De Novo Hybrid Assembly Unveils Multi-Chromosomal Mitochondrial Genomes in Ludwigia Species, Highlighting Genomic Recombination, Gene Transfer, and RNA Editing Events.

Biological invasions have been identified as the fifth cause of biodiversity loss, and their subsequent dispersal represents a major ecological challenge. The aquatic invasive species Ludwigia grandiflora subsp. hexapetala (Lgh) and Ludwigia peploides subsp. montevidensis (Lpm) are largely distributed in aquatic environments in North America and in Europe. However, they also present worrying terrestrial forms that are able to colonize wet meadows. To comprehend the mechanisms of the terrestrial adaptation of Lgh and Lpm, it is necessary to develop their genomic resources, which are currently poorly documented. We performed de novo assembly of the mitogenomes of Lgh and Lpm through hybrid assemblies, combining short reads (SR) and/or long reads (LR) before annotating both mitogenomes. We successfully assembled the mitogenomes of Lgh and Lpm into two circular molecules each, resulting in a combined total length of 711,578 bp and 722,518 bp, respectively. Notably, both the Lgh and Lpm molecules contained plastome-origin sequences, comprising 7.8% of the mitochondrial genome length. Additionally, we identified recombinations that were mediated by large repeats, suggesting the presence of multiple alternative conformations. In conclusion, our study presents the first high-quality mitogenomes of Lpm and Lgh, which are the only ones in the Myrtales order found as two circular molecules.

Safe and easy in vitro evaluation of tmRNA-SmpB-mediated trans-translation from ESKAPE pathogenic bacteria.

In bacteria, trans-translation is the major quality control system for rescuing stalled ribosomes. It is mediated by tmRNA, a hybrid RNA with properties of both a tRNA and a mRNA, and the small protein SmpB. Because trans-translation is absent in eukaryotes but necessary for bacterial fitness or survival, it is a promising target for the development of novel antibiotics. To facilitate screening of chemical libraries, various reliable in vitro and in vivo systems have been created for assessing trans-translational activity. However, the aim of the current work was to permit the safe and easy in vitro evaluation of trans-translation from pathogenic bacteria, which are obviously the ones we should be targeting. Based on green fluorescent protein (GFP) reassembly during active trans-translation, we have created a cell-free assay adapted to the rapid evaluation of trans-translation in ESKAPE bacteria, with 24 different possible combinations. It can be used for easy high-throughput screening of chemical compounds as well as for exploring the mechanism of trans-translation in these pathogens.

The genomic substrate for adaptive radiation in African cichlid fish.

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

Porphyromonas spp. have an extensive host range in ill and healthy individuals and an unexpected environmental distribution: A systematic review and meta-analysis.

Studies on the anaerobic bacteria Porphyromonas, mainly focused on P. gingivalis, have revealed new bacterial structures, metabolic pathways, and physiologic functionalities. Porphyromonas are mainly described as being associated with mammals and involved in chronic oral infections and secondary pathologies such as cancers or neurodegenerative diseases. In this review, we collected and analyzed information regarding Porphyromonas isolation sites and associated conditions and showed that Porphyromonas are detected in numerous pristine and anthropic environments and that their host range appears wider than previously believed, including aquatic animals, arthropods, and birds, even if their predominant hosts remain humans, pets, and farm animals. Our analyses also revealed their presence in multiple organs and in a substantial proportion of healthy contexts. Overall, the growing numbers of microbiota studies have allowed unprecedented advances in the understanding of Porphyromonas ecology but raise questions regarding their phylogenic assignment. In conclusion, this systematic and meta-analysis provides an overview of current knowledge regarding Porphyromonas ecological distribution and encourages additional research to fill the knowledge gaps to better understand their environmental distribution and inter- and intra-species transmission.

Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.

