The discovery of large DNA viruses has challenged the traditional perception of viral complexity due to their enormous genome size and physical dimensions. Previously, viruses were considered small, filterable agents until the discovery of large DNA viruses. Among large DNA viruses, the phylum Nucleocytoviricota and its members, which are often called "giant viruses" have large genome sizes (up to 2.5 Mbp) and virion sizes (up to 1.5 um). Due to having large virion and genome sizes, these viruses were often excluded from viral surveys and remained understudied for years. Luckily, the advancement of metagenomic analysis has facilitated the study of large DNA viruses by analyzing them directly from their environment without cultivating them in the lab, which could be challenging for viruses. In the first chapter of the thesis, I investigated 11 metagenome-assembled genomes (MAGs) of giant viruses previously surveyed from Station ALOHA in the Pacific Ocean. St. ALOHA is located near Hawaii and represents oligotrophic gyres which the majority of the ocean is made of them. I focused on 11 MAGs of giant viruses to get insight into their phylogenetic characteristics, genomic repertoire, and global distribution patterns. Despite the fact that metagenomic analysis has facilitated the study of genetic materials of microbes and viruses on a huge scale, it is essential to benchmark the performance of metagenomic tools and understand the associated biases, particularly in viral metagenomics. In the second chapter, I evaluated the performance of metagenomic tools (contigs assembler and binning tool) in recovering viral genomes using annotated dataset. We used a metagenome simulator (CAMISIM) to generate simulated short reads with known composition to assess these processes. Moreover, I emphasized the importance of binning contigs for viral genomes to fully recover the genomes of viruses along with discussing how diversity metrics were differed for contigs, bins populations. / Master of Science / Viruses are generally thought to be small biological agents with small genome (genetic material) sizes and tiny physical structures; for instance, the genome length of a Human Immunodeficiency Virus (HIV) is around 10 kilobase pair (a unit for measuring genetic material in an organism), and the virion size (physical dimension of a virus) can go up to 120 nm. The discovery of large DNA viruses has challenged the idea of considering viruses as small biological entities, as their genome sizes and physical dimensions can be up to 2.5 megabase pairs and 1500 nm, respectively. Famous members of large DNA viruses from the phylum Nucleocytoviricota are often known as "Giant Viruses'' because they have enormous genome sizes and physical dimensions. Due to having large viral particles, these viruses may usually be excluded from viral surveys. For instance, in field studies, samples must be filtered through a fraction (e.g., 0.2 um) to eliminate bacterial and archaeal genomes and cellular debris, which also results in excluding larger viruses. Since these viruses remain understudied for several years because of biases associated with having large viral particles, there is a solid need to discover and investigate more about them. Growing and cultivating viruses in the laboratory may be challenging, as they need specific hosts to be dependent on to produce more viral progeny and some specific laboratory environments. Luckily, with the advancement of biotechnology, scientists could find ways to evade the need for cultivating viruses in the lab and study them with computational tools such as metagenomic analysis and bioinformatic tools. Metagenomics analysis helps to study the genetic materials of microbial or viral populations directly from their habitat without growing them in a laboratory. In short, metagenomic analysis has multiple steps, including collecting and filtering samples, fragmenting DNA within the samples, generating short DNA sequences (short-read sequences) with NGS (Next Generation Sequencing) technology, assembling short-read sequences into large DNA fragments which can be contigs (contiguous DNA fragments) and metagenome-assembled genome (MAGs). With metagenomic analysis, we can recover the genome of multiple organisms, and we name the recovered genome as metagenome-assembled genome (MAGs) as it is generated through metagenomic processes. The metagenomic analysis will allow us to study microbes and viruses in their environment and gain insight into their taxonomic details, genomic content, and how widespread they are. In the first chapter, I studied 11 MAGs of giant viruses previously surveyed from St. ALOHA, Hawaii. St. ALOHA is a good field site for examining microbial processes and diversity and a good representative of oligotrophic waters (low in nutrients). I examined 11 MAGs of giant viruses to investigate their taxonomic characteristics to clarify which order they belong to within their phylum, their genomic content, and their global distribution pattern. Although studies have successfully recovered the genome of large DNA viruses from their habitats and then analyzed them, all these metagenomic processes need to be evaluated so the results will be valid to consider as the genome of our interested organisms. In the second chapter, I developed a workflow for viral metagenomic analysis to assess metagenomic tools' performance in recovering reliable viral genomes, particularly for large DNA viruses. Most of these benchmarking workflows are done for bacterial and archaeal genomes, and in this thesis, I used these metagenomic tools and applied them to recover large DNA viruses genomes. Also, I emphasized the importance of using binning tools to fully recover large DNA viruses genomes, as due to their large genome size, their genomes might remain fragmented into different contigs, which are longer sequences than reads but shorter than MAGs.

