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GcvB est un ARN bactérien conservé de 200 nucléotides, qui régule négativement l’expression de plusieurs gènes impliqués dans l’import et la biosynthèse des acides aminés. Bien que le rôle physiologique de GcvB ne soit pas complètement élucidé, il contribuerait vraisemblablement à équilibrer les ressources nutritionnelles en conditions de croissance rapide. GcvB inhibe la traduction des ARNm cibles en s’appariant avec des séquences à l’intérieur ou en amont du site de liaison du ribosome. Dans cette étude, la caractérisation d’un nouveau locus régulé par GcvB a permis de dévoiler des aspects singuliers du mode de fonctionnement de cet ARN régulateur. Nous avons découvert que GcvB réprime yifK - un gène très conservé, codant pour un transporteur d’acides aminés putatif - en ciblant un élément activateur de la traduction sur l’ARNm. Deux motifs ACA dans la séquence cible sont les déterminants principaux de la fonction activatrice. Le remplacement de l’un ou l’autre avec des triplets aléatoires, provoque une diminution de 10 fois du niveau d’expression de yifK, quelque soit l’allèle de GcvB (délétion ou changement de séquence permettant la reconnaissance de la cible mutante). Il apparait ainsi que l’efficacité de GcvB à réguler négativement sa cible serait liée a sa capacité d’antagoniser l’élément activateur. Lorsque l’activateur est éliminé, l’action de GcvB n’est plus un facteur limitant pour l’expression de yifK. Dans son ensemble, cette étude apporte une meilleure compréhension de la fonction de GcvB et révèle un nouvel aspect du processus d’initiation de la traduction. En plus du contrôle par GcvB, le locus yifK est régulé au niveau transcriptionnel par Lrp (leucine-responsive regulatory protein) et par HdfR (YifA) un régulateur transcriptionnel peu connu qui requerrait le produit du gène adjacent orienté de façon divergente, yifE, pour son expression ou activité. Enfin, la transcription initiée au niveau du promoteur yifK s’étend dans l’opéron d’ARNt argX-hisR-leuT-proM adjacent, donnant lieu à un transcrit primaire qui est à la fois un lARNm et un précurseur des ARNt. Cet ARN chimère est rapidement maturé par l’ARNase E. / GcvB is a conserved 200 nucleotide RNA that downregulates several genes involved in amino acid uptake or biosynthesis in bacteria. The physiological role of GcvB action is not entirely clear, but it is likely aimed at balancing of nutritional resources under fast growth conditions. GcvB inhibits translation of target messenger RNAs by pairing with sequences inside or upstream of ribosome binding sites. In the present study, characterization of a novel GcvB-regulated locus revealed some unique features in the mode of functioning of this regulatory RNA. We found that GcvB represses yifK - a highly conserved locus encoding a putative amino acid transporter - by targeting a translational enhancer element. Two ACA motifs within the target sequence are the main determinants of the enhancer activity. Replacing either of these motifs with random triplets caused up to a 10-fold decrease in yifK expression regardless of the GcvB allele (deleted or suitably modified to recognize the mutated target). It thus appears that GcvB effectiveness as a regulator results from countering the enhancer activity. When the enhancer is removed, GcvB action no longer constitutes a rate-limiting factor for yifK expression. Overall, this study is relevant not only to a better understanding of GcvB function but it also provides insight into an elusive aspect of the translation initiation process. Besides the GcvB control, the yifK locus is regulated at the transcriptional level by the leucine responsive regulator Lrp, and by HdfR (YifA) a poorly known transcriptional regulator, that appears to require the product of the adjacent, divergently oriented gene, yifE, for expression or activity. Transcription initiating at the yifK promoter extends into the adjacent argX-hisR-leuT-proM tRNA operon yielding an unusual primary transcript which both a messenger RNA and a tRNA precursor. This chimeric RNA si rapidly processed by RNAse E.

