ORCID Profile
0000-0002-5301-9624
Current Organisations
Telethon Kids Institute
,
University of Western Australia
,
The Harry Perkins Institute of Medical Research
,
Curtin Health Innovation Research Institute
,
Curtin University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Biochemistry and Cell Biology | Synthetic Biology | Genetics | Gene Expression (incl. Microarray and other genome-wide approaches) | Genome Structure and Regulation | Gene Expression | Microbial Genetics | Genomics | Bioinformatics |
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Biological Sciences | Technological and organisational innovation | Human Pharmaceutical Treatments (e.g. Antibiotics) | Veterinary Pharmaceutical Treatments (e.g. Antibiotics) | Treatments (e.g. chemicals, antibiotics) | Biological sciences | Industrial Chemicals and Related Products not elsewhere classified | Expanding Knowledge in the Information and Computing Sciences | Organic Industrial Chemicals (excl. Resins, Rubber and Plastics) | Manufacturing not elsewhere classified | Expanding Knowledge in Technology
Related Links
Publications
Conserved and Novel Functions for Arabidopsis thaliana MIA40 in Assembly of Proteins in Mitochondria and Peroxisomes
Publisher: Elsevier BV
Date: 11-2010
Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria
Publisher: Elsevier BV
Date: 12-2019
Energetic and spectroscopic properties of the low-lying C7 H2 isomers: A high-level: Ab initio perspective
Publisher: Royal Society of Chemistry (RSC)
Date: 2017
DOI: 10.1039/C7CP02848B
Abstract: We report here nine low-lying isomers of C 7 H 2 , which lie within 1 eV, investigated with high-level ab initio methods.
Secure Knowledge and Cluster-Based Intrusion Detection Mechanism for Smart Wireless Sensor Networks
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 2018
A modified yeast three-hybrid system enabling both positive and negative selections
Publisher: Springer Science and Business Media LLC
Date: 18-05-2018
DOI: 10.1007/S10529-018-2567-7
Abstract: To increase the reporter repertoire of the yeast three-hybrid system and introduce the option of negative selection. Two new versions of the yeast three-hybrid system were made by modifying the MS2 coat RNA-binding protein and fusing it to the Gal4 DNA-binding protein. This allows the use of Gal4 inducible reporters to measure RNA-protein interactions. We introduced two mutations, V29I and N55K into the tandem MS2 dimer and an 11 amino acid deletion to increase RNA-protein affinity and inhibit capsid formation. Introduction of these constructs into the yeast strains MaV204K and PJ69-2A (which contain more reporters than the conventional yeast three-hybrid strains L40-coat and YBZ-1) allows RNA-protein binding interactions with a wide range of affinities to be detected using histidine auxotrophy, and negative selection with 5-fluoroorotic acid. This yeast three-hybrid system has advantages over previous versions as demonstrated by the increased dynamic range of detectable binding interactions using yeast survival assays and colony forming assays with multiple reporters using known RNA-protein interactions.
CirGO: An alternative circular way of visualising gene ontology terms
Publisher: Springer Science and Business Media LLC
Date: 18-02-2019
Synthesizing cellular networks from evolved ribosome-mRNA pairs
Publisher: Portland Press Ltd.
Date: 04-2006
DOI: 10.1042/BST20060328
An Artificial Yeast Genetic Circuit Enables Deep Mutational Scanning of an Antimicrobial Resistance Protein
Publisher: American Chemical Society (ACS)
Date: 06-07-2018
DOI: 10.1021/ACSSYNBIO.8B00121
Abstract: Understanding the molecular mechanisms underlying antibiotic resistance requires concerted efforts in enzymology and medicinal chemistry. Here we describe a new synthetic biology approach to antibiotic development, where the presence of tetracycline antibiotics is linked to a life-death selection in Saccharomyces cerevisiae. This artificial genetic circuit allowed the deep mutational scanning of the tetracycline inactivating enzyme TetX, revealing key functional residues. We used both positive and negative selections to confirm the importance of different residues for TetX activity, and profiled activity hotspots for different tetracyclines to reveal substrate-specific activity determinants. We found that precise positioning of FAD and hydrophobic shielding of the tetracycline are critical for enzymatic inactivation of doxycycline. However, positioning of FAD is suboptimal in the case of anhydrotetracycline, potentially explaining its comparatively poor degradation and potential as an inhibitor for this family of enzymes. By combining artificial genetic circuits whose function can be modulated by antimicrobial resistance determinants, we establish a framework to select for the next generation of antibiotics.
A gold(I) phosphine complex selectively induces apoptosis in breast cancer cells: Implications for anticancer therapeutics targeted to mitochondria
Publisher: Elsevier BV
Date: 10-2007
DOI: 10.1016/J.BCP.2007.07.022
Abstract: Bis-chelated gold(I) phosphine complexes have shown great potential as anticancer agents, however, their efficacy has been limited by their high toxicity and lack of selectivity for cancer cells. Here, we have investigated the anticancer activity of a new bis-chelated Au(I) bidentate phosphine complex of the novel water soluble ligand 1,3-bis(di-2-pyridylphosphino)propane (d2pypp). We show that this gold complex [Au(d2pypp)(2)]Cl, at submicromolar concentrations, selectively induces apoptosis in breast cancer cells but not in normal breast cells. Apoptosis was induced via the mitochondrial pathway, which involved mitochondrial membrane potential depolarisation, depletion of the glutathione pool and caspase-3 and caspase-9 activation. The gold lipophilic complex was accumulated in mitochondria of cells, driven by the high mitochondrial membrane potential. To address the molecular basis of the observed selectivity between the two cell lines we investigated the effect of the gold complex on the thioredoxin/thioredoxin reductase system in normal and cancer breast cells. We show that [Au(d2pypp)(2)]Cl inhibits the activities of both thioredoxin and thioredoxin reductase and that this effect is more pronounced in the breast cancer cells. This difference may account for the selective cell death seen in the breast cancer cells but not in the normal cells. Our investigation has led to new insights into the mechanism of action of bis-chelated gold(I) diphosphine complexes and their future development as mitochondria targeted chemotherapeutics.
Is mitochondrial gene expression coordinated or stochastic?
Publisher: Portland Press Ltd.
Date: 09-10-2018
DOI: 10.1042/BST20180174
Abstract: Mitochondrial biogenesis is intimately dependent on the coordinated expression of the nuclear and mitochondrial genomes that is necessary for the assembly and function of the respiratory complexes to produce most of the energy required by cells. Although highly compacted in animals, the mitochondrial genome and its expression are essential for survival, development, and optimal energy production. The machinery that regulates gene expression within mitochondria is localised within the same compartment and, like in their ancestors, the bacteria, this machinery does not use membrane-based compartmentalisation to order the gene expression pathway. Therefore, the lifecycle of mitochondrial RNAs from transcription through processing, maturation, translation to turnover is mediated by a gamut of RNA-binding proteins (RBPs), all contained within the mitochondrial matrix milieu. Recent discoveries indicate that multiple processes regulating RNA metabolism occur at once but since mitochondria have a new complement of RBPs, many evolved de novo from nuclear genes, we are left wondering how co-ordinated are these processes? Here, we review recently identified ex les of the co-ordinated and stochastic processes that govern the mitochondrial transcriptome. These new discoveries reveal the complexity of mitochondrial gene expression and the need for its in-depth exploration to understand how these organelles can respond to the energy demands of the cell.
Cardiolipin is required for membrane docking of mitochondrial ribosomes and protein synthesis
Publisher: The Company of Biologists
Date: 2020
DOI: 10.1242/JCS.240374
Abstract: The mitochondrial inner membrane contains a unique phospholipid known as cardiolipin (CL), which stabilises the protein complexes embedded in the membrane and supports its overall structure. Recent evidence indicates that the mitochondrial ribosome may associate with the inner membrane to facilitate co-translational insertion of the hydrophobic oxidative phosphorylation (OXPHOS) proteins into the inner membrane. We generated three mutant knockout cell lines for the cardiolipin biosynthesis gene Crls1 to investigate the effects of cardiolipin loss on mitochondrial protein synthesis. Reduced CL levels caused altered mitochondrial morphology and transcriptome-wide changes that were accompanied by reduced uncoordinated mitochondrial translation rates and impaired respiratory supercomplex formation. Aberrant protein synthesis was caused by impaired formation and distribution of mitochondrial ribosomes. Reduction or loss of cardiolipin resulted in ergent mitochondrial and endoplasmic reticulum stress responses. We show that cardiolipin is required to stabilise the interaction of the mitochondrial ribosome with the membrane via its association with OXA1 during active translation. This interaction facilitates insertion of newly synthesised mitochondrial proteins into the inner membrane and stabilises the respiratory supercomplexes.