Die Endprodukte der Tetrapyrrolbiosynthese sind essentiell für die Schwefel- und Stickstoffassimilation (Sirohäm), der von Photorezeptoren abhängigen Genexpression (Phytochromobilin), Elektronenübertragungsreaktionen (Häm) und der Photosynthese (Chlorophyll). Die Synthese von Chlorophyllen wird durch eine Mg-Chelatase (MgCh) eingeleitet, die durch das GENOMES UNCOUPLED 4 (GUN4) Protein stimuliert wird. GUN4 ist essentiell für die Aktivierung der MgCh und die Synthese von Chlorophyllen. Das GUN4 aus Arabidopsis thaliana wird ausschließlich an der vorletzten Aminosäure (S264) des C-Terminus phosphoryliert. Die in vitro und in vivo MgCh-Aktivität wird hingegen durch phosphoryliertes GUN4 nicht mehr stimuliert. De-phosphoryliertes GUN4 bewirkt die lichtabhängige Aktivierung der MgCh im Übergang von der Nacht zum Tag in Angiospermen. Im Laufe der Evolution photosynthetisch aktiver Organismen hat sich die in den Angiospermen hochkonservierte Phosphorylierungsstelle entwickelt. GUN4-Homologe aus Synechocystis oder Chlamydomonas werden nicht phosphoryliert. Im Rahmen der Suche nach der GUN4-spezifischen Proteinkinase wurden vier in den Plastiden lokalisierte PLASTID PROTEIN KINASE WITH UNKNOWN FUNCTION identifiziert. In dieser Arbeit wurden zusätzlich Experimente zum durch die GUN-Proteine vermittelten retrograden Signalweg durchgeführt. gun Mutanten sind durch eine defizitäre cytosolische Anthocyan-/Flavonoidbiosynthese charakterisiert. Auf der Suche nach Hinweisen für einen Zusammenhang zwischen Anthocyanen und der De-repression von PHOTOSYNTHESIS-ASSOCIATED NUCLEAR GENES wurde eine neue gun Mutante identifiziert. Der knockout der durch TRANSPARENT TESTA 4 (TT4) kodierten CHALCON SYNTHASE führte zu einer mit den gun Mutanten vergleichbaren De-repression der PHANGs nach Norflurazon-Behandlung. Pharmakologische Experimente belegen eine mögliche Funktion der Phenylpropanoidbiosynthese in der durch die GUN-Proteine vermittelten retrograden Kommunikation. / Endproducts of the tetrapyrrole biosynthesis pathway are essential for the assimilation of sulfur and nitrogen (siroheme), photoreceptor mediated control of nuclear gene expression (phytochromobilin), electron transfer reactions (heme) and photosynthesis (chlorophyll). The synthesis of chlorophyll is initiated by a Mg-chelatase (MgCh) which is stimulated by the GUN4 protein. GUN4 is essential for the activation of MgCh and synthesis of chlorophyll. GUN4 from Arabidopsis thaliana is exclusively phosphorylated at the next-to-last amino acid of the C-terminus (S264). The stimulatory impact towards MgCh is reduced upon GUN4 phosphorylation. De-phosphorylated GUN4 stimulates MgCh activity during the transition from night to daytime. The phosphorylation site of GUN4 has evolved in the clade of angiosperms. GUN4 homologs of Synechocystis or Chlamydomonas are not phosphorylated. In an attempt to isolate the GUN4-kinase four formerly unknown PLASTID PROTEIN KINASE WITH UNKNOWN FUNCTION were identified. In addition to the elucidation of the post-translational GUN4 modifications, experiments concerning the GUN-dependent retrograde signaling pathway were performed. Under conditions which lead to a block of chloroplast development the de-repression of PHOTOSYNTHESIS-ASSOCIATED NUCLEAR GENES is paralleled by a reduced accumulation of anthocyanins in the gun mutants. When searching for a correlation between anthocyanin biosynthesis and expression of PHANGs a new gun mutant was identified. The knockout of CHALCONE SYNTHASE encoded by TRANSPARENT TESTA 4 (TT4) leads to a comparable de-repression of PHANGs after norflurazon treatment as it was observed for the gun mutants. Pharmacological modification of phenylpropanoid biosynthesis revealed that an intermediate of the pathway is a component of chloroplast-to-nucleus communication. Hence, first evidences for a function of the phenylpropanoid biosynthesis pathway in mediating the GUN-dependent retrograde signal were obtained.

