Éditeur(s) : HAL CCSD
Résumé : Evolution of organisms, genomes and genes does not strictly follow a tree-like process; symbiosis, horizontal gene transfers and gene fusions build high level composite objects with components of phylogenetically distinct origins. Such processes have been called introgressive events and are significant in evolution. They are involved in some major evolutionary transitions such as eukaryogenesis, photosynthesis acquisition in eukaryotes and the origins of major archaeal clades. Eukaryogenesis would have involved (at least) two kinds of partners: an archaeon and an alpha-proteobacterium. Photosynthetic eukaryotes arose from the integration of a cyanobacterium into a eukaryotic cell and recent findings suggested that most archaeal lineages emerged after massive acquisitions of bacterial genes. These composite lineages carry highly chimeric genomes where genes from symbiotic partners co-localize into the same genome. During my PhD thesis, I used sequence similarity networks and phylogenetic methods in order to study reticulate evolution. My research specifically focused on a previously hidden component of composite genomes: symbiogenetic genes (S genes). These chimeric genes are found in genetic mergers, and originate from the association of genes of symbiotic partners. Some association rules have been discovered. In a broad perspective, the discovery of S-genes extends the concept of genome chimerism to the within-gene level.
L'évolution des organismes, des génomes et des gènes n'est pas strictement arborescente; les symbioses, les transferts horizontaux de gènes ou encore la fusion de gènes créent des objets composites formés de parties dont les histoires évolutives sont différentes. Ces processus non arborescents sont appelés introgressifs et ont un impact non négligeable en évolution. Ils sont à l'origine de transitions évolutives majeures comme l'émergence des eucaryotes, des eucaryotes photosynthétiques ou encore de nombreux groupes d'Archaea. Dans le cas des eucaryotes, l'association et la stabilisation d'une Archaea et d'une alpha-protéobactérie a permis l'émergence d'un nouveau groupe d'organismes composites aux propriétés émergentes. L'acquisition de la photosynthèse chez les eucaryotes s'est faite via l'endosymbiose d'une cyanobactérie et, bien que débattue, l'apparition des grands groupes d'Archaea semble être concomitante avec l'acquisition de nombreux gènes d'origine bactérienne. Ces superorganismes ont la particularité d'avoir des génomes composés de gènes de différents partenaires symbiotiques. L'objectif de mon travail de thèse a constitué à étudier l'aspect introgressif de l'évolution par des méthodes de réseaux de similarité de séquence et des méthodes phylogénétiques. Je me suis particulièrement focalisé sur la détection de nouveaux gènes chimériques nommés gènes symbiogénétiques (S-gènes) car composés de parties originaires des différents partenaires symbiotiques. De tels gènes existent dans les génomes et plusieurs règles d'association ont pu être mises en évidence. Plus généralement, la présence de S-gènes étend la notion de mosaïcisme génomique au niveau infra-génique.
https://tel.archives-ouvertes.fr/tel-01536344

NNT : 2016PA066534
tel-01536344
https://tel.archives-ouvertes.fr/tel-01536344
https://tel.archives-ouvertes.fr/tel-01536344/document
https://tel.archives-ouvertes.fr/tel-01536344/file/2016PA066534.pdf

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699
Spontaneous gene flow between wild and cultivated chicory, Cichorium intybus L., may have implications for the genetic structure and evolution of populations and varieties. One aspect of this crop-wild gene flow is the dispersal of transgenes from genetically modified varieties, e.g. gene flow from GM chicory to natural chicory could have unwanted consequences. With the purpose to identify and quantify crop-wild gene flow in chicory, we analysed introgression in 19 wild chicory populations and 16 accessions of chicory varieties and landraces distributed across Northern, Central and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between landraces and wild populations, between different wild populations as well as between cultivars. Population structure visualized by distance-based clustering showed a North-South geographical structuring of the wild populations, and a general grouping of the cultivars corresponding to known origin. The results indicated, however, that the structuring between the two groups of wild and cultivated types was weak. As crop and wild recipients are genetically close and genes are transferred between the two types rather frequently, focus on mitigating crop-wild gene flow should be increased, before transgenic varieties are cultivated openly.
ISSN: 0925-9864

hal-01032184
https://hal.archives-ouvertes.fr/hal-01032184
DOI : 10.1007/s10722-008-9375-1

