Bulge-helix-bulge (BHB) elements guide the enzymatic splicing machinery that in Archaea excises introns from tRNAs, rRNAs from their primary precursor, and accounts for the assembly of piece-wise encoded tRNAs. This processing pathway renders the intronic sequences as circularized RNA species. Although archaeal transcriptomes harbor a large number of circular small RNAs, it remains unknown whether most or all of them are produced through BHB-dependent splicing. We therefore conduct a genome-wide survey of BHB elements of a phylogenetically diverse set of archaeal species and complement this approach by searching for BHB-like structures in the vicinity of circularized transcripts. We find that besides tRNA introns, the majority of box C/D snoRNAs is associated with BHB elements. Not all circularized sRNAs, however, can be explained by BHB elements, suggesting that there is at least one other mechanism of RNA circularization at work in Archaea. Pattern search methods were unable, however, to identify common sequence and/or secondary structure features that could be characteristic for such a mechanism.

Os elementos genéticos móveis (mobile genetic elements MGEs), são elementos extremamente importantes para plasticidade e evolução dos genomas. Uma das classes mais importantes de MGEs são as sequências de inserção (insertion sequences - IS). Estes elementos são encontrados em bactérias e archaea e apresentam grande diversidade de famílias e mecanismos de movimentação. Uma família interessante de IS é IS200/605, esta família encontra-se distribuída em bactérias, archaea e vírus e utiliza substratos de DNA de fita simples para seu processo de transposição. Neste trabalho, através da análise de dados públicos de transcritoma identificamos RNAs sobrepostos ao 3\' de genes tnpB de IS200/605 em archaea e bactérias, estes transcritos foram chamados de sense overlapping transcripts (sotRNAs). As extremidades 5\' e 3\' dos sotRNAs foram mapeadas através de dados de RNA-seq de pequenos RNAs (sRNA-seq) e validadas através da técnica de C-RACE. Análises de sequência e estrutura secundária demonstraram que estes RNAs apresentam um motivo conservado chamado de RE-like. Utilizando a sequência consenso deste motivo pudemos identificar RNAs intergênicos derivados de IS200/605 em H. salinarum NRC-1. Para caracterização funcional, construímos linhagens superexpressando os RNAs VNG_sot0042 e VNG_R0052, ambos contendo o motivo RE-like. Curvas de crescimento, utilizando as linhagens construídas demonstraram que a superexpressão destes RNAs aumenta o crescimento de H. salinarum demonstrando sua funcionalidade. Devido a presença do motivo RE-like, extremidades 5\' e 3\' determinadas e fenótipo visualizado em curva de crescimento padrão, o sotRNA VNG_sot0042 foi estudado mais a fundo. Realizamos experimentos de RNA-seq para avaliar o impacto desta superexpressão no transcritoma de H. salinarum NRC-1, assim como experimentos de SILAC para identificação de proteínas parceiras em larga escala. Nestes ensaios identificamos proteínas e genes associados ao processo de adesão, geração de células persistentes e resistência a metais pesados. Ensaios de adesão e sobrevivência a metais pesados demonstraram que a linhagem de superexpressão apresenta maior capacidade de aderir a vidro e maior sobrevivência em diversas condições de estresse. Deste modo, podemos sugerir que ncRNAs derivados de IS200/605 são importantes moléculas regulatórias em H. salinarum NRC-1 e nos ajudam a compreender a manutenção de IS200/605 e seus derivados nos genomas de procariotos. / Mobile genetic elements (MGEs) are extremely important for plasticity and evolution of genomes. Their impacts are diverse and could be related to antibiotic resistence or symbiosis. One of the most important class of MGEs are insertion sequences (ISs). These elements are found widespread throughout bacteria and archaea, presenting a great diversity of families. An interesting family is the IS200/605, this family is found widespread in bacteria, archaea and viruses and is divided in three subgroups according to it\'s genetic composition: IS200 with tnpA gene alone, IS605 with tnpA and tnpB and IS1341 with tnpB only. Another interesting aspect is the utilization of single-stranded DNA as a substrate during the transposition process. In this work, through the analysis of public available transcriptomic data we identified transcripts that overlaps the 3\' end of tnpB in IS200/605 in both bacteria and archaea. These transcripts were named sense overlapping transcripts (sotRNAs). Sequence and secondary structure analysis showed a conserved motif present in sotRNAs, the RE-like motif. Using the consensus sequence of this motif we identified novel intergenic ncRNAs containing this motif that are derived from IS200/605. For functional characterization we overexpressed a sotRNA (VNG_sot0042) and a intergenic (VNG_R0052), both containing the RE-like motif. Standard growth curves demonstrated that the overexpression of these ncRNAs improve H. salinarum growth showing that this RNA is functional. To further evaluate the impact of the overexpressions we prepared RNA-seq libraries of the strain overexpressing VNG_sot0042 and in parallel performed SILAC experiments to identify potential protein-RNA interaction partners. Differentially regulated genes and interacting proteins associated with adhesion and persistent cells generation were found. Adhesion and survival assays showed that the lineage overexpressing VNG_sot0042 has a better capability to adhere in glass surfaces and survive more in diverse stressful conditions.