The FASTK family proteins fine-tune mitochondrial RNA processing
Publisher: Public Library of Science (PLoS)
Date: 08-11-2021
DOI: 10.1371/JOURNAL.PGEN.1009873
Abstract: Transcription of the human mitochondrial genome and correct processing of the two long polycistronic transcripts are crucial for oxidative phosphorylation. According to the tRNA punctuation model, nucleolytic processing of these large precursor transcripts occurs mainly through the excision of the tRNAs that flank most rRNAs and mRNAs. However, some mRNAs are not punctuated by tRNAs, and it remains largely unknown how these non-canonical junctions are resolved. The FASTK family proteins are emerging as key players in non-canonical RNA processing. Here, we have generated human cell lines carrying single or combined knockouts of several FASTK family members to investigate their roles in non-canonical RNA processing. The most striking phenotypes were obtained with loss of FASTKD4 and FASTKD5 and with their combined double knockout. Comprehensive mitochondrial transcriptome analyses of these cell lines revealed a defect in processing at several canonical and non-canonical RNA junctions, accompanied by an increase in specific antisense transcripts. Loss of FASTKD5 led to the most severe phenotype with marked defects in mitochondrial translation of key components of the electron transport chain complexes and in oxidative phosphorylation. We reveal that the FASTK protein family members are crucial regulators of non-canonical junction and non-coding mitochondrial RNA processing.
Building a parallel metabolism within the cell
Publisher: American Chemical Society (ACS)
Date: 2008
DOI: 10.1021/CB700185E
Abstract: One of the key aims of synthetic biology is to engineer artificial processes inside living cells. This requires components that interact in a predictable manner, both with each other and with existing cellular systems. However, the activity of many components is constrained by their interactions with other cellular molecules and often their roles in maintaining cell health. To escape this limitation, researchers are pursuing an "orthogonal" approach, building a parallel metabolism within the cell. Components of this parallel metabolism can be sourced from evolutionarily distant species or reengineered from existing cellular molecules by using rational design and directed evolution. These approaches allow the study of basic principles in cell biology and the engineering of cells that can function as environmental sensors, simple computers, and drug factories.
Pentatricopeptide repeats: modular blocks for building RNA-binding proteins.
Publisher: Informa UK Limited
Date: 09-2013
DOI: 10.4161/RNA.24769
Multi‐omic profiling reveals an RNA processing rheostat that predisposes to prostate cancer
Publisher: EMBO
Date: 24-04-2023
Abstract: Prostate cancer is the most commonly diagnosed malignancy and the third leading cause of cancer deaths. GWAS have identified variants associated with prostate cancer susceptibility however, mechanistic and functional validation of these mutations is lacking. We used CRISPR‐Cas9 genome editing to introduce a missense variant identified in the ELAC2 gene, which encodes a dually localised nuclear and mitochondrial RNA processing enzyme, into the mouse Elac2 gene as well as to generate a prostate‐specific knockout of Elac2 . These mutations caused enlargement and inflammation of the prostate and nodule formation. The Elac2 variant or knockout mice on the background of the transgenic adenocarcinoma of the mouse prostate (TRAMP) model show that Elac2 mutation with a secondary genetic insult exacerbated the onset and progression of prostate cancer. Multiomic profiling revealed defects in energy metabolism that activated proinflammatory and tumorigenic pathways as a consequence of impaired noncoding RNA processing and reduced protein synthesis. Our physiologically relevant models show that the ELAC2 variant is a predisposing factor for prostate cancer and identify changes that underlie the pathogenesis of this cancer.
Stress signaling and cellular proliferation reverse the effects of mitochondrial mistranslation
Publisher: EMBO
Date: 13-11-2019
SLIRP stabilizes LRPPRC via an RRM–PPR protein interface
Publisher: Oxford University Press (OUP)
Date: 28-06-2016
DOI: 10.1093/NAR/GKW575
Building artificial genetic circuits to understand protein function
Publisher: Elsevier
Date: 2019
Setting up a specialist pleural disease service
Publisher: Wiley
Date: 27-09-2010
DOI: 10.1111/J.1440-1843.2010.01832.X
Abstract: The past decade has seen a dramatic rise in clinical and research interests in pleural disease in parallel with rising incidences of pleural cancers and infection worldwide. Development of specialist pleural services can streamline patient diagnosis and therapy, reduce health-care resource consumption, improve procedural training and safety and facilitate clinical research. Pleural ultrasound, pleuroscopy, indwelling pleural catheter services and pleural procedural education programmes for junior staff are important elements of most specialist pleural units. An integrated service including radiology, pathology, oncology and thoracic surgery input is pivotal to success. Establishing funding support and referral sources are the common initial hurdles. This article provides an overview of the need for specialist pleural disease units, the essential elements required and the likely challenges encountered in setting a service up.
Investigating Mitochondrial Transcriptomes and RNA Processing Using Circular RNA Sequencing
Publisher: Springer US
Date: 24-11-2021
Reduced mitochondrial translation prevents diet-induced metabolic dysfunction but not inflammation
Publisher: Impact Journals, LLC
Date: 06-10-2020
New Galactic Planetary nebulae selected by radio and multiwavelength characteristics
Publisher: Oxford University Press (OUP)
Date: 25-07-2018
Mitochondrial mistranslation modulated by metabolic stress causes cardiovascular disease and reduced lifespan
Publisher: Wiley
Date: 07-06-2021
DOI: 10.1111/ACEL.13408
Abstract: Changes in the rate and fidelity of mitochondrial protein synthesis impact the metabolic and physiological roles of mitochondria. Here we explored how environmental stress in the form of a high‐fat diet modulates mitochondrial translation and affects lifespan in mutant mice with error‐prone ( Mrps12 ep / ep ) or hyper‐accurate ( Mrps12 ha / ha ) mitochondrial ribosomes. Intriguingly, although both mutations are metabolically beneficial in reducing body weight, decreasing circulating insulin and increasing glucose tolerance during a high‐fat diet, they manifest ergent (either deleterious or beneficial) outcomes in a tissue‐specific manner. In two distinct organs that are commonly affected by the metabolic disease, the heart and the liver, Mrps12 ep / ep mice were protected against heart defects but sensitive towards lipid accumulation in the liver, activating genes involved in steroid and amino acid metabolism. In contrast, enhanced translational accuracy in Mrps12 ha / ha mice protected the liver from a high‐fat diet through activation of liver proliferation programs, but enhanced the development of severe hypertrophic cardiomyopathy and led to reduced lifespan. These findings reflect the complex transcriptional and cell signalling responses that differ between post‐mitotic (heart) and highly proliferative (liver) tissues. We show trade‐offs between the rate and fidelity of mitochondrial protein synthesis dictate tissue‐specific outcomes due to commonly encountered stressful environmental conditions or aging.
Mitochondria: Unusual features of the mammalian mitoribosome
Publisher: Elsevier BV
Date: 08-2014
DOI: 10.1016/J.BIOCEL.2014.05.011
Abstract: Mitochondria are responsible for generating most of the energy required by the cell. The oxidative phosphorylation (OXPHOS) system that produces the energy is composed of nuclear and mitochondrial encoded polypeptides. The 13 polypeptides encoded by the mitochondrial genome are synthesized by mitochondrial ribosomes (mitoribosomes). The evolutionary ergence of mitoribosomes has seen a reduction in their rRNA content and an increase in ribosomal proteins compared to their bacterial and cytoplasmic counterparts. Recent advances in cryo-electron microscopy (cryo-EM) mapping have revealed not all of these proteins simply replace the roles of the rRNA and that many have new roles. The mitoribosome has unique features that include a gatelike structure at the mRNA entrance that may facilitate recruitment of leaderless mitochondrial mRNAs and also a polypeptide exit tunnel that has an unusual nascent-polypeptide exit mechanism. Defects in the mitochondrial translation machinery are a common contributor to multi-system disorders known as mitochondrial diseases for which currently there are no cures or effective treatments.
Concerted regulation of mitochondrial and nuclear non-coding RNAs by a dual-targeted RNase Z
Publisher: EMBO
Date: 20-08-2018
Synthetic biology with RNA
Publisher: Royal Society of Chemistry
Date: 2014
The Effect of Aging on Acetaminophen Pharmacokinetics, Toxicity and Nrf2 in Fischer 344 Rats
Publisher: Oxford University Press (OUP)
Date: 17-07-2013
Risk reduction in pleural procedures: Sonography, simulation and supervision
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 07-2010
Tighter Ligand Binding Can Compensate for Impaired Stability of an RNA-Binding Protein
Publisher: American Chemical Society (ACS)
Date: 29-05-2018
DOI: 10.1021/ACSCHEMBIO.8B00424
Abstract: It has been widely shown that ligand-binding residues, by virtue of their orientation, charge, and solvent exposure, often have a net destabilizing effect on proteins that is offset by stability conferring residues elsewhere in the protein. This structure-function trade-off can constrain possible adaptive evolutionary changes of function and may h er protein engineering efforts to design proteins with new functions. Here, we present evidence from a large randomized mutant library screen that, in the case of PUF RNA-binding proteins, this structural relationship may be inverted and that active-site mutations that increase protein activity are also able to compensate for impaired stability. We show that certain mutations in RNA-protein binding residues are not necessarily destabilizing and that increased ligand-binding can rescue an insoluble, unstable PUF protein. We hypothesize that these mutations restabilize the protein via thermodynamic coupling of protein folding and RNA binding.
