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Статті в журналах з теми "Organellar genomes":
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Hertle, Alexander P., Benedikt Haberl, and Ralph Bock. "Horizontal genome transfer by cell-to-cell travel of whole organelles." Science Advances 7, no. 1 (January 2021): eabd8215. http://dx.doi.org/10.1126/sciadv.abd8215.
Анотація:
Recent work has revealed that both plants and animals transfer genomes between cells. In plants, horizontal transfer of entire plastid, mitochondrial, or nuclear genomes between species generates new combinations of nuclear and organellar genomes, or produces novel species that are allopolyploid. The mechanisms of genome transfer between cells are unknown. Here, we used grafting to identify the mechanisms involved in plastid genome transfer from plant to plant. We show that during proliferation of wound-induced callus, plastids dedifferentiate into small, highly motile, amoeboid organelles. Simultaneously, new intercellular connections emerge by localized cell wall disintegration, forming connective pores through which amoeboid plastids move into neighboring cells. Our work uncovers a pathway of organelle movement from cell to cell and provides a mechanistic framework for horizontal genome transfer.
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Greiner, Stephan, Pascal Lehwark, and Ralph Bock. "OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes." Nucleic Acids Research 47, W1 (April 5, 2019): W59—W64. http://dx.doi.org/10.1093/nar/gkz238.
Анотація:
Abstract Organellar (plastid and mitochondrial) genomes play an important role in resolving phylogenetic relationships, and next-generation sequencing technologies have led to a burst in their availability. The ongoing massive sequencing efforts require software tools for routine assembly and annotation of organellar genomes as well as their display as physical maps. OrganellarGenomeDRAW (OGDRAW) has become the standard tool to draw graphical maps of plastid and mitochondrial genomes. Here, we present a new version of OGDRAW equipped with a new front end. Besides several new features, OGDRAW now has access to a local copy of the organelle genome database of the NCBI RefSeq project. Together with batch processing of (multi-)GenBank files, this enables the user to easily visualize large sets of organellar genomes spanning entire taxonomic clades. The new OGDRAW server can be accessed at https://chlorobox.mpimp-golm.mpg.de/OGDraw.html.
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Ramsey, Adam J., David E. McCauley, and Jennifer R. Mandel. "Heteroplasmy and Patterns of Cytonuclear Linkage Disequilibrium in Wild Carrot." Integrative and Comparative Biology 59, no. 4 (June 11, 2019): 1005–15. http://dx.doi.org/10.1093/icb/icz102.
Анотація:
Abstract Organellar genomes are considered to be strictly uniparentally-inherited. Uniparental inheritance allows for cytonuclear coevolution and the development of highly coordinated cytonuclear interactions. Yet, instances of biparental inheritance have been documented across eukaryotes. Biparental inheritance in otherwise uniparentally-inherited organelles is termed leakage (maternal or paternal) and allows for the presence of multiple variants of the same organellar genome within an individual, called heteroplasmy. It is unclear what, if any, evolutionary consequences are placed on nuclear and/or organellar genomes due to heteroplasmy. One way of accessing cytonuclear interactions and potential coevolution is through calculating cytonuclear linkage disequilibrium (cnLD), or the non-random association of alleles between nuclear and organellar genomes. Patterns of cnLD can indicate positive or negative cytonuclear selection, coevolution between the nuclear and organellar genomes, non-traditional organellar inheritance, or instances of ancestral heteroplasmy. In plants, cytonuclear interactions have been shown to play a role in cytoplasmic male sterility which occurs in gynodioecious species and is associated with leakage. We used the gynodioecious species, Daucus carota L. spp. carota, or wild carrot, to investigate cnLD. We genotyped a total of 265 individuals from two regions of the USA at 15 nuclear microsatellites, the mitochondrial genes cox1 and atp9, and an intergenic region between trnS and trnG (StoG) in the plastid genome to calculate nuclear–nuclear LD (nucLD), cnLD, and organellar LD (i.e., within the mtDNA and between mtDNA and ptDNA) within the two regions. We were further able to identify cox1 and StoG heteroplasmy and calculate some of the same LD measures within heteroplasmic and homoplasmic (non-heteroplasmic) datasets. We used a Z-transformation test to demonstrate that heteroplasmic individuals display significantly higher levels of cnLD within both regions. In spite of this, within and between organellar LD is low to moderate. Given these patterns of LD in two regions of the USA in which gene flow has been shown to occur between crop and wild carrot, we suggest that heteroplasmy is an evolutionary mechanism which permits the maintenance of cnLD while also acting to disrupt organellar LD.
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Wang, Haoqi, Xuezhu Liao, Luke R. Tembrock, Zuoren Yang, and Zhiqiang Wu. "Evaluation of Intracellular Gene Transfers from Plastome to Nuclear Genome across Progressively Improved Assemblies for Arabidopsis thaliana and Oryza sativa." Genes 13, no. 9 (September 9, 2022): 1620. http://dx.doi.org/10.3390/genes13091620.
Анотація:
DNA originating from organellar genomes are regularly discovered in nuclear sequences during genome assembly. Nevertheless, such insertions are sometimes omitted during the process of nuclear genome assembly because the inserted DNA is assigned to organellar genomes, leading to a systematic underestimation of their frequency. With the rapid development of high-throughput sequencing technology, more inserted fragments from organelle genomes can now be detected. Therefore, it is necessary to be aware of the insertion events from organellar genomes during nuclear genome assembly to properly attribute the impact and rate of such insertions in the evolution of nuclear genomes. Here, we investigated the impact of intracellular gene transfer (IGT) from the plastome to the nuclear genome using genome assemblies that were refined through time with technological improvements from two model species, Arabidopsis thaliana and Oryza sativa. We found that IGT from the plastome to the nuclear genome is a dynamic and ongoing process in both A. thaliana and O. sativa, and mostly occurred recently, as the majority of transferred sequences showed over 95% sequence similarity with plastome sequences of origin. Differences in the plastome-to-nuclear genome IGT between A. thaliana and O. sativa varied among the different assembly versions and were associated with the quality of the nuclear genome assembly. IGTs from the plastome to nuclear genome occurred more frequently in intergenic regions, which were often associated with transposable elements (TEs). This study provides new insights into intracellular genome evolution and nuclear genome assembly by characterizing and comparing IGT from the plastome into the nuclear genome for two model plant species.
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Leister, Dario. "Towards understanding the evolution and functional diversification of DNA-containing plant organelles." F1000Research 5 (March 11, 2016): 330. http://dx.doi.org/10.12688/f1000research.7915.1.
Анотація:
Plastids and mitochondria derive from prokaryotic symbionts that lost most of their genes after the establishment of endosymbiosis. In consequence, relatively few of the thousands of different proteins in these organelles are actually encoded there. Most are now specified by nuclear genes. The most direct way to reconstruct the evolutionary history of plastids and mitochondria is to sequence and analyze their relatively small genomes. However, understanding the functional diversification of these organelles requires the identification of their complete protein repertoires – which is the ultimate goal of organellar proteomics. In the meantime, judicious combination of proteomics-based data with analyses of nuclear genes that include interspecies comparisons and/or predictions of subcellular location is the method of choice. Such genome-wide approaches can now make use of the entire sequences of plant nuclear genomes that have emerged since 2000. Here I review the results of these attempts to reconstruct the evolution and functions of plant DNA-containing organelles, focusing in particular on data from nuclear genomes. In addition, I discuss proteomic approaches to the direct identification of organellar proteins and briefly refer to ongoing research on non-coding nuclear DNAs of organellar origin (specifically, nuclear mitochondrial DNA and nuclear plastid DNA).
