a disruptive insertion in the RNA-dependent RNA polymerase 1 gene, Rdr1(4-6). For a plant so routinely used in research, the origin, ersity and evolution of the species, and the basis of its unusual abilities, have been relatively unexplored. Here, by comparison with wild accessions from across the spectrum of the species' natural distribution, we show that the laboratory strain of N. benthamiana is an extremophile originating from a population that has retained a mutation in Rdr1 for ∼0.8 Myr and thereby traded its defence capacity for early vigour and survival in the extreme habitat of central Australia. Reconstituting Rdr1 activity in this isolate provided protection. Silencing the functional allele in a wild strain rendered it hypersusceptible and was associated with a doubling of seed size and enhanced early growth rate. These findings open the way to a deeper understanding of the delicate balance between protection and vigour.
Publisher: Frontiers Media SA
Date: 29-09-2016
Publisher: Springer New York
Date: 2007
Publisher: Public Library of Science (PLoS)
Date: 23-02-2017
Publisher: Elsevier BV
Date: 2016
Publisher: Cold Spring Harbor Laboratory
Date: 25-11-2021
DOI: 10.1101/2021.11.24.469772
Abstract: Topical application of double-stranded RNA (dsRNA) as RNA interference(RNAi) based biopesticides represents a sustainable alternative to traditional transgenic, breeding-based or chemical crop protection strategies. A key feature of RNAi is its ability to act non-cell autonomously, a process that plays a critical role in plant protection. However, the uptake of dsRNA upon topical application, and its ability to move and act non-cell autonomously remains debated and largely unexplored. Here we show that when applied to a leaf, unprocessed full-length dsRNA enters the vasculature and rapidly moves to multiple distal below ground, vegetative and reproductive tissue types in several model plant and crop hosts. Intact unprocessed dsRNA was detected in the apoplast of leaves, roots and flowers after leaf application and maintained in subsequent new growth. Furthermore, we show mobile dsRNA is functional against root infecting fungal and foliar viral pathogens. Our demonstration of the uptake and maintained movement of intact and functional dsRNA stands to add significant benefit to the emerging field of RNAi-based plant protection.
Publisher: American Society of Hematology
Date: 19-02-2009
DOI: 10.1182/BLOOD-2008-05-155812
Abstract: We demonstrate that in zebrafish, the microRNA miR-451 plays a crucial role in promoting erythroid maturation, in part via its target transcript gata2. Zebrafish miR-144 and miR-451 are processed from a single precursor transcript selectively expressed in erythrocytes. In contrast to other hematopoietic mutants, the zebrafish mutant meunier (mnr) showed intact erythroid specification but diminished miR-144/451 expression. Although erythropoiesis initiated normally in mnr, erythrocyte maturation was morphologically retarded. Morpholino knockdown of miR-451 increased erythrocyte immaturity in wild-type embryos, and miR-451 RNA duplexes partially rescued erythroid maturation in mnr, demonstrating a requirement and role for miR-451 in erythrocyte maturation. mnr provided a selectively miR-144/451-deficient background, facilitating studies to discern miRNA function and validate candidate targets. Among computer-predicted miR-451 targets potentially mediating these biologic effects, the pro-stem cell transcription factor gata2 was an attractive candidate. In vivo reporter assays validated the predicted miR-451/gata2-3′UTR interaction, gata2 down-regulation was delayed in miR-451-knockdown and mnr embryos, and gata2 knockdown partially restored erythroid maturation in mnr, collectively confirming gata2 down-regulation as pivotal for miR-451-driven erythroid maturation. These studies define a new genetic pathway promoting erythroid maturation (mnr/miR-451/gata2) and provide a rare ex le of partial rescue of a mutant phenotype solely by miRNA overexpression.
Publisher: Elsevier BV
Date: 08-2016
Publisher: Frontiers Media SA
Date: 2013
Publisher: Springer Science and Business Media LLC
Date: 10-08-2023
DOI: 10.1038/S41477-023-01489-8
Abstract: Nicotiana benthamiana is an invaluable model plant and biotechnology platform with a ~3 Gb allotetraploid genome. To further improve its usefulness and versatility, we have produced high-quality chromosome-level genome assemblies, coupled with transcriptome, epigenome, microRNA and transposable element datasets, for the ubiquitously used LAB strain and a related wild accession, QLD. In addition, single nucleotide polymorphism maps have been produced for a further two laboratory strains and four wild accessions. Despite the loss of five chromosomes from the ancestral tetraploid, expansion of intergenic regions, widespread segmental allopolyploidy, advanced diploidization and evidence of recent bursts of Copia pseudovirus (Copia) mobility not seen in other Nicotiana genomes, the two subgenomes of N. benthamiana show large regions of synteny across the Solanaceae. LAB and QLD have many genetic, metabolic and phenotypic differences, including disparate RNA interference responses, but are highly interfertile and amenable to genome editing and both transient and stable transformation. The LAB/QLD combination has the potential to be as useful as the Columbia-0/Landsberg errecta partnership, utilized from the early pioneering days of Arabidopsis genomics to today.