BACKGROUND: Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes are only working drafts, an incompleteness that causes numerous problems and constitutes a major obstacle to genotypic and phenotypic interpretation. In this work, we began with an example from the class Bacteroidia in the phylum Bacteroidetes, which is preponderant among human orodigestive microbiota. We successfully identify the genetic loci responsible for assembly breaks and misassemblies and demonstrate the importance and usefulness of long-read sequencing and curated reannotation. RESULTS: We showed that the fragmentation in Bacteroidia draft genomes assembled from massively parallel sequencing linearly correlates with genomic repeats of the same or greater size than the reads. We also demonstrated that some of these repeats, especially the long ones, correspond to misassembled loci in three reference Porphyromonas gingivalis genomes marked as circularized (thus complete or finished). We prove that even at modest coverage (30X), long-read resequencing together with PCR contiguity verification (rrn operons and an integrative and conjugative element or ICE) can be used to identify and correct the wrongly combined or assembled regions. Finally, although time-consuming and labor-intensive, consistent manual biocuration of three P. gingivalis strains allowed us to compare and correct the existing genomic annotations, resulting in a more accurate interpretation of the genomic differences among these strains. CONCLUSIONS: In this study, we demonstrate the usefulness and importance of long-read sequencing in verifying published genomes (even when complete) and generating assemblies for new bacterial strains/species with high genomic plasticity. We also show that when combined with biological validation processes and diligent biocurated annotation, this strategy helps reduce the propagation of errors in shared databases, thus limiting false conclusions based on incomplete or misleading information.

Signature of Microbial Dysbiosis in Periodontitis.

Periodontitis is driven by disproportionate host inflammatory immune responses induced by an imbalance in the composition of oral bacteria; this instigates microbial dysbiosis, along with failed resolution of the chronic destructive inflammation. The objectives of this study were to identify microbial signatures for health and chronic periodontitis at the genus level and to propose a model of dysbiosis, including the calculation of bacterial ratios. Published sequencing data obtained from several different studies (196 subgingival samples from patients with chronic periodontitis and 422 subgingival samples from healthy subjects) were pooled and subjected to a new microbiota analysis using the same Visualization and Analysis of Microbial Population Structures (VAMPS) pipeline, to identify microbiota specific to health and disease. Microbiota were visualized using CoNet and Cytoscape. Dysbiosis ratios, defined as the percentage of genera associated with disease relative to the percentage of genera associated with health, were calculated to distinguish disease from health. Correlations between the proposed dysbiosis ratio and the periodontal pocket depth were tested with a different set of data obtained from a recent study, to confirm the relevance of the ratio as a potential indicator of dysbiosis. Beta diversity showed significant clustering of periodontitis-associated microbiota, at the genus level, according to the clinical status and independent of the methods used. Specific genera (Veillonella, Neisseria, Rothia, Corynebacterium, and Actinomyces) were highly prevalent (>95%) in health, while other genera (Eubacterium, Campylobacter, Treponema, and Tannerella) were associated with chronic periodontitis. The calculation of dysbiosis ratios based on the relative abundance of the genera found in health versus periodontitis was tested. Nonperiodontitis samples were significantly identifiable by low ratios, compared to chronic periodontitis samples. When applied to a subgingival sample set with well-defined clinical data, the method showed a strong correlation between the dysbiosis ratio, as well as a simplified ratio (Porphyromonas, Treponema, and Tannerella to Rothia and Corynebacterium), and pocket depth. Microbial analysis of chronic periodontitis can be correlated with the pocket depth through specific signatures for microbial dysbiosis.IMPORTANCE Defining microbiota typical of oral health or chronic periodontitis is difficult. The evaluation of periodontal disease is currently based on probing of the periodontal pocket. However, the status of pockets "on the mend" or sulci at risk of periodontitis cannot be addressed solely through pocket depth measurements or current microbiological tests available for practitioners. Thus, a more specific microbiological measure of dysbiosis could help in future diagnoses of periodontitis. In this work, data from different studies were pooled, to improve the accuracy of the results. However, analysis of multiple species from different studies intensified the bacterial network and complicated the search for reproducible microbial signatures. Despite the use of different methods in each study, investigation of the microbiota at the genus level showed that some genera were prevalent (up to 95% of the samples) in health or disease, allowing the calculation of bacterial ratios (i.e., dysbiosis ratios). The correlation between the proposed ratios and the periodontal pocket depth was tested, which confirmed the link between dysbiosis ratios and the severity of the disease. The results of this work are promising, but longitudinal studies will be required to improve the ratios and to define the microbial signatures of the disease, which will allow monitoring of periodontal pocket recovery and, conceivably, determination of the potential risk of periodontitis among healthy patients.

Identification and characterization of cichlid TAAR genes and comparison with other teleost TAAR repertoires.