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Lyu, Jun. "Editing plant organellar genomes." Nature Plants 8, no. 1 (December 6, 2021): 4. http://dx.doi.org/10.1038/s41477-021-01059-w.
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Gray, Michael W. "Evolution of organellar genomes." Current Opinion in Genetics & Development 9, no. 6 (December 1999): 678–87. http://dx.doi.org/10.1016/s0959-437x(99)00030-1.
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Havey, M. J., J. McCreight, W. Rhodes, and G. Taurick. "Inheritance and Evolution of the Cucurbit Organellar Genomes." HortScience 31, no. 4 (August 1996): 601e—601. http://dx.doi.org/10.21273/hortsci.31.4.601e.
Анотація:
The cucurbits have several-fold size differences in their mitochondrial genomes. Watermelon possesses a relatively small mitochondrial genome of 330 kb. Squash has a larger mitochondrial genome of 840 kb. Cucumber and melon possess huge mitochondrial genomes of 1500 and 2400 kb, respectively. We demonstrated predominately paternal transmission of the mitochondrial genome in cucumber. Squash shows maternal transmission of the chloroplast genome. We generated reciprocal crosses and identified restriction fragment length polymorphisms in the chloroplast and mitochondrial genomes of melon, squash, and watermelon to establish their transmission. Our analyses also revealed that intergenomic transfers contributed to the evolution of extremely large mitochondrial genomes.
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Barbrook, Adrian C., Christopher J. Howe, Davy P. Kurniawan, and Sarah J. Tarr. "Organization and expression of organellar genomes." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1541 (March 12, 2010): 785–97. http://dx.doi.org/10.1098/rstb.2009.0250.
Анотація:
Protist mitochondrial genomes show a very wide range of gene content, ranging from three genes for respiratory chain components in Apicomplexa and dinoflagellates to nearly 100 genes in Reclinomonas americana . In many organisms the rRNA genes are fragmented, although still functional. Some protist mitochondria encode a full set of tRNAs, while others rely on imported molecules. There is similarly a wide variation in mitochondrial genome organization, even among closely related groups. Mitochondrial gene expression and control are generally poorly characterized. Transcription probably relies on a ‘viral-type’ RNA polymerase, although a ‘bacterial-type’ enzyme may be involved in some cases. Transcripts are heavily edited in many lineages. The chloroplast genome generally shows less variation in gene content and organization, although greatly reduced genomes are found in dinoflagellate algae and non-photosynthetic organisms. Genes in the former are located on small plasmids in contrast to the larger molecules found elsewhere. Control of gene expression in chloroplasts involves transcriptional and post-transcriptional regulation. Redox poise and the ATP/ADP ratio are likely to be important determinants. Some protists have an additional extranuclear genome, the nucleomorph, which is a remnant nucleus. Nucleomorphs of two separate lineages have a number of features in common.
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Shatskaya, Natalia V., Vera S. Bogdanova, Oleg E. Kosterin, and Gennadiy V. Vasiliev. "New Insights into Plastid and Mitochondria Evolution in Wild Peas (Pisum L.)." Diversity 15, no. 2 (February 2, 2023): 216. http://dx.doi.org/10.3390/d15020216.
Анотація:
Plastids and mitochondria are organelles of plant cells with small genomes, which may exhibit discordant microevolution as we earlier revealed in pea crop wild relatives. We sequenced 22 plastid and mitochondrial genomes of Pisum sativum subsp. elatius and Pisum fulvum using Illumina platform, so that the updated sample comprised 64 accessions. Most wild peas from continental southern Europe and a single specimen from Morocco were found to share the same organellar genome constitution; four others, presumably hybrid constitutions, were revealed in Mediterranean islands and Athos Peninsula. A mitochondrial genome closely related to that of Pisum abyssinicum, from Yemen and Ethiopia, was unexpectedly found in an accession of P. sativum subsp. elatius from Israel, their plastid genomes being unrelated. Phylogenetic reconstructions based on plastid and mitochondrial genomes revealed different sets of wild peas to be most related to cultivated P. sativum subsp. sativum, making its wild progenitor and its origin area enigmatic. An accession of P. fulvum representing ‘fulvum-b’ branch, according to a nuclear marker, appeared in the same branch as other fulvum accessions in organellar trees. The results stress the complicated evolution and structure of genetic diversity of pea crop wild relatives.
Дисертації з теми "Organellar genomes":
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Postel, Zoé. "Speciation and organellar genome evolution in lineages of Silene nutans (Caryophyllaceae)." Electronic Thesis or Diss., Université de Lille (2022-....), 2022. http://www.theses.fr/2022ULILR080.
Анотація:
Via l'émergence de barrières à la reproduction qui isolent les populations les unes des autres, la spéciation est le processus qui conduit à la formation de nouvelles espèces. Par ailleurs, les génomes organellaires peuvent être impliqués dans ce processus, par le biais d'incompatibilités cytonucléaires. Leur mode de transmission peut également influencer l'évolution de l'isolement reproducteur (IR) entre populations. Dans ce travail de thèse, j'ai travaillé sur l'influence des génomes organellaires sur l'évolution de l'isolement reproducteur entre quatres lignées de Silene nutans et ai tenté de reconstruire le scénario évo-démographique qui a façonné leur évolution. Dans un premier temps, via l'utilisation de données génomiques et transcriptomiques, nous avons tenté d'identifier des candidats d'incompatibilités chloro-nucléaires impliquées dans l'IR entre ces lignées. Nous avons ensuite approfondi l'analyse d'un complexe candidat: le ribosome chloroplastique. Par ailleurs, l'IR semble être incomplet entre ces lignées puisque certains hybrides ont survécu. Nous avons donc testé une transmission paternelle du génome chloroplastique chez cette espèce, qui pourrait avoir sauvé certains de ces hybrides. Nous avons génotypé les hybrides survivants pour six SNP chloroplastiques et déterminé s'ils avaient hérité du génome chloroplastique paternel ou maternel. En permettant la transmission d'un génome chloroplastique moins incompatible, la fuite paternelle semble bien avoir sauvé certains de ces hybrides. Les génomes mitochondriaux pourraient également être impliqués dans l'IR, par le biais d'incompatibilités mito-nucléaires. Du fait de leur co-transmission, les génomes organellaires sont supposés être en déséquilibre de liaison étroit, présentant ainsi des schémas évolutifs similaires. Nous les avons comparés en utilisant les données génomiques des deux génomes organellaires, pour des individus des quatre lignées. Ces schémas évolutifs se sont révélés particulièrement contrastés, les gènes mitochondriaux présentant du polymorphisme partagé à l'inverse des gènes chloroplastiques contenant des substitutions fixées différemment entre lignées. Des événements de type recombinaison ont également été identifiés dans les gènes mitochondriaux. Enfin, nous avons reconstruit l'histoire évo-démographique des quatre lignées de S. nutans, en utilisant les données RNAseq et des méthodes ABC. Un scénario de spéciation allopatrique a été identifiée entre les quatre lignées, avec des temps de séparation cohérent avec les maximums glaciairesSpeciation is the process by which the emergence of reproductive barriers isolate populations from one another and ultimately lead to the formation of new species. How these reproductive barriers emerge is a core question when thinking of speciation. Organellar genomes might be involved in the speciation process, through cytonuclear incompatibilities. Their mode of transmission might also influence the pace of reproductive isolation evolution. In my PhD, I worked on how organellar genomes influence the evolution of reproductive isolation between isolated lineages of S. nutans and which evo-demographic scenario shaped their evolution. Using plastid genomic and nuclear transcriptomic data we tried, in the first chapter, to identify candidates for plastid-nuclear incompatibilities involved in RI between lineages of S. nutans. We further dug into one plastid candidate complexe, the plastid ribosome. Because RI seems to be incomplete between lineages of S. nutans as some inter-lineage hybrids survived, we tested for paternal leakage of the plastid genome. We genotyped the surviving hybrids for plastid SNPs and analyzed whether they inherited the paternal or maternal plastid genomes. By allowing the transmission of the less incompatible plastid genome, paternal leakage rescued some of the inter-lineage hybrids. The mitochondrial genome could also be involved in the RI, through mito-nuclear incompatibilities. Because of their co-transmission, organellar genomes are supposed to be in tight linkage-disequilibrium, so exhibiting similar evolutionary patterns. Using genomic data for both organellar genomes for individuals of the four lineages we compared their evolutionary patterns. They were different with mitochondrial genes exhibiting many shared polymorphisms while plastid genomes many fixed substitutions between lineages. Recombination-like events were also identified in the mitochondrial genes. Lastly, we reconstructed the evo-demographic histories of the four lineages of S. nutans, using RNAseq data and ABC methods. Allopatric speciation was identified between the four lineages, with split times consistent with the glacial maxima
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Silva, Saura Rodrigues da. "Genômica organelar e evolução de Genlisea e Utricularia (lentibulariaceae)." Botucatu, 2018. http://hdl.handle.net/11449/153889.
