Os microrganismos atraem considerável atenção por serem uma fonte de compostos biotecnológicos e farmacêuticos. Diversos produtos naturais peptídicos produzidos por fungos e bactérias são sintetizados por grandes enzimas, conhecidas como peptídeo sintetase não ribossômica (NRPS) e policetídeo sintase (PKS). A bioprospecção dos microrganismos isolados do solo de Terra Preta Antropogênica (TPA) da Amazônia Ocidental é de grande importância para o conhecimento deste bioma tropical. Este estudo correlacionou a presença de sideróforos e de compostos antimicrobianos produzidos pelos microrganismos isolados de TPA e dos solos adjacentes com a presença dos genes que codificam para NRPS e PKS. Linhagens bacterianas foram isoladas das amostras do solo coletadas de 10, 20 e 40 cm de profundidade. Os isolados foram cultivados em meio líquido específico por 2 dias a 28oC. Um total de 143 isolados foi testado para a atividade de sideróforo e para isso, as linhagens foram inoculadas em um meio com baixa concentração de ferro (MM9) contendo o complexo cromoazurol S-Fe3. Do total, 72 isolados apresentaram reação positiva para a produção de sideróforo. O DNA genômico dos isolados foi extraído e a amplificação por PCR foi realizada usando iniciadores específicos para NRPS e PKS. Os resultados mostraram que quinze isolados apresentaram o gene que codifica para NRPS, vinte isolados para PKS e somente dez isolados apresentaram ambos os genes. A presença de genes de NRPS e PKS em 31% dos isolados testados sugere que a produção dos sideróforos possa ocorrer pela via não ribossomal. Dois isolados foram selecionados para estudos de identificação e caracterização dos compostos. O isolado TP11 foi identificado como Pseudomonas putida através de seqüenciamento do 16S rRNA e apresentou resultado negativo para hidroxamato e catecol, sugerindo que o tipo de sideróforo não possui nenhum destes grupos funcionais. O isolado TP16 foi identificado como Pseudomonas putida e apresentou produção de sideróforo do tipo catecol e hidroxamato, sugerindo a produção de mais de um sideróforo. Além disso, esta linhagem produziu um composto antimicrobiano, com atividade de sideróforo identificado por espectrometria de massas como pseudomonina com massa molar de 330 Da. / Microorganisms have attracted considerable attention as a source for biotechnological and pharmaceutical agents. Several peptidic natural products synthesized by fungi and bacteria are assembled by large enzymes, referred as nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS). Bioprospection of microorganisms isolated from Anthropological Dark Earth soil of Brazilian Occidental Amazon is of great importance to the knowledge of this tropical biome. This study aimed to correlate the presence of siderophores and antimicrobial compounds produced by microorganisms isolated from Dark Earth and adjacent soils of Brazilian Amazon with the presence of genes encoding NRPS and PKS. Bacterial strains were isolated from soil samples collected at 10, 20 and 40 cm depth. The isolates were grown in specific liquid medium for 2 d at 28oC. A total of 143 isolates were screened for siderophore activity and for this, bacterial strains were inoculated on plates containing an iron-limited medium (MM9) amended with a chromeazurol S-Fe3 complex. From the total, seventy-two isolates showed positive reaction for siderophore production. Genomic DNA of the isolates was extracted and PCR amplification was carried out using specific primers for NRPS and PKS. The results showed that fifteen isolates presented NRPS, twenty isolates presented PKS and only ten isolates showed both genes. The presence of NRPS and PKS genes in 31% of the isolates tested suggests that production of siderophores may occur by a nonribosomal pathway. Two isolates were selected for further studies. Isolate TP11 was identified as Pseudomonas putida by 16S rDNA sequencing analysis and was negative for hydroxamate and catechol, suggesting that the siderophore type has no hydroxamate- or catechol-type functional groups. The isolate TP16 was identified as Pseudomonas putida and showed the production of catechol and hydroxamate siderophore-type, suggesting the production of more than one siderophore. In addition, this strain produced an antimicrobial compound, with siderophore activity identified through mass spectrometry as pseudomonine with a molar mass of 330 Da.