Surprisingly little is known about the organization and distribution of tRNAs and tRNA-related sequences on a genome-wide scale. While tRNA complements are usually reported in passing as part of genome annotation efforts, and peculiar features such as the tandem arrangements of tRNAs in Entamoeba histolytica have been described in some detail, comparative studies are rare. We therefore set out to systematically survey the genomic arrangement of tRNAs in a wide range of eukaryotes to identify common patterns and taxon-specific peculiarities. We found that tRNA complements evolve rapidly and that tRNA locations are subject to rapid turnover. At the phylum level, distributions of tRNA numbers are very broad, with standard deviations on the order of the mean. Even within fairly closely related species, we observe dramatic changes in local organization. Consistent with this variability, syntenic conservation of tRNAs is also poor in general, with turn-over rates comparable to those of unconstrained sequence elements. We conclude that the genomic organization of tRNAs shows complex, lineage-specific patterns characterized by extensive variability, and that this variability is in striking contrast to the extreme levels of sequence-conservation of the tRNA genes themselves. Our comprehensive analysis of eukaroyotic tRNA distributions provides a basis for further studies into the interplay between tRNA gene arrangements and genome organization in general. Secondly, we focused on the investigation of small non-coding RNAs (ncRNAs) from whole transcriptome data. Since ncRNAs constitute a significant part of the transcriptome, we explore this data to detect and classify patterns derived from transcriptome-associated loci. We selected three distinct ncRNA classes: microRNAs, snoRNAs and tRNAs, all of which undergo maturation processes that lead to the production of shorter RNAs. After mapping the sequences to the reference genome, specific patterns of short reads were observed. These read patterns appeared to reflect RNA processing and, if so, should specify the RNA transcripts from which they are derived. In order to investigate whether the short read patterns carry information on the particular ncRNA class from which they orginate, we performed a random forest classification on the three distinct ncRNA classes listed above. Then, after exploring the potential classification of general groups of ncRNAs, we focused on the identification of small RNA fragments derived from tRNAs. After mapping transcriptome sequence data to reference genomes, we searched for specific short read patterns reflecting tRNA processing. In this context, we devised a common tRNA coordinate system based on conservation and secondary structure information that allows vector representation of processing products and thus comparison of different tRNAs by anticodon and amino acid. We report patterns of tRNA processing that seem to be conserved across species. Though the mechanisms and functional implications underlying these patterns remain to be clarified, our analysis suggests that each type of tRNA exhibits a specific pattern and thus appears to undergo a characteristic maturation process.

GcvB is a conserved 200 nucleotide RNA that downregulates several genes involved in amino acid uptake or biosynthesis in bacteria. The physiological role of GcvB action is not entirely clear, but it is likely aimed at balancing of nutritional resources under fast growth conditions. GcvB inhibits translation of target messenger RNAs by pairing with sequences inside or upstream of ribosome binding sites. In the present study, characterization of a novel GcvB-regulated locus revealed some unique features in the mode of functioning of this regulatory RNA. We found that GcvB represses yifK - a highly conserved locus encoding a putative amino acid transporter - by targeting a translational enhancer element. Two ACA motifs within the target sequence are the main determinants of the enhancer activity. Replacing either of these motifs with random triplets caused up to a 10-fold decrease in yifK expression regardless of the GcvB allele (deleted or suitably modified to recognize the mutated target). It thus appears that GcvB effectiveness as a regulator results from countering the enhancer activity. When the enhancer is removed, GcvB action no longer constitutes a rate-limiting factor for yifK expression. Overall, this study is relevant not only to a better understanding of GcvB function but it also provides insight into an elusive aspect of the translation initiation process. Besides the GcvB control, the yifK locus is regulated at the transcriptional level by the leucine responsive regulator Lrp, and by HdfR (YifA) a poorly known transcriptional regulator, that appears to require the product of the adjacent, divergently oriented gene, yifE, for expression or activity. Transcription initiating at the yifK promoter extends into the adjacent argX-hisR-leuT-proM tRNA operon yielding an unusual primary transcript which both a messenger RNA and a tRNA precursor. This chimeric RNA si rapidly processed by RNAse E.