Анотація:
Orientador: Vitor Fernandes Oliveira de MirandaResumo: Utricularia e Genlisea são gêneros irmãos de plantas carnívoras da família Lentibulariaceae. Possuem aproximadamente 260 espécies representadas em diversas formas de vida. Para o Brasil foram catalogadas 82 espécies, das quais 27 são consideradas endêmicas. Além de dispor das armadilhas carnívoras mais complexas entre plantas, algumas de suas espécies apresentam os menores genomas e as maiores taxas de mutações entre as angiospermas relatadas até o momento. A respeito de seus genomas organelares, os estudos são pífios. Neste contexto, há a necessidade de se investigar como são os genomas organelares, suas estruturas, seus genes e como se deu a evolução das organelas nos gêneros. Portanto este estudo teve como objetivo, a partir de sequenciamento de nova geração e montagem de genomas, estudar e comparar os genomas organelares de Utricularia e Genlisea. Neste âmbito, foram montados e sequenciados os cloroplastos das espécies Utricularia foliosa, U. reniformis, G. aurea, G. filiformis, G. pygmaea, G. repens e G. tuberosa, e o genoma mitocondrial de U. reniformis. Os resultados obtidos revelaram que possivelmente há relação entre forma de vida e presença de genes ndhs nos gêneros, em razão de que para as espécies terrestres há deleção e “pseudogenização” de genes ndhs, já as espécies aquáticas detêm todo repertório de ndhs intacto. A partir das evidências encontradas, foi possível constatar transferência horizontal de genes, inclusive de genes ndhs, em mitocôndrias.
Abstract: Utricularia and Genlisea are sister genera in the carnivorous family Lentibulariaceae. There are aprproximately 260 species representing diverse life forms. For Brasil there are 82 species, 27 considered endemic. At the moment, besides having the most complex carnivorous traps between all plants, some of its species have miniature genomes and the highest mutational rates among angiosperms. There are few studies regarding its organellar genome. In this context, it is necessary to investigate how are these organellar genomes, its structure, genes, and how evolutionary forces govern these organelles in the different genera. Therefore, the aim of this study is to study and compare the organellar genomes of Utricularia and Genlisea, using next generation sequencing and genome assembly. In this context, chloroplasts of the species Utricularia foliosa, U. reniformis, Genlisea aurea, G. filiformis, G. pygmaea, G. repens and G. tuberosa, and the mitochondrial genome of U. reniformis were assembled and sequenced. The results show that possibly there is a connection between life form and the presence of ndhs genes in the genera, since for the terrestrial species there are ndhs genes that are deleted and pseudogenization, in contrary to the aquatic species which have all intact ndhs repertoir. Concerning the evidences, it was possible to verify horizontal transfer of ndhs and other genes as there are chloroplasts genes in the mitochondria.
Doutor
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Dierckxsens, Nicolas. "Targeted organelle genome assembly and heteroplamsy detection." Doctoral thesis, Universite Libre de Bruxelles, 2018. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/277507.
Анотація:
Thanks to the development of next-generation sequencing (NGS) technology, whole genome data can be readily obtained from a variety of samples. Since the massive increase in available sequencing data, the development of efficient assembly algorithms has become the new bottleneck. Almost every new released tool is based on the De Brujin graph method, which focuses on assembling complete datasets with mathematical models. Although the decreasing sequencing costs made whole genome sequencing (WGS) the most straightforward and least laborious approach of gathering sequencing data, many research projects are only interested in the extranuclear genomes. Unfortunately, few of the available tools are specifically designed to efficiently retrieve these extranuclear genomes from WGS datasets. We developed a seed-and-extend algorithm that assembles organelle circular genomes from WGS data, starting from a single short seed sequence. The algorithm has been tested on several new (Gonioctena intermedia and Avicennia marina) and public (Arabidopsis thaliana and Oryza sativa) whole genome Illumina datasets and always outperformed other assemblers in assembly accuracy and contiguity. In our benchmark, NOVOPlasty assembled all genomes in less than 30 minutes with a maximum RAM memory requirement of 16 GB. NOVOPlasty is the only de novo assembler that provides a fast and straightforward manner to extract the extranuclear sequences from WGS data and generates one circular high quality contig.Heteroplasmy, the existence of multiple mitochondrial haplotypes within an individual, has been researched across different fields. Mitochondrial genome polymorphisms have been linked to multiple severe disorders and are of interest to evolutionary studies and forensic science. By utilizing ultra-deep sequencing, it is now possible to uncover previously undiscovered patterns of intra-individual polymorphism. However, it remains challenging to determine its source. Current available software can detect polymorphic sites but are not capable of determining the link between them. We therefore developed a new method to not only detect intra-individual polymorphisms within mitochondrial and chloroplast genomes, but also to look for linkage among polymorphic sites by assembling the sequence around each detected polymorphic site. Our benchmark study shows that this method can detect heteroplasmy more accurately than any method previously available and is the first tool that is able to completely or partially reconstruct the origin sequences for each intra-individual polymorphism.Doctorat en Sciences
info:eu-repo/semantics/nonPublished
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Fisk, Dianna G. "CRP1 : founding member of a novel protein family that functions in organellar gene expression /." view abstract of download file of text, 2000. http://wwwlib.umi.com/cr/uoregon/fullcit?p9987422.
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Munoz, Víctor Hugo Anaya. "A theoretical model on the role of lateral gene transfer in the evolution of endosymbiotic genomes." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2012. http://dx.doi.org/10.18452/16446.
