京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第19188号 / 工博第4065号 / 新制||工||1627(附属図書館) / 32180 / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 跡見 晴幸, 教授 森 泰生, 教授 濵地 格 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

No description available.

No description available.

L'objectif de cette thèse est d'appliquer la méthode d'identification bactérienne par spectrométrie de masse MALDI-TOF pour une utilisation en routine dans un laboratoire de microbiologie clinique. Dans un 1er temps et de manière prospective, nous avons évalué la performance et le coût-efficacité de l'identification bactérienne de routine par MALDI-TOF par rapport aux techniques conventionnelles d'identification phénotypique. Durant la période des 16 semaines d'étude, nous avons comparé la performance de la technique par MALDI-TOF aux techniques conventionnelles d'identification phénotypique comprenant la coloration de Gram, la galerie API ANA et le Vitek 2. En cas de résultats discordants entre ces deux techniques, l'identification était réalisée par biologie moléculaire. Nous avons montré que le MALDI-TOF est un moyen efficace et rentable pour l'identification des bactéries de routine. Le MALDI-TOF peut être utilisée en 1ère intention dans l'identification bactérienne avant l'ensemble de techniques phénotypiques. Dans un 2ème temps, nous avons évalué rétrospectivement la performance et le coût-efficacité de l'utilisation exclusive de MALDI-TOF en diagnostic bactériologique de routine en comparaison avec les techniques conventionnelles. En analysant les données des 11 dernières années, nous avons montré que le MALDI-TOF est efficace et tout à fait adaptée pour l'identification d'espèce bactérienne en routine. Nous avons également prouvé que MALDI-TOF est un outil puissant pour identifier les espèces bactériennes rarement impliquées dans les infections humaines. Cette technique pourrait être une alternative aux méthodes moléculaires dans le laboratoire clinique. / The objective of this thesis is to apply the method of bacterial identification by MALDI-TOF MS in daily practice in a routine clinical microbiological laboratory. Firstly, we prospectively evaluated the performance and the cost-effective of bacterial identification by MALDI-TOF in comparison with conventional phenotypic identification methods. During a 16-week study, we compared the performance of MALDI-TOF with conventional techniques of identification including Gram staining, API ANA identification strip and automated identification using the Vitek 2. The unmatched identifications between MALDI-TOF and conventional methods were resolved by molecular identification. In this study, we showed that MALDI-TOF was an effective tool and less expensive for the rapid identification of bacterial species in clinical microbiology laboratory. MALDI-TOF can be used in first intention for identification before Gram staining or other phenotypic identification techniques based on physicochemical properties of bacteria. Secondly, we retrospectively evaluated the performance and the cost-effectiveness of the exclusive use of MALDI-TOF in bacteriological diagnosis in comparison with conventional phenotypic identification. 11-year retrospective analysis of data showed that MALDI-TOF was efficient and completely adapted for the routine identification of bacterial species. We also showed that MALDI-TOF had capacity to identify bacterial species that were rarely involved in human diseases. This technique could be an alternative to molecular methods in the clinical laboratory.

