The Experts below are selected from a list of 309 Experts worldwide ranked by ideXlab platform
David Roy Smith - One of the best experts on this subject based on the ideXlab platform.
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Pervasive Transcription of Mitochondrial, Plastid, and Nucleomorph Genomes across Diverse Plastid-Bearing Species.
Genome biology and evolution, 2017Co-Authors: Matheus Sanita Lima, David Roy SmithAbstract:Organelle Genomes exhibit remarkable diversity in content, structure, and size, and in their modes of gene expression, which are governed by both Organelle- and nuclear-encoded machinery. Next generation sequencing (NGS) has generated unprecedented amounts of genomic and transcriptomic data, which can be used to investigate Organelle Genome transcription. However, most of the available eukaryotic RNA-sequencing (RNA-seq) data are used to study nuclear transcription only, even though large numbers of Organelle-derived reads can typically be mined from these experiments. Here, we use publicly available RNA-seq data to assess Organelle Genome transcription in 59 diverse plastid-bearing species. Our RNA mapping analyses unraveled pervasive (full or near-full) transcription of mitochondrial, plastid, and nucleomorph Genomes. In all cases, 85% or more of the Organelle Genome was recovered from the RNA data, including noncoding (intergenic and intronic) regions. These results reinforce the idea that Organelles transcribe all or nearly all of their genomic material and are dependent on post-transcriptional processing of polycistronic transcripts. We explore the possibility that transcribed intergenic regions are producing functional noncoding RNAs, and that Organelle Genome noncoding content might provide raw material for generating regulatory RNAs.
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the in complete Organelle Genome exploring the use and nonuse of available technologies for characterizing mitochondrial and plastid chromosomes
Molecular Ecology Resources, 2016Co-Authors: Matheus Sanita Lima, Laura C Woods, Matthew W Cartwright, David Roy SmithAbstract:Not long ago, scientists paid dearly in time, money and skill for every nucleotide that they sequenced. Today, DNA sequencing technologies epitomize the slogan 'faster, easier, cheaper and more', and in many ways, sequencing an entire Genome has become routine, even for the smallest laboratory groups. This is especially true for mitochondrial and plastid Genomes. Given their relatively small sizes and high copy numbers per cell, Organelle DNAs are currently among the most highly sequenced kind of chromosome. But accurately characterizing an Organelle Genome and the information it encodes can require much more than DNA sequencing and bioinformatics analyses. Organelle Genomes can be surprisingly complex and can exhibit convoluted and unconventional modes of gene expression. Unravelling this complexity can demand a wide assortment of experiments, from pulsed-field gel electrophoresis to Southern and Northern blots to RNA analyses. Here, we show that it is exactly these types of 'complementary' analyses that are often lacking from contemporary Organelle Genome papers, particularly short 'Genome announcement' articles. Consequently, crucial and interesting features of Organelle chromosomes are going undescribed, which could ultimately lead to a poor understanding and even a misrepresentation of these Genomes and the genes they express. High-throughput sequencing and bioinformatics have made it easy to sequence and assemble entire chromosomes, but they should not be used as a substitute for or at the expense of other types of genomic characterization methods.
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The mutational hazard hypothesis of Organelle Genome evolution: 10 years on.
Molecular ecology, 2016Co-Authors: David Roy SmithAbstract:Why is there such a large variation in size and noncoding DNA content among Organelle Genomes? One explanation is that this genomic variation results from differences in the rates of Organelle mutation and random genetic drift, as opposed to being the direct product of natural selection. Along these lines, the mutational hazard hypothesis (MHH) holds that 'excess' DNA is a mutational liability (because it increases the potential for harmful mutations) and, thus, has a greater tendency to accumulate in an Organelle system with a low mutation rate as opposed to one with a high rate of mutation. Various studies have explored this hypothesis and, more generally, the relationship between Organelle Genome architecture and the mode and efficiency of Organelle DNA repair. Although some of these investigations are in agreement with the MHH, others have contradicted it; nevertheless, they support a central role of mutation, DNA maintenance pathways and random genetic drift in fashioning Organelle chromosomes. Arguably, one of the most important contributions of the MHH is that it has sparked crucial, widespread discussions about the importance of nonadaptive processes in Genome evolution.