A importância da praga Spodoptera frugiperda (Lepidoptera: Noctuidae) deve-se não somente aos danos provocados às lavouras de milho, mas a capacidade de se alimentar de uma ampla variedade de famílias de plantas. Lagartas desta espécie são capazes de se adaptar a dietas contendo inibidores de peptidase de soja (IPS). Há uma hipótese de que a microbiota intestinal neste inseto poderia estar envolvida com estes mecanismos de adaptação. Neste contexto, um dos objetivos do trabalho foi verificar se estas bactérias poderiam alterar a expressão gênica de serino peptidases e atividade enzimática nestes lepidópteros em ensaios in vitro. Observouse que no tratamento com tetraciclina, não houve influência na alteração da expressão gênica e da atividade quantitativa das respectivas serino peptidases nas lagartas provenientes dos ambientes diferentes. Ao mesmo tempo, objetivou-se estudar se haveria uma contribuição das bactérias na atividade proteolítica intestinal de S. frugiperda ao longo do processo digestivo de insetos, analisando se influenciam no perfil qualitativo das serino peptidases intestinais destas lagartas em zimograma. As lagartas de campo que sofreram a primeira exposição à uma dieta com antibiótico aumentaram a atividade de duas peptidases provavelmente trípticas, também sintetizadas nos tratamentos com IPS e IPS com antibiótico provavelmente como provável resposta adaptativa. Para analisar o efeito do IPS e da tetraciclina em folhas ingeridas por lagartas criadas em laboratório e coletadas em campo, além da influência da dieta natural (cartucho de milho) e da dieta artificial sobre a composição e diversidade da microbiota fecal de S. frugiperda, foi feito o sequenciamento das regiões V3-V4 do gene 16S rRNA de procariotos utilizando a plataforma de alto desempenho Illumina Miseq. Os valores médios de diversidade de UTOs do índice Shannon detectados nas fezes de S. frugiperda foram mais baixos nas amostras de dieta artificial e o segundo índice médio mais baixo foi calculado naquelas provenientes de cartucho de milho no campo, revelando que ambas as amostras apresentaram menor diversidade de espécies na composição da comunidade bacteriana. A abundância relativa em nível de filo bacteriano gerada para todos os conjuntos de amostras fecais demonstrou que os filos mais predominantes foram Proteobacteria (73,3%) e Firmicutes (24,2%), sendo ambos os filotipos mais abundantes nos grupos de insetos. Os quatro filotipos mais abundantes em nível de gênero corresponderam a Enterococcus (23,5%), Acinetobacter (20,5%), Stenotrophomonas (11,4%) e Klebsiella (10,4%). Verificamos que a dieta foi a principal variável que modulou a estrutura das comunidades bacterianas das fezes de S. frugiperda. Entretanto, não é possível afirmar se haveria uma contribuição das peptidases das bactérias simbiontes ao processo digestivo de insetos. Com estes novos dados taxonômicos, poderemos isolar as bactérias a partir das fezes destas lagartas e estudar a significância funcional destes simbiontes tais como, detoxificação de compostos tóxicos como inibidores de peptidases de plantas, papel digestivo e nutricional destas bactérias para as lagartas desta espécie. / The importance of the pest Spodoptera frugiperda (Lepidoptera: Noctuidae) is due not only to corn crops damage, but the ability to attack a wide variety of plant families. Caterpillars of this species are able to circumvent diets containing soybean peptidase inhibitors (SPI). There is a hypothesis that this insect gut microbiota might be involved in these adaptation mechanisms. One of the goals of this study was to determine whether these bacteria could alter the serine peptidase gene expression or enzymatic activity in vitro assays in these Lepidoptera. It was observed that there was no alteration of the gene expression and the quantitative activity of serine peptidases in the caterpillars collected from both different environments fed with tetracycline leaves. At the same time, other objective was to study if there was a contribution from bacteria in the gut proteolytic activity of S. frugiperda in the digestive process of insects, analyzing its influence in the qualitative profile of serine peptidase gut worms in zymogram. The field caterpillars that suffered the first exposure to a diet with antibiotic increased the activity of two probably tryptic type peptidases which were also synthesized in IPS and IPS plus antibiotic treatments, probably as likely adaptive response. In order to analyze the effect of IPS and tetracycline in leaves eaten by caterpillars reared in the laboratory and collected in the field, beyond the influence of the natural diet (maize cartridge) and artificial diet on the composition and diversity of fecal microbiota of S. frugiperda, the sequencing using high performance Miseq Illumina platform was done in V3-V4 regions of 16S rRNA gene typical of prokaryotes. The average values of Shannon index related to OTUs diversity detected in the feces of S. frugiperda were lower in artificial diet samples and second lower mean index was calculated from those collected in the field, showing that both samples showed lower species diversity in the composition of bacterial communities. The relative abundance of bacterial phylum level generated for all fecal samples showed that the most prevalent phyla were Proteobacteria (73.3%) and Firmicutes (24.2%). Both phylotypes are predominant in insect groups. The four most abundant phylotypes at genus level accounted for Enterococcus (23.5%), Acinetobacter (20.5%), Stenotrophomonas (11.4%) and Klebsiella (10.4%). We found that the diet was the main variable that modulated the bacterial communities structure in the feces of S. frugiperda. However, it is not possible to state that there would be a contribution of peptidase bacterial symbionts to the digestive process of insects. With these new taxonomic data, we may isolate bacteria from S. frugiperda feces and study the functional significance of these symbionts such as detoxification of toxic plant compounds as inhibitors of peptidases, the digestive and nutrition role of these bacteria for the caterpillars species.