No description available.

Indiana University-Purdue University Indianapolis (IUPUI) / My thesis comprises of two individual projects: 1) we have developed a database for operon prediction using high-throughput sequencing datasets for bacterial genomes. 2) Genomics and mechanistic insights of convergent transcription in bacterial genomes. In the first project we developed a database for the prediction of operons for bacterial genomes using RNA-seq datasets, we predicted operons for bacterial genomes. RNA-seq datasets with different condition for each bacterial genome were taken into account and predicted operons using Rockhopper. We took RNA-seq datasets from NCBI with distinct experimental conditions for each bacterial genome into account and analyzed using tool for operon prediction. Currently our database contains 9 bacterial organisms for which we predicted operons. User interface is simple and easy to use, in terms of visualization, downloading and querying of data. In our database user can browse through reference genome, genes present in that genome and operons predicted from different RNA-seq datasets. Further in the second project, we studied the genomic and mechanistic insights of convergent transcription in bacterial genomes. We know that convergent gene pairs with overlapping head-to-head configuration are widely spread across both eukaryotic and prokaryotic genomes. They are believed to contribute to the regulation of genes at both transcriptional and post-transcriptional levels, although factors contributing to their abundance across genomes and mechanistic basis for their prevalence are poorly understood. In this study, we explore the role of various factors contributing to convergent overlapping transcription in bacterial genomes. Our analysis shows that the proportion of convergent overlapping gene pairs (COGPs) in a genome is affected due to endospore formation, bacterial habitat, oxygen requirement, GC content and the temperature range. In particular, we show that bacterial genomes thriving in specialized habitats, such as thermophiles, exhibit a high proportion of COGPs. Our results also conclude that the density distribution of COGPs across the genomes is high for shorter overlaps with increased conservation of distances for decreasing overlaps. Our study further reveals that COGPs frequently contain stop codon overlaps with the middle base position exhibiting mismatches between complementary strands. Further, for the functional analysis using cluster of orthologous groups (COGs) annotations suggested that cell motility, cell metabolism, storage and cell signaling are enriched among COGPs, suggesting their role in processes beyond regulation. Our analysis provides genomic insights into this unappreciated regulatory phenomenon, allowing a refined understanding of their contribution to bacterial phenotypes.

Oenococcus oeni joue un rôle essentiel dans l’élaboration du vin. Adaptée aux environnements acides et riches en alcool, elle est la bactérie lactique naturellement sélectionnée pour mener la fermentation malolactique (FML). Elle est ainsi la principale espèce recherchée et utilisée industriellement comme levain malolactique. Toutefois, il existe une grande diversité phénotypique au sein des souches d’O. oeni et notamment une variabilité des propriétés technologiques que sont la résistance à la lyophilisation, la résistance à l’inoculation dans le vin et la capacité à réaliser rapidement la FML. De nombreux gènes impliqués dans l’adaptation au vin ont déjà été identifiés mais, ne se sont pas toujours révélés efficaces pour la sélection de souches œnologiques. Dans ce contexte, cette étude a consisté à identifier des gènes spécifiques des souches d’intérêt technologique à travers l’analyse des plasmides et génomes. Face aux difficultés rencontrées pour purifier les grands plasmides, seul le plasmide pOENI-1 a été étudié. Ce travail a révélé différentes formes plasmidiques regroupées en une famille nommée « pOENI-1 ». Plusieurs gènes accessoires ont été identifiés et deux d’entre eux ont été détectés chez les souches associées aux fermentations malolactiques spontanées. La comparaison des génomes de souches aux propriétés technologiques diverses a également révélé des séquences génétiques qui leur sont spécifiques. L’ensemble de ces travaux a permis d’identifier plusieurs gènes dont la distribution statistique parmi les souches d’O. oeni a été analysée par la construction de courbes ROC. Ces courbes permettent d’évaluer la qualité des gènes en tant que marqueurs génétiques des souches d’intérêt technologique. Il est donc maintenant possible d’orienter la sélection des nouveaux levains malolactiques par l’utilisation des données génétiques et des outils statistiques décrits dans cette étude. / Oenococcus oeni plays an essential role in the production of wine. Adapted to acidic and alcohol rich environments, it is the lactic acid bacterium species that is naturally selected to conduct malolactic fermentation (MLF). It is also the main species that is selected and used industrially as malolactic starter. However, there is a huge phenotypic diversity among strains of O. oeni, which includes a variability of technological properties such as resistance to freeze-drying, resistance to inoculation into the wine and the ability to quickly achieve the MLF. Many genes involved in adaptation to wine have been identified but have not always proven