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Inflated Organelle Genomes and a circular-mapping mtDNA probably existed at the origin of coloniality in volvocine green algae
European Journal of Phycology, 2016Co-Authors: Jonathan Featherston, Pierre M. Durand, Hisayoshi Nozaki, Yoko Arakaki, David Roy SmithAbstract:The volvocine lineage is a monophyletic grouping of unicellular, colonial and multicellular algae, and a model for studying the evolution of multicellularity. In addition to being morphologically diverse, volvocine algae boast a surprising amount of Organelle genomic variation. Moreover, volvocine Organelle Genome complexity appears to scale positively with organismal complexity. However, the Organelle DNA architecture at the origin of colonial living is not known. To examine this issue, we sequenced the plastid and mitochondrial DNAs (ptDNA and mtDNA) of the 4-celled alga Tetrabaena socialis, which is basal to the colonial and multicellular volvocines.Tetrabaena socialis has a circular-mapping mitochondrial Genome, contrasting with the linear mtDNA architecture of its relative Chlamydomonas reinhardtii. This suggests that a circular-mapping mtDNA conformation emerged at or near the transition to group living in the volvocines, or represents the ancestral state of the lineage as a whole. The T. socialis p...
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Mitochondrial and plastid Genomes of the colonial green alga Gonium pectorale give insights into the origins of Organelle DNA architecture within the volvocales.
PloS one, 2013Co-Authors: Takashi Hamaji, David Roy Smith, Hideki Noguchi, Atsushi Toyoda, Masahiro Suzuki, Hiroko Kawai-toyooka, Asao Fujiyama, Ichiro Nishii, Tara N. Marriage, Bradley J. S. C. OlsonAbstract:Volvocalean green algae have among the most diverse mitochondrial and plastid DNAs (mtDNAs and ptDNAs) from the eukaryotic domain. However, nearly all of the Organelle Genome data from this group are restricted to unicellular species, like Chlamydomonas reinhardtii, and presently only one multicellular species, the ∼4,000-celled Volvox carteri, has had its Organelle DNAs sequenced. The V. carteri Organelle Genomes are repeat rich, and the ptDNA is the largest plastome ever sequenced. Here, we present the complete mtDNA and ptDNA of the colonial volvocalean Gonium pectorale, which is comprised of ∼16 cells and occupies a phylogenetic position closer to that of V. carteri than C. reinhardtii within the volvocine line. The mtDNA and ptDNA of G. pectorale are circular-mapping AT-rich molecules with respective lengths and coding densities of 16 and 222.6 kilobases and 73 and 44%. They share some features with the Organelle DNAs of V. carteri, including palindromic repeats within the plastid compartment, but show more similarities with those of C. reinhardtii, such as a compact mtDNA architecture and relatively low Organelle DNA intron contents. Overall, the G. pectorale Organelle Genomes raise several interesting questions about the origin of linear mitochondrial chromosomes within the Volvocales and the relationship between multicellularity and Organelle Genome expansion.
Normand Brisson - One of the best experts on this subject based on the ideXlab platform.
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short range inversions rethinking Organelle Genome stability
BioEssays, 2015Co-Authors: Samuel Tremblaybelzile, Éric Zampini, Étienne Lepage, Normand BrissonAbstract:In the Organelles of plants and mammals, recent evidence suggests that genomic instability stems in large part from template switching events taking place during DNA replication. Although more than one mechanism may be responsible for this, some similarities exist between the different proposed models. These can be separated into two main categories, depending on whether they involve a single-strand-switching or a reciprocal-strand-switching event. Single-strand-switching events lead to intermediates containing Y junctions, whereas reciprocal-strand-switching creates Holliday junctions. Common features in all the described models include replication stress, fork stalling and the presence of inverted repeats, but no single element appears to be required in all cases. We review the field, and examine the ideas that several mechanisms may take place in any given Genome, and that the presence of palindromes or inverted repeats in certain regions may favor specific rearrangements.