An artificial PPR scaffold for programmable RNA recognition
Publisher: Springer Science and Business Media LLC
Date: 17-12-2014
DOI: 10.1038/NCOMMS6729
Abstract: Pentatricopeptide repeat (PPR) proteins control erse aspects of RNA metabolism in eukaryotic cells. Although recent computational and structural studies have provided insights into RNA recognition by PPR proteins, their highly insoluble nature and inconsistencies between predicted and observed modes of RNA binding have restricted our understanding of their biological functions and their use as tools. Here we use a consensus design strategy to create artificial PPR domains that are structurally robust and can be programmed for sequence-specific RNA binding. The atomic structures of these artificial PPR domains elucidate the structural basis for their stability and modelling of RNA-protein interactions provides mechanistic insights into the importance of RNA-binding residues and suggests modes of PPR-RNA association. The modular mode of RNA binding by PPR proteins holds great promise for the engineering of new tools to target RNA and to understand the mechanisms of gene regulation by natural PPR proteins.
Specialization from synthesis: How ribosome diversity can customize protein function
Publisher: Wiley
Date: 26-02-2013
DOI: 10.1016/J.FEBSLET.2013.02.032
Abstract: It was thought that the proteins produced by ribosomes were dictated only by the sequences of the mRNAs they translated, however it is becoming apparent that subpopulations of ribosomes can have unique properties that influence the functions of the proteins they produce. Ribosomes have been engineered to discriminate between different mRNA templates or with unique decoding properties, and many new applications of unnatural ribosomes can be foreseen. In natural systems ribosomes with alternate protein and RNA composition have been shown to selectively translate specific mRNAs. As more is learned about ribosome structure and the mechanisms of translation, new opportunities to engineer ribosomes for applications in biotechnology and synthetic biology can be developed and new ex les of ribosome-mediated regulation of translation are likely to emerge in nature.
Mitochondrial gene expression is required for platelet function and blood clotting
Publisher: Elsevier BV
Date: 11-2023
Engineered rRNA enhances the efficiency of selenocysteine incorporation during translation.
Publisher: American Chemical Society (ACS)
Date: 27-12-2012
DOI: 10.1021/JA3069177
Abstract: We developed a new genetic selection approach to screen for mutations that can alter the efficiency of selenocysteine incorporation. We identified mutations in 16S rRNA that increase or decrease the efficiency of selenocysteine incorporation in Escherichia coli without influencing the efficiency or fidelity of canonical translation. Engineered ribosomes with improved selenocysteine incorporation provide valuable tools for synthetic biology and biotechnology.
ANGEL2 phosphatase activity is required for non-canonical mitochondrial RNA processing
Publisher: Springer Science and Business Media LLC
Date: 30-09-2022
DOI: 10.1038/S41467-022-33368-9
Abstract: Canonical RNA processing in mammalian mitochondria is defined by tRNAs acting as recognition sites for nucleases to release flanking transcripts. The relevant factors, their structures, and mechanism are well described, but not all mitochondrial transcripts are punctuated by tRNAs, and their mode of processing has remained unsolved. Using Drosophila and mouse models, we demonstrate that non-canonical processing results in the formation of 3′ phosphates, and that phosphatase activity by the carbon catabolite repressor 4 domain-containing family member ANGEL2 is required for their hydrolysis. Furthermore, our data suggest that members of the FAST kinase domain-containing protein family are responsible for these 3′ phosphates. Our results therefore propose a mechanism for non-canonical RNA processing in metazoan mitochondria, by identifying the role of ANGEL2.
Big Data Security and Privacy Concerns: A Review
Publisher: Springer International Publishing
Date: 2019
The quest for the carbene bent-pentadiynylidene isomer of C5 H2
Publisher: Elsevier BV
Date: 11-2018
Modular recognition of nucleic acids by PUF, TALE and PPR proteins
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C2MB05392F
Abstract: Sequence specific binding of DNA and RNA is of fundamental importance in the regulation of cellular gene expression. Because of their modular structure repeat domain proteins are particularly well suited for these processes and have been widely adopted throughout evolution. Detailed biochemical and structural data has revealed the key residues responsible for recognition of RNA by Pumilio and FBF homology (PUF) repeat proteins and shown that the base specificity can be predicted and re-engineered. Recent work on the DNA-binding properties of transcription activator-like effector (TALE) proteins has shown that their specificity also relies on only a few key residues with a predictable code that can be used to design new DNA-binding proteins. Although less well understood, pentatricopeptide repeat (PPR) proteins contain motifs that appear to contribute to RNA recognition and comparisons to TALE and PUF proteins may help elucidate the code by which they recognize their RNA targets. Understanding how repeat proteins bind nucleic acids enables their biological roles to be uncovered and the design of engineered proteins with predictable RNA and DNA targets for use in biotechnology.
A network of orthogonal ribosome·mrna pairs
Publisher: Springer Science and Business Media LLC
Date: 17-07-2005
DOI: 10.1038/NCHEMBIO719
Abstract: Synthetic biology promises the ability to program cells with new functions. Simple oscillators, switches, logic functions, cell-cell communication and pattern-forming circuits have been created by the connection of a small set of natural transcription factors and their binding sites in different ways to produce different networks of molecular interactions. However, the controlled synthesis of more complex synthetic networks and functions will require an expanded set of functional molecules with known molecular specificities. Here, we tailored the molecular specificity of duplicated Escherichia coli ribosome x mRNA pairs with respect to the wild-type ribosome and mRNAs to produce multiple orthogonal ribosome x orthogonal mRNA pairs that can process information in parallel with, but independent of, their wild-type progenitors. In these pairs, the ribosome exclusively translates the orthogonal mRNA, and the orthogonal mRNA is not a substrate for cellular ribosomes. We predicted and measured the network of interactions between orthogonal ribosomes and orthogonal mRNAs, and showed that they can be used to post-transcriptionally program the cell with Boolean logic.
Stepwise maturation of the peptidyl transferase region of human mitoribosomes
Publisher: Springer Science and Business Media LLC
Date: 16-06-2021
DOI: 10.1038/S41467-021-23811-8
Abstract: Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes have erged considerably from the ancestral bacterial ribosomes and feature dramatically reduced ribosomal RNAs. The structural basis of the mammalian mitochondrial ribosome assembly is currently not well understood. Here we present eight distinct assembly intermediates of the human large mitoribosomal subunit involving seven assembly factors. We discover that the NSUN4-MTERF4 dimer plays a critical role in the process by stabilizing the 16S rRNA in a conformation that exposes the functionally important regions of rRNA for modification by the MRM2 methyltransferase and quality control interactions with the conserved mitochondrial GTPase MTG2 that contacts the sarcin-ricin loop and the immature active site. The successive action of these factors leads to the formation of the peptidyl transferase active site of the mitoribosome and the folding of the surrounding rRNA regions responsible for interactions with tRNAs and the small ribosomal subunit.
CCSDT(Q)/CBS thermochemistry for the D5h → D10h isomerization in the C10 carbon cluster: Getting the right answer for the right reason
Publisher: Elsevier BV
Date: 08-2018
Organelle transcriptomes: products of a deconstructed genome
Publisher: Elsevier BV
Date: 10-2013
DOI: 10.1016/J.MIB.2013.07.011
Abstract: Genetic drift and mutational pressure have shaped the evolution of mitochondrial and chloroplast genomes, giving rise to mechanisms that regulate their gene expression, which often differ from those in their prokaryotic ancestors. Advances in next generation sequencing technologies have enabled highly detailed characterization of organelle transcriptomes and the discovery of new transcripts and mechanisms for controlling gene expression. Here we discuss the common features of organelle transcriptomes that stem from their prokaryotic origin and some of the new innovations that are unique to organelles of multicellular organisms.
Designer RNA-binding proteins: New tools for manipulating the transcriptome
Publisher: Informa UK Limited
Date: 11-2011
Abstract: Post-transcriptional regulation of gene expression is ubiquitous and fundamental for the control of cell growth, differentiation and the complex developmental programs of multicellular eukaryotes. Despite this realization, the current tools that are available to study RNAs are limited in many respects. Recently we expanded the RNA recognition code of Pumilio and FBF homology (PUF) proteins, enabling RNA-binding proteins with programmable specificities to be designed. The design of proteins that can bind any RNA sequence of interest and modulate its function will be important to elucidate the mechanisms by which gene expression is controlled at the level of RNA and may provide potential therapeutics in the future.