effective in selecting wine strains. In this context, this study aimed to identify genes that are specific strains of technological interest through the analysis of genomes and plasmids. Due to difficulties encountered to purify large plasmids, only the plasmid pOENI-1 was studied. This work has revealed several different but related plasmids that were grouped into a family named "pOENI-1". Several accessory genes have been identified and two of them were detected in O. oeni strains associated with spontaneous MLF. Comparing the genomes of strains showing various technological properties also revealed genetic sequences that are specific of those strains. Altogether, these works have revealed several genes whose statistical distribution among O. oeni strains was analyzed by constructing ROC curves. These curves are used to assess the quality of genes as genetic markers of strains of technological interest. It is now possible to guide the selection of new malolactic starters by the use of genetic data and statistical tools described in this study.

A recombinação durante a transcrição reversa é um fator importante no aumento da diversidade genética e adaptação do HIV-1, permitindo que mutações vantajosas presentes em diferentes linhagens sejam combinadas em um mesmo genoma. No Brasil, vários recombinantes foram descritos e seis formas recombinantes circulantes (CRFs) já foram identificados, demonstrando a relevância destes recombinantes na epidemia brasileira. Portanto, um dos objetivos desta tese foi analisar os dados gerados pela Rede de Diversidade Genética Viral (VGDN) (sequências parciais de gag, pol e env), a fim de identificar recombinantes inter-subtipos de HIV-1 e avaliar a frequência e distribuição geográfica destes vírus. Utilizando diferentes técnicas foram identificados 152/1083 pacientes portadores de recombinantes BF. A frequência destes recombinantes foi maior em cidades como São Vicente (30%) e Sorocaba (22,6%), sendo que os recombinantes circulantes em São Vicente foram geralmente relacionados às CRF28 e CRF29, enquanto que os vírus presentes na região de Sorocaba comumente apresentam um envelope subtipo F1, independente do subtipo nos demais genes. Além disso, o gene da integrase de 159 pacientes foi amplificado e sequenciado. A análise deste gene revelou mais 10 pacientes infectados com recombinantes BF e nenhuma mutação de resistência primária aos inibidores da integrase foi encontrada. O segundo objetivo foi isolar e caracterizar recombinantes BF in vitro. O isolamento viral foi realizado por co-cultivo e ao final foram obtidos 10 isolados primários. O sequenciamento do genoma quase completo desses dez isolados primários revelou que três isolados primários pertencem ao grupo da CRF28_BF, três ao grupo da CRF29_BF e quatro foram classificados como formas recombinantes únicas (URFs). Ainda, o uso de correceptores desses isolados foi avaliado in vitro em ensaios com as células GHOST(3), e revelou três duplo-trópicos (X4/R5) vírus, quatro CXCR4 (X4) e três isolados utilizaram apenas CCR5 (R5). Em suma, uma alta frequência de URFs foi encontrada em algumas cidades do Estado de São Paulo, e também foi desenvolvido e caracterizado um painel de isolados primários representando as CRF28_BF, CRF29_BF e algumas URFs. / Recombination during reverse transcription is an important factor promoting HIV-1 diversity and adaptive change, allowing advantageous mutations arising on different genomes to undergo linkage in the same progeny recombinant genome more frequently than what would be expected under random mutation alone. In Brazil, several recombinant viruses were reported, and six circulating recombinant forms (CRFs) have already been identified. Therefore, the first objective of this Thesis was to analyze the data generated by the Viral Genetic Diversity Network (VGDN) (gag, pol and env partial sequences), in order to identify HIV-1 intersubtype recombinants and evaluate the frequency and geographical distribution of these viruses. Using different techniques we identified 152/1083 patients harboring BF recombinants. The frequency of these recombinants was higher in cities like São Vicente (30%) and Sorocaba (22.6 %). The recombinant viruses circulating in São Vicente were generally related to CRF28 and CRF29, while those viruses circulating in Sorocaba commonly presented an envelope region of subtype F1, irrespective the subtype composition on the remaining genes. Additionally, the integrase gene of HIV-1 from 159 patients was further amplified and sequenced. The analysis of this viral gene revealed ten more patients infected with BF recombinants and no primary mutations related to integrase inhibitor resistance were found. The second objective was to isolate and characterize BF recombinants in vitro, which resulted in ten primary HIV-1 isolates. The near full-length genomes of these ten primary isolates revealed that three were related to CRF28_BF, three to CRF29_BF and four were unique recombinant forms (URFs), according to their breakpoints profile determined with the jpHMM program. Additionally, the coreceptor usage of these isolate was investigated in vitro using GHOST assays, which revealed three dual-tropic (X4/R5) viruses, four CXCR4 (X4) viruses and three CCR5 (R5) viruses. In sum, we report a high frequency of URFs in some cities of São Paulo State, and also developed a well-characterized panel of viruses representing CRF28_BF, CRF29_BF and URFs.