Em procariotos, RNAs antisense (asRNAs) constituem a classe de RNAs não codificantes (ncRNAs) mais numerosa detectada por métodos de avaliação de transcritoma em larga escala. Apesar da grande abundância, pouco se sabe sobre mecanismos regulatórios e aspectos da conservação evolutiva dessas moléculas, principalmente em arquéias, onde o mecanismo de degradação de RNAs dupla fita (dsRNAs) é um fenômeno pouco conhecido. No presente estudo, utilizando dados de dRNA-seq, identificamos 1626 inícios de transcrição primários antisense (aTSSs) no genoma de Halobacterium salinarum NRC-1, importante organismo modelo para estudos de regulação gênica no domínio Archaea. Integrando dados de expressão gênica obtidos a partir de 18 bibliotecas de RNA-seq paired-end, anotamos 846 asRNAs a partir dos aTSSs mapeados. Encontramos asRNAs em ~21% dos genes anotados, alguns desses relacionados a importantes características desse organismo como: codificadores de proteínas que constituem vesículas de gás e da proteína bacteriorodopsina, além de vários genes relacionados a maquinaria de tradução e transposases. Além desses, encontramos asRNAs em genes pertencentes a sistemas de toxinas-antitoxinas do tipo II e utilizando dados públicos de dRNA-seq, evidenciamos que esse é um fenômeno que ocorre em bactérias e arquéias. A interação de um ncRNA com seu RNA alvo pode ser dependente de proteínas, em arquéias, a proteína LSm é uma chaperona de RNA homóloga a Hfq de bactérias, implicada no controle pós-transcricional. Utilizamos dados de RIP-seq de RNAs imunoprecipitados com LSm e identificamos 91 asRNAs interagindo com essa proteína, para 81 desses, o mRNA do gene sense também foi encontrado interagindo. Buscando por aTSSs presentes nas mesmas regiões de genes ortólogos, identificamos 160 aTSSs que dão origem a asRNAs em H. salinarum possivelmente conservados em Haloferax volcanii. A expressão dos asRNAs anotados foi avaliada ao longo de uma curva de crescimento e em uma linhagem knockout de um gene que codifica uma RNase R, possível degradadora de dsRNAs em arquéias. Encontramos um total de 144 asRNAs diferencialmente expressos ao longo da curva de crescimento, para 56 desses o gene sense também está diferencialmente expresso, caracterizando possíveis mecanismos de regulação em cis por esses RNAs. Na linhagem knockout, encontramos cinco asRNAs diferencialmente expressos e apenas para um desses o gene sense também está diferencialmente expresso, resultado que não nos permitiu inferir um possível papel de degradação de dsRNAs da RNAse R em H. salinarum NRC-1. Nesse trabalho apresentamos um mapeamento completo do transcritoma antisense primário de H. salinarum NRC-1 com resultados que consistem em um importante passo na direção da compreensão do envolvimento da transcrição antisense na regulação gênica pós-transcricional desse organismo modelo do terceiro domínio da vida. / Antisense RNAs (asRNAs) constitute the most numerous class of non-coding RNAs (ncRNAs) detected by transcriptome highthroughput methods in prokaryotes. Despite this abundance, little is known about regulatory mechanisms and evolutionary aspects of these molecules, mainly in archaea, where the mechanism of double-strand RNA (dsRNA) degradation remains poorly understood. In this study, using dRNA-seq data, we identified 1626 antisense transcription start sites (aTSSs) in the genome of Halobacterium salinarum NRC-1, an important model organism for gene expression regulation studies in Archaea. By integrating gene expression data from 18 RNA-seq paired-end libraries, we were able to annotate 846 asRNAs from mapped aTSSs. We found asRNAs in ~21% of annotated genes including genes related to important characteristics of this organism, such as: gas vesicle proteins, bacteriorhodopsin, translation machinery and transposases. We also found asRNAs in type II toxin-antitoxin systems and using public dRNA-seq data, we show evidences that this phenomenon might be conserved in archaea and bacteria. The interaction of a ncRNA with its target may depend on intermediary proteins action. In archaea, the LSm protein is a RNA chaperone homologous to bacterial Hfq, involved in post-transcriptional regulation. We used RIP-seq data from RNAs immunoprecipitated with LSm and identified 91 asRNAs interacting with this protein, for 81 of these the mRNA of the sense gene is also interacting. We searched for aTSSs present in the same region of orthologous genes in the Haloferax volcanii. We found 160 aTSSs that originated asRNAs in H. salinarum NRC-1 that might be conserved in this two archaea. The expression of annotated asRNAs was analyzed over a growth curve and in a knockout strain for RNase R gene. We found 144 asRNA differentially expressed over the growth curve, for 56 of these the sense gene was also differentially expressed, characterizing possible cis regulators asRNAs. In the knockout strain we found five differentially expressed asRNAs and only one asRNA/gene pair, this result does not allow us to infer a dsRNA degradation in vivo activity for this RNase in H. salinarum NRC- 1. This work contributes to the discovery of the antisense transcriptome in H. salinarum NRC- 1 a relevant step to uncover the post-transcriptional gene regulatory network in this archaeon.