Politics and Constitutions in Southeast Asia
Publisher: Routledge
Date: 15-07-2016
Substrate and inhibitor specificities differ between human cytosolic and mitochondrial thioredoxin reductases: Implications for development of specific inhibitors.
Publisher: Elsevier BV
Date: 03-2010
DOI: 10.1016/J.FREERADBIOMED.2010.12.015
Abstract: The cytosolic and mitochondrial thioredoxin reductases (TrxR1 and TrxR2) and thioredoxins (Trx1 and Trx2) are key components of the mammalian thioredoxin system, which is important for antioxidant defense and redox regulation of cell function. TrxR1 and TrxR2 are selenoproteins generally considered to have comparable properties, but to be functionally separated by their different compartments. To compare their properties we expressed recombinant human TrxR1 and TrxR2 and determined their substrate specificities and inhibition by metal compounds. TrxR2 preferred its endogenous substrate Trx2 over Trx1, whereas TrxR1 efficiently reduced both Trx1 and Trx2. TrxR2 displayed strikingly lower activity with dithionitrobenzoic acid (DTNB), lipoamide, and the quinone substrate juglone compared to TrxR1, and TrxR2 could not reduce lipoic acid. However, Sec-deficient two-amino-acid-truncated TrxR2 was almost as efficient as full-length TrxR2 in the reduction of DTNB. We found that the gold(I) compound auranofin efficiently inhibited both full-length TrxR1 and TrxR2 and truncated TrxR2. In contrast, some newly synthesized gold(I) compounds and cisplatin inhibited only full-length TrxR1 or TrxR2 and not truncated TrxR2. Surprisingly, one gold(I) compound, [Au(d2pype)(2)]Cl, was a better inhibitor of TrxR1, whereas another, [(iPr(2)Im)(2)Au]Cl, mainly inhibited TrxR2. These compounds also inhibited TrxR activity in the cytoplasm and mitochondria of cells, but their cytotoxicity was not always dependent on the proapoptotic proteins Bax and Bak. In conclusion, this study reveals significant differences between human TrxR1 and TrxR2 in substrate specificity and metal compound inhibition in vitro and in cells, which may be exploited for development of specific TrxR1- or TrxR2-targeting drugs.
Empirical Estimation of Nearshore Waves From a Global Deep-Water Wave Model
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 10-2006
Circularized visualisation of genetic interactions
Publisher: ACM Press
Date: 2017
Functional epitopes at the ribosome subunit interface
Publisher: Springer Science and Business Media LLC
Date: 02-04-2006
DOI: 10.1038/NCHEMBIO783
Abstract: The ribosome is a 2.5-MDa molecular machine that synthesizes cellular proteins encoded in mRNAs. The 30S and 50S subunits of the ribosome associate through structurally defined intersubunit bridges burying 6,000 A(2), 80% of which is buried in conserved RNA-RNA interactions. Intersubunit bridges bind translation factors, may coordinate peptide bond formation and translocation and may be actively remodeled in the post-termination complex, but the functional importance of numerous 30S bridge nucleotides had been unknown. We carried out large-scale combinatorial mutagenesis and in vivo selections on 30S nucleotides that form RNA-RNA intersubunit bridges in the Escherichia coli ribosome. We determined the covariation and functional importance of bridge nucleotides, allowing comparison of the structural interface and phylogenetic data to the functional epitope. Our results reveal how information for ribosome function is partitioned across bridges, and suggest a subset of nucleotides that may have measurable effects on in idual steps of the translational cycle.
Analysis of the Human Mitochondrial Transcriptome Using Directional Deep Sequencing and Parallel Analysis of RNA Ends
Publisher: Humana Press
Date: 2014
DOI: 10.1007/978-1-62703-971-0_21
Abstract: RNA sequencing using next-generation technologies provides comprehensive coverage of transcriptomes at a much greater depth than conventional transcriptomic methods. The human mitochondrial genome is relatively small, and sequencing its transcriptome provides a valuable method to investigate changes in RNA metabolism in great detail. Here we describe two methods that use next-generation technologies to investigate mitochondrial RNAs. Directional RNA sequencing enables the analyses of RNA abundance from each strand of the mitochondrial DNA. Parallel analysis of RNA ends enables the analyses of processing of mitochondrial transcripts, their termini, and annotation of any new transcripts.
A bifunctional protein regulates mitochondrial protein synthesis
Publisher: Oxford University Press (OUP)
Date: 05-03-2014
DOI: 10.1093/NAR/GKU179
Hierarchical RNA Processing Is Required for Mitochondrial Ribosome Assembly
Publisher: Elsevier BV
Date: 08-2016
DOI: 10.1016/J.CELREP.2016.07.031
Abstract: The regulation of mitochondrial RNA processing and its importance for ribosome biogenesis and energy metabolism are not clear. We generated conditional knockout mice of the endoribonuclease component of the RNase P complex, MRPP3, and report that it is essential for life and that heart and skeletal-muscle-specific knockout leads to severe cardiomyopathy, indicating that its activity is non-redundant. Transcriptome-wide parallel analyses of RNA ends (PARE) and RNA-seq enabled us to identify that in vivo 5' tRNA cleavage precedes 3' tRNA processing, and this is required for the correct biogenesis of the mitochondrial ribosomal subunits. We identify that mitoribosomal biogenesis proceeds co-transcriptionally because large mitoribosomal proteins can form a subcomplex on an unprocessed RNA containing the 16S rRNA. Taken together, our data show that RNA processing links transcription to translation via assembly of the mitoribosome.
Mapping of mitochondrial RNA-protein interactions by digital rnase footprinting
Publisher: Elsevier BV
Date: 11-2013
DOI: 10.1016/J.CELREP.2013.09.036
Abstract: Human mitochondrial DNA is transcribed as long polycistronic transcripts that encompass each strand of the genome and are processed subsequently into mature mRNAs, tRNAs, and rRNAs, necessitating widespread posttranscriptional regulation. Here, we establish methods for massively parallel sequencing and analyses of RNase-accessible regions of human mitochondrial RNA and thereby identify specific regions within mitochondrial transcripts that are bound by proteins. This approach provides a range of insights into the contribution of RNA-binding proteins to the regulation of mitochondrial gene expression.
Estrogen-mediated regulation of mitochondrial gene expression
Publisher: The Endocrine Society
Date: 2015
DOI: 10.1210/ME.2014-1077
Cellular logic with orthogonal ribosomes
Publisher: American Chemical Society (ACS)
Date: 22-11-2005
DOI: 10.1021/JA055338D
Abstract: The creation and use of unnatural molecules to control cellular function is a long standing goal of the chemical community, but in general, these efforts have been directed at finding molecules to inhibit or activate a particular molecular target or function, or to elicit a particular phenotype. Here we show that multiple unnatural molecules (orthogonal ribosomes) can be used combinatorially, in a single cell, to program Boolean logic functions. These experiments show how attention to the molecular specificity of noncovalent interactions between unnatural macromolecules allows the synthesis of complex function from the "bottom-up" in living matter.
Mice lacking the mitochondrial exonuclease MGME1 accumulate mtDNA deletions without developing progeria
Publisher: Springer Science and Business Media LLC
Date: 23-03-2018
DOI: 10.1038/S41467-018-03552-X
Abstract: Replication of mammalian mitochondrial DNA (mtDNA) is an essential process that requires high fidelity and control at multiple levels to ensure proper mitochondrial function. Mutations in the mitochondrial genome maintenance exonuclease 1 ( MGME1 ) gene were recently reported in mitochondrial disease patients. Here, to study disease pathophysiology, we generated Mgme1 knockout mice and report that homozygous knockouts develop depletion and multiple deletions of mtDNA. The mtDNA replication stalling phenotypes vary dramatically in different tissues of Mgme1 knockout mice. Mice with MGME1 deficiency accumulate a long linear subgenomic mtDNA species, similar to the one found in mtDNA mutator mice, but do not develop progeria. This finding resolves a long-standing debate by showing that point mutations of mtDNA are the main cause of progeria in mtDNA mutator mice. We also propose a role for MGME1 in the regulation of replication and transcription termination at the end of the control region of mtDNA.
Fidelity of translation initiation is required for coordinated respiratory complex assembly
Publisher: American Association for the Advancement of Science (AAAS)
Date: 06-12-2019
Abstract: The initiation of mitochondrial protein synthesis fine-tunes the assembly of respiratory complexes and energy production.