Анотація:
Laterale Gentransfer wurde zuerst von Schwartz und Dayhoff (1978) entdeckt, die es aber als eine Exzentrizität werteten und als solche ignorierten. Später, als mehrere DNS- und Eiweißsequenzen sequenziert und raffiniertere Phylogenien rekonstruiert wurden, hat die Rolle an Relevanz gewonnen, die der laterale (oder horizontale) Gentransfer in der evolutionären Geschichte von lebendigen Organismen gespielt hat. Außerdem existiert auch zwischen Endosymbionten und Zellkernen statt. Ich habe ein theoretisches Modell entwickelt, das den lateralen Gentransfer zwischen Endosymbionten und dem Zellkern repräsentiert. Das Modell erforscht die Bedeutung des Fehlens von Rekombination in den Organellen (Muller’s Ratchet) sowie Abweichungen von Muller’s Ratchet in Form der non-symmetrical homologous recombination in Gentransfermechanismen. Ich habe zum einen Zellkern-Inkompatibilitäten, die aus der Übertragung eines Gens resultieren, und zum anderen Zyto- und Zellkern-Inkompatibilitäten zwischen den mutierten endosymbiotischen Genomen und dem modifizierten Zellenkern untersucht. Die Ergebnisse zeigen, dass unter bestimmten Bedingungen die Existenz oder Nicht-Existenz von Rekombination die gleiche Wirkung haben können. Es zeigte sich auch, dass Rekombination, wenn sie vorkommt und wenn sie nicht symmetrisch ist, starke Auswirkungen auf die Allelenfrequenz einer Population haben kann. Es wurde auch klar, dass es eine starke Beziehung zwischen dem Zellkern und endosymbiotischen Genomen gibt, und dass das evolutionäre Schicksal des einen größtenteils von den evolutionären Kräften abhängig ist, die das andere beeinflussen. Wenn man Zellkern- und Cyto-Zellkerninkompatibilitäten in das Modell einführt, dann zeigen die Ergebnisse, dass die Inkompatibilitäten, die der laterale Gentransfer produziert hat, möglicherweise eine ähnliche Rolle im Speziationsmechanismus spielen könnten wie die Inkompatibilitäten zwischen Mitochondrien und Zellkernen in verschiedenen Nasonia-Arten.Lateral gene transfer has played a key role in the evolution of living beings. This process was first acknowledged in 1978 by Schwartz and Dayhoff but considered a relatively infrequent eccentricity and ignored. Later on, as DNA and protein sequences accumulated and more refined phylogenies were reconstructed, the contribution of lateral (or horizontal) gene transfer to the evolutionary history of living organisms gained relevance. Besides, gene transfer is known to occur not only between independent organisms but also, and more frequently between endosymbionts including eukaryotic organelles. I developed a theoretical model to study the lateral gene transfer process between cell organelles (but extendible to other endosymbionts) and the cell nucleus. The model explores the role of the lack of recombination in the organelles (Muller''s ratchet) as well as deviations from Muller''s ratchet in the form of non-symmetrical homologous recombination in relation with the gene transfer process. Also, nuclear incompatibilities resulting from the inclusion of a transferred gene, and cyto-nuclear incompatibilities between the mutant endosymbiotic genomes and the modified nuclear genome are investigated. The results obtained show that under certain circumstances the existence recombination or its non-existence produce the same results, and that deviations from symmetry in the recombination process might have important effects on the frequency of different alleles. It is also clear that there is a strong relation between nuclear and endosymbiotic genomes, and that the evolutionary fate of one largely depends on the forces affecting the other. When nuclear and cyto-nuclear incompatibilities are introduced in the model, the results show that lateral gene transfer-induced incompatibilities could potentially play a role in the speciation process similar to the one produced by mitochondria in the Nasonia species.
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Meeusen, Shelly Lyn. "Analysis of the machinery regulating mitochondrial organelle and genome dynamics /." For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2003. http://uclibs.org/PID/11984.
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Ohniwa, Ryosuke L. "Comparative analyses of genome architectures among prokaryote, organelle and eukaryote by nano-scale imaging, molecular genetics and bioinformatics." 京都大学 (Kyoto University), 2007. http://hdl.handle.net/2433/136993.
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Richly, Erik. "Structural and functional genomics in semi-autonomous organelles composition and origin of proteomes of chloroplasts and mitochondria and related transcriptomics /." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=969512104.
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Serafini, Annalisa. "A FRET-based genome wide high content screen identifies a novel role for the Parkinson's disease gene LRRK2 as modulator of endoplasmic reticulum-mitochondria tethering." Doctoral thesis, Università degli studi di Padova, 2017. http://hdl.handle.net/11577/3422263.
Анотація:
Inter-organelle communication is a key feature of eukaryotic cells and has been found to be fundamental in many different cellular processes. One of the best characterized interorganelle cross talk due to membrane contact sites is that between Endoplasmic Reticulum (ER) and mitochondria. Also referred to as mitochondria associated ER-membranes (MAMs) or Mitochondria-ER contact sites (MERCs), their existence was discovered 50 years ago through electron microscopic studies, but their functional significance started to emerge only in late 90s when the role of MERCs in calcium exchange from ER to mitochondria was demonstrated. Despite the importance of these contacts sites in physiology and pathology, only few proteins have so far been identifed involved in the structural maintenace of the distance between the two organelles in mammals. Mitofusin 2 (MFN2) was the first structural tether to be identified. MFN2 has been found on both OMM and ER cytosolic face and is able to form homo and heterotypic interactions with MFN1, thus tethering the two organelles. As residual juxtaposition between the two organelles is still observed in Mfn2-/- cells, additional tethering proteins have to exist. To identify them, we set out to perform two replicates of a genome wide screening in mouse embryonic fibroblasts (MEFs). In order to perform the genome wide screening, we capitalized on the FRET based biosensor, where CFP fused with FRB domain and YFP fused with FKBP domain were targeted to ER (by a Sac 1 signaling sequence) and mitochondria (by an Akap signaling sequence) respectively (Csordas et al., 2010). We modified this probe by introducing between the cDNAs of the two fluorescent proteins a self-cleaving Tav2A peptide in order to have a single mRNA construct that allows the expression of equimolar level of the proteins. FKBP and FRB binding domain are able to heterodymerize upon addition of rapamycin, thus allowing the measurement not only of the basal level of juxtaposition between the two organelles, but also of the maximum level of contacts that can occur in a cell. We called this new construct FRET ER-mitochondria probe (FEMP). FEMP unique features allow us to discriminate between proteins whose role is keeping the two organelles closer, termed as "tethers", and proteins that keep the two organelles apart, defined as "spacers".
We analyzed raw images from the screen and calculated two indexes, namely basal and maximum MERC index, mirroring the level of contacts observed at any given timepoint and the maximum possible level of contacts respectively. Following automated image analysis and statistical analysis performed on ~10,000 genes, after candidate selection we identified 205 genes as ER-mitochondria tethers (i.e., genes that once ablated increase the distance between the two organelles) and 59 genes as spacers (i.e., genes that once ablated decrease the distance between the two organelles) affecting both basal and maximum MERC index in both replicates. Moreover, we identified 625 tehters and 696 spacers affecting only the basal MERC index; 519 tethers and 67 spacers affecting only the maximum MERC indexes. Protein classes analysis of these three groups of genes by Panther predicted both already known and new protein classes that are yet to explored in terms of ER-mitochondria communication. Subcellular localization analysis to identify predicted proteins to be present in both ER and outer mitochondrial membrane (OMM) of the gene lists detailed before, revealed 13 proteins among the common tethers and spacers, 30 proteins affecting only the basal MERC index and 16 proteins affecting only the maximum MERC index localized on both organelles. One of the protein present in the last group is Leucine Rich Repeat Kinase 2 (LRRK2) and we have further characterized it as ER-mitochondria tether. Subcellular fractionation experiments showed that LRKK2 localized mostly in MAMs. As expected for a tether, levels of ER-mitochondria juxtaposition, measured with FEMP, were decrased in LRRK2-/- MEF. ER-mitochondria proximity was fully restored by reintroduction in MEF LRRK2-/- of wt protein but not of the familial PD associated mutants.