As Terras Pretas de Índio (TPI), também conhecida por Amazonian Dark Earth, apresentam horizonte A antrópico, elevado pH, nutrientes importantes para o crescimento das plantas, elevado teor de carvão pirogênico e intensa atividade biológica quando comparadas aos seus solos de origem. A comunidade microbiana do solo é essencial para o funcionamento dos ecossistemas, sendo fundamentais em processos de decomposição da matéria orgânica, na disponibilização de nutrientes para as plantas e na ciclagem de nutrientes. Este estudo teve como objetivo acessar as estruturas e composição das comunidades de Bacteria e Archaea em fragmentos de carvão pirogênico (provenientes de TPI), TPI e solo adjacente (ADJ) utilizando as técnicas moleculares. Os solos foram coletados em quatro sítios arqueológicos (Balbina, Barro Branco, Costa do Açutuba e Hatahara), localizados na Amazônia Central. Em geral, as TPIs apresentaram elevados valores de pH, P e Ca corroborando com resultados anteriores em TPIs. As amostras de TPI dos sítios Balbina, Barro Branco e Hatahara apresentaram maior número de cópias do gene 16S rRNA de Bacteria quando comparadas com as amostras de solo ADJ. Os resultados obtidos pelas técnicas de fingerprinting (Terminal Restriction Fragment Length Polymorphism - T-RFLP e Denaturing Gradient Gel Electrophoresis - DGGE) utilizando o gene 16S rRNA de Bacteria e Archaea revelaram que as estruturas das comunidades bacterianas em fragmentos de carvão apresentaram diferenças significativas quando comparados com os solos ADJ. A partir da técnica de pirosequenciamento, os filos Proteobacteria, Actinobacteria e Crenarchaeota apresentaram predominância nos fragmentos de carvão. Observou-se também que em fragmentos de carvão, os microorganismos encontrados podem estar diretamente relacionados aos ciclos do N e C. Além disso, a presença desses micro-organismos em fragmentos de carvão pode favorecer a microbiota do solo e, consequentemente, sua qualidade. Neste sentido, o carvão pode também servir como elemento de recuperação em ambientes degradados, agindo como condicionador do solo sendo esta uma alternativa promissora no manejo de solos agrícolas. / Amazonian Dark Earth (ADE), also known as Terra Preta de Índio, present tropical A horizon, high pH, important nutrients for plant growth, high pyrogenic charcoal levels and intense biological activity when compared to its soil of origin. Soil microbial community is essential for ecosystem function, which is involved in fundamental processes such as the decomposition of organic matter, availability of nutrients to plants and the nutrient cycling. The objective of this study was to assess the structure and composition of bacterial and archaeal communities in fragments of pyrogenic charcoal (from ADE), ADE and adjacent soil (ADJ) using molecular techniques. The soils were collected in four archaeological sites (Balbina, Barro Branco, Costa do Açutuba and Hatahara), located in the central Amazon. In general, ADE presented high values of pH, P and Ca agreeing with previous results in ADE. ADE samples in Balbina, Barro Branco and Hatahara sites presented higher bacterial 16S rRNA gene copy number in comparison with ADJ soil samples. The results obtained with the fingerprinting techniques (Terminal Restriction Length Polymorphism, T-RFLP and Denaturing Gradient Gel Electrophoresis, DGGE) using the bacterial and archaeal 16S rRNA genes revealed that bacterial community structure in charcoal fragments differed significantly when compared to the ADJ soils. Using the pyrosequencing technique, the phyla Proteobacteria, Actinobacteria and Crenarchaeota were predominant in charcoal fragments. It was also observed that microorganisms from charcoal fragments may be directly related to the N and C cycles. Furthermore, the presence of these microorganisms in charcoal fragments may favor the soil microbiota and, consequently, its quality. In this context, pyrogenic charcoal can serve as an element to recover degraded areas acting as soil conditioner and a promising alternative to the management of agricultural soils.