O presente estudo teve como objetivo avaliar a comunidade envolvida na desnitrificação autotrófica pela oxidação de sulfetos, aplicada ao pós-tratamento de efluentes anaeróbios. O enriquecimento da comunidade bacteriana e da comunidade desnitrificante autotrófica foi realizado a partir de amostras da biomassa coletadas de três reatores verticais de leito fixo operados em condições distintas, sendo, redução autotrófica de nitrato, redução autotrófica de nitrito e redução autotrófica de nitrato com excesso de sulfeto. Após a determinação da melhor condição de enriquecimento, a cultura foi purificada, identificada por meio de ferramentas da biologia molecular e caracterizada quanto às melhores condições de crescimento. O enriquecimento foi bem sucedido com a biomassa dos três reatores. No entanto, a condição de redução de nitrato com relação \'N\'/\'S\' igual a 0,8 foi a que apresentou maior concentração de microrganismos desnitrificantes autotróficos. A bactéria isolada foi identificada como Pseudomonas stutzeri. A velocidade específica máxima de crescimento da cultura (\'mü\'máx) foi de 0,037/h, com tempo de duplicação de 18,7 horas. O rendimento celular (Y) do composto nitrogenado foi de 0,15 gSSV.g/\'N\' e a velocidade de desnitrificação foi de aproximadamente 0,24 g\'N\'/gSSV.h. Os dados obtidos indicaram a viabilidade da aplicação da espécie isolada no processo de desnitrificação autotrófica utilizando sulfeto como doador de elétrons. / The aim of this study was to evaluate the community involved on autotrophic denitrification by sulfide oxidation applied to the post-treatment of anaerobic effluents. The enrichment of the bacterial community and autotrophic denitrifier community was accessed in three immobilized bed reactors operated at the conditions of autotrophic reduction of nitrate, autotrophic reduction of nitrite and autotrophic reduction of nitrate under excess of sulfide. Following the determination of the best enrichment conditions, the culture was purified, identified by molecular biology tools and the best growth conditions were characterized. Enriched cultures were obtained for the three operational conditions, but the best condition for the growth of autotrophic denitrifiers microorganisms was at \'N\'/\'S\' ratio of 0,8. The isolated microorganism was identified as Pseudomonas stutzeri. The maximum specific growth rate (\'mü\'máx) was 0.037/h, with a doubling time of 18.7 hours. The growth yield (Y) of nitrogen compound was 0.15 gSSV/g\'N\' and the specific rate of nitrogen utilization was approximately 0.24 g\'N\'/gSSV.h. The results indicated the viability of application of this microorganism for autotrophic denitrification using sulfide as electron donor.

Les abcès cérébraux sont des infections potentiellement mortelles, entraînant souvent des séquelles graves. La prise en charge médicale en reste empirique en raison d’un manque de connaissance approfondie des microorganismes responsables de cette condition. Dans la plupart des laboratoires microbiologiques, le diagnostic d’abcès cérébral est basé sur la culture du pus recueilli chirurgicalement. Malheureusement, cette procédure a de nombreuses limites et ne permet l’identification que d’une petite partie de la population microbienne en cause. L’amplification par PCR et le séquençage du gène codant la fraction 16S de l’ADN ribosomal ont récemment été utilisées pour surmonter les limites de la culture, et ont été démontré leur efficacité dans la documentation des infections bactériennes. Malheureusement, cette procédure présente un degré de discrimination limité en cas d’infection polymicrobienne. Des études métagénomiques de flores complexes de l’homme, basées sur une combinaison de PCR, clonage et séquençage des produits de PCR se sont avérées utiles pour évaluer la diversité bactérienne des flores dentaires, vaginales et intestinales. Nous avons appliqué cette technique à des échantillons d’abcès cérébral pour étudier la flore associée à cette maladie. Dans une première étape, nous avons réalisé une enquête en utilisant la culture et les techniques moléculaires. Le but de cette étude était d’analyser et d’évaluer les bactéries de la flore responsable des abcès cérébraux, en comparant la culture à trois techniques moléculaires basées sur le gène 16S rDNA, incluant le séquençage direct, le clonage suivi de séquençage par méthode de Sanger, et le séquençage direct des produits de PCR par pyroséquençage. Cette enquête a déterminé que la variété des espèces bactériennes associée aux abcès cérébraux est beaucoup plus grande que précédemment décrite, et inclut de nombreuses bactéries anaérobies et des bactéries incultivables de la flore buccale. Cette étude préliminaire a identifié 49 agents bactériens différents, et a permis l’identification de 27 bactéries jamais détectées auparavant