In conclusion, we have developed a new method to assess the proximity between ER and mitochondria and we have utilized this technology to perform two replicates of a high content screen identifying novel structural components of the ER-mitochondria contact sites.La comunicazione tra organelli cellulari è una caratteristica fondamentale delle cellule eucariotiche ed esercita un ruolo fondamentale in molti processi cellulari. Uno dei processi di comunicazione tra organelli cellulari tra i più caratterizzati è quello dovuto ai siti di contatto tra le membrane di mitocondri e reticolo endoplasmatico (ER). Anche noti come "Mitochondria-associated ER membranes" (MAMs) o "Mitochondria-ER contact sites" (MERCs), la loro esistenza è stata scoperta 50 anni fa tramite studi di microscopia elettronica, ma il loro significato funzionale è iniziato ad emergere solo alla fine degli anni 90 quando è stato dimosdtrato il ruolo dei MERCs nello scambio di calcio dall'ER. Nonostante l'importanza di questi siti di contatto tra organelli sia in fisiologia sia in patologia, solo poche proteine coinvolte nel mantenimento strutturale della distanza tra i due organelli sono state finora identificate nei mammiferi. Mitofusina2 (MFN2) è stato il primo "tether" strutturale ad essere identificato. E' stato rilevato che MFN2 è localizzata sia nella membrana mitocondriale esterna (OMM) sia sulla superficie citosolica dell'ER ed ' in grado di formare intrazioni omo- ed eterotipiche con MFN1, mantenendo quindi la distanza tra i due organelli. Poiché una residua giustapposizione tra i due organelli è stata osservata in cellule MFN2-/-, ulteriori proteine che esercitano questo ruolo devono esistere. Per identificarle, abbiamo stabilito un protocollo ed eseguito due repliche di uno screening genomico su larga scala in fibroblasti embrionali di topo (MEF). Per eseguire questo screening, abbiamo sfruttato un biosensore basato sulla FRET, dove la proteina fluorescente CFP fusa con il dominio funzionale FRB e la proteina fluorescente YFP fusa con il dominio funzionale FKBP vengono fatte localizzare rispettivamente all'ER (grazie alla sequenza di segnale Sac1) ed ai mitocondri (grazie alla sequenza di segnale Akap1) (Csordas G. et al., 2010). Abbiamo modificato questo costrutto inserendo tra i cDNA delle due proteine il peptide autocatalitico Tav2A per ottenere un singolo mRNA e quindi l'espressione equimolare delle due proteine. I domini funzionali FKBP e FRB sono in grado di eterodimerizzare con l'aggiunta di Rapamicina, permettendo così la misurazione non solo dei livelli di giustapposizione basale tra i due organelli, ma anche del massimo livello di contatti che possono avvenire in una cellula. Abbiamo chiamato questo nuovo costrutto FRET ER-mitochondria probe (FEMP). Le caratteristiche uniche del FEMP ci consentono didiscriminare tra le proteine il cui ruolo è quello di mantenere i due organelli vicini, chiamate "tethers", e proteine che invece tengono i due organelli più distanti, definiti "spacers". Le immagini ottenute dallo screening sono state analizzate e sono stati calcolati due indici, chiamati "basal MERC index" e "maximum MERC index", che rappresentano rispettivamente il livello di contatti osservabili in qualsiasi momento in una cellula e il massimo livello di contatti possibile. A seguito di un'analisi delle immagini automatizzata e di un'analisi statistica effettutata su ~10,000 geni, dopo un processo di selezione abbiamo identificato 205 geni come "tethers" (geni che una volta eliminati aumentano la distanza tra i due organelli) tra mitocondri e ER e 59 geni come "spacers" (geni che una volta eliminati diminuiscono la distanza tra i due organelli) che influenzano sia il basal sia il maximum MERC index in entrambe le repliche. Inoltre, sono stati identificati 625 tethers e 696 spacers che influenzano solo il basal MERC index; e 519 tethers e 67 spacers che modificano solo il maximum MERC index. Analisi delle classi di proteine presenti in questi tre gruppi tramite Panther ha rivelato sia classi di proteine il cui ruolo in questo processo era noto, sia nuove classi di proteine il cui ruolo nella comunicazione tra ER e mitocondri deve ancora essere esplorato. Analisi della localizzazione cellulare per identificare proteine localizzate sia nell'ER sia nei mitocondri delle liste di geni esposte in precedenza, ha rivelato l'esistenza di 13 proteine tra i tethers e gli spacers comuni, 30 proteine che influenzano solo il basal MERC index e 16 proteine che influenzano solo il maximum MERC index localizzate in entrambi gli organelli. Una delle proteine presente nell'ultimo gruppo è "Leucine Rich Repeat Kinase 2" (LRRK2) che abbiamo ulteriormente caratterizzato come tether tra ER e mitocondri. Esperimenti di frazionamento cellulare dimostrano che LRRK2 è localizzata principalmente nelle MAMs. Come previsto per un tether, il livello di prossimità tra ER e mitocondri, misurato tramite FEMP, sono diminuiti in MEF LRRK2-/-. La prossimità tra i due organelli è pienamente recuperata dalla reintroduzione in MEF LRRK2-/- della proteina WT, ma non dei mutanti associati alle forme di Parkinson familiare. In conclusione, abbiamo sviluppato un nuovo metodo per determinare la prossimità tra ER e mitocondri e abbiamo utilizzato questa tecnologia per eseguire due repliche di uni screening gnomico su larga scala identificando nuovi componenti strutturali dei contatti tra mitocondri e ER.
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Tourmente, Sylvette. "Evolution des mitochondries pendant l'ovogenese de drosophile : morphologie, distribution, replication et expression du genome." Clermont-Ferrand 2, 1987. http://www.theses.fr/1987CLF21073.
Книги з теми "Organellar genomes":
1
Gillham, Nicholas W. Organelle genes and genomes. New York: Oxford University Press, 1994.
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P, Hirt Robert, and Horner David S, eds. Organelles, genomes and eukaryote phylogeny: An evolutionary synthesis in the age of genomics. Boca Raton, Fla: CRC Press, 2004.
3
Tachezy, Jan. Hydrogenosomes and Mitosomes. New York: Springer, 2008.
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Gillham, Nicholas. Organelle genes and genomes. Oxford University Press, 1994.
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Hirt, Robert P., and David S. Horner. Organelles Genomes and Eukaryote Phylogeny. Taylor & Francis Group, 2019.
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Bullerwell, Charles E. Organelle Genetics: Evolution of Organelle Genomes and Gene Expression. Springer, 2011.
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Organelle Genetics Evolution Of Organelle Genomes And Gene Expression. Springer, 2011.
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Bullerwell, Charles E. Organelle Genetics: Evolution of Organelle Genomes and Gene Expression. Springer, 2011.