Les microorganismes du domaine du vivant Archaea sont très divers sur le plan biologique et sont présents dans de nombreux types d'écosystèmes. Ils sont majoritaires dans les environnements dits extrêmes. Parmi les virus d'archées, ceux infectant les espèces d'un phylum majeur des archées, Crenarchaeota, constitué d'hyperthermophiles, forment un groupe exceptionnel. En effet, leurs morphotypes sont uniques, variés, et complexes. Le contenu de leur génome est également unique. Enfin, la plupart de ces virus se maintiennent dans la cellule hôte en état porteur, une relation chronique qui permet un équilibre entre production de virions et division cellulaire. J'ai d'abord démontré que le virus de crenarchée Sulfolobus islandicus rod-shaped virus 2 est un virus virulent, et non chronique comme il avait été suggéré. Un mécanisme de lyse unique a été découvert. La paroi cellulaire est modifiée en plusieurs points, avec l'apparition de structures pyramidales saillantes. Celles-ci s'ouvrent en fin de cycle infectieux, permettant aux virions, assemblés auparavant dans le cytoplasme, de quitter la cellule. Puis j'ai travaillé sur des échantillons de sources géothermiques de la péninsule de Kamchatka (Russie) et contribué à l'isolement et la caractérisation d'un virus de morphotype filamenteux. Des protéines structurales supplémentaires ont ainsi été identifiées. Enfin, des mots courts exceptionnels ont été identifiés dans un grand nombre de génomes d'archées et de leurs éléments extra-chromosomiques. Ce sont potentiellement des motifs fonctionnels non-codants, impliqués dans des mécanismes biologiques importants. Typiquement, les motifs palindromiques sont évités dans les génomes / The microorganisms from the Archaea domain are very diverse at the biological level and they are present in many types of ecosystems. They are dominant in the so-called extreme environments. Among their viruses, those infecting species of the Crenarchaeota phylum, a major archaeal phylum comprising hyperthermophiles, form an exceptional group. Indeed, their morphotypes are unique, diverse, and complex. Their genome content is also unique. Finally, most of these viruses persist in the host cell in a carrier state, a chronic relationship allowing an equilibrium between virion production and cell division. I first proved that Sulfolobus islandicus rod-shaped virus 2 is a virulent virus, and not chronic, as had previously been suggested. A unique lysis mechanism was discovered. The cell wall is modified in several locations, with the appearance of pyramidal prominent structures. Those burst open at the end of the infection cycle, allowing the virions, previously assembled in the cytoplasm, to leave the cell. Then, I worked on environmental samples from geothermal springs of the Kamchatka peninsula (Russia) and contributed to the isolation and characterization of a virus of filamentous morphotype. Additional structural proteins were in particular identified. Finally, short exceptional words were identified in a great number of genomes from archaea and their extra-chromosomal elements. These are potentially functional non-coding motifs involved in important biological mechanisms. Typically, palindromic motifs are avoided in the genomes

Trotz der zunehmenden Bedeutung, die der Biogasprozess in der Reihe der regenerativen Energiequellen seit einigen Jahren einnimmt, sind dessen mikrobiologische Prozesse häufig nur zum Teil verstanden und die Zusammensetzung der mikrobiellen Biozönose oft unbekannt. Um jedoch die Biogasgewinnung möglichst effektiv zu gestalten, ist es essentiell, die physikochemischen Bedingungen im Reaktor an die Mikroorganismen anzupassen. Daher war es ein Ziel dieser Arbeit, die mikrobielle Gemeinschaft in verschiedenen Biogasanlagen abhängig vom eingesetzten Substrat zu charakterisieren. Dabei zeigte sich, dass insbesondere die archaeelle Diversität in NawaRo-Anlagen sehr limitiert ist und die Organismen in den