Résumé : Aux Antilles, la faible fréquence des coronaropathies pourrait être liée à des facteurs génétiques, ethniques et/ou une distribution spécifique des facteurs de risque cardio-vasculaire (FDRCV). Les propriétés l'ANP (Atrial Natriuretic Peptide) et l'influence de certains polymorphismes de son gène, fréquents dans les populations d'ascendance Africaine pourraient également être en cause. L'analyse des dossiers de 638 patients coronariens consécutifs a mis en évidence une forte prévalence de l'hypertension artérielle et du diabète dans cette population et révélé des différences significatives dans la prévalence des FDRCV entre Afro-Caribéens (AC), Caucasiens et descendants de migrants Indiens. L'analyse angiographique de 420 patients AC a révélé que le diabète était le FDRCV le plus fortement lié à la sévérité des lésions coronaires alors l'obésité apparaissait comme un facteur protecteur. La transfection in vitro, de cellules musculaires lisses artérielles par une construction adénovirale porteuse du gène de l'ANP a entrainé une inhibition de la prolifération et de la migration cellulaire de 31 % et 25% respectivement. In vivo, cet effet s'est traduit par une réduction de 25% de la formation néotimale et de 28% du rapport intima/média dans un modèle d'hyperplasie de carotide de rat. Dans étude transversale incluant 210 sujets diabétiques AC nous avons mis en évidence une association entre le polymorphisme rs5065 (22381>C) du gène de l'ANP et l'existence d'une coronaropatbie. Dans cette étude, l'odds ratio de la présence d'une coronaropathie chez les porteurs de l'allèle mineur de cette mutation (TC/CC) était de 0,50 (0,26- 0,96; P = 0,038).
In Guadeloupe and Martinique, the low frequency ofcoronary artery disease (CAD) could be related to genetic or ethniefactors and/or specifie distribution ofcardiovascular risk factors (CRFs). Atrial Natriuretic Peptide (ANP) properties and influence of sorne of ANP gene polymorphism that are frequent in populations of African descent could also be involved in CAD occurrence. We retrospectively studied 638 consecutive patients with documented CAO and found a high prevalence of hypertension and diabetes in this population. This study also demonstrated significant differences in the prevalence of CRFs between Afro-Caribbean (AC), Caucasians and Indians migrants. The angiographie analysis of420 patients revealed that in AC, diabetes emerged as the strongest CFR related to the severity ofcoronary lesions while obesity appeared as a protective factor. After transfection by an adenoviral construct carrying the ANP gene, vascular smooth muscle cell proliferation stimulated by 10% fetal calf serum was reduced by 31% and migration by 25%. In vivo, in rat carotid artery model ofvascular injury, neointima formation and intima/media ratio was reduced by 25% and 28% respectively. In a cross-sectional study inc1uding 210 AC diabetics we found an association between rs5065 (22381> C) polymorpbism and the presence of coronary artery disease suggesting that the minor allele could have a protective effect against CAD. The odds ratio for the presence ofCAD in carriers ofthe minor allele ofthis mutation (TC / CC) was 0.50 (0.26-0.96, P = 0.038).

http://www.theses.fr/2012AGUY0553/document

Éditeur(s) : HAL CCSD Society for Molecular Biology and Evolution
Résumé : International audience
Vibrio metoecus is the closest relative of Vibrio cholerae, the causative agent of the potent diarrheal disease cholera. Although the pathogenic potential of this new species is yet to be studied in depth, it has been co-isolated with V. cholerae in coastal waters and found in clinical specimens in the USA. We used these two organisms to investigate the genetic interaction between closely related species in their natural environment. The genomes of twenty V. cholerae and four V. metoecus strains isolated from a brackish coastal pond on the US east coast, as well as four clinical V. metoecus strains were sequenced and compared to reference strains. Whole genome comparison shows 86-87% average nucleotide identity (ANI) in their core genes between the two species. On the other hand, the chromosomal integron, which occupies approximately 3% of their genomes, shows higher conservation in ANI between species than any other region of their genomes. The ANI of 93-94% observed in this region is not significantly greater within than between species, meaning that it does not follow species boundaries. V. metoecus does not encode toxigenic V. cholerae major virulence factors, the cholera toxin and toxin co-regulated pilus. However, some of the pathogenicity islands found in pandemic V. cholerae were either present in the common ancestor it shares with V. metoecus, or acquired by clinical and environmental V. metoecus in partial fragments. The virulence factors of V. cholerae are therefore both more ancient and more widespread than previously believed. There is high interspecies recombination in the core genome, which has been detected in 24% of the single-copy core genes, including genes involved in pathogenicity. V. metoecus was six times more often the recipient of DNA from V. cholerae as it was the donor, indicating a strong bias in the direction of gene transfer in the environment.
ISSN: 1759-6653