dans des abcès du cérébraux, dont 15 n’avaient jamais été cultivées. Un tel nombre d’espèces bactériennes impliquées dans les abcès cérébraux a motivé l’étude de 51 nouveaux spécimens dans le but de décrire plus en détail la flore associée aux abcès cérébraux en fonction de leurs étiologies. Ainsi, nous avons effectué une analyse métagénomique, basé sur le gène 16S rDNA, de 51 patients ayant développé un abcès cérébral. Notre stratégie a été beaucoup plus discriminatoire et a permis à l’identification d’un plus grand nombre de bactéries que la culture et l’amplification et le séquençage direct de l’ANRr 16S. La combinaison des données de 71 patients (20 de la première étude et 51 de la deuxième étude) a permis l’identification de plusieurs associations à l’aide de la méthode de data mining.En outre, notre étude a permis l’identification de deux nouvelles bactéries, la première étant une nouvelle espèce de genre Staphylococcus (Staphylococcus massiliensis) et la seconde étant une bactérie anaérobie qui représente une nouvelle espèce dans un nouveau genre au sein du phylum des Bacteroidetes (Phocaeicola abscesses). En outre, nous avons décrit deux cas inhabituels d’abcès du cerveau, à Mycoplasma hominis après curetage utérin, et à Nocardia carnea chez un greffé rénal. Malgré les limites inhérentes à la procédure de clonage, nos résultats suggèrent que le clonage et le séquençage de gène DNAr 16S est une méthode très performante pour identifier les agents bactériens associés aux abcès cérébraux. / Brain abscess is a life-threatening infection with frequent serious sequelae. The medical management remains empirical due to a lack of comprehensive knowledge of the microorganisms responsible for this condition. In most microbiology laboratories the diagnosis of brain abscess is based on culture from pus collected surgically. Unfortunately, this procedure has many limitations and reveals only a small portion of the true microbial population. PCR-amplified 16S rDNA sequencing has recently been used to overcome the limitations of culture-based bacterial detection in brain abscess pus, and it was demonstrated to be effective in the documentation of monomicrobial infections. Unfortunately, this procedure failed to discriminate among polymicrobial floras.Metagenomic studies of complex human floras using a combination of 16S rDNA PCR and cloning-sequencing of PCR products proved useful to evaluate the bacterial diversity of dental, vaginal and intestinal floras. Thus, we applied this technique to brain abscess samples to study the flora associated with this condition. In a first step, we performed an investigation using culture and molecular techniques. The purpose of this investigation was to analyze and evaluate the bacterial flora responsible for brain abscess by comparing standard culture technique to three techniques using 16S rDNA amplification, that is, direct sequencing, multiple sequencing following cloning, and multiple sequencing via high throughput pyrosequencing. This investigation has determined that the variety of brain abscess-associated bacterial species is much larger than previously reported, and it includes many anaerobes and uncultured bacteria from the oral cavity flora. This preliminary study identified 49 distinct brain abscess bacterial agents, and enabled the identification of 27 bacteria never detected before in brain abscess, 15 of which were uncultured.Such a high number of bacterial species involved in brain abscess prompted the study of 51 new specimens in an effort to describe further the flora associated with brain abscesses and their etiologies. Thus, we performed a 16S rDNA-based metagenomic analysis of cerebral abscesses from 51 patients. Our strategy was significantly more discriminatory and enabled the identification of greater number of bacterial taxa, than culture and conventional 16S rDNA PCR/sequencing, respectively. The combination of data from 71 patients (20 from the first study and 51 from the second study) enabled the identification of several associations using the data mining analysis. Also, these studies permitted the identification of two novel bacteria, the first being a novel Staphylococcus species (Staphylococcus massiliensis) and the second being a novel anaerobic bacterium that represents a novel species in a new genus within the phylum Bacteroidetes (Phocaeicola abscesses). In addition, we reported tow unusual cases of brain abscess, the first case was a Mycoplasma hominis brain abscess following uterus curettage and the second case was a Nocardia carnea infection in a kidney transplant recipient patient.Despite limitations inherent to the cloning procedure, our results suggest that cloning and sequencing of PCR-amplified 16S rDNA is a highly valuable method to identify bacterial agents of brain abscesses.