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Bullerwell, Charles E. Organelle Genetics: Evolution of Organelle Genomes and Gene Expression. Springer, 2014.
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Hirt, Robert P., and David S. Horner. Organelles, Genomes and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics. Taylor & Francis Group, 2004.
Частини книг з теми "Organellar genomes":
1
Ohyama, Kanji, Yutaka Ogura, Kenji Oda, Katsuyuki Yamato, Ehji Ohta, Yasukazu Nakamura, Miho Takemura, et al. "Evolution of Organellar Genomes." In Evolution of Life, 187–98. Tokyo: Springer Japan, 1991. http://dx.doi.org/10.1007/978-4-431-68302-5_13.
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Handa, Hirokazu. "Organellar Genomes in Barley." In Compendium of Plant Genomes, 363–76. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-92528-8_20.
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Boopathi, N. Manikanda, R. Veera Ranjani, and M. Raveendran. "Genome Sequencing, Organellar Genomes and Comparative Genomics in Moringa." In Compendium of Plant Genomes, 101–32. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-80956-0_10.
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Kumar, Nitin, Khushbu Islam, and Nirala Ramchiary. "Sequencing of Capsicum Organellar Genomes." In Compendium of Plant Genomes, 153–72. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-319-97217-6_9.
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Havey, Michael J. "Organellar Genomes of the Cucurbits." In Genetics and Genomics of Cucurbitaceae, 241–52. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/7397_2016_8.
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Choubey, Ami, and Manchikatla Venkat Rajam. "Organellar Genomes of Flowering Plants." In Plant Biology and Biotechnology, 179–204. New Delhi: Springer India, 2015. http://dx.doi.org/10.1007/978-81-322-2283-5_8.
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Ohta, Niji, Naoki Sato, and Tsuneyoshi Kuroiwa. "The Organellar Genomes of Cyanidioschyzon merolae." In Enigmatic Microorganisms and Life in Extreme Environments, 139–49. Dordrecht: Springer Netherlands, 1999. http://dx.doi.org/10.1007/978-94-011-4838-2_11.
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Pehu, E. "RFLP analysis of organellar genomes in somatic hybrids." In Plant Tissue Culture Manual, 695–702. Dordrecht: Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-009-0103-2_39.
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Shearman, Jeremy R., Wirulda Pootakham, and Sithichoke Tangphatsornruang. "The BPM 24 Rubber Tree Genome, Organellar Genomes and Synteny Within the Family Euphorbiaceae." In The Rubber Tree Genome, 55–66. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-42258-5_4.
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Burger, Gertraud, Chris J. Jackson, and Ross F. Waller. "Unusual Mitochondrial Genomes and Genes." In Organelle Genetics, 41–77. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-22380-8_3.
Тези доповідей конференцій з теми "Organellar genomes":
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Jung, Jaehee, and Gangman Yi. "A computational model based on long short-term memory for predicting organellar genes in plastid genomes." In 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2019. http://dx.doi.org/10.1109/bibm47256.2019.8983030.
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"Symmetry and asymmetry in bacterial and organellae genomes." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-216.
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"The variability of organelle genomes in barley." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-190.
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Amorim, Marianny Rodrigues Costa, Letícia Oliveira Martins, and Andreia Juliana Rodrigues Caldeira. "ORIGEM E IMPORTÂNCIA FILOGENÉTICA DO CPDNA." In I Congresso Nacional On-line de Biologia Celular e Estrutural. Revista Multidisciplinar em Saúde, 2021. http://dx.doi.org/10.51161/rems/1946.
Анотація:
Introdução: O genoma do cloroplasto é mais conservado que o genoma nuclear e as mudanças de estrutura, ordem ou conteúdo de sequências do DNA cloroplasmático (cpDNA) são frequentemente usadas para mensurar a diversidade genética vegetal. Objetivo: Realizar uma revisão bibliográfica sobre a origem e importância filogenética do cpDNA. Material e métodos: foi realizada uma busca a partir de base dados como SciELO Brasil e Web of Science. Resultado: Cloroplasto é plastídio com DNA próprio. É considerada uma organela semiautônoma, devido a capacidade de sintetizar algumas proteínas. A origem evolutiva de plastídios está relacionada a antigos procariotos que viviam em simbiose dentro de eucariotos e que, ao longo da evolução, no ambiente citoplasmático, perdeu a maioria dos seus genes. Neste processo evolutivo, as bactérias precursoras do cloroplasto, transferiram parte de seu material genético para o DNA da célula hospedeira, contando assim com o genoma da célula hospedeira para produzir muitas de suas proteínas. O genoma cloroplástico é relativamente simples e possui uma estrutura circular com apenas 60 a 200 Kpb. Poucos genes cloroplasmáticos possuem íntrons e o espaço intergênico é pequeno, separados por poucos pares de bases. O número de proteínas codificadas pelo cpDNA é pequeno, mas o cloroplasto realiza sua própria replicação e transcrição de DNA e síntese proteica. Esses processos ocorrem na matriz, e, embora as proteínas que medeiam esse processo genético sejam específicas das organelas, a maioria delas é codificada pelo genoma nuclear, por isso o cpDNA é considerado uma organela especializada. Cada cloroplasto possui várias cópias do cpDNA e existem vários cloroplastos por célula. Isto multiplica o conteúdo da sequência básica de cpDNA por célula em dezenas a centenas de vezes. Conclusão: Estudos de cpDNA podem ser utilizados em várias áreas da biologia de plantas como: estudos evolutivos e filogenéticos (estabelecer relações filogenéticas entre espécies, gêneros e famílias), busca da base genética de doenças, clonagem gênica e reprodução, contribuindo para a expansão das pesquisas botânicas e agronômicas. Além disso, o sequenciamento de cpDNA revela características específicas de cada grupo de planta e de seu funcionamento, os quais podem ser amplamente aplicados através de técnicas da biotecnologia.
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CHERNYSHOVA, A. I., Yu A. PUTINTSEVA, and M. G. SADOVSKY. "VERY HIGH SYNCHRONY IN EVOLUTION OF ORGANELLES AND HOST GENOMES." In International Symposium on Mathematical and Computational Biology. WORLD SCIENTIFIC, 2015. http://dx.doi.org/10.1142/9789814667944_0017.
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Romanova, E. V., Yu S. Bukin, V. V. Aleoshin, and D. Yu Sherbakov. "TRANSPORT RNA GENES REMOLDING IN MITOCHONDRIAL GENOMES." In The Second All-Russian Scientific Conference with international participation "Regulation Mechanisms of Eukariotic Cell Organelle Functions". SIPPB SB RAS, 2018. http://dx.doi.org/10.31255/978-5-94797-318-1-109-110.
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Lang, Franz. "Comparative analysis of organelle genomes, a biologist's view of computational challenges (abstract only)." In the fifth annual international conference. New York, New York, USA: ACM Press, 2001. http://dx.doi.org/10.1145/369133.369201.
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"Longread-only approach to the organellar genome assembly of a rare endemic non-model species Crepis callicephala Juz. (Asteraceae)." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-008.
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"DNA import into plant mitochondria: studying of the translocation pathways in organello and in vivo." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/plantgen2019-189.