Droits : http://creativecommons.org/licenses/by/
hal-01264332
http://hal.upmc.fr/hal-01264332
http://hal.upmc.fr/hal-01264332/document
http://hal.upmc.fr/hal-01264332/file/Genome%20Biol%20Evol-2015-Orata-gbe_evv193.pdf
DOI : 10.1093/gbe/evv193

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
This study investigated the clinical epidemiology and resistance mechanisms of Acinetobacter baumannii and characterised the clonal diversity of carbapenem-resistant A. baumannii (CRAB) during an ICU-associated outbreak at Cayenne Hospital, French Guiana. All non-duplicate A. baumannii isolates from 2008 to 2014 were tested for antibiotic susceptibility by disk diffusion. Multilocus sequence typing, pulsed-field gel electrophoresis (PFGE) and characterisation of carbapenemase-encoding genes were performed on CRAB. Of the 441 A. baumannii isolates, most were from males (54.0%) and were detected mainly from the ICU (30.8%) and medicine wards (21.8%). In the ICU, strains were mainly isolated from the respiratory tract (44.1%) and bloodstream (14.0%), whereas in medicine wards they mainly were from wound/drainage (36.5%) and bloodstream (25.0%). A. baumannii showed the greatest susceptibility to piperacillin/tazobactam (92.7%), imipenem (92.5%), colistin (95.6%) and amikacin (97.2%), being lower in the ICU and medicine wards compared with other wards. An outbreak of OXA-23-producing CRAB occurred in the 13-bed ICU in 2010. CRAB strains were more co-resistant to other antimicrobials compared with non-CRAB. Molecular genetics analysis revealed five sequence types [ST78, ST107 and ST642 and two new STs (ST830 and ST831)]. Analysis of PFGE profiles indicated cross-transmissions of CRAB within the ICU, between the ICU and one medicine ward during transfer of patients, and within that medicine ward. This study provides the first clinical and molecular data of A. baumannii from French Guiana and the Amazon basin. The ICU was the highest risk unit of this nosocomial outbreak of OXA-23-producing CRAB, which could subsequently disseminate within the hospital.
ISSN: 0924-8579

hal-01506828
https://hal.archives-ouvertes.fr/hal-01506828
PUBMED : 27236843

Éditeur(s) : Nature Publishing Group
Résumé : Vibrio nigripulchritudo is an emerging pathogen of farmed shrimp in New Caledonia and other regions in the Indo-Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have suggested that pathogenicity is linked to particular lineages. Here, we performed high-throughput sequencing-based comparative genome analysis of 16 V. nigripulchritudo strains to explore the genomic diversity and evolutionary history of pathogen-containing lineages and to identify pathogen-specific genetic elements. Our phylogenetic analysis revealed three pathogen-containing V. nigripulchritudo clades, including two clades previously identified from New Caledonia and one novel clade comprising putatively pathogenic isolates from septicemic shrimp in Madagascar. The similar genetic distance between the three clades indicates that they have diverged from an ancestral population roughly at the same time and recombination analysis indicates that these genomes have, in the past, shared a common gene pool and exchanged genes. As each contemporary lineage is comprised of nearly identical strains, comparative genomics allowed differentiation of genetic elements specific to shrimp pathogenesis of varying severity. Notably, only a large plasmid present in all highly pathogenic (HP) strains encodes a toxin. Although less/non-pathogenic strains contain related plasmids, these are differentiated by a putative toxin locus. Expression of this gene by a non-pathogenic V. nigripulchritudo strain resulted in production of toxic culture supernatant, normally an exclusive feature of HP strains. Thus, this protein, here termed 'nigritoxin', is implicated to an extent that remains to be precisely determined in the toxicity of V. nigripulchritudo.
Isme Journal (1751-7362) (Nature Publishing Group), 2013-10 , Vol. 7 , N. 10 , P. 1985-1996