Ability of Procalcitonin to Discriminate Infection from Non-Infective Inflammation Using Two Pleural Disease Settings
Publisher: Public Library of Science (PLoS)
Date: 12-12-2012
Intrapleural Use of Tissue Plasminogen Activator and DNase in Pleural Infection
Publisher: Massachusetts Medical Society
Date: 11-08-2011
Early-onset Parkinson disease caused by a mutation in CHCHD2 and mitochondrial dysfunction
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 10-2018
DOI: 10.1212/NXG.0000000000000276
Abstract: Our goal was to identify the gene(s) associated with an early-onset form of Parkinson disease (PD) and the molecular defects associated with this mutation. We combined whole-exome sequencing and functional genomics to identify the genes associated with early-onset PD. We used fluorescence microscopy, cell, and mitochondrial biology measurements to identify the molecular defects resulting from the identified mutation. Here, we report an association of a homozygous variant in CHCHD2 , encoding coiled-coil-helix-coiled-coil-helix domain containing protein 2, a mitochondrial protein of unknown function, with an early-onset form of PD in a 26-year-old Caucasian woman. The CHCHD2 mutation in PD patient fibroblasts causes fragmentation of the mitochondrial reticular morphology and results in reduced oxidative phosphorylation at complex I and complex IV. Although patient cells could maintain a proton motive force, reactive oxygen species production was increased, which correlated with an increased metabolic rate. Our findings implicate CHCHD2 in the pathogenesis of recessive early-onset PD, expanding the repertoire of mitochondrial proteins that play a direct role in this disease.
Computationally designed hyperactive Cas9 enzymes
Publisher: Springer Science and Business Media LLC
Date: 31-05-2022
DOI: 10.1038/S41467-022-30598-9
Abstract: The ability to alter the genomes of living cells is key to understanding how genes influence the functions of organisms and will be critical to modify living systems for useful purposes. However, this promise has long been limited by the technical challenges involved in genetic engineering. Recent advances in gene editing have bypassed some of these challenges but they are still far from ideal. Here we use FuncLib to computationally design Cas9 enzymes with substantially higher donor-independent editing activities. We use genetic circuits linked to cell survival in yeast to quantify Cas9 activity and discover synergistic interactions between engineered regions. These hyperactive Cas9 variants function efficiently in mammalian cells and introduce larger and more erse pools of insertions and deletions into targeted genomic regions, providing tools to enhance and expand the possible applications of CRISPR-based gene editing.
Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins
Publisher: Cold Spring Harbor Laboratory
Date: 25-10-2011
Abstract: Human mitochondrial long noncoding RNAs (lncRNAs) have not been described to date. By analysis of deep-sequencing data we have identified three lncRNAs generated from the mitochondrial genome and confirmed their expression by Northern blotting and strand-specific qRT–PCR. We show that the abundance of these lncRNAs is comparable to their complementary mRNAs and that nuclear-encoded mitochondrial proteins involved in RNA processing regulate their expression. We also identify the 5′ and 3′ transcript ends of the three lncRNAs and show that mitochondrial RNase P protein 1 (MRPP1) is important for the processing of these transcripts. Finally, we show that mitochondrial lncRNAs form intermolecular duplexes and that their abundance is cell- and tissue-specific, suggesting a functional role in the regulation of mitochondrial gene expression.
Pentatricopeptide repeat domain protein 3 associates with the mitochondrial small ribosomal subunit and regulates translation
Publisher: Wiley
Date: 08-05-2009
DOI: 10.1016/J.FEBSLET.2009.04.048
Abstract: The basic components and mechanisms of mitochondrial transcription in mammals have been described, however, the components involved in mRNA processing, translation and stability remain largely unknown. In plants, pentatricopeptide domain RNA-binding proteins regulate the stability, expression and translation of mitochondrial transcripts. Here, we investigated the role of an uncharacterized mammalian pentatricopeptide domain protein, pentatricopeptide repeat domain protein 3 (PTCD3), and showed that it is a mitochondrial protein that associates with the small subunit of mitochondrial ribosomes. PTCD3 knockdown and over expression did not affect mitochondrial mRNA levels, suggesting that PTCD3 is not involved in RNA processing and stability. However, lowering PTCD3 in 143B osteosarcoma cells decreased mitochondrial protein synthesis, mitochondrial respiration and the activity of Complexes III and IV, suggesting that PTCD3 has a role in mitochondrial translation.
Structure of the heterodimer of human NONO and paraspeckle protein component 1 and analysis of its role in subnuclear body formation
Publisher: Proceedings of the National Academy of Sciences
Date: 13-03-2012
Abstract: Proteins of the Drosophila behavior/human splicing (DBHS) family include mammalian SFPQ (PSF), NONO (p54nrb), PSPC1, and invertebrate NONA and Hrp65. DBHS proteins are predominately nuclear, and are involved in transcriptional and posttranscriptional gene regulatory functions as well as DNA repair. DBHS proteins influence a wide gamut of biological processes, including the regulation of circadian rhythm, carcinogenesis, and progression of cancer. Additionally, mammalian DBHS proteins associate with the architectural long noncoding RNA NEAT1 (Men ε/β) to form paraspeckles, subnuclear bodies that alter gene expression via the nuclear retention of RNA. Here we describe the crystal structure of the heterodimer of the multidomain conserved region of the DBHS proteins, PSPC1 and NONO. These proteins form an extensively intertwined dimer, consistent with the observation that the different DBHS proteins are typically copurified from mammalian cells, and suggesting that they act as obligate heterodimers. The PSPC1/NONO heterodimer has a right-handed antiparallel coiled-coil that positions two of four RNA recognition motif domains in an unprecedented arrangement on either side of a 20-Å channel. This configuration is supported by a protein:protein interaction involving the NONA araspeckle domain, which is characteristic of the DBHS family. By examining various mutants and truncations in cell culture, we find that DBHS proteins require an additional antiparallel coiled-coil emanating from either end of the dimer for paraspeckle subnuclear body formation. These results suggest that paraspeckles may potentially form through self-association of DBHS dimers into higher-order structures.
A mutation in MT-TW causes a tRNA processing defect and reduced mitochondrial function in a family with Leigh syndrome
Publisher: Elsevier BV
Date: 11-2015
DOI: 10.1016/J.MITO.2015.10.008
Abstract: Leigh syndrome (LS) is a progressive mitochondrial neurodegenerative disorder, whose symptoms most commonly include psychomotor delay with regression, lactic acidosis and a failure to thrive. Here we describe three siblings with LS, but with additional manifestations including hypertrophic cardiomyopathy, hepatosplenomegaly, cholestatic hepatitis, and seizures. All three affected siblings were found to be homoplasmic for an m. 5559A>G mutation in the T stem of the mitochondrial DNA-encoded MT-TW by next generation sequencing. The m.5559A>G mutation causes a reduction in the steady state levels of tRNA(Trp) and this decrease likely affects the stability of other mitochondrial RNAs in the patient fibroblasts. We observe accumulation of an unprocessed transcript containing tRNA(Trp), decreased de novo protein synthesis and consequently lowered steady state levels of mitochondrial DNA-encoded proteins that compromise mitochondrial respiration. Our results show that the m.5559A>G mutation at homoplasmic levels causes LS in association with severe multi-organ disease (LS-plus) as a consequence of dysfunctional mitochondrial RNA metabolism.
Transcriptome-wide effects of aPOLR3Agene mutation in patients with an unusual phenotype of striatal involvement
Publisher: Oxford University Press (OUP)
Date: 09-08-2016
DOI: 10.1093/HMG/DDW263
Abstract: RNA polymerase III is essential for the transcription of non-coding RNAs, including tRNAs. Mutations in the genes encoding its largest subunits are known to cause hypomyelinating leukodystrophies (HLD7) with pathogenetic mechanisms hypothesised to involve impaired availability of tRNAs. We have identified a founder mutation in the POLR3A gene that leads to aberrant splicing, a premature termination codon and partial deficiency of the canonical full-length transcript. Our clinical and imaging data showed no evidence of the previously reported white matter or cerebellar involvement instead the affected brain structures included the striatum and red nuclei with the ensuing clinical manifestations. Our transcriptome-wide investigations revealed an overall decrease in the levels of Pol III-transcribed tRNAs and an imbalance in the levels of regulatory ncRNAs such as small nuclear and nucleolar RNAs (snRNAs and snoRNAs). In addition, the Pol III mutation was found to exert complex downstream effects on the Pol II transcriptome, affecting the general regulation of RNA metabolism.
PTCD1 Is Required for 16S rRNA Maturation Complex Stability and Mitochondrial Ribosome Assembly
Publisher: Elsevier BV
Date: 04-2018
DOI: 10.1016/J.CELREP.2018.03.033
Abstract: The regulation of mitochondrial RNA life cycles and their roles in ribosome biogenesis and energy metabolism are not fully understood. We used CRISPR/Cas9 to generate heart- and skeletal-muscle-specific knockout mice of the pentatricopeptide repeat domain protein 1, PTCD1, and show that its loss leads to severe cardiomyopathy and premature death. Our detailed transcriptome-wide and functional analyses of these mice enabled us to identify the molecular role of PTCD1 as a 16S rRNA-binding protein essential for its stability, pseudouridylation, and correct biogenesis of the mitochondrial large ribosomal subunit. We show that impaired mitoribosome biogenesis can have retrograde signaling effects on nuclear gene expression through the transcriptional activation of the mTOR pathway and upregulation of cytoplasmic protein synthesis and pro-survival factors in the absence of mitochondrial translation. Taken together, our data show that impaired assembly of the mitoribosome exerts its consequences via differential regulation of mitochondrial and cytoplasmic protein synthesis.