Em procariotos, RNAs antisense (asRNAs) constituem a classe de RNAs não codificantes (ncRNAs) mais numerosa detectada por métodos de avaliação de transcritoma em larga escala. Apesar da grande abundância, pouco se sabe sobre mecanismos regulatórios e aspectos da conservação evolutiva dessas moléculas, principalmente em arquéias, onde o mecanismo de degradação de RNAs dupla fita (dsRNAs) é um fenômeno pouco conhecido. No presente estudo, utilizando dados de dRNA-seq, identificamos 1626 inícios de transcrição primários antisense (aTSSs) no genoma de Halobacterium salinarum NRC-1, importante organismo modelo para estudos de regulação gênica no domínio Archaea. Integrando dados de expressão gênica obtidos a partir de 18 bibliotecas de RNA-seq paired-end, anotamos 846 asRNAs a partir dos aTSSs mapeados. Encontramos asRNAs em ~21% dos genes anotados, alguns desses relacionados a importantes características desse organismo como: codificadores de proteínas que constituem vesículas de gás e da proteína bacteriorodopsina, além de vários genes relacionados a maquinaria de tradução e transposases. Além desses, encontramos asRNAs em genes pertencentes a sistemas de toxinas-antitoxinas do tipo II e utilizando dados públicos de dRNA-seq, evidenciamos que esse é um fenômeno que ocorre em bactérias e arquéias. A interação de um ncRNA com seu RNA alvo pode ser dependente de proteínas, em arquéias, a proteína LSm é uma chaperona de RNA homóloga a Hfq de bactérias, implicada no controle pós-transcricional. Utilizamos dados de RIP-seq de RNAs imunoprecipitados com LSm e identificamos 91 asRNAs interagindo com essa proteína, para 81 desses, o mRNA do gene sense também foi encontrado interagindo. Buscando por aTSSs presentes nas mesmas regiões de genes ortólogos, identificamos 160 aTSSs que dão origem a asRNAs em H. salinarum possivelmente conservados em Haloferax volcanii. A expressão dos asRNAs anotados foi avaliada ao longo de uma curva de crescimento e em uma linhagem knockout de um gene que codifica uma RNase R, possível degradadora de dsRNAs em arquéias. Encontramos um total de 144 asRNAs diferencialmente expressos ao longo da curva de crescimento, para 56 desses o gene sense também está diferencialmente expresso, caracterizando possíveis mecanismos de regulação em cis por esses RNAs. Na linhagem knockout, encontramos cinco asRNAs diferencialmente expressos e apenas para um desses o gene sense também está diferencialmente expresso, resultado que não nos permitiu inferir um possível papel de degradação de dsRNAs da RNAse R em H. salinarum NRC-1. Nesse trabalho apresentamos um mapeamento completo do transcritoma antisense primário de H. salinarum NRC-1 com resultados que consistem em um importante passo na direção da compreensão do envolvimento da transcrição antisense na regulação gênica pós-transcricional desse organismo modelo do terceiro domínio da vida. / Antisense RNAs (asRNAs) constitute the most numerous class of non-coding RNAs (ncRNAs) detected by transcriptome highthroughput methods in prokaryotes. Despite this abundance, little is known about regulatory mechanisms and evolutionary aspects of these molecules, mainly in archaea, where the mechanism of double-strand RNA (dsRNA) degradation remains poorly understood. In this study, using dRNA-seq data, we identified 1626 antisense transcription start sites (aTSSs) in the genome of Halobacterium salinarum NRC-1, an important model organism for gene expression regulation studies in Archaea. By integrating gene expression data from 18 RNA-seq paired-end libraries, we were able to annotate 846 asRNAs from mapped aTSSs. We found asRNAs in ~21% of annotated genes including genes related to important characteristics of this organism, such as: gas vesicle proteins, bacteriorhodopsin, translation machinery and transposases. We also found asRNAs in type II toxin-antitoxin systems and using public dRNA-seq data, we show evidences that this phenomenon might be conserved in archaea and bacteria. The interaction of a ncRNA with its target may depend on intermediary proteins action. In archaea, the LSm protein is a RNA chaperone homologous to bacterial Hfq, involved in post-transcriptional regulation. We used RIP-seq data from RNAs immunoprecipitated with LSm and identified 91 asRNAs interacting with this protein, for 81 of these the mRNA of the sense gene is also interacting. We searched for aTSSs present in the same region of orthologous genes in the Haloferax volcanii. We found 160 aTSSs that originated asRNAs in H. salinarum NRC-1 that might be conserved in this two archaea. The expression of annotated asRNAs was analyzed over a growth curve and in a knockout strain for RNase R gene. We found 144 asRNA differentially expressed over the growth curve, for 56 of these the sense gene was also differentially expressed, characterizing possible cis regulators asRNAs. In the knockout strain we found five differentially expressed asRNAs and only one asRNA/gene pair, this result does not allow us to infer a dsRNA degradation in vivo activity for this RNase in H. salinarum NRC- 1. This work contributes to the discovery of the antisense transcriptome in H. salinarum NRC- 1 a relevant step to uncover the post-transcriptional gene regulatory network in this archaeon.

No description available.