O objetivo deste trabalho foi caracterizar uma nova família de retrotransposons Copia em cana-de-açúcar, e também compreender a diversidade de retrotransposons com LTR transcricionalmente ativos em cana, com base na análise filogenética de cDNAs provenientes do projeto SUCEST. Foi assim isolada uma nova família de retrotransposons de cana, denominada SURE (SUgarcane REtrotransposon). O genoma da cana apresentou grande colinearidade com os genomas de sorgo e arroz em segmentos contendo SURE. Foram também classificados filogeneticamente cDNAs e seqüências completas de retrotransposons com LTR de cana-de-açúcar. A maioria das linhagens evolutivas descritas apresenta ao menos um representante em cana. O grupo de retrotransposons com LTR mais representado no transcriptoma de cana foi reunido como um novo membro da superfamília Copia Garapa. Trata-se de um elemento com mais cópias e maior variabiliadade que SURE. Dessa forma, SURE e Garapa apresentam-se como duas linhagens de retrotransposons que apresentam padrões distintos de amplificação no genoma de cana. / The aim of this work was to characterize a sugarcane element belonging to a new Copia retrotransposon-family in sugarcane and also study the diversity of transcriptional active LTR-retrotransposons in sugarcane, based in a phylogenetic analysis of cDNAs from SUCEST. The new retrotransposon family identified in sugarcane was named SURE (Sugarcane REtrotransposon). BAC clones bearing one copy of SURE showed that sugarcane genome have a high sinteny with sorghum and rice genomes in coding regions. Other sugarcane sequences containing LTR-retroelements were characterized and compared to pre existent in the plant kingdom. Most of these lineages had at least one sugarcane element. The most representative group of these sequences was reunited as a new group of Copia superfamily in sugarcane and named Garapa. It comprises elements highly distributed in sugarcane chromosomes and with a higher variability when compared to SURE. Finally, SURE and Garapa represent two distinct lineages of Copia retrotransposons that had different amplification pattern in the sugarcane genome.

Os vírus Influenza A infectam um largo espectro de hospedeiros e causam epidemias anuais. São vírus com alta variabilidade genética e RNA segmentado, que podem sofrer rearranjos entre os genes de diferentes vírus. Em 2006, foram analisadas 521 amostras de crianças menores de 5 anos atendidas no HU-USP e 25 foram positivas para Influenza A, sendo H3N2 o mais prevalente (68%). Cinco genes de 18 amostras foram seqüenciados e obtivemos 13 sequencias de HA, 12 da NP, 12 de NA, 14 da M e 10 da NS. Verificou-se a presença de várias mutações, especialmente na HA e NA, que favoreceram a substituição da cepa vacinal naquele ano. Todas as amostras H3N2 apresentaram sítios de resistências aos inibidores da M2. Diferentes linhagens circularam no mesmo ano, tanto de H1 como de H3, favorecendo rearranjos entre elas. Foram verificados, também rearranjos envolvendo os genes da HA e NP, indicando o complexo mecanismo de evolução desses vírus e enfatizando a necessidade de monitoramento da circulação e caracterização de seus genes. / Influenza A virus infects a wide range of hosts and cause annual outbreaks. RNA segmented virus has high genetic variability and may have rearrangements between the genes of different viruses. In 2006, 521 samples of children younger than 5 years were analyzed and 25 tested positive for Influenza A virus, of which the subtype H3N2 is the most prevalent (68%). Five genes of 18 samples were sequenced and 13 sequences of HA, 12 of NP, 14 of M and 10 of NS obtained were. The presence of this several mutations, especially in the HA and NA genes probably helped the replacement of the vaccine strain in that year. All H3N2 subtype samples showed points of resistance to M2 inhibitors. The phylogenetic analysis revealed the circulation of different lineages in the same year, for both H1 and H3, and the presence of two rearrangements involving the HA and NP genes. These results indicate the influence of rearrangements in the evolution of the virus and emphasize the need for monitoring of circulation and characterization of genes.