einzelnen Anlagen nah verwandt sind. Von großer Bedeutung waren dabei die Genera Methanoculleus und Methanosarcina (bei hoher Acetatkonzentration) bzw. Methanothrix (bei geringer Acetatkonzentration). Deren genaues Verhältnis in den verschiedenen Anlagen hing wesentlich von den zugesetzten Co-Substraten ab und vor allem in Anlage A konnte eine Abhängigkeit der Abundanz von Methanosarcina je nach Zusatz von Hühnertrockenkot bzw. Rindermist beobachtet werden. Im Gegensatz dazu spielten die untersuchten chemischen Parameter eine geringere Rolle und es konnten kaum Korrelationen zwischen der Abundanz einzelner archaeeller Genera und physikochemischen Parametern beobachtet werden. In der mit Klärschlamm betriebenen Anlage KA waren außerdem verschiedene Methanobacteriales und Organismen der WCHA1-57-Klade von Bedeutung. Neben methanogenen Archaea konnten in den Anlagen C, KA und KL außerdem Crenarchaeota nachgewiesen werden, die wahrscheinlich in das erst kürzlich neu postulierte Phylum der „Bathyarchaeota“ einzuordnen sind. Deren genaue physiologische Funktion im Biogasprozess ist jedoch noch ungeklärt. Zusätzlich zu den Archaea wurden exemplarisch auch Proben aus den einzelnen Anlagen hinsichtlich ihrer bakteriellen Population untersucht. Dabei waren in den NawaRo-Anlagen A, B, C und KL vor allem Firmicutes und Cloacimonetes zu finden. Letztere stellen dabei eine bisher nur wenig charakterisierte Gruppe dar, die wahrscheinlich im hydrolytischen Abbau von Cellulose und/oder Aminosäuren eine entscheidende Rolle spielen. Innerhalb der Firmicutes übten insbesondere die Clostridiales vielseitige physiologische Funktionen innerhalb der anaeroben Fermentation aus. Überraschend gering war jedoch der Anteil der syntrophen Organismen. Es ist möglich, dass einige der nicht näher klassifizierbaren OTUs dieser Gruppe angehören, da der syntrophe Abbau verschiedener Säuren von essentieller Bedeutung für den Biogasprozess ist. In der mit kommunalem Abwasserschlamm betriebenen Anlage KA war der Anteil der Firmicutes und Cloacimonetes deutlich geringer. Abundantestes Phylum waren hier die Proteobacteria, unter denen zusätzlich Syntrophe zu finden sind. Zusätzlich zur Untersuchung der mikrobiellen Gemeinschaft während des Normalbetriebes von Biogasanlagen wurden außerdem häufige Prozessstörungen simuliert. Dabei zeigte sich, dass es trotz rückläufiger Methanbildung häufig nicht zu Veränderungen in der Zusammensetzung der Mikroorganismen kommt und stattdessen deren Aktivität sinkt. Erst bei dramatischer Veränderung der physikochemischen Parameter, wie es im Rahmen des ersten Versuchs zur Ammonium-Intoxiaktion der Fall war, wurden deutliche Veränderungen in der archaeellen Biozönose detektiert. Die bakterielle Gemeinschaft blieb dabei kaum verändert. Bei geringerer Ammoniumkonzentration hingegen konnte eine gute Anpassungsfähigkeit der Archaea gezeigt werden. Dennoch war es nicht möglich, anhand dieser Versuche einen allgemein gültigen Grenzwert der Ammoniumkonzentration, ab der inhibitorische Effekte auftreten, festzulegen, da in Anlage A bei ähnlichen Konzentrationen die archaeelle Abundanz durchaus zurückging. Auch im Rahmen der Versuche zur Versauerung konnte eine gute Anpassungsfähigkeit der Archaea gegenüber erhöhten FOS-Konzentrationen gezeigt werden. Dabei war insbesondere eine erhöhte Abundanz der Syntrophomonadaceae mit Stressresistenz verbunden, während eine erhöhte Abundanz von Methanobacterium mit verminderter Säuretoleranz einher ging. Insgesamt liefern die Ergebnisse dieser Arbeit einen aufschlussreichen Einblick in die mikrobielle Population in NawaRo-Anlagen sowohl während des Normalbetriebes als auch im Verlauf von Prozessstörungen, die zu einem besseren Verständnis der ablaufenden Prozesse beitragen können. Dennoch ist die Rolle vieler beteiligter Organismen noch nicht gänzlich geklärt. Es sind daher weitere Studien nötig, um die mikrobiologischen Prozesse in Biogasanlagen vollständig zu verstehen.