La PCR universelle ciblant le gène codant pour l'ARNr 16S à l'aide d'amorces universelles, a d'abord été développée pour des études phylogénétiques. En effet ce gène est universellement retrouvé chez les bactéries et sa fonction est conservée. Ainsi, il peut servir d'« horloge moléculaire » pour mesurer les distances phylogénétiques entre les différentes espèces bactériennes. La PCR universelle a ensuite été appliquée en microbiologie clinique dans deux domaines distincts : la détection et l'identification bactériennes. Dans ce travail, nous avons évalué l'applicabilité de la PCR « universelle » 16S comme outil diagnostique dans un centre hospitalier universitaire (hôpital la Timone, Marseille, France). Tout d'abord, nous avons décrit comment la PCR universelle permet l'identification de souches bactériennes mal identifiées par les techniques phénotypiques conventionnelles. Puis, nous avons montré que la PCR universelle peut être utilisée pour détecter l'ADN bactérien dans des prélèvements à culture négative, soit parce que le patient a reçu une antibiothérapie préalable, soit parce que le microorganisme responsable est de croissance difficile. Enfin, nous avons montré que la PCR 16S utilisée pour l'identification permet de mettre en évidence des souches susceptibles de représenter de nouvelles espèces et/ou de nouveaux genres bactériens. Ainsi, la PCR universelle est applicable dans un laboratoire de bactériologie de routine dans les trois objectifs ci-dessus. Elle permet une identification précise des souches bactériennes et l'amélioration du diagnostic des infections associées à des cultures négatives et, par là-même, l'amélioration de la prise en charge des patients. / Broad-range 16S rDNA PCR using universal primers was first developed for phylogenetic purpose since 16S rRNA gene is found in every bacterial species with a conserved function; consequently 16S rRNA gene can be used as a molecular clock for assessing bacterial phylogeny. Broad-range PCR was then applied to medical microbiological diagnosis in two distinct fields: molecular detection and bacteria identification. In the present work, we evaluated the applicability of broad-range PCR as a diagnostic tool in a teaching hospital (Timone Hospital, Marseilles, France). First, we showed that broad-range PCR allows identification of bacteria obtained in culture but misidentified by conventional phenotypic methods. Second, we showed that universal PCR permits bacterial detection in culture-negative infection. Third, we exemplified that using broad-range PCR is a valuable tool to identify new bacterial species and/or genera. Consequently, universal PCR is applicable in routine laboratories in the three above fields; it allows a more accurate identification of bacterial strains and permits to diagnose culture-negative bacterial infections, thus improving patient's management. It also improves our knowledge of infectious diseases together with bacterial diversity and phylogeny. Although universal PCR presents certain limitations (discussed in this work), it remains today the gold-standard for molecular identification and detection in routine laboratories.

Chapter 2 The sea surface microlayer is a biogenic thin layer, comprising less than one millimeter of the ocean surface. This surface layer has gained much attention due to its dampening effect on ocean capillary ripples. The chemistry of the air-sea interface has been studied for decades; however, the structure and function of the marine bacterial community within the sea surface microlayer are still understudied. Although various sea surface microlayer sampling techniques were developed over the past decades, aseptic bacterial sampling in the open ocean is a rather challenging task. In this study, a new approach is presented. It is designed for bacterial sampling of the sea surface microlayer, which intends to reduce sampling contamination from the vessel, subsurface water and the investigators. A 47mm polycarbonate membrane was utilized at each sampling site. In addition, the metagenomic approach using the new generation 454 high-throughput DNA sequencing system was employed to compensate for the small sample size. Two sample sets were collected in summer 2010 and fall 2011 from the sea surface microlayer and underlying water (20 cm deep). A contamination assessment was carried out to determine that contamination might have been caused during the use of the sampling techniques. A total of 14,120 bacterial 16S rRNA gene sequences with an average length of 437.8 bp were obtained. A total of 1,254 Operational Taxonomic Units (OTUs) were constructed and 268 genera were identified. The results indicated that the bacterial compositions of the sea surface microlayer samples were distinct from those of the underlying water samples. This experiment demonstrated that the new generation sequencing platform and microbial metagenomics analysis software together served as powerful tools to gain a deeper understanding of microbial communities within the sea surface microlayer. Furthermore, it is suggested that the newly employed sampling methods could be used to obtain a snapshot of bacterial community structure as well as environmental conditions. Chapter 3 Synthetic aperture radar (SAR) remote sensing captures various fine-scale features on the ocean surface such as coastal discharge, oil pollution, vessel traffic, algal blooms and sea slicks. Although numerous factors potentially affect the SAR imaging process, the influence of biogenic and anthropogenic surfactants has been suggested as one of the primary parameters, especially under relatively low wind conditions. Surfactants have a tendency to dampen the short gravity-capillary ocean waves causing the sea surface to smoothen, thus allowing the radar to detect areas of surfactants. Surfactants are found in sea slicks, which are the accumulation of organic material shaped as elongated bands on the ocean’s surface. Sea slicks are often observable with the naked eye due to their glassy appearance and can also be seen on SAR images as dark scars. While the sources of surfactants can vary, some are known to be associated with marine bacteria. Countless numbers of marine bacteria are present in the oceanic environment, and their biogeochemical contributions cannot be overlooked. Not only do marine bacteria produce surfactants, but they also play an important role in the transformation of surfactants. In this study, we profiled the surfactant-associated bacteria composition within the biogenic thin layer of the ocean surface more commonly referred as the sea surface microlayer (SML). Bacterial samples were collected from the SML for comparative analysis from both within and outside of sea slick areas as well as the respective underlying subsurface water. The bacterial microlayer sampling coincided with SAR satellite, RADARSAT-2, overpasses to demonstrate the simultaneous in-situ measurements during a satellite image capture. The SML sampling method was designed to enable aseptic bacterial sampling. A 47 mm polycarbonate membrane was utilized at each sampling site to obtain a snapshot of the bacterial community structure at a specific space and time. Also, a new generation high-throughput sequencing method was employed to compensate for the small sample size acquired. A total of 27,006 nucleotide sequences (16S rRNA genes) with an average 437.8 bp in length were analyzed. The results revealed the presence of industrially important surfactant-producing marine bacteria, Acinetobacter, Bacillus, Corynebacterium and surfactant-degrading marine bacteria, Escherichia. In addition, Pseudomonas was detected which can be either a producer, decomposer or both. Recognizing that there is still a large number of marine bacterial species that have not been taxonomically classified nor recognized as surfactant-associated species, the effects on SAR imaging due to a high number of surfactant-associated marine bacteria is expected. This study has provided the basis for the biological importance for fine-scale synthetic aperture satellite imaging. Moreover, this new approach is expected to have applications in monitoring biological and chemical properties of the sea surface across the globe.