O presente estudo teve como objetivo realizar a triagem de PHA sintases numa biblioteca metagenômica de solo de Mata Atlântica, empregando duas técnicas de busca: o método de detecção fenotípica e a técnica de PCR. Resultados positivos foram obtidos com este último, empregando iniciadores descritos na literatura e iniciadores descritos neste trabalho. Em 10.67% dos clones da biblioteca foram obtidos amplicons, dos quais 7 foram seqüenciados, apresentando similaridade para os genes phaC dos tipos II e IV. Adicionalmente, 67 clones positivos para a classe III foram obtidos e 4 destes foram seqüenciados. Duas das seqüências obtidas mostraram alta similaridade com o gene codificador da enzima glutamina sintetase tipo I, outro deles para a proteína hipotética conservada pertencente à família de enzimas oxidoredutases e a outra para o componente D do gene hidrogenase-4. A partir da análise dos resultados, iniciadores mais específicos são propostos. Assim, a técnica de PCR foi mais eficiente na detecção de genes da biossíntese de PHA na biblioteca metagenômica estudada. / To perform a PHA synthase screening in a metagenomic library from Atlantic forest soil two search methods were applied: phenotypic detection and PCR. Positive results with PCR were obtained by using primers described in the literature and proposed in this study. Amplicons were obtained in 10.67% of the library, 7 of them were sequenced showing similarity with class II and IV phaC genes. In addition, 67 positive clones for class III were obtained and 4 of them were sequenced. Two of these sequences showed high similarity to the glutamine synthase gene type I, the third one showed similarity to the conserved hypothetical protein of the reductase family, and the forth presented similarity to the component D of the hidrogenase-4. According to the results, more specific primers are suggested. Therefore, PCR was more efficient in the detection of PHA biosynthesis genes in the studied metagenomic library.

Caulobacter crescentus pertence ao grupo das proteobactérias e apresenta a característica distinta de diferenciação celular a cada divisão. Este trabalho visou desvendar os mecanismos de reparo de DNA em C. crescentus. Identificamos 44 genes pertecentes ao regulon SOS através da construção de um mutante para o repressor deste, LexA. Caracterizamos funcionalmente alguns dos genes do regulon, como CC_2272 (que codifica uma proteína da família das endonucleases III) e CC_2433. A cepa deficiente em LexA apresentou morfologia filamentosa, e por esse motivo, buscamos também desvendar quais seriam os fatores genéticos responsáveis por esta morfologia. Investigamos também os processos de controle do ciclo celular após a introdução de danos na molécula de DNA pela luz UVC, em mutantes deficientes para diferentes vias de reparo. Estes experimentos nos mostraram que as células procariontes possuem mecanismos para acoplar a progressão do ciclo celular a integridade do material genético. Este trabalho abre novas e excitantes possibilidades no campo da biologia bacteriana. / Caulobacter crescentus belongs to the proteobacteria group and exhibts the distinctive feature of cellular differentiation after each division. This work aimed to reveal the DNA repair mechanisms in C. crescentus. We have identified 44 genes belonging to the SOS regulon through the construction of a mutant strain to its repressor. We have functionally characterized some of its genes, like CC_2272 (that encodes an endonuclease III family protein) and CC_2433. The lexA strain showed filamentous morphology, e because of that, we have tried to discover which the genetic factors responsible for this morphology were. We have also investigated the cell cycle control processes after the introduction of damages in the DNA by the UVC light, in mutant strains deficient in different repair pathways. These experiments showed us that prokaryotic cells possess mechanisms to couple the cell cycle progression to the integrity of the genetic material. This work opens new and exciting possibilities in the field of bacterial biology.