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Made available in DSpace on 2016-06-02T19:26:22Z (GMT). No. of bitstreams: 1 SOARES_Lais_2013.pdf: 1502301 bytes, checksum: 5eb3bd554b98070bc2586ad2fed479d4 (MD5) Previous issue date: 2013-05-17 / Universidade Federal de Sao Carlos / This work aimed to quantifier the archaeal and bacterial communities by real time PCR, that shown the number of copies of 16S gene, rDNA into the water samples and to compare the archaeal and bacterial profiles on the PCR/DGGE technique as well as relate them with environmental variables in two points, dam and input on the Itupararanga reservoir, Sorocaba s basin. The bacterial density on the sediment (6,09 x108 e 2,56 x 109, dam and input, respectively) was more than water column (6,79 x 107 e 6,55 x 107, dam and input, respectively) this can be attributed to increase of the nutrients concentration from the surface to bottom. The bacterial (6,09 x 108 e 2,56 x 109 dam and input, respectively ) and archaeal (2,31 x 102 e 4,49 x 102 dam and input, respectively) quantities on the reservoir were more in the water column than in the sediment, which can be caused by the higher nutrients concentration in the top and the lees nutrients concentration in the bottom of Itupararanga reservoir. Since the canonical correspondence analysis has been possible, identify that the archaeal community has correlated with profundity and ammonia concentration suggesting ammonia oxidizing archaea s presence and abundance. The bacterial community quantity has correlated with physical chemical properties like pH and dissolved oxygen suggesting the environmental variables influence the group s abundance. Richness has correlated with nutrients distribution like orthophosphate concentration suggesting that the resources may limit the communities. / Com este trabalho objetivou-se quantificar a comunidade de bactérias e arqueias por meio de PCR em tempo real que determina o número de cópias do gene 16S de rDNA presentes nas amostras ambientais e comparar as comunidades de arqueia e bactérias em um perfil de bandas de PCR/DGGE, bem como relacioná-las às variáveis ambientais de dois pontos, Entrada e Barragem do reservatório de Itupararanga, bacia do rio Sorocaba. A quantidade de bactérias (6,09 x 108 e 2,56 x 109 barragem e entrada, respectivamente) e de arqueias (2,31 x 102 e 4,49 x 102 barragem e entrada, respectivamente) no sedimento foi maior do que na coluna d água o que pode ser atribuído ao aumento da concentração de nutrientes da superfície para o fundo do reservatório. A partir de análise de correspondência canônica foi possível observar que a quantidade de arqueias relacionou-se a profundidade e à concentração de íons amônio indicando possível presença e abundância de arqueias amônio oxidantes (AOA), enquanto que as bactérias foram mais relacionadas às variáveis físico-químicas, como temperatura e oxigênio dissolvido indicando que este grupo é mais sensível às variações ambientais. A riqueza de ambos os grupos foi relacionada à disponibilidade de nutrientes, indicando que os recursos podem ser limitantes às comunidades.