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Short‐range inversions: Rethinking Organelle Genome stability
BioEssays : news and reviews in molecular cellular and developmental biology, 2015Co-Authors: Samuel Tremblay-belzile, Étienne Lepage, Éric Zampini, Normand BrissonAbstract:In the Organelles of plants and mammals, recent evidence suggests that genomic instability stems in large part from template switching events taking place during DNA replication. Although more than one mechanism may be responsible for this, some similarities exist between the different proposed models. These can be separated into two main categories, depending on whether they involve a single-strand-switching or a reciprocal-strand-switching event. Single-strand-switching events lead to intermediates containing Y junctions, whereas reciprocal-strand-switching creates Holliday junctions. Common features in all the described models include replication stress, fork stalling and the presence of inverted repeats, but no single element appears to be required in all cases. We review the field, and examine the ideas that several mechanisms may take place in any given Genome, and that the presence of palindromes or inverted repeats in certain regions may favor specific rearrangements.
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Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair
The Plant cell, 2010Co-Authors: Laurent Cappadocia, Alexandre Marechal, Étienne Lepage, Jean-sébastien Parent, Jurgen Sygusch, Normand BrissonAbstract:DNA double-strand breaks are highly detrimental to all organisms and need to be quickly and accurately repaired. Although several proteins are known to maintain plastid and mitochondrial Genome stability in plants, little is known about the mechanisms of DNA repair in these Organelles and the roles of specific proteins. Here, using ciprofloxacin as a DNA damaging agent specific to the Organelles, we show that plastids and mitochondria can repair DNA double-strand breaks through an error-prone pathway similar to the microhomology-mediated break-induced replication observed in humans, yeast, and bacteria. This pathway is negatively regulated by the single-stranded DNA (ssDNA) binding proteins from the Whirly family, thus indicating that these proteins could contribute to the accurate repair of plant Organelle Genomes. To understand the role of Whirly proteins in this process, we solved the crystal structures of several Whirly-DNA complexes. These reveal a nonsequence-specific ssDNA binding mechanism in which DNA is stabilized between domains of adjacent subunits and rendered unavailable for duplex formation and/or protein interactions. Our results suggest a model in which the binding of Whirly proteins to ssDNA would favor accurate repair of DNA double-strand breaks over an error-prone microhomology-mediated break-induced replication repair pathway.
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recombination and the maintenance of plant Organelle Genome stability
New Phytologist, 2010Co-Authors: Alexandre Marechal, Normand BrissonAbstract:Contents Summary 299 I. Introduction 299 II. Roles of recombination in Organelle Genome stability 301 III. Recombination surveillance machinery in plant Organelles 304 IV. Conclusion and perspectives 312 Acknowledgements 313 References 313 Summary Like their nuclear counterpart, the plastid and mitochondrial Genomes of plants have to be faithfully replicated and repaired to ensure the normal functioning of the plant. Inability to maintain Organelle Genome stability results in plastid and/or mitochondrial defects, which can lead to potentially detrimental phenotypes. Fortunately, plant Organelles have developed multiple strategies to maintain the integrity of their genetic material. Of particular importance among these processes is the extensive use of DNA recombination. In fact, recombination has been implicated in both the replication and the repair of Organelle Genomes. Revealingly, deregulation of recombination in Organelles results in genomic instability, often accompanied by adverse consequences for plant fitness. The recent identification of four families of proteins that prevent aberrant recombination of Organelle DNA sheds much needed mechanistic light on this important process. What comes out of these investigations is a partial portrait of the recombination surveillance machinery in which plants have co-opted some proteins of prokaryotic origin but have also evolved whole new factors to keep their Organelle Genomes intact. These new features presumably optimized the protection of plastid and mitochondrial Genomes against the particular genotoxic stresses they face.