Droits : 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13
http://archimer.ifremer.fr/doc/00160/27117/28369.pdf
DOI:10.1038/ismej.2013.90
http://archimer.ifremer.fr/doc/00160/27117/

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: Increasingly, similarity networks are being used for evolutionary analyses of molecular datasets. These networks are very useful, in particular for the analysis of gene sharing, lateral gene transfer and for the detection of distant homologs. Currently, such analyses require some computer programming skills due to the limited availability of user-friendly freely distributed software. Consequently, although appealing, the construction and analyses of these networks remain less familiar to biologists than do phylogenetic approaches. Results: In order to ease the use of similarity networks in the community of evolutionary biologists, we introduce a software program, EGN, that runs under Linux or MacOSX. EGN automates the reconstruction of gene and genome networks from nucleic and proteic sequences. EGN also implements statistics describing genetic diversity in these samples, for various user-defined thresholds of similarities. In the interest of studying the complexity of evolutionary processes affecting microbial evolution, we applied EGN to a dataset of 571,044 proteic sequences from the three domains of life and from mobile elements. We observed that, in Borrelia, plasmids play a different role than in most other eubacteria. Rather than being genetic couriers involved in lateral gene transfer, Borrelia's plasmids and their genes act as private genetic goods, that contribute to the creation of genetic diversity within their parasitic hosts. Conclusion: EGN can be used for constructing, analyzing, and mining molecular datasets in evolutionary studies. The program can help increase our knowledge of the processes through which genes from distinct sources and/or from multiple genomes co-evolve in lineages of cellular organisms.
ISSN: 1471-2148

hal-01544799
https://hal.archives-ouvertes.fr/hal-01544799
DOI : 10.1186/1471-2148-13-146

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: Microbial genetic diversity is often investigated via the comparison of relatively similar 16S molecules through multiple alignments between reference sequences and novel environmental samples using phylogenetic trees, direct BLAST matches, or phylotypes counts. However, are we missing novel lineages in the microbial dark universe by relying on standard phylogenetic and BLAST methods? If so, how can we probe that universe using alternative approaches? We performed a novel type of multi-marker analysis of genetic diversity exploiting the topology of inclusive sequence similarity networks. Results: Our protocol identified 86 ancient gene families, well distributed and rarely transferred across the 3 domains of life, and retrieved their environmental homologs among 10 million predicted ORFs from human gut samples and other metagenomic projects. Numerous highly divergent environmental homologs were observed in gut samples, although the most divergent genes were over-represented in non-gut environments. In our networks, most divergent environmental genes grouped exclusively with uncultured relatives, in maximal cliques. Sequences within these groups were under strong purifying selection and presented a range of genetic variation comparable to that of a prokaryotic domain. Conclusions: Many genes families included environmental homologs that were highly divergent from cultured homologs: in 79 gene families (including 18 ribosomal proteins), Bacteria and Archaea were less divergent than some groups of environmental sequences were to any cultured or viral homologs. Moreover, some groups of environmental homologs branched very deeply in phylogenetic trees of life, when they were not too divergent to be aligned. These results underline how limited our understanding of the most diverse elements of the microbial world remains, and encourage a deeper exploration of natural communities and their genetic resources, hinting at the possibility that still unknown yet major divisions of life have yet to be discovered.
ISSN: 1745-6150

Droits : http://creativecommons.org/licenses/by/
hal-01257771
http://hal.upmc.fr/hal-01257771
http://hal.upmc.fr/hal-01257771/document
http://hal.upmc.fr/hal-01257771/file/s13062-015-0092-3.pdf
DOI : 10.1186/s13062-015-0092-3