Foi estudada a degradação do pentaclorofenol (PCP) em reator aneróbio horizontal de leito fixo (RAHLF) de volume de 2000 mL. O reator foi inoculado com microrganismos oriundos de reatores aneróbios não previamente adaptados a PCP. Atividade microbiana foi monitorada através de técnicas clássicas na presença do organoclorado na faixa de 2,0 a 13 mg/L de PCP. O reator apresentou eficiência de 97% na remoção de DQO e completo desaparecimento do composto de PCP em todas as concentrações testadas. A fração orgânica foi consumida totalmente na primeira terça parte do reator de acordo com os valores determinados de ácidos voláteis, DQD e PCP. Não foi verificada inibição da atividade de culturas microbianas. Os exames microscópicos, fluorescência e varredura, permitiram verificar o predomínio de microrganismos pertencentes ao Domínio Archea. As técnicas moleculares PCR, ARDRA e hibridação slot-blot confirmaram o predomínio do Domínio Archaea e possibilitaram a verificação de alterações na diversidade das populações após adição de 2 mg PCP/L. Conclui-se que o reator sem prévia adaptação do inóculo foi eficiente para o tratamento do PCP, e os microrganismos relacionados às Archaea metanogênicas acetocláticas podem estar envolvidas na degradação deste composto. / The degradation of pentachlorophenol (PCP) was studied in a 2000 mL. Horizontal Anaerobic Immobilized System (HAIS). The reactor was inoculated with microorganisms obtained from an anaerobic reactor without previous adaptation to the PCP. The microbial activity was evaluated by using classic techniques in order to . monitor its behavior during the HAIS fed with a range of PCP between 2.0 to 13 mg/L. The reactor presented 97% of efficiency in the removal of COD and complete decrease of PCP in alI concentrations tested. The total consumption of organic fraction took place mainly in the first third part of the reactor according the values of volatile fatty acids, COD and PCP obtained. Microbial inhibition was not verified in during HAIS operation. Microscopic examinations allowed certifying the Archaea Domain predominance according the morphologies observed. The molecular techniques polimerase chain reaction (PCR), ARDRA and slot-blot hibridation confirmed the predominance of Archaea Domain and alIowed verifying some changes in the population\'s diversity under additions of 2mg PCP/L. The efficiency of PCP decreased in the anaerobic reactor was related to the presence of Archaea Domain, especially the acetoclastic methanogens, whose where probably involved with the organochlorine compound degradation.

A caracterização em larga escala do transcritoma de diferentes organismos revelou um cenário complexo da expressão gênica, levando a identificação de inúmeros transcritos produzidos ao longo dos genomas de eucariotos e procariotos. Esse fenômeno recebeu o nome de transcrição pervasiva e tem sido fonte de estudos na busca de novos RNAs com importâncias regulatórias e também transcritos envolvidos na tradução de proteínas ainda não caracterizadas. A abundância de dados de transcritômica e proteômica, além de informações completas a respeito do genoma, fazem do extremófilo halofílico Halobacterium salinarum, um organismo modelo ideal para os estudos da transcrição pervasiva. Esse micro-organismo pertence ao grupo Archaea, o último dos três domínios da vida a ser descrito e com características compartilhadas entre bactérias e eucariotos. Através do uso da técnica de differential RNA-seq (dRNA-seq), a qual permite a distinção entre transcritos primários e processados, identificamos 179 TSSaRNAs em H. salinarum, esses pequenos RNAs estão associados ao início de transcrição e ainda não haviam sido descritos em archaea. A aplicação do dRNA-seq em amostras de RNA extraídas ao longo da curva de crescimento permitiu a identificação de 4540 TSS no genoma de H. salinarum NRC-1. Parte desses inícios de transcrição está localizada upstream a genes conhecidos, permitindo a identificação de inícios de transcrição em 1545 genes. 59,2% desses inícios de transcrição estão localizados até 10 pb. de distância do códon de início de tradução, confirmando a ausência de regiões UTRs em grande parte dos genes. A análise de expressão, em diferentes condições, das regiões relacionadas a inícios de transcrição antisense a genes revelou que a maioria dessas regiões apresenta um perfil de expressão correlacionado com os genes na fita oposta, indicando um possível papel regulatório desses transcritos. De forma similar, a análise da expressão de inícios de transcrição intergênicos permitiu a identificação de 132 regiões diferencialmente expressas e que não estão relacionadas a nenhum outro elemento no genoma de H. salinarum NRC-1. A análise comparativa com dados de proteômica revela que