CSIR / Translation initiation is a rate limiting step during protein biosynthesis. Initiation occurs by formation of an initiation complex comprising 30S subunit of ribosome, mRNA, initiator tRNA, and initiation factors. The initiator tRNA has a specialized function of binding to ribosomal P site whereas all the other tRNAs are selected in the ribosomal A site. The presence of a highly conserved 3 consecutive G-C base pairs in the anticodon stem of the initiator tRNA has been shown to be responsible for its P-site targeting. The exact molecular mechanism involved in the P-site targeting of the initiator tRNA is still unclear and focus of our study. Using genetic methods, we obtained mutant E. coli strains where initiator tRNA mutants lacking the characteristic 3-GC base pairs can also initiate translation. One such mutant strain, A30, was selected for this study. Using standard molecular genetic tools, the mutation was mapped and identified to be a mutation in a transcription remodeling factor, RapA (A511V). RapA is a transcription recycling factor and it displaces S1 when it performs its transcription recycling activity. We found this mutation to cause an increase in the S1-depleted ribosomes leading to decreased fidelity of translation initiation as the mutant RapA inefficiently displaces S1 from RNA polymerase complex. The mutation in the RapA was also found to cause changes in the transcriptome which leads to downregulation of major genes important for methionine and purine metabolism. Using mass spectrometric analysis, we identified deficiencies of methionine and adenine in the strain carrying mutant RapA. Our lab had previously reported that methionine and S-adenosyl methionine deficiency cause deficiency of methylations in ribosome which in turn decreases the fidelity of protein synthesis initiation. We used strains deleted for two newly identified methyltransferases, namely RlmH and RlmI, for our study and these strains also showed decreased fidelity of initiation. RlmH and RlmI methylate 1915 and 1962 positions of 23S rRNA respectively. We found that deletion of these methyltransferases also caused defects in ribosome biogenesis and compromised activity of ribosome recycling factor. We constructed phylogenetic trees of the initiator tRNA from 158 species which distinctly assembled into three domains of life. We also constructed trees using the minihelix or the whole sequence of species specific tRNAs, and iterated our analysis on 50 eubacterial species. We identified tRNAPro, tRNAGlu, or tRNAThr (but surprisingly not elongator tRNAMet) as probable ancestors of tRNAi. We then determined the factors imposing selection of methionine as the initiating amino acid. Overall frequency of occurrence of methionine, whose metabolic cost of synthesis is the highest among all amino acids, remains almost unchanged across the three domains of life. Our results indicate that methionine selection, as the initiating amino acid was possibly a consequence of the evolution of one-carbon metabolism, which plays an important role in regulating translation initiation. In conclusion, the current study reveals the importance of methylations in ribosome biogenesis and fidelity of translation initiation. It also strongly suggests a co-evolution of the metabolism and translation apparatus giving adaptive advantage to the cells where presence of methionine in the environment can be a signal to initiate translation with methionine initiator tRNA.