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Recombination and the maintenance of plant Organelle Genome stability
The New phytologist, 2010Co-Authors: Alexandre Marechal, Normand BrissonAbstract:Like their nuclear counterpart, the plastid and mitochondrial Genomes of plants have to be faithfully replicated and repaired to ensure the normal functioning of the plant. Inability to maintain Organelle Genome stability results in plastid and/or mitochondrial defects, which can lead to potentially detrimental phenotypes. Fortunately, plant Organelles have developed multiple strategies to maintain the integrity of their genetic material. Of particular importance among these processes is the extensive use of DNA recombination. In fact, recombination has been implicated in both the replication and the repair of Organelle Genomes. Revealingly, deregulation of recombination in Organelles results in genomic instability, often accompanied by adverse consequences for plant fitness. The recent identification of four families of proteins that prevent aberrant recombination of Organelle DNA sheds much needed mechanistic light on this important process. What comes out of these investigations is a partial portrait of the recombination surveillance machinery in which plants have co-opted some proteins of prokaryotic origin but have also evolved whole new factors to keep their Organelle Genomes intact. These new features presumably optimized the protection of plastid and mitochondrial Genomes against the particular genotoxic stresses they face.
Alexandre Marechal - One of the best experts on this subject based on the ideXlab platform.
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Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair
The Plant cell, 2010Co-Authors: Laurent Cappadocia, Alexandre Marechal, Étienne Lepage, Jean-sébastien Parent, Jurgen Sygusch, Normand BrissonAbstract:DNA double-strand breaks are highly detrimental to all organisms and need to be quickly and accurately repaired. Although several proteins are known to maintain plastid and mitochondrial Genome stability in plants, little is known about the mechanisms of DNA repair in these Organelles and the roles of specific proteins. Here, using ciprofloxacin as a DNA damaging agent specific to the Organelles, we show that plastids and mitochondria can repair DNA double-strand breaks through an error-prone pathway similar to the microhomology-mediated break-induced replication observed in humans, yeast, and bacteria. This pathway is negatively regulated by the single-stranded DNA (ssDNA) binding proteins from the Whirly family, thus indicating that these proteins could contribute to the accurate repair of plant Organelle Genomes. To understand the role of Whirly proteins in this process, we solved the crystal structures of several Whirly-DNA complexes. These reveal a nonsequence-specific ssDNA binding mechanism in which DNA is stabilized between domains of adjacent subunits and rendered unavailable for duplex formation and/or protein interactions. Our results suggest a model in which the binding of Whirly proteins to ssDNA would favor accurate repair of DNA double-strand breaks over an error-prone microhomology-mediated break-induced replication repair pathway.
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recombination and the maintenance of plant Organelle Genome stability
New Phytologist, 2010Co-Authors: Alexandre Marechal, Normand BrissonAbstract:Contents Summary 299 I. Introduction 299 II. Roles of recombination in Organelle Genome stability 301 III. Recombination surveillance machinery in plant Organelles 304 IV. Conclusion and perspectives 312 Acknowledgements 313 References 313 Summary Like their nuclear counterpart, the plastid and mitochondrial Genomes of plants have to be faithfully replicated and repaired to ensure the normal functioning of the plant. Inability to maintain Organelle Genome stability results in plastid and/or mitochondrial defects, which can lead to potentially detrimental phenotypes. Fortunately, plant Organelles have developed multiple strategies to maintain the integrity of their genetic material. Of particular importance among these processes is the extensive use of DNA recombination. In fact, recombination has been implicated in both the replication and the repair of Organelle Genomes. Revealingly, deregulation of recombination in Organelles results in genomic instability, often accompanied by adverse consequences for plant fitness. The recent identification of four families of proteins that prevent aberrant recombination of Organelle DNA sheds much needed mechanistic light on this important process. What comes out of these investigations is a partial portrait of the recombination surveillance machinery in which plants have co-opted some proteins of prokaryotic origin but have also evolved whole new factors to keep their Organelle Genomes intact. These new features presumably optimized the protection of plastid and mitochondrial Genomes against the particular genotoxic stresses they face.