algumas dessas regiões podem estar envolvidas com a produção de pequenas proteínas. Além disso, a identificação de 1365 inícios de transcrição internos a genes sugere que a produção de transcritos intragênicos (intraRNAs) seja um fenômeno amplamente distribuído no genoma desse halófilo. Experimentos de Northern blot confirmaram a produção de um transcrito correspondente a porção final do gene VNG_RS05220, e experimentos de Western blot revelaram que a tradução desses intraRNAs é responsável pela produção de pequenas proteínas correspondentes a domínios proteicos individuais, com importante papel funcional em condições específicas de crescimento. A análise de inícios de transcrição upstream a regiões codificantes de domínios similares em bactérias e outras archaea sugere que a produção de intraRNAs codificantes é um fenômeno amplamente distribuído em procariotos e pode ser responsável pelo aumento da diversidade do proteoma através da geração de isoformas de proteínas a partir de um único gene. Por fim, a análise de dados de RNA-seq, em conjunto com a busca por assinaturas conhecidas de término de transcrição em archaea, permitiu a identificação da posição final de 58 genes. Os dados obtidos a partir dos experimentos e análises realizados ajudam a traçar um panorama mais completo do transcritoma de H. salinarum NRC-1 e revelam a presença de novos transcritos que podem ser amplamente distribuídos em procariotos e apresentar importantes papéis funcionais. / The large-scale transcriptome characterization of different organisms revealed a highly complex scenario of gene expression, leading to the identification of numerous transcripts in the genomes of eukaryotes and prokaryotes. This phenomenon has been named pervasive transcription and has been an important source for the search of new RNAs with regulatory functions or involved in the translation of unknown proteins. The abundance of transcriptomic and proteomic data, as well as complete information regarding the genome, allowed the halophilic extremophile Halobacterium salinarum to be an ideal model organism for studies of pervasive transcription. This microorganism belongs to the Archaea group, the last one of the three domains of life to be described, which presents shared characteristics with bacteria and eukaryotes. The use of differential RNA-seq (dRNA-seq) approach, which allows the distinction between primary and processed transcripts, allowed the identification of 179 TSSaRNAs, small RNAs associated with the transcription initiation in H. salinarum. The application of dRNA-seq in RNA samples collected along the growth curve allowed the identification of 4540 transcription start sites (TSS) in H. salinarum NRC-1. Some of these transcription initiation are located upstream to known genes, enabling the identification of TSSs for 1545 genes. 59.2% of these positions are located up to 10 bp away from the translation initiation codon, confirming that most of genes are leaderless. The expression analysis of regions related to antisense TSS under different conditions revealed that most of these regions have a correlated expression profile with genes in the opposite strand, indicating a possible regulatory role. Similarly, analysis of the expression of intergenic TSS allowed the identification of 132 differentially expressed regions that are not related to any other element in H. salinarum NRC-1 genome. Integration with proteomic data reveals that some of these regions may be involved in the production of small proteins. The identification of 1365 TSS located within genes suggests that the production of intragenic RNAs (intraRNAs) is a widely distributed phenomenon in H. salinarum NRC-1 genome. Northern blot experiments confirmed the production of a transcript corresponding to the final portion of VNG_RS05220 gene and Western blot experiments also revealed that the translation of intraRNAs is responsible for producing small proteins corresponding to individual protein domains with important functional role in specific growth conditions. Analysis of TSS upstream to the coding regions of similar protein domains in bacteria and other archaea suggests that the production of coding intraRNAs is a widely distributed phenomenon in prokaryotes and may be responsible for the increased proteome diversity through the generation of protein isoforms from a unique gene. Finally, the RNA-seq data analysis, combined with a search for known signatures for transcription termination in archaea, allowed the identification of the final position of 58 genes. The present work help to give a more complete picture of H. salinarum transcriptional landscape and reveals the presence of new transcripts that can be widely distributed in prokaryotes, with important functional roles.