Deux réacteurs, R1 et R2, ont été alimentés quotidiennement avec les effluents à traiter à des TRH de 13 jours et de 20 jours, respectivement. Les résultats obtenus ont montré un taux d'abattement de la dégradation de la matière organique de 53% pour R2, contre 35% pour R1. Afin de mieux comprendre le fonctionnement biologique de ces réacteurs, nous avons exploré les communautés microbiennes d'importance écologique impliquées dans la dégradation de la matière organique contenue dans ces effluents. Cela a été réalisé dans un premier temps par des approches moléculaires en utilisant la technique de DGGE et le pyroséquençage 454. Nous avons alors montré que les représentants du domaine des Bacteria étaient les plus représentés dans les deux réacteurs par rapport aux Archaea avec une plus grande diversité au niveau du réacteur R2. Les séquences de Bacteria obtenues sont affiliées principalement aux phylums des Firmicutes, des Bacteroïdetes, et des Synergistetes, impliquées dans l'hydrolyse et la fermentation de la matière organique des effluents. Une mention particulière est à accorder aux membres du phylum des Synergistetes qui ont été également détectés par pyroséquençage 454. Dans les deux réacteurs, ce phylum majoritaire était représenté par deux familles, celle des "Dethiosulfovibrionaceae" et celle des "Aminiphilaceae" dont on sait qu'elles interviennant dans la dégradation des acides aminés. Enfin, l'approche culturale nous a permis d'isoler dans nos réacteurs plusieurs souches bactériennes anaérobies mésophiles hétérotrophes. Parmi celles-ci, nous avons pu décrire deux nouvelles espèces Desulfocurvus thunnarius et A thunnarium. / For this purpose, two ASBR reactors R1 and R2 were tested. They were fed daily with the industrial effluents at HRT of 13 days and 20 days, respectively. The results obtained during the anaerobic treatment showed a degradation rate of the organic matter of 53% for R2 against 35% for R1. In order to better understand this process, we explored the microbial communities of ecological importance involved in the degradation of organic matter in the effluent to be treated. This was accomplished by initiating molecular approaches. Using the DGGE technique and 454 pyrosequencing, we showed that representatives of the domain Bacteria were the most dominant in both reactors as compared to Archaea with a greater diversity observed in R2 reactor. Bacteria sequences were affiliated to the phyla Firmicutes, Bacteroidetes and Synergistetes, known to be involved in the hydrolysis and fermentation of organic matter. A particular mention is given to members of the phylum Synergistetes which were also detected by pyrosequencing 454. In both reactors, this phylum was represented by two families, the "Dethiosulfovibrionaceae" and that of "Aminiphilaceae" which are recognized as significant amino acids degraders. Finally, the cultivation approach allowed us to isolate several mesophilic heterotrophic anaerobic bacteria. Among them, a new sulfate-reducing species belonging to the family Desulfovibrionaceae, Desulfocurvus thunnarius, and A thunnarium.

Les transferts horizontaux de gènes (THG) ont été démontrés pour jouer un rôle important dans l'évolution des procaryotes. Leur impact a été le sujet de débats intenses, ceux-ci allant même jusqu'à l'abandon de l'arbre des espèces. Selon certaines études, un signal historique dominant est présent chez les procaryotes, puisque les transmissions horizontales stables et fonctionnelles semblent beaucoup plus rares que les transmissions verticales (des dizaines contre des milliards). Cependant, l'effet cumulatif des THG est non-négligeable et peut potentiellement affecter l'inférence phylogénétique. Conséquemment, la plupart des chercheurs basent leurs inférences phylogénétiques sur un faible nombre de gènes rarement transférés, comme les protéines ribosomales. Ceux-ci n'accordent cependant pas autant d'importance au modèle d'évolution utilisé, même s'il a été démontré que celui-ci est important lorsqu'il est question de résoudre certaines divergences entre ancêtres d'espèces, comme pour les animaux par exemple. Dans ce mémoire, nous avons utilisé des simulations et analyser des jeux de données d'Archées afin d'étudier l'impact relatif des THG ainsi que l'impact des modèles d'évolution sur la précision phylogénétique. Nos simulations prouvent que (1) les THG ont un impact limité sur les phylogénies, considérant un taux de transferts réaliste et que (2) l'approche super-matrice est plus précise que l'approche super-arbre. Nous avons également observé que les modèles complexes expliquent non seulement mieux les données que les modèles standards, mais peuvent avoir un impact direct sur différents groupes phylogénétiques et sur la robustesse de l'arbre obtenu. Nos résultats contredisent une publication récente proposant que les Thaumarchaeota apparaissent à la base de l'arbre des Archées. / Horizontal gene transfer (HGT) had been demonstrated to play an important role in the evolution of prokaryotes. Their impact on phylogeny was the subject of a heated debate, with some proposing that the concept of a species tree should be abandoned. The phylogeny of prokaryotes does contain a major part of the historical signal, because stable and functional horizontal transmissions appear to be by far rarer than vertical transmissions (tens versus billions). However, the cumulative effect of HGT is non-negligible and can potentially affect phylogenetic inference. Therefore, most researchers base their phylogenetic inference on a low number of rarely transferred genes such as ribosomal proteins, but they assume the selection of the model of evolution as less important, this despite the fact that it has been shown of prime importance for much less deep divergences, e.g. like animals. Here, we used a combination of simulations and of real data from Archaea to study the relative impact of HGT and of the inference methods on the phylogenetic accuracy. Our simulations prove that (1) HGTs have a limited impact on phylogeny, assuming a realistic rate and (2) the supermatrix is much more accurate than the supertree approach. We also observed that more complex models of evolution not only have a better fit to the data, but can also have a direct impact on different phylogenetic groups and on the robustness of the tree. Our results are in contradiction to a recent publication proposing that the Thaumarchaeota are at the base of the Archaeal tree.