Bordetella pertussis, l’agent responsable de la coqueluche, provoque près de 200000 morts par an dans le monde. Malgré une forte couverture vaccinale, une réémergence de la maladie a été observée dans les pays développés, liée en partie à une adaptation à la pression vaccinale. Les souches capables d’échapper à la réponse immunitaire montrent des réarrangements génomiques importants, provoqués par des éléments génétiques mobiles (IS) présents en plus de 230 copies, qui pourraient impacter sur la transcription des gènes et ARN régulateurs du pathogène.Pour élucider l’impact des IS sur le transcriptome global de Bordetella pertussis, nous avons d’abord déterminé le transcriptome codant et non-codant du pathogène par des approches de séquençage d’ARN couplées à des prédictions bioinformatiques. Cette étude a permis d’identifier les structures codantes mono- et polycistroniques, incluant des structures régulatrices telles que des riboswitches, un excludon et de longs 5’ et 3’UTR chevauchants. Une cartographie de candidats ARN régulateurs non-codant a été édifiée à partir de nouveaux transcrits localisés en régions intergéniques (IGR) et de transcrits orientés en antisens de séquences codantes. Des prolongements de transcriptions des IS ont été observés, prenant leur origine de promoteurs internes à l’IS ou formés par insertion de celles-ci. Ces transcrits sont spécifiques d’une souche à l’autre du pathogène, et s’orientent en sens ou en antisens des gènes environnant, ou dans des IGR. Le potentiel caractère régulateur de ces transcrits a été étudié par la caractérisation et l’étude du mode d’action d’un ARN régulateur, BPnc264, orienté en antisens du gène de virulence fim2. / Bordetella pertussis, the causative agent of whooping cough, is responsible of more than 200000 deaths worldwide. Despite a high vaccine coverage in developed countries, a reemergence of the disease has been observed, which is in part linked to vaccine-pressure. Strains able to evade vaccine-induced immunity show high genome organization rearrangements, essentially due to mobile genetic elements (IS) present in more than 230 copies, which could impact on messenger and regulatory transcription of the pathogene.To assess the impact of IS on the global transcriptome of Bordetella pertussis, we first determined the coding and non-coding primary transcriptome by a combination of differents RNA-sequencing approaches and predictive bioinformatics analysis software packages. We identify mono- and polycistronic coding structures, including regulatories structures like riboswitches, excludon, and long overlapping 5’ and 3’UTR. A list of candidates regulating transcripts (small RNA) has been mapped from new transcripts located in intergenic regions (IGR) and transcripts oriented in antisense of annotated coding sequences. Extended transcriptions emerging from IS elements have been observed, originating from internal promoters or newly formed promoters by insertion in a specific genomic region. Those transcripts can extend in sense or in antisense of the flanking gene, or in IGR. The regulatory function of those transcripts has been studied from the characterization and the mode of action of an extended regulatory RNA, BPnc264, oriented in antisense of the virulence gene fim2.

Parmi les régulateurs nucléiques, les petits ARN régulateurs sont un moyen rapide d’adaptation. On les retrouve dans tous les domaines du vivant. Chez les bactéries, l’action d’un grand nombre d’entre eux dépend de la protéine chaperonne d’ARN Hfq. Leur mode d’action consiste à d’apparier directement à l’ARNm cible par complémentarité imparfaite de séquence. Il en résulte une régulation positive ou négative, de la traduction et/ou de la stabilité de l’ARNm cible.Au cours de la première partie cette thèse, nous avons essayé de caractériser la régulation des ARNm par les petits ARN régulateurs. Pour ce faire, nous avons étudiés les différents composants de cette régulation et nous avons pu montrer que les sites de fixation à la protéine Hfq sur les ARN devaient être compatibles pour obtenir une régulation optimale des ARNm par les petits ARN régulateurs.Lors de la seconde partie de la thèse, nous avons pu identifier un nouveau type de régulation des ARNm par les petits ARN régulateurs : la polarité transcriptionnelle. Nous avons pu montrer que la fixation du petit ARN ChiX sur la région 5’UTR de l’ARNm chiPQ entrainer l’inhibition de la traduction de chiP mais