Éditeur(s) : Academic Press Ltd- Elsevier Science Ltd
Résumé : Bonamiosis due to the parasite Bonamia ostreae has been associated with massive mortality in flat oyster stocks in Europe. Control of the disease currently relies on disease management practices and transfer restriction. Previously, massal selections based on survival to challenge to infection with B. ostreae have been applied to produce flat oyster families with resistant progeny. In an attempt to understand the molecular mechanisms involved in disease resistance, differentially expressed sequence tags between resistant and wild Ostrea edulis haemocytes, both infected with the parasite, were identified using suppression subtractive hybridisation. Expression of seven ESTs has been studied using quantitative reverse-transcriptase PCR. The base-line expression of an extracellular superoxide dismutase, inhibitor of apoptosis (OeIAP), Fas ligand (OeFas-ligand) and Cathepsin B was significantly increased, whilst cyclophilin B appeared significantly decreased in resistant oysters. Considering their great interest for further studies, the open reading frames of the OeFas-ligand and OeIAP were completely sequenced. Highlights ► Bonamia ostreae is an intra-haemocytes parasite. ► Flat oyster Ostrea edulis, is the natural host of B. ostreae. ► In this study we have studied genes expressed in response to the parasite. ► Extracellular superoxide dismutase (OeEcSOD) is up regulated in resistant haemocyte. ► Genes involved in apoptosis is up regulated in resistant haemocytes from flat oyster.
Fish & Shellfish Immunology (1050-4648) (Academic Press Ltd- Elsevier Science Ltd), 2012-06 , Vol. 32 , N. 6 , P. 958-968

Droits : 2012 Elsevier Ltd. All rights reserved.
http://archimer.ifremer.fr/doc/00071/18218/15790.pdf
DOI:10.1016/j.fsi.2012.01.026
http://archimer.ifremer.fr/doc/00071/18218/

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The common endosymbiotic Wolbachia bacteria influence arthropod hosts in multiple ways. They are mostly recognized for their manipulations of host reproduction, yet, more recent studies demonstrate that Wolbachia also impact host behavior, metabolic pathways and immunity. Besides their biological and evolutionary roles Wolbachia are new potential biological control agents for pest and vector management. Importantly, Wolbachia-based control strategies require controlled symbiont transfer between host species and predictable outcomes of novel Wolbachia-host associations. Theoretically, this artificial horizontal transfer could inflict genetic changes within transferred Wolbachia populations. This could be facilitated through de novo mutations in the novel recipient host or changes of haplotype frequencies of polymorphic Wolbachia populations when transferred from donor to recipient hosts. Here we show that Wolbachia resident in the European cherry fruit fly, Rhagoletis cerasi, exhibit ancestral and cryptic sequence polymorphism in three symbiont genes, which are exposed upon microinjection into the new hosts Drosophila simulans and Ceratitis capitata. Our analyses of Wolbachia in microinjected D. simulans over 150 generations after microinjection uncovered infections with multiple Wolbachia strains in trans-infected lines that had previously been typed as single infections. This confirms the persistence of low-titer Wolbachia strains in microinjection experiments that had previously escaped standard detection techniques. Our study demonstrates that infections by multiple Wolbachia strains can shift in prevalence after artificial host transfer driven by either stochastic or selective processes. Trans-infection of Wolbachia can claim fitness costs in new hosts and we speculate that these costs may have driven the shifts of Wolbachia strains that we saw in our model system.
ISSN: 1932-6203

hal-01544765
https://hal.archives-ouvertes.fr/hal-01544765
DOI : 10.1371/journal.pone.0082402

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Based on their small size and genomic properties, ultrasmall prokaryotic groups like the Candidate Phyla Radiation have been proposed as possible symbionts dependent on other bacteria or archaea. In this study, we use a bipartite graph analysis to examine patterns of sequence similarity between draft and complete genomes from ultrasmall bacteria and other complete prokaryotic genomes, assessing whether the former group might engage in significant gene transfer (or even endosymbioses) with other community members. Our results provide preliminary evidence for many lateral gene transfers with other prokaryotes, including members of the archaea, and report the presence of divergent, membrane-associated proteins among these ultrasmall taxa. In particular, these divergent genes were found in TM6 relatives of the intracellular parasite Babela massiliensis.
ISSN: 1462-2912