Pentatricopeptide repeat domain protein 1 lowers the levels of mitochondrial leucine tRNAs in cells
Publisher: Oxford University Press (OUP)
Date: 03-08-2009
DOI: 10.1093/NAR/GKP627
Theoretical Studies of Two Key Low-Lying Carbenes of C5H2Missing in the Laboratory
Publisher: American Chemical Society (ACS)
Date: 03-07-2019
Abstract: The equilibrium geometries and spectroscopic properties of two key singlet carbenes, buta-1,3-diynylcarbene (
The role of mammalian PPR domain proteins in the regulation of mitochondrial gene expression
Publisher: Elsevier BV
Date: 09-2012
DOI: 10.1016/J.BBAGRM.2011.10.007
Abstract: Pentatricopeptide repeat (PPR) domain proteins are a large family of RNA-binding proteins that are involved in the maturation and translation of organelle transcripts in eukaryotes. They were first identified in plant organelles and their important role in mammalian mitochondrial gene regulation is now emerging. Mammalian PPR proteins, like their plant counterparts, have erse roles in mitochondrial transcription, RNA metabolism and translation and consequently are important for mitochondrial function and cell health. Here we discuss the current knowledge about the seven mammalian PPR proteins identified to date and their roles in the regulation of mitochondrial gene expression. Furthermore we discuss the mitochondrial RNA targets of the mammalian PPR proteins and methods to investigate the RNA targets of these mitochondrial RNA-binding proteins. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
Frankenstein Cas9: engineering improved gene editing systems
Publisher: Portland Press Ltd.
Date: 28-10-2022
DOI: 10.1042/BST20220873
Abstract: The discovery of CRISPR–Cas9 and its widespread use has revolutionised and propelled research in biological sciences. Although the ability to target Cas9's nuclease activity to specific sites via an easily designed guide RNA (gRNA) has made it an adaptable gene editing system, it has many characteristics that could be improved for use in biotechnology. Cas9 exhibits significant off-target activity and low on-target nuclease activity in certain contexts. Scientists have undertaken ambitious protein engineering c aigns to bypass these limitations, producing several promising variants of Cas9. Cas9 variants with improved and alternative activities provide exciting new tools to expand the scope and fidelity of future CRISPR applications.
Promoter polymorphisms in two overlapping 6p25 genes implicate mitochondrial proteins in cognitive deficit in schizophrenia
Publisher: Springer Science and Business Media LLC
Date: 04-10-2011
DOI: 10.1038/MP.2011.129
Abstract: In a previous study, we detected a 6p25-p24 region linked to schizophrenia in families with high composite cognitive deficit (CD) scores, a quantitative trait integrating multiple cognitive measures. Association mapping of a 10 Mb interval identified a 260 kb region with a cluster of single-nucleotide polymorphisms (SNPs) significantly associated with CD scores and memory performance. The region contains two colocalising genes, LYRM4 and FARS2, both encoding mitochondrial proteins. The two tagging SNPs with strongest evidence of association were located around the overlapping putative promoters, with rs2224391 predicted to alter a transcription factor binding site (TFBS). Sequencing the promoter region identified 22 SNPs, many predicted to affect TFBSs, in a tight linkage disequilibrium block. Luciferase reporter assays confirmed promoter activity in the predicted promoter region, and demonstrated marked downregulation of expression in the LYRM4 direction under the haplotype comprising the minor alleles of promoter SNPs, which however is not driven by rs2224391. Experimental evidence from LYRM4 expression in lymphoblasts, gel-shift assays and modelling of DNA breathing dynamics pointed to two adjacent promoter SNPs, rs7752203-rs4141761, as the functional variants affecting expression. Their C-G alleles were associated with higher transcriptional activity and preferential binding of nuclear proteins, whereas the G-A combination had opposite effects and was associated with poor memory and high CD scores. LYRM4 is a eukaryote-specific component of the mitochondrial biogenesis of Fe-S clusters, essential cofactors in multiple processes, including oxidative phosphorylation. LYRM4 downregulation may be one of the mechanisms involved in inefficient oxidative phosphorylation and oxidative stress, increasingly recognised as contributors to schizophrenia pathogenesis.
RNA processing in human mitochondria
Publisher: Informa UK Limited
Date: 09-2011
Abstract: Mammalian mitochondrial DNA is transcribed as precursor polycistronic transcripts containing 13 mRNAs, 2 rRNAs, punctuated by 22 tRNAs. The mechanisms involved in the excision of mitochondrial tRNAs from these polycistronic transcripts have remained largely unknown. We have investigated the roles of ELAC2, mitochondrial RNase P proteins 1 and 3, and pentatricopeptide repeat domain protein 1 in the processing of mitochondrial polycistronic transcripts. We used a deep sequencing approach to characterize the 5' and 3' ends of processed mitochondrial transcripts and provide a detailed map of mitochondrial tRNA processing sites affected by these proteins. We show that MRPP1 and MRPP3 process the 5' ends of tRNAs and the 5' unconventional, non tRNA containing site of the CO1 transcript. By contrast, we find that ELAC2 and PTCD1 affect the 3' end processing of tRNAs. Finally, we found that MRPP1 is essential for transcript processing, RNA modification, translation and mitochondrial respiration.
Supernumerary proteins of mitochondrial ribosomes
Publisher: Elsevier BV
Date: 04-2014
DOI: 10.1016/J.BBAGEN.2013.08.010
Abstract: Messenger RNAs encoded by mitochondrial genomes are translated on mitochondrial ribosomes that have unique structure and protein composition compared to prokaryotic and cytoplasmic ribosomes. Mitochondrial ribosomes are a patchwork of core proteins that share homology with prokaryotic ribosomal proteins and new, supernumerary proteins that can be unique to different organisms. In mammals, there are specific supernumerary ribosomal proteins that are not present in other eukaryotes. Here we discuss the roles of supernumerary proteins in the regulation of mitochondrial gene expression and compare them among different eukaryotic systems. Furthermore, we consider if differences in the structure and organization of mitochondrial genomes may have contributed to the acquisition of mitochondrial ribosomal proteins with new functions. The distinct and erse compositions of mitochondrial ribosomes illustrate the high evolutionary ergence found between mitochondrial genetic systems. Elucidating the role of the organism-specific supernumerary proteins may provide a window into the regulation of mitochondrial gene expression through evolution in response to distinct evolutionary paths taken by mitochondria in different organisms. This article is part of a Special Issue entitled Frontiers of Mitochondrial Research.
Blood culture bottle culture of pleural fluid in pleural infection
Publisher: BMJ
Date: 04-2011
Abstract: Pleural infection is common, and has a >30% major morbidity and mortality-particularly when infection is caused by Gram-negative, Staphylococcus aureus or mixed aerobic pathogens. Standard pleural fluid culture is negative in ∼40% of cases. Culturing pleural fluid in blood culture bottles may increase microbial yield, and is cheap and easy to perform. To determine whether inoculating pleural fluid into blood culture bottles increases the culture positivity of pleural infection over standard laboratory culture, and to assess the optimum volume of inoculum to introduce. 62 patients with pleural infection were enrolled. Pairs of aerobic and anaerobic blood culture bottles were inoculated at the bedside with 2, 5 or 10 ml of pleural fluid, and two pleural fluid specimens were sent for standard culture. Pleural fluid from nine control patients was cultured to test for 'false-positive' results. The addition of blood culture bottle culture to standard culture increased the proportion of patients with identifiable pathogens by 20.8% (20/53 (37.7%) to 31/53 (58.5%) (difference 20.8%, 95% CI difference 8.9% to 20.8%, p<0.001)). The second standard culture did not similarly improve the culture positivity (19/49 (38.8%) to 22/49 (44.9%) (difference 6.1%, 95% CI difference -2.5% to 6.1%, p=0.08)). The culture inoculum volume did not influence bacterial isolation frequency. The control fluids were culture negative. Blood culture bottle culture of infected pleural fluid increases microbial yield when used in addition to standard culture. This technique should be part of routine care.
A common genetic variant of a mitochondrial RNA processing enzyme predisposes to insulin resistance
Publisher: American Association for the Advancement of Science (AAAS)
Date: 24-09-2021
Abstract: A variant in an RNA processing enzyme predisposes to insulin resistance by reducing calcium release and insulin secretion.