O gênero Yersinia compreende 12 espécies. Y. enterocolitica, Y. pseudotuberculosis e Y. pestis são patógenos de vários animais, incluindo os humanos. Y. aldovae, Y. bercovieri, Y. frederiksenii, Y. intermedia, Y. kristensenii, Y. aleksiciae, Y. mollaretti e Y. rhodei são encontradas sobretudo no meio ambiente e alimentos e consideradas, usualmente, como bactérias oportunistas não-patogênicas e Y. ruckeri é um importante patógeno de peixes. Usualmente, as linhagens de Yersinia são classificadas em espécies de acordo com suas características bioquímicas. O Laboratório Nacional de Referência em Yersinia spp. outras que Y. pestis recebeu mais de 700 linhagens que foram identificadas bioquimicamente. Entretanto, sete linhagens de Yersinia não puderam ser identificadas pelos testes bioquímicos convencionais em nenhuma das espécies até o momento conhecidas e, por esse motivo, foram denominadas Yersinia atípicas. Os objetivos desse trabalho foram identificar as linhagens atípicas de Yersinia spp. em espécies por técnicas moleculares como Enterobacterial Repetitive Intergenic Consensus PCR (ERIC-PCR), Eletroforese em Campo Pulsado (PFGE), sequenciamento do gene 16S rRNA e Multilocus Sequencing Typing (MLST) e definir dentre as metodologias empregadas a que mais contribui para a identificação precisa dessas linhagens. Foi estudado um total de 59 linhagens de Yersinia spp., sendo 52 linhagens representantes das diferentes espécies do gênero e sete as linhagens bioquimicamente atípicas de Yersinia. As técnicas de ERIC-PCR, sequenciamento do gene 16S rRNA e o MLST foram eficientes na identificação molecular do gênero Yersinia, uma vez que conseguiram reunir todas as espécies em ramos espécie-específicos, com exceção de algumas linhagens de Y. frederiksenii e Y. kristensenii. A técnica de PFGE, pelo contrário, não agrupou as linhagens estudadas em clusters espécie-específicos. Os dados de ERIC-PCR, sequenciamento do gene 16S rRNA e MLST, sugerem que as linhagens atípicas FCF 229 e FCF 231 pertençam à espécie Y. ruckeri. Os dados de ERIC-PCR e MLST sugerem que a linhagem atípica FCF 487 pertença à espécie Y. enterocolitica. Ademais, os dados de ERIC-PCR, sequenciamento do gene 16S rRNA e MLST sugerem que as linhagens atípicas FCF 216, FCF 465, FCF 457 e FCF 494 pertençam a espécie Y. massiliensis. Os resultados obtidos nesse trabalho fornecem dados importantes para a caracterização molecular de linhagens bioquimicamente atípicas de Yersinia e contribuem para uma melhor descrição do gênero quanto a sua diversidade e reforçam o MLST como uma técnica confiável e reprodutível a ser usada na identificação de bactérias pertencentes a esse gênero, sendo dentre as metodologias utilizadas nesse estudo a mais indicada para tipagem molecular de yersiniae. / The genus Yersinia comprises 12 species. Y. enterocolitica, Y. pseudotuberculosis and Y. pestis are pathogens of various animals, including humans. Y. aldovae, Y. bercovieri, Y. frederiksenii, Y. intermedia, Y. kristensenii, Y. aleksiciae, Y. mollaretti and Y. rohdei have been mostly found in the environment and food sources and are commonly considered to be opportunistic nonpathogenic bacteria and Y. ruckeri is an important fish pathogen. Usually, Yersinia strains are classified into species according to their biochemical characteristics. The Brazilian Reference Center on Yersinia spp. other than Y. pestis received more than 700 strains that were biochemically identified. However, seven strains that were typed as Yersinia could not be biochemically identified in any one of the currently known Yersinia species and for this reason they were named as atypical strains. The aims of this work were to identify into species the atypical Yersinia strains using molecular techniques as Enterobacterial Repetitive Intergenic Consensus PCR (ERIC-PCR), Pulsed Field Gel Electrophoresis (PFGE), 16S rRNA gene sequencing and Multilocus Sequencing Typing (MLST) and to define which methodology better contribute to the identification of those strains. A total of 59 Yersinia spp. strains were studied, being 52 representative strains of the defined Yersinia species and seven atypical Yersinia strains. ERIC-PCR, 16S rRNA gene sequencing and MLST were efficient in molecular identifying the genera Yersinia once they grouped the strains into species-specific clusters, with exception of some Y. frederiksenii and Y. kristensenii strains. However, PFGE was not capable to cluster the defined Yersinia strains into species-specific clusters. The data obtained by ERIC-PCR, 16S rRNA gene sequencing and MLST suggest that the atypical strains FCF 229 and FCF 231 belong to Y. ruckeri species. The data obtained by ERIC-PCR and MLST suggest that FCF 487 belong to the Y. enterocolitica species. Additionally, ERIC-PCR, 16S rRNA gene sequencing and MLST suggest that the atypical strains FCF 216, FCF 465, FCF 457 and FCF 494 belong to the Y. massiliensis species. The results obtained provide important data for the molecular characterization of biochemically atypical strains and contribute for a better description of the genera regardless its diversity. Furthermore, the results reinforce MLST as a trustful and reproducible technique to be used in the identification of bacteria of this genus, being among the methodologies studied the most recommended one to molecular type yersiniae.