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Peretolchina, T. E., T. Ya Sitnikova, and D. Yu Sherbakov. "THE COMPLETE MITOCHONDRIAL GENOMES OF FOUR ENDEMIC BAIKAL MOLLUSKS (MOLLUSCA: CAENOGASTROPODA)." In The Second All-Russian Scientific Conference with international participation "Regulation Mechanisms of Eukariotic Cell Organelle Functions". SIPPB SB RAS, 2018. http://dx.doi.org/10.31255/978-5-94797-318-1-87-88.
Звіти організацій з теми "Organellar genomes":
1
Ostersetzer-Biran, Oren, and Alice Barkan. Nuclear Encoded RNA Splicing Factors in Plant Mitochondria. United States Department of Agriculture, February 2009. http://dx.doi.org/10.32747/2009.7592111.bard.
Анотація:
Mitochondria are the site of respiration and numerous other metabolic processes required for plant growth and development. Increased demands for metabolic energy are observed during different stages in the plants life cycle, but are particularly ample during germination and reproductive organ development. These activities are dependent upon the tight regulation of the expression and accumulation of various organellar proteins. Plant mitochondria contain their own genomes (mtDNA), which encode for a small number of genes required in organellar genome expression and respiration. Yet, the vast majority of the organellar proteins are encoded by nuclear genes, thus necessitating complex mechanisms to coordinate the expression and accumulation of proteins encoded by the two remote genomes. Many organellar genes are interrupted by intervening sequences (introns), which are removed from the primary presequences via splicing. According to conserved features of their sequences these introns are all classified as “group-II”. Their splicing is necessary for organellar activity and is dependent upon nuclear-encoded RNA-binding cofactors. However, to-date, only a tiny fraction of the proteins expected to be involved in these activities have been identified. Accordingly, this project aimed to identify nuclear-encoded proteins required for mitochondrial RNA splicing in plants, and to analyze their specific roles in the splicing of group-II intron RNAs. In non-plant systems, group-II intron splicing is mediated by proteins encoded within the introns themselves, known as maturases, which act specifically in the splicing of the introns in which they are encoded. Only one mitochondrial intron in plants has retained its maturaseORF (matR), but its roles in organellar intron splicing are unknown. Clues to other proteins required for organellar intron splicing are scarce, but these are likely encoded in the nucleus as there are no other obvious candidates among the remaining ORFs within the mtDNA. Through genetic screens in maize, the Barkan lab identified numerous nuclear genes that are required for the splicing of many of the introns within the plastid genome. Several of these genes are related to one another (i.e. crs1, caf1, caf2, and cfm2) in that they share a previously uncharacterized domain of archaeal origin, the CRM domain. The Arabidopsis genome contains 16 CRM-related genes, which contain between one and four repeats of the domain. Several of these are predicted to the mitochondria and are thus postulated to act in the splicing of group-II introns in the organelle(s) to which they are localized. In addition, plant genomes also harbor several genes that are closely related to group-II intron-encoded maturases (nMats), which exist in the nucleus as 'self-standing' ORFs, out of the context of their cognate "host" group-II introns and are predicted to reside within the mitochondria. The similarity with known group-II intron splicing factors identified in other systems and their predicted localization to mitochondria in plants suggest that nuclear-encoded CRM and nMat related proteins may function in the splicing of mitochondrial-encoded introns. In this proposal we proposed to (i) establish the intracellular locations of several CRM and nMat proteins; (ii) to test whether mutations in their genes impairs the splicing of mitochondrial introns; and to (iii) determine whether these proteins are bound to the mitochondrial introns in vivo.
2
Ostersetzer-Biran, Oren, and Jeffrey Mower. Novel strategies to induce male sterility and restore fertility in Brassicaceae crops. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7604267.bard.
Анотація:
Abstract Mitochondria are the site of respiration and numerous other metabolic processes required for plant growth and development. Increased demands for metabolic energy are observed during different stages in the plants life cycle, but are particularly ample during germination and reproductive organ development. These activities are dependent upon the tight regulation of the expression and accumulation of various organellar proteins. Plant mitochondria contain their own genomes (mtDNA), which encode for rRNAs, tRNAs and some mitochondrial proteins. Although all mitochondria have probably evolved from a common alpha-proteobacterial ancestor, notable genomic reorganizations have occurred in the mtDNAs of different eukaryotic lineages. Plant mtDNAs are notably larger and more variable in size (ranging from 70~11,000 kbp in size) than the mrDNAs in higher animals (16~19 kbp). Another unique feature of plant mitochondria includes the presence of both circular and linear DNA fragments, which undergo intra- and intermolecular recombination. DNA-seq data indicate that such recombination events result with diverged mitochondrial genome configurations, even within a single plant species. One common plant phenotype that emerges as a consequence of altered mtDNA configuration is cytoplasmic male sterility CMS (i.e. reduced production of functional pollen). The maternally-inherited male sterility phenotype is highly valuable agriculturally. CMS forces the production of F1 hybrids, particularly in predominantly self-pollinating crops, resulting in enhanced crop growth and productivity through heterosis (i.e. hybrid vigor or outbreeding enhancement). CMS lines have been implemented in some cereal and vegetables, but most crops still lack a CMS system. This work focuses on the analysis of the molecular basis of CMS. We also aim to induce nuclear or organellar induced male-sterility in plants, and to develop a novel approach for fertility restoration. Our work focuses on Brassicaceae, a large family of flowering plants that includes Arabidopsis thaliana, a key model organism in plant sciences, as well as many crops of major economic importance (e.g., broccoli, cauliflower, cabbage, and various seeds for oil production). In spite of the genomic rearrangements in the mtDNAs of plants, the number of genes and the coding sequences are conserved among different mtDNAs in angiosperms (i.e. ~60 genes encoding different tRNAs, rRNAs, ribosomal proteins and subunits of the respiratory system). Yet, in addition to the known genes, plant mtDNAs also harbor numerous ORFs, most of which are not conserved among species and are currently of unknown function. Remarkably, and relevant to our study, CMS in plants is primarily associated with the expression of novel chimericORFs, which likely derive from recombination events within the mtDNAs. Whereas the CMS loci are localized to the mtDNAs, the factors that restore fertility (Rfs) are identified as nuclear-encoded RNA-binding proteins. Interestingly, nearly all of the Rf’s are identified as pentatricopeptide repeat (PPR) proteins, a large family of modular RNA-binding proteins that mediate several aspects of gene expression primarily in plant organelles. In this project we proposed to develop a system to test the ability of mtORFs in plants, which are closely related to known CMS factors. We will induce male fertility in various species of Brassicaceae, and test whether a down-relation in the expression of the recombinantCMS-genes restores fertility, using synthetically designed PPR proteins.
3
Palmer, Guy, Varda Shkap, Wendy Brown, and Thea Molad. Control of bovine anaplasmosis: cytokine enhancement of vaccine efficacy. United States Department of Agriculture, March 2007. http://dx.doi.org/10.32747/2007.7695879.bard.