Copy number variation in tRNA isodecoder genes impairs mammalian development and balanced translation
Publisher: Springer Science and Business Media LLC
Date: 18-04-2023
DOI: 10.1038/S41467-023-37843-9
Abstract: The number of tRNA isodecoders has increased dramatically in mammals, but the specific molecular and physiological reasons for this expansion remain elusive. To address this fundamental question we used CRISPR editing to knockout the seven-membered phenylalanine tRNA gene family in mice, both in idually and combinatorially. Using ATAC-Seq, RNA-seq, ribo-profiling and proteomics we observed distinct molecular consequences of single tRNA deletions. We show that tRNA-Phe-1-1 is required for neuronal function and its loss is partially compensated by increased expression of other tRNAs but results in mistranslation. In contrast, the other tRNA-Phe isodecoder genes buffer the loss of each of the remaining six tRNA-Phe genes. In the tRNA-Phe gene family, the expression of at least six tRNA-Phe alleles is required for embryonic viability and tRNA-Phe-1-1 is most important for development and survival. Our results reveal that the multi-copy configuration of tRNA genes is required to buffer translation and viability in mammals.
Modulation of miRNA function by natural and synthetic RNA-binding proteins in cancer
Publisher: Springer Science and Business Media LLC
Date: 04-06-2019
DOI: 10.1007/S00018-019-03163-9
Abstract: RNA-binding proteins (RBPs) and microRNAs (miRNAs) are the most important regulators of mRNA stability and translation in eukaryotic cells however, the complex interplay between these systems is only now coming to light. RBPs and miRNAs regulate a unique set of targets in either a positive or negative manner and their regulation is mainly opposed to each other on overlapping targets. In some cases, the levels of RBPs or miRNAs regulate the cellular levels of one another and decreased levels of either results in changes in translation of their targets. There is growing evidence that these regulatory circuits are crucial in the development and progression of cancer however, the rules underlying synergism and antagonism between miRNAs and RNA-binding proteins remain unclear. Synthetic biology seeks to develop artificial systems to better understand their natural counterparts and to develop new, useful technologies for manipulation of gene expression at the RNA level. The recent development of artificial RNA-binding proteins promises to enable a much greater understanding of the importance of the functional interactions between RNA-binding proteins and miRNAs, as well as enabling their manipulation for therapeutic purposes.
In silico evolution of nucleic acid-binding proteins from a nonfunctional scaffold
Publisher: Springer Science and Business Media LLC
Date: 24-02-2022
DOI: 10.1038/S41589-022-00967-Y
Abstract: Directed evolution emulates the process of natural selection to produce proteins with improved or altered functions. These approaches have proven to be very powerful but are technically challenging and particularly time and resource intensive. To bypass these limitations, we constructed a system to perform the entire process of directed evolution in silico. We employed iterative computational cycles of mutation and evaluation to predict mutations that confer high-affinity binding activities for DNA and RNA to an initial de novo designed protein with no inherent function. Beneficial mutations revealed modes of nucleic acid recognition not previously observed in natural proteins, highlighting the ability of computational directed evolution to access new molecular functions. Furthermore, the process by which new functions were obtained closely resembles natural evolution and can provide insights into the contributions of mutation rate, population size and selective pressure on functionalization of macromolecules in nature.
Murine cytomegalovirus infection exacerbates complex IV deficiency in a model of mitochondrial disease
Publisher: Public Library of Science (PLoS)
Date: 04-03-2020
Visualization of RNA-protein interactions in living cells: FMRP and IMP1 interact on mRNAs
Publisher: Wiley
Date: 29-07-2004
Simultaneous processing and degradation of mitochondrial RNAs revealed by circularized RNA sequencing
Publisher: Oxford University Press (OUP)
Date: 15-02-2017
DOI: 10.1093/NAR/GKX104
Stepwise maturation of the peptidyl transferase region of human mitoribosomes
Publisher: Cold Spring Harbor Laboratory
Date: 29-03-2021
DOI: 10.1101/2021.03.29.437532
Abstract: Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes erged considerably from the ancestral bacterial ribosomes and feature dramatically reduced ribosomal RNAs. Structural basis of the mammalian mitochondrial ribosome assembly is currently not understood. Here we present eight distinct assembly intermediates of the human large mitoribosomal subunit involving 7 assembly factors. We discover that NSUN4-MTERF4 dimer plays a critical role in the process by stabilizing the 16S rRNA in a conformation that exposes the functionally important regions of rRNA for modification by MRM2 methyltransferase and quality control interactions with a conserved mitochondrial GTPase MTG2 that contacts the sarcin ricin loop and the immature active site. The successive action of these factors leads to the formation of the peptidyl transferase active site of the mitoribosome and the folding of the surrounding rRNA regions responsible for interactions with tRNAs and the small ribosomal subunit.
Manipulating and elucidating mitochondrial gene expression with engineered proteins
Publisher: The Royal Society
Date: 02-12-2020
Abstract: Many conventional, modern genome engineering tools cannot be used to study mitochondrial genetics due to the unusual structure and physiology of the mitochondrial genome. Here, we review a number of newly developed, synthetic biology-based approaches for altering levels of mutant mammalian mitochondrial DNA and mitochondrial RNAs, including transcription activator-like effector nucleases, zinc finger nucleases and engineered RNA-binding proteins. These approaches allow researchers to manipulate and visualize mitochondrial processes and may provide future therapeutics. This article is part of the theme issue ‘Linking the mitochondrial genotype to phenotype: a complex endeavour’.
Defects in RNA metabolism in mitochondrial disease
Publisher: Elsevier BV
Date: 04-2017
DOI: 10.1016/J.BIOCEL.2017.02.003
Abstract: The expression of mitochondrially-encoded genes requires the efficient processing of long precursor RNAs at the 5' and 3' ends of tRNAs, a process which, when disrupted, results in disease. Two such mutations reside within mt-tRNA
ATFS-1 counteracts mitochondrial DNA damage by promoting repair over transcription
Publisher: Springer Science and Business Media LLC
Date: 17-07-2023
Association of menopausal symptom severity and osteoporotic fractures: a case-control study
Publisher: Informa UK Limited
Date: 22-08-2020
Theoretical Studies of SiC4H2 Isomers Delineate Three Low-Lying Silylidenes Are Missing in the Laboratory
Publisher: American Chemical Society (ACS)
Date: 06-01-2020
Abstract: Eleven isomers of SiC
Modular ssDNA binding and inhibition of telomerase activity by designer PPR proteins
Publisher: Springer Science and Business Media LLC
Date: 07-06-2018
DOI: 10.1038/S41467-018-04388-1
Abstract: DNA is typically found as a double helix, however it must be separated into single strands during all phases of DNA metabolism including transcription, replication, recombination and repair. Although recent breakthroughs have enabled the design of modular RNA- and double-stranded DNA-binding proteins, there are currently no tools available to manipulate single-stranded DNA (ssDNA). Here we show that artificial pentatricopeptide repeat (PPR) proteins can be programmed for sequence-specific ssDNA binding. Interactions occur using the same code and specificity as for RNA binding. We solve the structures of DNA-bound and apo proteins revealing the basis for ssDNA binding and how hydrogen bond rearrangements enable the PPR structure to envelope its ssDNA target. Finally, we show that engineered PPRs can be designed to bind telomeric ssDNA and can block telomerase activity. The modular mode of ssDNA binding by PPR proteins provides tools to target ssDNA and to understand its importance in cells.
Shackled ribosomes unleashed
Publisher: Springer Science and Business Media LLC
Date: 14-07-2022
MRPS27 is a pentatricopeptide repeat domain protein required for the translation of mitochondrially encoded proteins
Publisher: Wiley
Date: 25-07-2012
DOI: 10.1016/J.FEBSLET.2012.07.043
Abstract: Mammalian pentatricopeptide repeat domain (PPR) proteins are involved in regulation of mitochondrial RNA metabolism and translation and are required for mitochondrial function. We investigated an uncharacterised PPR protein, the supernumerary mitochondrial ribosomal protein of the small subunit 27 (MRPS27), and show that it associates with the 12S rRNA and tRNA(Glu), however it does not affect their abundance. We found that MRPS27 is not required for mitochondrial RNA processing or the stability of the small ribosomal subunit. However, MRPS27 is required for mitochondrial protein synthesis and its knockdown causes decreased abundance in respiratory complexes and cytochrome c oxidase activity.
A universal code for RNA recognition by PUF proteins
Publisher: Springer Science and Business Media LLC
Date: 15-05-2011
DOI: 10.1038/NCHEMBIO.577
Abstract: The design of proteins that can bind any RNA sequence of interest has many potential biological and medical applications. Here we have expanded the recognition of Pumilio and FBF homology protein (PUF) repeats beyond adenine, guanine and uracil and evolved them to specifically bind cytosine. These repeat sequences can be used to create PUF domains capable of selectively binding RNA targets of erse sequence and structure.