Archaea ainda não foi reconhecido como patógeno de doença humana. O objetivo deste estudo foi determinar a prevalência, diversidade, níveis e proporções de Archaea no biofilme subgengival de indivíduos com periodontite agressiva (PA) e saúde periodontal (SP). Sessenta indivíduos foram selecionados para este estudo (n=30/grupo). A análise de diversidade foi realizada em 10 indivíduos/grupo. Quatro sítios/indivíduo do grupo PA e 2 sítios/indivíduo do grupo SP foram analisados por qPCR. A freqüência de Archaea foi de 60% dos indivíduos/ 15,2% dos sítios em PA e de 63,3% dos indivíduos/ 15,6% dos sítios em SP (p>0,05). Um a três filotipos foi identificado por amostra. O número de cópias e a proporção de Archaea e Bacteria foram menores no grupo SP do que no grupo PA (p<0,05). Archaea são encontrados no biofilme subgengival de indivíduos com PA e SP. Methanobrevibacter oralis é o filotipo mais prevalente, podendo ser considerado residente da cavidade bucal. A alteração ecológica na microbiota de indivíduos com PA inclui o aumento dos níveis e proporções de Archaea. / Membrers of Archaea domain may be detected in the microbiota of mucous surfaces of human and animals, but their association with diesase have not been yet stablished Some studies have suggested that Archaea domain may be indirectly associated with pathogenesis of periodontitis, since they are found restrict to subgingival sites with severe periodontal destruction. The aim of this study was to determine the prevalence, diversity, levels and proportions of microorganisms of Archaea domain in subgingival biofilm of aggressive periodontitis and periodontally healthy subjects. Thirty generalized aggressive periodontitis (GAgP) and 30 periodontally healthy (PH) subjects were selected. Archaea detection was performed by PCR using domain-specific primers in 9 subgingival samples taken from each subject. Archaea diversity was determined by evaluating a single positive sample per subject, randomly selected from 10 GAgP and 10 PH subjects. Archaeal 16S rRNA gene library were constructed to each sample and the identity of phylotypes were determined for the comparison of unrecognized sequences with gene database. The levels and proportions of Archaea in relation to total microbial load were analysed by quantitative PCR (qPCR) in 4 sites per GAgP subject and 2 sites per PH subject. A total of 540 subgingival samples were analysed to Archaea presence. This domain were detected in 18 GAgP (60%) and in 19 PH (63.3%) subjects. Forty-one (15.2%) and 42 (15.6%) samples were positive for this domain in GAgP and PH subjects, respectively. There was not difference in prevalence of this domain between subjects from GAgP and PH groups, as well as there was not difference in prevalence between sites with different probing depthsin GAgP group. Thenumber of 16S rRNA clones available to identification per sample varies from 33 to 47 in GAgP group, and from 15 to 23 in PH group, with a mean of 42.8+3.9 e 20.2 +2.2, respectively. The analysis of 629 sequencies permits an identification of 1 to 3 phylotypes of Archaea domain per sample. Methanobrevibacter oralis was detected in all archaeal positive samples, being the single detected specie of this domain in 5 subjects from GAgP group, and in 3 subjects from PH group. Methanobacterium curvum/congolense was detected in 3/10 GAgP and 6/10 PH samples, whereas Methanosarcina mazeii was detected in 4/10 samples from both groups. Archaea analysis by qPCR was carried out in 103 sites and 28 GAgP subjects and in 60 sites and 30 PH individuals. Archaea has been detected in 27/28 subjects and in 68% of studied sites in GAgP group and in 26/30 subjects and 58,3% of total analysed sites in PH group. Archaeal and bacterial 16S rRNA mean levels were smaller in PH group than in GAgP group (Mann Whitney, p<0.05). There was no statistic significance of difference in the levels of Archaea in regard to probing depth categories in GAgP group (p>0.05). Moreover, the proportion of Archaea in relation to total microbial load (Archaea + Bacteria) was 0.02% and 0.08% in PH and GAgP group (p<0.05), respectively. These data suggest that Archaea is commonly found in the subgingival biofilm of humans, and that M. oralis may be considered a member of the resident microbiota of subgingival sites. The ecological shift in the microbiota of aggressive periodontitis subjects includes the increase of levels and proportions of Archaea domain.