Анотація:
Anaplasmosis an arthropod-born disease of cattle caused by the rickettsia Anaplasma marginale and is an impediment to efficient production of healthy livestock in both Israel and the United States. Currently the only effective vaccines are derived from the blood of infected cattle. The risk of widespread transmission of both known and newly emergent pathogens has prevented licensure of live blood-based vaccines in the U.S. and is a major concern for their continued use in Israel. Consequently development of a safe, effective vaccine is a high priority. In this collaborative project we focused on two approaches to vaccine development. The first focused o n improving antigen delivery to livestock and specifically examined how DNA vaccines could be improved to enhance priming and expansion of the immune response. This research resulted in development and testing of two novel vaccine delivery systems--one that targeted antigen spread among dendritic cells (the key cell in priming immune responses and a follow-on construct that also specifically targeted antigen to the endosomal-lysosomal compartment the processing organelle within the dendritic cell that directs vaccine antigen to the MHC class ll-CD4* T cell priming pathway). The optimized construct targeting vaccine antigen to the dendritic cell MHC class II pathway was tested for ability to prime A. marginale specific immune responses in outbred cattle. The results demonstrated both statistically significant effects of priming with a single immunization, continued expansion of the primary immune response including development of high affinity lgG antibodies and rapid recall of the memory response following antigen challenge. This portion of the study represented a significant advance in vaccine delivery for livestock. Importantly the impact of these studies is not limited to A. marginale a s the targeting motifs are optimized for cattle and can be adapted to other cattle vaccinations by inserting a relevant pathogen-specific antigen. The second approach (which represented an addition to the project for which approval was requested as part of the first annual report) was a comparative approach between A . marginale and the Israel A . centrale vaccines train. This addition was requested as studies on Major Surface Protein( MSP)- 2 have shown that this antigen is highly antigenically variable and presented solely as a "static vaccine" antigen does not give cross-strain immunity. In contrast A. . centrale is an effective vaccine which Kimron Veterinary institute has used in the field in Israel for over 50 years. Taking advantage of this expertise, a broad comparison of wild type A. marginale and vaccine strain was initiated. These studies revealed three primary findings: i) use of the vaccine is associated with superinfection, but absence of clinical disease upon superinfection with A. marginale; ii) the A. centrale vaccine strain is not only less virulent but transmission in competent in Dermacentor spp. ticks; and iii) some but not all MSPs are conserved in basic orthologous structure but there are significant polymorphisms among the strains. These studies clearly indicated that there are statistically significant differences in biology (virulence and transmission) and provide a clear path for mapping of biology with the genomes. Based on these findings, we initiated complete genome sequencing of the Israel vaccine strain (although not currently funded by BARD) and plant to proceed with a comparative genomics approach using already sequenced wild-type A. marginale. These findings and ongoing collaborative research tie together filed vaccine experience with new genomic data, providing a new approach to vaccine development against a complex pathogen.
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Stern, David B., and Gadi Schuster. Manipulation of Gene Expression in the Chloroplast: Control of mRNA Stability and Transcription Termination. United States Department of Agriculture, December 1993. http://dx.doi.org/10.32747/1993.7568750.bard.
Анотація:
Chloroplasts are the site of photosynthesis and of other essential biosynthetic activities in plant cells. Chloroplasts are semi-autonomous organelles, since they contain their own genomes and protein biosynthetic machinery, but depend on the coordinate expression of nuclear genes to assemble macromolecular complexes. The bioeingineering of plants requires manipulation of chloroplast gene expression, and thus a knowledge of the molecular mechanisms that modulate mRNA and protein production. In this proposal the heterotrophic green alga Chlamydomonas reinhardtii has been used as a model system to understand the control and interrelationships between transcription termination, mRNA 3' end processing and mRNA stability in chloroplasts. Chlamydomonas is a unique and ideal system in which to address these issues, because the chloroplast can be easily manipulated by genetic transformation techniques. This research uncovered new and important information on chloroplast mRNA 3' end formation and mRNA stability. In particular, the 3' untranslated regions of chloroplast mRNAs were shown not to be efficient transcription terminators. The endonucleolytic site in the 3' untranslated region was characterized by site directed mutagensis and the role of several 3' untranslated regions in modulating RNA stability and translation has been studied. This information will allow us to experimentally manipulate the expression of chloroplast genes in vivo by post-transcriptional mechanisms, and should be widely applicable to other higher plant systems.
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Wang, X. F., and M. Schuldiner. Systems biology approaches to dissect virus-host interactions to develop crops with broad-spectrum virus resistance. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134163.bard.
Анотація:
More than 60% of plant viruses are positive-strand RNA viruses that cause billion-dollar losses annually and pose a major threat to stable agricultural production, including cucumber mosaic virus (CMV) that infects numerous vegetables and ornamental trees. A highly conserved feature among these viruses is that they form viral replication complexes (VRCs) to multiply their genomes by hijacking host proteins and remodeling host intracellular membranes. As a conserved and indispensable process, VRC assembly also represents an excellent target for the development of antiviral strategies that can be used to control a wide-range of viruses. Using CMV and a model virus, brome mosaic virus (BMV), and relying on genomic tools and tailor-made large-scale resources specific for the project, our original objectives were to: 1) Identify host proteins that are required for viral replication complex assembly. 2) Dissect host requirements that determine viral host range. 3) Provide proof-of-concept evidence of a viral control strategy by blocking the viral replication complex-localized phospholipid synthesis. We expect to provide new ways and new concepts to control multiple viruses by targeting a conserved feature among positive-strand RNA viruses based on our results. Our work is going according to the expected timeline and we are progressing well on all aims. For Objective 1, among ~6,000 yeast genes, we have identified 96 hits that were possibly play critical roles in viral replication. These hits are involved in cellular pathways of 1) Phospholipid synthesis; 2) Membrane-shaping; 3) Sterol synthesis and transport; 4) Protein transport; 5) Protein modification, among many others. We are pursuing several genes involved in lipid metabolism and transport because cellular membranes are primarily composed of lipids and lipid compositional changes affect VRC formation and functions. For Objective 2, we have found that CPR5 proteins from monocotyledon plants promoted BMV replication while those from dicotyledon plants inhibited it, providing direct evidence that CPR5 protein determines the host range of BMV. We are currently examining the mechanisms by which dicot CPR5 genes inhibit BMV replication and expressing the dicot CPR5 genes in monocot plants to control BMV infection. For Objective 3, we have demonstrated that substitutions in a host gene involved in lipid synthesis, CHO2, prevented the VRC formation by directing BMV replication protein 1a (BMV 1a), which remodels the nuclear membrane to form VRCs, away from the nuclear membrane, and thus, no VRCs were formed. This has been reported in Journal of Biological Chemistry. Based on the results from Objective 3, we have extended our plan to demonstrate that an amphipathic alpha-helix in BMV 1a is necessary and sufficient to target BMV 1a to the nuclear membrane. We further found that the counterparts of the BMV 1a helix from a group of viruses in the alphavirus-like superfamily, such as CMV, hepatitis E virus, and Rubella virus, are sufficient to target VRCs to the designated membranes, revealing a conserved feature among the superfamily. A joint manuscript describing these exciting results and authored by the two labs will be submitted shortly. We have also successfully set up systems in tomato plants: 1) to efficiently knock down gene expression via virus-induced gene silencing so we could test effects of lacking a host gene(s) on CMV replication; 2) to overexpress any gene transiently from a mild virus (potato virus X) so we could test effects of the overexpressed gene(s) on CMV replication. In summary, we have made promising progress in all three Objectives. We have identified multiple new host proteins that are involved in VRC formation and may serve as good targets to develop antiviral strategies; have confirmed that CPR5 from dicot plants inhibited viral infection and are generating BMV-resistance rice and wheat crops by overexpressing dicot CPR5 genes; have demonstrated to block viral replication by preventing viral replication protein from targeting to the designated organelle membranes for the VRC formation and this concept can be further employed for virus control. We are grateful to BARD funding and are excited to carry on this project in collaboration.