également une terminaison prématurée rho-dépendante de la transcription de l’ARNm.Nous avons par la suite cherché à savoir si ce type de régulation pouvait se retrouver dans la régulation d’autre ARNm comme l’opéron dppABCDF et l’opéron pgaABCD. En parallèle de ces études, nous avons également essayé de caractérisé la terminaison Rho-dépendante entre S. Typhimurium et E.coli au sein de l’ARNm chiPQ. / Among the nucleic regulators, small regulatory RNAs are a quick way to adapt. They are found in all areas of life. In bacteria, the action of a large number of them depends on the chaperone protein of Hfq RNA. Their mode of action consists of matching directly to the target mRNA by imperfect complementary sequence. This results in a positive or negative control, translation and/or stability of the target mRNA.During the first part of this thesis, we have tried to characterize the regulation of mRNA by small regulatory RNAs. To do this, we studied the different components of this regulation and we have shown that the binding sites on protein Hfq on RNA should be consistent for optimal regulation of mRNA by small regulatory RNAs.In the second part of the thesis, we identified a new type of mRNA regulation by small RNA regulators: transcriptional polarity. We could show that the fixing of small RNA ChiX on the 5 'UTR region of the mRNA chiPQ cause inhibition of translation of chiP but also a Rho-dependent premature termination of mRNA transcription.We subsequently investigated whether this type of regulation could be in the control of other mRNAs as dppABCDF’s operon and pgaABCD’s operon. In parallel with these studies, we have also tried characterized Rho-dependent termination between S. Typhimurium and E. coli in mRNA chiPQ.

京都大学 / 新制・課程博士 / 博士(生命科学) / 甲第23330号 / 生博第448号 / 新制||生||60(附属図書館) / 京都大学大学院生命科学研究科統合生命科学専攻 / (主査)教授 垣塚 彰, 教授 上村 匡, 教授 豊島 文子 / 学位規則第4条第1項該当 / Doctor of Philosophy in Life Sciences / Kyoto University / DFAM

<p>The relatively recent discoveries of bacterial small RNAs (sRNAs) and their important regulatory functions prompted us to conduct a genome wide survey for sRNAs in <em>Streptomyces coelicolor</em>. We used a combined bioinformatics and experimental approach to identify and characterize six sRNAs. sRNA expression profiles were determined throughout <em>S. coelicolor</em> development, including vegetative and reproductive growth, during growth on minimal and rich media. Additionally, we also tested sRNA expression in various <em>S. coelicolor</em> developmental mutants. Two sRNAs were expressed exclusively during growth on one medium type and all but one were expressed constitutively throughout growth apart from the late sporulation timepoint. One of the identified sRNAs, scr1906, appeared to be closely associated with development. scr1906 was only expressed in nutrient limiting conditions just prior to aerial development and sporulation. Expression of scr1906 was abolished in a mutant that was defective in sporulation (due to a mutation in the sporulation sigma factor gene, <em>whiG</em>); however, expression was detected in mutants of both known σ^WhiG target genes, <em>whiH</em> and <em>whiI</em>, which encode sporulation transcription factors. Intriguingly, <em>in silico</em> analysis predicted <em>whiH</em> to be a direct target for scr1906-mediated regulation based on potential nucleotide binding sites. The effects of deletion and overexpression of <em>scr1906</em> on WhiH levels were tested, but require further experimentation.</p> <p>In a separate line of investigation, we sought to characterize a novel actinobacterial-specific protein named sIHF. The <em>sIHF</em> mutant strain revealed that sIHF influenced DNA compaction and segregation during <em>S. coelicolor</em> sporulation and also affected antibiotic production. sIHF associated with the nucleoid, and <em>in vitro</em>, it bound to DNA non-specifically in a length dependent manner, although it was determined to have a preference for three distinct DNA motifs. Like most nucleoid-associated proteins, sIHF affected gene expression indicating the potential for an additional role as a transcription factor. Interestingly, sIHF impacted the activity of topoisomerase. Leveraging information that we have gained from the sIHF-DNA co-crystal complex, studies aimed at characterizing the sIHF regions that are important for DNA interaction and topoisomerase modulation are currently underway.</p> / Doctor of Philosophy (PhD)