Droits : http://creativecommons.org/licenses/by/
hal-01480348
http://hal.upmc.fr/hal-01480348
http://hal.upmc.fr/hal-01480348/document
http://hal.upmc.fr/hal-01480348/file/emi13477.pdf
DOI : 10.1111/1462-2920.13477

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Since the first molecular study of the suborder Notothenioidei in 1994, many phylogenetic studies have been published. Among these, those with a sufficient number of taxa have all suggested that the Nototheniidae, as currently defined, is monophyletic only with the inclusion of the Channichthyidae, Artedidraconidae, Bathydraconidae and Harpagiferidae. This is corroborated by more recent studies including more taxa, but in these studies either the number of nuclear markers or the number of taxa included remained low. We obtained sequences for a large sampling covering most nototheniid genera for five markers described previously for other samplings (COI, Rhodopsin retrogene, Pkd1, HECW2, and SSRP1) and one nuclear marker never used before in phylogenetic inference (PPM1d). The topology for the combined analysis of the nuclear coding genes, as well as the topology for SSRP1 (non-coding) and the combined analysis for all markers all support the paraphyly of Nototheniidae, the genus Notothenia (including Paranotothenia) is the sister group of the clade Channichthyidae, Artedidraconidae, Bathydraconidae and Harpagiferidae, and genus Gobionotothen is a sister group to both. As in previous studies, Trematomus, Lepidonotothen and Patagonotothen form a clade that also includes Indonotothenia cyanobrancha. The position of Pleuragramma antarctica, Dissostichus species and Aethotaxis mitopteryx remains unstable and dependant on markers and analyses. We therefore propose the inclusion of the four families of the High Antarctic clade in the Nototheniidae, and their transformation into subfamilies. We transfer Paranotothenia magellanica to the genus Notothenia, as Notothenia magellanica.
ISSN: 1874-7787

hal-01544914
https://hal.archives-ouvertes.fr/hal-01544914
DOI : 10.1016/j.margen.2012.02.003

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The tree model and tree-based methods have played a major, fruitful role in evolutionary studies. However, with the increasing realization of the quantitative and qualitative importance of reticulate evolutionary processes, affecting all levels of biological organization, complementary network-based models and methods are now flourishing, inviting evolutionary biology to experience a network-thinking era. We show how relatively recent comers in this field of study, that is, sequence-similarity networks, genome networks, and gene families–genomes bipartite graphs, already allow for a significantly enhanced usage of molecular datasets in comparative studies. Analyses of these networks provide tools for tackling a multitude of complex phenomena, including the evolution of gene transfer, composite genes and genomes, evolutionary transitions, and holobionts.
ISSN: 0966-842X

Droits : http://creativecommons.org/licenses/by-nc-nd/
hal-01300043
http://hal.upmc.fr/hal-01300043
http://hal.upmc.fr/hal-01300043/document
http://hal.upmc.fr/hal-01300043/file/Network-Thinking.pdf
DOI : 10.1016/j.tim.2015.12.003

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Mitochondrial DNA integrity is ensured by several nuclear-encoded proteins in vertebrates, and a number of mtDNA alterations in human diseases, including deletions and duplications, have been suspected to result from errors in the mitochondrial recombination pathway. However, the presence of the latter system is still a matter of controversy as RecA proteins display various functions in vitro. In Escherichia coli, RecA plays a central role in homologous recombination by pairing and transferring a single strand to a homologous duplex DNA. To address indirectly the issue of a mitochondrial recombination pathway in vivo, we have constructed a chimeric gene containing an N terminal mitochondrial targeting sequence and the E. coli RecA gene. Cells were transfected by the recombinant plasmid, then tested for their mtDNA repair upon bleomycin treatment. We found an increased repair rate of the mitochondrial DNA in cells expressing RecA as compared to control cells. These results indicate that the transfected cells display an improved mtDNA repair replication pathway due to the exogenous RecA, likely in synergy with an endogenous rate-limiting mitochondrial recombination pathway.
ISSN: 0027-5107