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Recombination and the maintenance of plant Organelle Genome stability
The New phytologist, 2010Co-Authors: Alexandre Marechal, Normand BrissonAbstract:Like their nuclear counterpart, the plastid and mitochondrial Genomes of plants have to be faithfully replicated and repaired to ensure the normal functioning of the plant. Inability to maintain Organelle Genome stability results in plastid and/or mitochondrial defects, which can lead to potentially detrimental phenotypes. Fortunately, plant Organelles have developed multiple strategies to maintain the integrity of their genetic material. Of particular importance among these processes is the extensive use of DNA recombination. In fact, recombination has been implicated in both the replication and the repair of Organelle Genomes. Revealingly, deregulation of recombination in Organelles results in genomic instability, often accompanied by adverse consequences for plant fitness. The recent identification of four families of proteins that prevent aberrant recombination of Organelle DNA sheds much needed mechanistic light on this important process. What comes out of these investigations is a partial portrait of the recombination surveillance machinery in which plants have co-opted some proteins of prokaryotic origin but have also evolved whole new factors to keep their Organelle Genomes intact. These new features presumably optimized the protection of plastid and mitochondrial Genomes against the particular genotoxic stresses they face.
Chantal Cabello - One of the best experts on this subject based on the ideXlab platform.
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Mitochondrial T3 receptor and targets
Molecular and Cellular Endocrinology, 2017Co-Authors: Chantal Cabello, Francois Casas, Gerard CabelloAbstract:The demonstration that TRa1 mRNA encodes a nuclear thyroid hormone receptor and two proteins imported into mitochondria with molecular masses of 43 and 28 kDa has brought new clues to better understand the pleiotropic influence of iodinated hormones. If p28 activity remains unknown, p43 binds to T3 responsive elements occurring in the Organelle Genome, and, in the T3 presence, stimulates mitochondrial transcription and the subsequent synthesis of mitochondrial encoded proteins. This influence increases mitochondrial activity and through changes in the mitochondrial/nuclear cross talk affects important nuclear target genes regulating cell proliferation and differentiation, oncogenesis, or apoptosis. In addition, this pathway influences muscle metabolic and contractile phenotype, as well as glycaemia regulation. Interestingly, according to the process considered, p43 exerts opposite or cooperative effects with the well-known T3 pathway, thus allowing a fine tuning of the physiological influence of this hormone.
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Mice lacking the p43 mitochondrial T3 receptor become glucose intolerant and insulin resistant during aging
PLoS ONE, 2013Co-Authors: Christelle Bertrand, Gerard Cabello, E. Blanchet, J. S. Annicotte, L. Pessemesse, Jonathan Levin, L. Fajas, Christine Coudray, Béatrice Chabi, Chantal CabelloAbstract:Thyroid hormones (TH) play an important regulatory role in energy expenditure regulation and are key regulators of mitochondrial activity. We have previously identified a mitochondrial triiodothyronine (T3) receptor (p43) which acts as a mitochondrial transcription factor of the Organelle Genome, which leads in vitro and in vivo, to a stimulation of mitochondrial biogenesis. Recently, we generated mice carrying a specific p43 invalidation. At 2 months of age, we reported that p43 depletion in mice induced a major defect in insulin secretion both in vivo and in isolated pancreatic islets, and a loss of glucose-stimulated insulin secretion. The present study was designed to determine whether p43 invalidation influences life expectancy and modulates blood glucose and insulin levels as well as glucose tolerance or insulin sensitivity during aging. We report that from 4 months old onwards, mice lacking p43 are leaner than wild-type mice. p43-/- mice also have a moderate reduction of life expectancy compared to wild type. We found no difference in blood glucose levels, excepted at 24 months old where p43-/- mice showed a strong hyperglycemia in fasting conditions compared to controls animals. However, the loss of glucose-stimulated insulin secretion was maintained whatever the age of mice lacking p43. If up to 12 months old, glucose tolerance remained unchanged, beyond this age p43-/- mice became increasingly glucose intolerant. In addition, if up to 12 months old p43 deficient animals were more sensitive to insulin, after this age we observed a loss of this capacity, culminating in 24 months old mice with a decreased sensitivity to the hormone. In conclusion, we demonstrated that during aging the depletion of the mitochondrial T3 receptor p43 in mice progressively induced an increased glycemia in the fasted state, glucose intolerance and an insulin-resistance several features of type-2 diabetes.