O exossomo é um complexo de exorribonucleases composto por onze proteínas envolvidas no processamento de rRNA, snRNAs, snoRNAs e na degradação de mRNAs. Todas as subunidades do complexo possuem possíveis domínios de RNase porém apenas quatro delas já tiveram a sua atividade de exorribonuclease caracterizada in vitro. Este complexo foi identificado inicialmente em levedura, sendo também encontrado em outros organismos eucarióticos e também em archaea. O estudo das interações entre suas subunidades resultou em modelos estruturais para o exossomo de H sapiens e T. brucei. A despeito do exossomo ter sido caracterizado em levedura, um estudo das possíveis interações entre as subunidades neste organismo ainda não foi realizado. Com a proposta de identificar estas interações em levedura, neste trabalho foi usado o sistema do duplo híbrido, uma poderosa ferramenta para analisar as interações proteína-proteína. Os resultados obtidos através deste sistema mostraram que a subunidade Rrp4p interagiu com as proteínas Rrp41p, Rrp44p, Mtr3p e Rrp6p. A subunidade Rrp41p mostrou uma forte interação com Rrp45p e a subunidade Rrp42p com Mtr3p. A proteína Rrp45p interagiu com Rrp41p e Rrp43p. A proteína Mtr3p interagiu com Rrp4p, Rrp42p e com Csl4p. Em nossos testes a subunidade Rrp40p não mostrou qualquer interação com as outras subunidades do complexo. Outras proteínas envolvidas no processamento RNA como Noplp, Nop58p, Nop8p e Lsm8p também foram testadas para interações com as subunidades do exossomo e mostraram que interagem com Rrp4p e Mtr3p. Estes resultados inéditos trouxeram novas informações para o futuro modelo estrutural do exossomo e novos da dos sobre a participação deste complexo no processamento de RNA. A determinação da sua estrutura pode contribuir para entender a versatilidade deste complexo em vários processos nos quais ele está envolvido na célula. / Exossome is a complex of exorribonucleases composed for eleven proteins involved in the processing of rRNA, snRNAs, snoRNAs and in the degradation of mRNAs. All the subunits of this complex possess possible RNase domains, however only four of them already had its exorribonucleases activity of characterized in vitro. This complex was identified initially in yeast, being also found in other eukaryotes organisms and also in archaea. The study of the interactions between its subunits resulted in structural models for the exossome of H. sapiens and T. bracei. The spite of exossome has been previously characterized in yeast a study of the possible interactions between the subunits in this organism was still not carried through. With the proposal of identifying these interactions in yeast, we used this work system of yeast two hybrid, a powerful tool analyze protein-protein interactions. The results obtained through this system showed that the subunit Rrp4p internet with the proteins Rrp41p, Rrp44p, Mtr3p and Rrp6p. The subunit Rrp41p showed to one strong interaction with Rrp45p and the subunit Rrp42p with Mtr3p. The Rrp45p protein interacted with Rrp41p and Rrp43p. The Mtr3p protein interacted with Rrp4p, Rrp42p and with Cs14p. In our tests the subunit Rrp40p did not show any interaction with the other subunits of the complex. Other proteins involved in processing RNA as Nop1p, Nop58p, Nop8p and Lsm8p had also been tested for interactions with the subunits of the exossome and had shown that they internet with Rrp4p and Mtr3p. These results had brought new inforrnation for a future structural model of the exossome and new data on the participation of this complex in the processing of RNA. The deterrnination of its structure can contribute to better understand the versatility of this complex in the various processes in which it is involved within the cell.

Um método baseado na extração de rRNA, seguido de RT-PCR rRNA 16S, clonagem e ARDRA foi otimizado e validado para a identificação das bactérias ativas em biofilmes. O método foi analisado primeiro com consórcios artificiais de três organismos. As etapas de clonagem e RT não causaram variações importantes na composição destes consórcios, do contrário da etapa de PCR, onde foi necessária a redução de 30 para 10 ciclos para limitar a distorção da proporção de templates. A análise de biofilmes reais indicou que clones dominantes podem ser identificados com o critério de ocorrência de >2% na biblioteca, mas que a reprodutibilidade de análises ainda é insatisfatória, possivelmente devido a fatores como a micro heterogeneidade espacial do biofilme, viés na reação de PCR e formação de mais de um clone de ARDRA por organismo. O armazenamento do biofilme a -20 °C por 2 meses não levou à alterações expressivas em sua composição. O perfil de clones detectado com o kit (Mo Bio) de extração de RNA foi muito diferente do perfil detectado com o método otimizado neste trabalho. / A method based on extraction of rRNA, followed by RT-PCR of 16S rRNA, cloning and ARDRA was optimized and validated for identification of bacteria active in biofilms. The method was first tested with artificial three-membered consortia. Cloning and RT did not lead to significant changes in the composition of the artificial consortia, but a reduction in cycle number in the PCR reaction from 30 to 10 was necessary for limiting the distortion in the proportion of amplicons relative to that of the templates. Analysis of real biofilms revealed that clones from active organisms occurred in frequencies >2% in the clone library, but reproducibility of analysis was unsatisfactory, probably due to factors such as the spatial heterogeneity of colonization of biofilms by microbes, PCR bias and more than one ARDRA clone per organism. Storage of biofilm samples at -20 °C for 2 months did not lead to important changes in composition. Very different clone profiles were obtained in the analysis of the same biofilm sample with the optimized method and with a kit (Mo Bio) for extraction of RNA.