hal-01680533
https://hal.univ-antilles.fr/hal-01680533
PUBMED : 11356332

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Analysis of microbial biodiversity is hampered by a lack of reference genomes from most bacteria, viruses, and algae. This necessitates either the cultivation of a restricted number of species for standard sequencing projects or the analysis of highly complex environmental DNA metagenome data. Single-cell genomics (SCG) offers a solution to this problem by constraining the studied DNA sample to an individual cell and its associated symbionts, prey, and pathogens. We used SCG to study marine heterotrophic amoebae related to Paulinella ovalis (A. Wulff) P.W. Johnson, P.E. Hargraves & J.M. Sieburth (Rhizaria). The genus Paulinella is best known for its photosynthetic members such as P.chromatophora Lauterborn that is the only case of plastid primary endosymbiosis known outside of algae and plants. Here, we studied the phagotrophic sister taxa of P.chromatophora that are related to P.ovalis and found one SCG assembly to contain -cyanobacterial DNA. These cyanobacterial contigs are presumably derived from prey. We also uncovered an associated cyanophage lineage (provisionally named phage PoL_MC2). Phylogenomic analysis of the fragmented genome assembly suggested a minimum genome size of 200Kbp for phage PoL_MC2 that encodes 179 proteins and is most closely related to Synechococcus phage S-SM2. For this phage, gene network analysis demonstrates a highly modular genome structure typical of other cyanophages. Our work demonstrates that SCG is a powerful approach for discovering algal and protist biodiversity and for elucidating biotic interactions in natural samples.
ISSN: 0022-3646

hal-01544797
https://hal.archives-ouvertes.fr/hal-01544797
DOI : 10.1111/jpy.12028

Éditeur(s) : HAL CCSD International Phycological Society
Résumé : International audience
We studied a group of monoraphid diatom species (Bacillariophyceae, Achnanthidiaceae) found in the marine coastal environment of tropical islands of the Caribbean Sea, western Atlantic Ocean, Indian Ocean, South Pacific Ocean, the Adriatic Sea and the Black Sea. Based on light and electron microscope examination, Madinithidium was formally described as a genus new to science with the generitype defined as Madinithidium undulatum. The characteristic features of the valve structure are a strongly developed sternum and raphe sternum, transapical striae formed by a single areola (macroareolae) positioned in small depressions, elevated virgae and coaxial internal central raphe endings. Furthermore, the striae of both raphe and sternum valves are closed by finely perforated hymenes. Madinithidium and Achnanthidium species are difficult to identify correctly with light microscopy since their valves are small and finely structured. Four species recently described from the western Indian Ocean and assigned to Achnanthidium sensu lato – Achnanthidium capitatum, A. flexuistriatum, A. pseudodelicatissimum and A. scalariforme – possessed morphological features permitting their placement into Madinithidium gen. nov. The above-mentioned species were formally transferred to the new genus.
ISSN: 2330-2968

hal-01333391
https://hal-univ-perp.archives-ouvertes.fr/hal-01333391
DOI : 10.2216/14-21R2

Éditeur(s) : HAL CCSD National Academy of Sciences
Résumé : International audience
All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.
ISSN: 0027-8424

hal-01544803
https://hal.archives-ouvertes.fr/hal-01544803
DOI : 10.1073/pnas.1206541109

Éditeur(s) : HAL CCSD
Résumé : International audience
Despite their dynamic nature, certain chromatin marks must be maintained over the long term. This is particulary true for histone 3 lysine 9 (H3K9) trimethylation, that is involved in the maintenance of healthy differentiated cellular states by preventing inappropriate gene expression, and has been recently identified as the most efficient barrier to cellular reprogramming in nuclear transfer experiments. We propose that the capacity of the enzymes SUV39H1/2 to rebind to a minor fraction of their products, either directly or via HP1α/β, contributes to the solidity of this mark through (i) a positive feedback involved in its establishment by the mutual enforcement of H3K9me3 and SUV39H1/2 and then (ii) a negative feedback sufficient to strongly stabilize H3K9me3 heterochromatin in post-mitotic cells by generating local enzyme concentrations capable of counteracting transient bursts of demethylation. This model does not require direct molecular interactions with adjacent nucleosomes and is favoured by a series of additional mechanisms including (i) the protection of chromatin-bound SUV39H1/2 from the turnovers of soluble proteins, which can explain the uncoupling between the cellular contents in SUV39H1 mRNA and protein; (ii) the cooperative dependence on the local density of the H3K9me3 of HP1α/β-dependent heterochomatin condensation and, dispensably (iii) restricted enzyme exchanges with chromocenters confining the reactive bursts of SUV39H1/2 in heterochromatin. This mechanism illustrates how seemingly static epigenetic states can be firmly maintained by dynamic and reversible modifications. © 2016 Elsevier B.V.
Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

hal-01467548
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01467548
DOI : 10.1016/j.bbagrm.2016.11.006
PUBMED : 27876670