Heroen Verbruggen - One of the best experts on this subject based on the ideXlab platform.
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The Organelle Genomes in the photosynthetic red algal parasite Pterocladiophila hemisphaerica (Florideophyceae, Rhodophyta) have elevated substitution rates and extreme gene loss in the plastid Genome
Journal of phycology, 2020Co-Authors: Maren Preuss, Heroen Verbruggen, Giuseppe C. ZuccarelloAbstract:Comparative Organelle Genome studies of parasites can highlight genetic changes that occur during the transition from a free-living to a parasitic state. Our study focuses on a poorly studied group of red algal parasites, which are often closely related to their red algal hosts and from which they presumably evolved. Most of these parasites are pigmented and some show photosynthetic capacity. Here, we assembled and annotated the complete Organelle Genomes of the photosynthetic red algal parasite, Pterocladiophila hemisphaerica. The plastid Genome is the smallest known red algal plastid Genome at 68,701 bp. The plastid Genome has many genes missing, including all photosynthesis-related genes. In contrast, the mitochondrial Genome is similar in architecture to that of other free-living red algae. Both Organelle Genomes show elevated mutation rates and significant changes in patterns of selection, measured as dN/dS ratios. This caused phylogenetic analyses, even of multiple aligned proteins, to be unresolved or give contradictory relationships. Full plastid datasets interfered by selected best gene evolution models showed the supported relationship of P. hemisphaerica within the Ceramiales, but the parasite was grouped with support as sister to the Gracilariales when interfered under the GHOST model. Nuclear rDNA showed a supported grouping of the parasite within a clade containing several red algal orders including the Gelidiales. This photosynthetic parasite, which is unable to photosynthesize with its own plastid due to the total loss of all photosynthesis genes, raises intriguing questions on parasite-host Organelle Genome capabilities and interactions.
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Phylogeny and Molecular Evolution of the Green Algae
Critical Reviews in Plant Sciences, 2012Co-Authors: Frederik Leliaert, Herve Moreau, Matthew D. Herron, Heroen Verbruggen, Charles F. Delwiche, David R Smith, Olivier De ClerckAbstract:The green lineage (Viridiplantae) comprises the green algae and their descendants the land plants, and is one of the major groups of oxygenic photosynthetic eukaryotes. Current hypotheses posit the earlydivergence of two discrete clades froman ancestral green flag- ellate. One clade, the Chlorophyta, comprises the early diverging prasinophytes, which gave rise to the core chlorophytes. The other clade, the Streptophyta, includes the charophyte green algae from which the land plants evolved. Multi-marker and Genome scale phylogenetic studies have greatly improved our understanding of broad-scale relationships of the green lineage, yet many questions persist, including the branching orders of the prasinophyte lin- eages, the relationshipsamongcore chlorophyte clades (Chloroden- drophyceae, Ulvophyceae,Trebouxiophyceae and Chlorophyceae), and the relationships among the streptophytes. Current phyloge- netic hypotheses provide an evolutionary framework for molecular evolutionary studies and comparative genomics. This review sum- marizes our current understanding of Organelle Genome evolution in the green algae, genomic insights into the ecology of oceanic picoplanktonic prasinophytes, molecular mechanisms underlying the evolution of complexity in volvocine green algae, and the evo- lution of genetic codes and the translational apparatus in green seaweeds. Finally, we discuss molecular evolution in the strepto- phyte lineage, emphasizing the genetic facilitation of land plant origins.