Depuis la découverte d’archées capables d’oxyder l’ammoniac en milieu aérobie, de nombreuses études ont mesuré en simultané les taux de nitrification et la diversité des organismes oxydant l’ammoniac dans la colonne d’eau des milieux marins. Malgré l’importance globale des lacs d’eau douce, beaucoup moins d’études ont fait la même chose dans ces milieux. Dans cette étude, nous avons évalué l’importance de la nitrification et caractérisé la communauté microbienne responsable de la première étape limitante de la nitrification dans un lac tempéré durant une année entière. L’utilisation de traceur isotopique 15NH4 nous a permis de mesurer des taux d’oxydation d’ammoniac à deux profondeurs dans la zone photique tout au long de l’année. Les taux d’oxydation d’ammoniac varient de non détectable à 333 nmol L-1 j-1 avec un pic d’activité sous la glace. De toutes les variables environnementales mesurées, la concentration d’ammonium dans la colonne d’eau semble avoir le plus grand contrôle sur les taux d’oxydation d’ammoniac. Nous avons détecté la présence d’archées (AOA) et de bactéries oxydante d’ammoniac (BOA) à l’aide de tests par réaction en chaîne de la polymérase (PCR) ciblant une partie du gène ammoniac monoxygénase (amoA). Les AOA et les BOA ont été détectées dans la zone photique du lac, cependant seules les AOA étaient omniprésentes durant l’année. Le séquençage du gène amoA des archées révèle que la majorité des AOA dans le lac sont membres du groupe phylogénétique Nitrosotalea (également appelé SAGMGC-1 ou groupe I.1a associé), ce qui confirme la pertinence écologique de ce groupe dans les eaux douces oligotrophes. Globalement, nos résultats indiquent l’hiver comme étant un moment propice pour l’oxydation de l’ammoniac dans les lacs tempérés. Cette étude fournit un point de référence pour la compréhension du processus d’oxydation de l’ammoniac dans les petits lacs oligotrophes. / Since the discovery that some archaea are able to oxidize ammonia aerobically, several studies have focused on measuring nitrification rates and identifying the diversity of planktonic ammonia oxidizers in marine systems. Despite the global importance of freshwater lakes, far fewer studies have done the same in these ecosystems. Here we investigated the importance of nitrification and characterize the microbial community catalyzing the first rate-limiting step of nitrification over an annual cycle in a temperate lake. The measurements of ammonia oxidation rates, using the 15NH4+ isotope tracer method, at two depths in the photic zone show that this process occurred throughout the entire year in the lake. Rates of ammonia oxidation ranged from undetectable to 333 nmol L-1 d-1 with a peak of activity during winter. Off all environmental variables measured, ammonium concentrations in the water-column seem to have the strongest effect on the magnitude of ammonia oxidation rates. We detected the presence of ammonia-oxidizing archaea (AOA) and bacteria (AOB) using polymerase chain reaction (PCR) assays targeting part of the ammonia monooxygenase (amoA) gene. Both AOA and AOB were detected in the photic zone of the lake, although only AOA were omnipresent over the year. The sequencing of archaeal amoA genes reveals that most of the AOA in the lake are members of the Nitrosotalea cluster (also referred as SAGMGC-1 or group I.1a associated), which confirms the ecological relevance of this cluster in oligotrophic freshwaters. Altogether, our results indicate that winter may be a critical time for ammonia oxidation in temperate lakes and provide a baseline for the understanding of ammonia oxidation in small oligotrophic lakes.