Éditeur(s) : Academic Press Ltd- Elsevier Science Ltd
Résumé : Extracellular products (ECPs) of the pathogenic Vibrio aestuarianus 01/32 were previously reported to display lethality in Crassostrea gigas oysters and to cause morphological changes and immunosuppression in oyster hemocytes. To identify the source of this toxicity, biochemical and genetic approaches were developed. ECP protease activity and lethality were shown to be significantly reduced following incubation with metal chelators, suggesting the involvement of a zinc metalloprotease. An open reading frame of 1836 bp encoding a 611-aa metalloprotease (designated yam) was identified. The deduced protein sequence showed high homology to other Vibrio metalloproteases reported to be involved in pathogenicity. To further confirm the role of this enzyme in ECP toxicity, a plasmid carrying the yarn gene under the control of an araC-P-BAD expression cassette was transferred to a Vibrio splendidus related strain, LMC20012(T), previously characterized as non-pathogenic to oysters. Expression of Vam conferred a toxic phenotype to LMG20012(T) ECPs in vivo and cytotoxicity to oyster hemocytes in vitro. Collectively, these data suggest that the Vam metalloprotease is a major contributor to the toxicity induced by V aestuarianus ECPs and is involved in the impairment of oyster hemocyte functions. (C) 2010 Elsevier Ltd. All rights reserved.
Fish & Shellfish Immunology (1050-4648) (Academic Press Ltd- Elsevier Science Ltd), 2010-11 , Vol. 29 , N. 5 , P. 753-758

Droits : 2010 Elsevier Ltd All rights reserved.
http://archimer.ifremer.fr/doc/00015/12649/9588.pdf
DOI:10.1016/j.fsi.2010.07.007
http://archimer.ifremer.fr/doc/00015/12649/

Éditeur(s) : HAL CCSD HUMANA PRESS INC
Résumé : International audience
Ever since Darwin, the familiar genealogical pattern known as the Tree of Life (TOL) has been prominent in evolutionary thinking and has dominated not only systematics, but also the analysis of the units of evolution. However, recent findings indicate that the evolution of DNA, especially in prokaryotes and such DNA vehicles as viruses and plasmids, does not follow a unique tree-like pattern. Because evolutionary patterns track a greater range of processes than those captured in genealogies, genealogical patterns are in fact only a subset of a broader set of evolutionary patterns. This fact suggests that evolutionists who focus exclusively on genealogical patterns are blocked from providing a significant range of genuine evolutionary explanations. Consequently, we highlight challenges to tree-based approaches, and point the way toward more appropriate methods to study evolution (although we do not present them in technical detail). We argue that there is significant benefit in adopting wider range of models, evolutionary representations, and evolutionary explanations, based on an analysis of the full range of evolutionary processes. We introduce an ecosystem orientation into evolutionary thinking that highlights the importance of ``type 1 coalitions'' (functionally related units with genetic exchanges, aka ``friends with genetic benefits''), ``type 2 coalitions'' (functionally related units without genetic exchanges), ``communal interactions,'' and ``emergent evolutionary properties.'' On this basis, we seek to promote the study of (especially prokaryotic) evolution with dynamic evolutionary networks, which are less constrained than the TOL, and to provide new ways to analyze an expanded range of evolutionary units (genetic modules, recombined genes, plasmids, phages and prokaryotic genomes, pangenomes, microbial communities) and evolutionary processes. Finally, we discuss some of the conceptual and practical questions raised by such network-based representation.
EVOLUTIONARY GENOMICS: STATISTICAL AND COMPUTATIONAL METHODS, VOL 2

ISBN : 978-1-61779-584-8
hal-01544801
https://hal.archives-ouvertes.fr/hal-01544801
DOI : 10.1007/978-1-61779-585-5_4