The human mitochondrial transcriptome and the rna-binding proteins that regulate its expression
Publisher: Wiley
Date: 09-07-2012
DOI: 10.1002/WRNA.1128
Abstract: The human mitochondrial transcriptome, although produced from a small and compact genome, has revealed surprising complexity in its composition and regulation. Wide variation between in idual tRNAs, mRNAs, and rRNAs indicate the importance of post-transcriptional processing, maturation, and degradation mechanisms in the regulation of mitochondrial gene expression. RNA-binding proteins play essential roles in controlling the mitochondrial transcriptome from its synthesis to its destruction and have evolved unique features to complement the unusual features of mitochondrial RNAs. Recent studies have shown how changes in mitochondrial RNAs and their binding proteins can have significant effects on human health. This opens new avenues for investigation of mitochondrial RNA-binding proteins and the mechanisms by which they regulate mitochondrial gene expression.
The surface electronic structure of silicon terminated (100) diamond.
Publisher: IOP Publishing
Date: 23-05-2016
DOI: 10.1088/0957-4484/27/27/275201
Abstract: A combination of synchrotron-based x-ray spectroscopy and contact potential difference measurements have been used to examine the electronic structure of the (3 × 1) silicon terminated (100) diamond surface under ultra high vacuum conditions. An occupied surface state which sits 1.75 eV below the valence band maximum has been identified, and indications of mid-gap unoccupied surface states have been found. Additionally, the pristine silicon terminated surface is shown to possess a negative electron affinity of -0.86 ± 0.1 eV.
Organization and expression of the mammalian mitochondrial genome
Publisher: Springer Science and Business Media LLC
Date: 22-04-2022
DOI: 10.1038/S41576-022-00480-X
Abstract: The mitochondrial genome encodes core subunits of the respiratory chain that drives oxidative phosphorylation and is, therefore, essential for energy conversion. Advances in high-throughput sequencing technologies and cryoelectron microscopy have shed light on the structure and organization of the mitochondrial genome and revealed unique mechanisms of mitochondrial gene regulation. New animal models of impaired mitochondrial protein synthesis have shown how the coordinated regulation of the cytoplasmic and mitochondrial translation machineries ensures the correct assembly of the respiratory chain complexes. These new technologies and disease models are providing a deeper understanding of mitochondrial genome organization and expression and of the diseases caused by impaired energy conversion, including mitochondrial, neurodegenerative, cardiovascular and metabolic diseases. They also provide avenues for the development of treatments for these conditions.
Regulation of a minimal transcriptome by repeat domain proteins
Publisher: Elsevier BV
Date: 04-2018
DOI: 10.1016/J.SEMCDB.2017.08.037
Abstract: Repeat proteins regulate the expression of the mammalian mitochondrial genome at the level of transcription, processing, maturation, and translation. Defects in the regulation of mitochondrial gene expression due to mutations in genes encoding repeat proteins can lead to mitochondrial dysfunction and disease, however the molecular mechanisms that regulate mitochondrial gene expression and how defects in these processes cause disease still remains poorly understood. Recently solved crystal structures, characterisation of the new genetic models, and use of RNA sequencing (RNA-Seq) technologies have greatly expanded our current understanding of mitochondrial repeat proteins and biology.
From High-Energy C7H2 Isomers with A Planar Tetracoordinate Carbon Atom to An Experimentally Known Carbene
Publisher: American Chemical Society (ACS)
Date: 26-10-2018
Abstract: In this work, we use high-level ab initio procedures to show that the high-energy isomers of C
Fidelity and coordination of mitochondrial protein synthesis in health and disease
Publisher: Wiley
Date: 15-08-2021
DOI: 10.1113/JP280359
Abstract: The evolutionary acquisition of mitochondria has given rise to the ersity of eukaryotic life. Mitochondria have retained their ancestral α‐proteobacterial traits through the maintenance of double membranes and their own circular genome. Their genome varies in size from very large in plants to the smallest in animals and their parasites. The mitochondrial genome encodes essential genes for protein synthesis and has to coordinate its expression with the nuclear genome from which it sources most of the proteins required for mitochondrial biogenesis and function. The mitochondrial protein synthesis machinery is unique because it is encoded by both the nuclear and mitochondrial genomes thereby requiring tight regulation to produce the respiratory complexes that drive oxidative phosphorylation for energy production. The fidelity and coordination of mitochondrial protein synthesis are essential for ATP production. Here we compare and contrast the mitochondrial translation mechanisms in mammals and fungi to bacteria and reveal that their erse regulation can have unusual impacts on the health and disease of these organisms. We highlight that in mammals the rate of protein synthesis is more important than the fidelity of translation, enabling coordinated biogenesis of the mitochondrial respiratory chain with respiratory chain proteins synthesised by cytoplasmic ribosomes. Changes in mitochondrial protein fidelity can trigger the activation of the erse cellular signalling networks in fungi and mammals to combat dysfunction in energy conservation. The physiological consequences of altered fidelity of protein synthesis can range from liver regeneration to the onset and development of cardiomyopathy. image
LRPPRC-mediated folding of the mitochondrial transcriptome
Publisher: Springer Science and Business Media LLC
Date: 16-11-2017
DOI: 10.1038/S41467-017-01221-Z
Abstract: The expression of the compact mammalian mitochondrial genome requires transcription, RNA processing, translation and RNA decay, much like the more complex chromosomal systems, and here we use it as a model system to understand the fundamental aspects of gene expression. Here we combine RNase footprinting with PAR-CLIP at unprecedented depth to reveal the importance of RNA–protein interactions in dictating RNA folding within the mitochondrial transcriptome. We show that LRPPRC, in complex with its protein partner SLIRP, binds throughout the mitochondrial transcriptome, with a preference for mRNAs, and its loss affects the entire secondary structure and stability of the transcriptome. We demonstrate that the LRPPRC–SLIRP complex is a global RNA chaperone that stabilizes RNA structures to expose the required sites for translation, stabilization, and polyadenylation. Our findings reveal a general mechanism where extensive RNA–protein interactions ensure that RNA is accessible for its biological functions.
Mutation in MRPS34 Compromises Protein Synthesis and Causes Mitochondrial Dysfunction
Publisher: Public Library of Science (PLoS)
Date: 27-03-2015
Loss of the RNA-binding protein TACO1 causes late-onset mitochondrial dysfunction in mice
Publisher: Springer Science and Business Media LLC
Date: 20-06-2016
DOI: 10.1038/NCOMMS11884
Abstract: The recognition and translation of mammalian mitochondrial mRNAs are poorly understood. To gain further insights into these processes in vivo, we characterized mice with a missense mutation that causes loss of the translational activator of cytochrome oxidase subunit I (TACO1). We report that TACO1 is not required for embryonic survival, although the mutant mice have substantially reduced COXI protein, causing an isolated complex IV deficiency. We show that TACO1 specifically binds the mt-Co1 mRNA and is required for translation of COXI through its association with the mitochondrial ribosome. We determined the atomic structure of TACO1, revealing three domains in the shape of a hook with a tunnel between domains 1 and 3. Mutations in the positively charged domain 1 reduce RNA binding by TACO1. The Taco1 mutant mice develop a late-onset visual impairment, motor dysfunction and cardiac hypertrophy and thus provide a useful model for future treatment trials for mitochondrial disease.
The determinants of a firm’s strategic orientation and its implication on performance: A study on Indonesia state owned enterprises
Publisher: Informa UK Limited
Date: 27-06-2023
Transterm: a database of mRNAs and translational control elements
Publisher: Oxford University Press (OUP)
Date: 2002
DOI: 10.1093/NAR/30.1.310
Abstract: Transterm is a database that facilitates studies of translation and the translational control of protein synthesis. It contains a curated collection of elements in mRNAs that control translation, and biologically relevant mRNA regions extracted from GenBank. It is organised largely on a taxonomic basis with files and summaries for each species. Global patterns that may affect translation in particular species, for ex le bias in the context of initiation codons (Kozak's consensus or Shine-Dalgarno sequences) or termination codons, can be detected in the consensus and information content bias summaries. Several types of access are provided via a web browser interface. Transterm defined elements may be matched in a user's sequence or in the database. Alternatively, elements can be entered by the user to search specific sections of the database (for ex le, coding regions or 3' flanking regions or the 3'-UTRs) or the user's sequence. Each Transterm defined element has an associated biological description with references. The database is accessible at uther.otago.ac.nz/Transterm.html.
Molecular basis of translation termination at noncanonical stop codons in human mitochondria
Publisher: American Association for the Advancement of Science (AAAS)
Date: 05-05-2023
Abstract: The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the standard genetic code, including the reassignment of two arginine codons to stop codons. The protein required for translation termination at these noncanonical stop codons to release the newly synthesized polypeptides is not currently known. In this study, we used gene editing and ribosomal profiling in combination with cryo–electron microscopy to establish that mitochondrial release factor 1 (mtRF1) detects noncanonical stop codons in human mitochondria by a previously unknown mechanism of codon recognition. We discovered that binding of mtRF1 to the decoding center of the ribosome stabilizes a highly unusual conformation in the messenger RNA in which the ribosomal RNA participates in specific recognition of the noncanonical stop codons.
The Human Mitochondrial Transcriptome
Publisher: Elsevier BV
Date: 08-2011
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