Publisher: Elsevier BV
Date: 02-2012
Publisher: Elsevier BV
Date: 08-2019
DOI: 10.1016/J.TPLANTS.2019.05.003
Abstract: The commercial release of third-generation sequencing technologies (TGSTs), giving long and ultra-long sequencing reads, has stimulated the development of new tools for assembling highly contiguous genome sequences with unprecedented accuracy across complex repeat regions. We survey here a wide range of emerging sequencing platforms and analytical tools for de novo assembly, provide background information for each of their steps, and discuss the spectrum of available options. Our decision tree recommends workflows for the generation of a high-quality genome assembly when used in combination with the specific needs and resources of a project.
Publisher: Frontiers Media SA
Date: 15-03-2019
Publisher: Springer Science and Business Media LLC
Date: 05-05-2005
DOI: 10.1007/S10142-005-0145-2
Abstract: Plant and animal microRNAs (miRNAs) are evolutionarily ancient small RNAs, approximately 19-24 nucleotides in length, that are generated by cleavage from larger highly structured precursor molecules. In both plants and animals, miRNAs posttranscriptionally regulate gene expression through interactions with their target mRNAs, and these targets are often genes involved with regulating key developmental events. Despite these similarities, plant and animal miRNAs exert their control in fundamentally different ways. Generally, animal miRNAs repress gene expression by mediating translational attenuation through (multiple) miRNA-binding sites located within the 3' untranslated region of the target gene. In contrast, almost all plant miRNAs regulate their targets by directing mRNA cleavage at single sites in the coding regions. These and other differences suggest that the two systems may have originated independently, possibly as a prerequisite to the development of complex body plans.
Publisher: American Chemical Society (ACS)
Date: 12-06-2020
Publisher: Oxford University Press (OUP)
Date: 11-05-2012
Abstract: Upward long-distance mobile silencing has been shown to be phloem mediated in several different solanaceous species. We show that the Arabidopsis (Arabidopsis thaliana) seedling grafting system and a counterpart inducible system generate upwardly spreading long-distance silencing that travels not in the phloem but by template-dependent reiterated short-distance cell-to-cell spread through the cells of the central stele. Examining the movement of the silencing front revealed a largely unrecognized zone of tissue, below the apical meristem, that is resistant to the silencing signal and that may provide a gating or protective barrier against small RNA signals. Using a range of auxin and actin transport inhibitors revealed that, in this zone, alteration of vesicular transport together with cytoskeleton dynamics prevented or retarded the spread of the silencing signal. This suggests that small RNAs are transported from cell to cell via plasmodesmata rather than diffusing from their source in the phloem.
Publisher: Elsevier BV
Date: 03-2013
Publisher: PeerJ
Date: 23-12-2014
DOI: 10.7717/PEERJ.701
Publisher: Springer Science and Business Media LLC
Date: 15-01-2014
Publisher: Wiley
Date: 02-12-2016
DOI: 10.1111/PBI.12506
Publisher: EMBO
Date: 13-10-2006
Publisher: Wiley
Date: 14-07-2008
DOI: 10.1016/J.FEBSLET.2008.07.004
Abstract: Dicers are associated with double-stranded RNA-binding proteins (dsRBPs) in animals. In the plant, Arabidopsis, there are four dicer-like (DCL) proteins and five potential dsRBPs. These DCLs act redundantly and hierarchically. However, we show there is little or no redundancy or hierarchy amongst the DRBs in their DCL interactions. DCL1 operates exclusively with DRB1 to produce micro (mi)RNAs, DCL4 operates exclusively with DRB4 to produce trans-acting (ta) siRNAs and 21nt siRNAs from viral RNA. DCL2 and DCL3 produce viral siRNAs without requiring assistance from any dsRBP. DRB2, DRB3 and DRB5 appear unnecessary for mi-, tasi-, viral si-, or heterochromatinising siRNA production but act redundantly in a developmental pathway.
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: Australia
Start Date: 2010
End Date: 2013
Funder: Australian Research Council
View Funded ActivityStart Date: 2016
End Date: 2020
Funder: Australian Research Council
View Funded ActivityStart Date: 2007
End Date: 2013
Funder: Australian Research Council
View Funded ActivityStart Date: 2010
End Date: 2010
Funder: Australian Research Council
View Funded ActivityStart Date: 2010
End Date: 2010
Funder: Australian Research Council
View Funded Activity