BACKGROUND: TAARs (trace amine-associated receptors) are among the principal receptors expressed by the olfactory epithelium. We used the recent BROAD Institute release of the genome sequences of five representative fishes of the cichlid family to establish the complete TAAR repertoires of these species and to compare them with five other fish TAAR repertoires. RESULTS: The genome sequences of O. niloticus, P. nyererei, H. burtoni, N. brichardi and M. zebra were analyzed by exhaustive TBLASTN searches with a set of published TAAR gene sequences used as positive bait. A second TBLASTN analysis was then performed on the candidate genes, with a set of non-TAAR class A GPCR (G protein-coupled receptors) used as negative bait. The resulting cichlid repertoire contained 44 complete TAAR genes from O. niloticus, 18 from P. nyererei, 23 from H. burtoni, 12 from N. brichardi and 20 from M. zebra, plus a number of pseudogenes, edge genes and fragments. A large proportion of these sequences (80%) consisted of two coding exons, separated in all but two cases by an intron in the interloop 1 coding sequence. We constructed phylogenetic trees. These trees indicated that TAARs constitute a distinct clade, well separated from ORs (olfactory receptors) and other class A GPCRs. Also these repertoires consist of several families and subfamilies, a number of which are common to fugu, tetraodon, stickleback and medaka. Like all other TAARs identified to date, cichlid TAARs have a characteristic two-dimensional structure and contain a number of amino-acid motifs or amino acids, such cysteine, in particular conserved positions. CONCLUSIONS: Little is known about the functions of TAARs: in most cases their ligands have yet to be identified, partly because appropriate methods for such investigations have not been developed. Sequences analyses and comparisons of TAARs in several animal species, here fishes living in the same environment, should help reveal their roles and whether they are complementary to that of ORs.

Inventory of the cichlid olfactory receptor gene repertoires: identification of olfactory genes with more than one coding exon.

BACKGROUND: To help understand the molecular mechanisms underlying the remarkable phenotypic diversity displayed by cichlids, the genome sequences of O. niloticus, P. nyererei, H. burtoni, N. brichardi and M. zebra were recently determined. Here, we present the contents of the olfactory receptor (OR) repertoires in the genomes of these five fishes. RESULTS: We performed an exhaustive TBLASTN search of the five cichlid genomes to identify their OR repertoires as completely as possible. We used as bait a set of ORs described in the literature. The cichlid repertoires thereby extracted contained large numbers of complete genes (O. niloticus 158; H. burtoni 90; M. zebra 102; N. brichardi 69; P. nyererei 88), a small numbers of pseudogenes and many "edge genes" corresponding to incomplete genes located at the ends of contigs. A phylogenetic tree was constructed and showed these repertoires include a large number of families and subfamilies. It also allowed the identification of a large number of OR analogues between cichlids with very high amino-acid identity (≥ 99%). Nearly 9% of the full-length cichlid OR genes are composed of several coding exons. This is very unusual for vertebrate OR genes. Nevertheless, the evidence is strong, and includes the donor and acceptor splice junction sequences; also, the positions of these genes in the phylogenetic tree indicate that they constitute subfamilies well apart from non-OR G protein-coupled receptor families. CONCLUSIONS: Cichlid OR repertoires are made up of a larger number of genes and fewer pseudogenes than those in other teleosts except zebrafish. These ORs share all identified properties common to all fish ORs; however, the large number of families and subfamilies, each containing few ORs implies that they have evolved more rapidly. This high level of OR diversity is consistent with the substantial phenotypic diversity that characterizes cichlids.

Strong mutator phenotype drives faster adaptation from growth on glucose to growth on acetate in Salmonella.

The metabolic adaptation of strong mutator strains was studied to better understand the link between the strong mutator phenotype and virulence. Analysis of the growth curves of isogenic strains of Salmonella, which were previously grown in M63 glucose media, revealed that the exponential phase of growth was reached earlier in an M63 acetate medium with strong mutator strains (mutated in mutS or in mutL) than with normomutator strains (P<0.05). Complemented strains confirmed the direct role of the strong mutator phenotype in this faster metabolic adaptation to the assimilation of acetate. In a mixed cell population, proliferation of strong mutators over normomutators was observed when the carbon source was switched from glucose to acetate. These results add to the sparse body of knowledge about strong mutators and highlight the selective advantage conferred by the strong mutator phenotype to adapt to a switch of carbon source in the environment. This work may provide clinically useful information given that there is a high prevalence of strong mutators among pathogenic strains of Salmonella and that acetate is the principal short chain fatty acid of the human terminal ileum and colon where Salmonella infection is localized.

Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers.

Transcription factors (TFs) bind specifically to discrete regions of mammalian genomes called cis-regulatory elements. Among those are enhancers, which play key roles in regulation of gene expression during development and differentiation. Despite the recognized central regulatory role exerted by chromatin in control of TF functions, much remains to be learned regarding the chromatin structure of enhancers and how it is established. Here, we have analyzed on a genomic-scale enhancers that recruit FOXA1, a pioneer transcription factor that triggers transcriptional competency of these cis-regulatory sites. Importantly, we found that FOXA1 binds to genomic regions showing local DNA hypomethylation and that its cell-type-specific recruitment to chromatin is linked to differential DNA methylation levels of its binding sites. Using neural differentiation as a model, we showed that induction of FOXA1 expression and its subsequent recruitment to enhancers is associated with DNA demethylation. Concomitantly, histone H3 lysine 4 methylation is induced at these enhancers. These epigenetic changes may both stabilize FOXA1 binding and allow for subsequent recruitment of transcriptional regulatory effectors. Interestingly, when cloned into reporter constructs, FOXA1-dependent enhancers were able to recapitulate their cell type specificity. However, their activities were inhibited by DNA methylation. Hence, these enhancers are intrinsic cell-type-specific regulatory regions of which activities have to be potentiated by FOXA1 through induction of an epigenetic switch that includes notably DNA demethylation.

Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers.

Enhancers are developmentally controlled transcriptional regulatory regions whose activities are modulated through histone modifications or histone variant deposition. In this study, we show by genome-wide mapping that the newly discovered deoxyribonucleic acid (DNA) modification 5-hydroxymethylcytosine (5hmC) is dynamically associated with transcription factor binding to distal regulatory sites during neural differentiation of mouse P19 cells and during adipocyte differentiation of mouse 3T3-L1 cells. Functional annotation reveals that regions gaining 5hmC are associated with genes expressed either in neural tissues when P19 cells undergo neural differentiation or in adipose tissue when 3T3-L1 cells undergo adipocyte differentiation. Furthermore, distal regions gaining 5hmC together with H3K4me2 and H3K27ac in P19 cells behave as differentiation-dependent transcriptional enhancers. Identified regions are enriched in motifs for transcription factors regulating specific cell fates such as Meis1 in P19 cells and PPARγ in 3T3-L1 cells. Accordingly, a fraction of hydroxymethylated Meis1 sites were associated with a dynamic engagement of the 5-methylcytosine hydroxylase Tet1. In addition, kinetic studies of cytosine hydroxymethylation of selected enhancers indicated that DNA hydroxymethylation is an early event of enhancer activation. Hence, acquisition of 5hmC in cell-specific distal regulatory regions may represent a major event of enhancer progression toward an active state and participate in selective activation of tissue-specific genes.

Complete genome sequence of the strong mutator Salmonella enterica subsp. enterica serotype Heidelberg strain B182.

In bacteria, normal mutation frequencies are mostly around 10(-10) per base pair. However, there exists natural isolates, called "mutators," that exhibit permanent mutation occurrences up to 1,000-fold greater than usual. As mutations play essential roles, particularly in the evolution of antibiotic resistance, bacteria showing elevated mutation rates could have an important responsibility in the emergence of antibiotic resistance, especially in the clinical background. In this announcement, we report the first complete genome sequence of the Salmonella enterica subsp. enterica serotype Heidelberg B182 mutator strain, isolated from bovine feces (France), which consists of a 4,750,465-bp circular chromosome (cB182_4750; GC, 52.2%) and one circular plasmid of 37,581 bp (pB182_37; GC, 42.8%).

SORGOdb: Superoxide Reductase Gene Ontology curated DataBase.

BACKGROUND: Superoxide reductases (SOR) catalyse the reduction of superoxide anions to hydrogen peroxide and are involved in the oxidative stress defences of anaerobic and facultative anaerobic organisms. Genes encoding SOR were discovered recently and suffer from annotation problems. These genes, named sor, are short and the transfer of annotations from previously characterized neelaredoxin, desulfoferrodoxin, superoxide reductase and rubredoxin oxidase has been heterogeneous. Consequently, many sor remain anonymous or mis-annotated. DESCRIPTION: SORGOdb is an exhaustive database of SOR that proposes a new classification based on domain architecture. SORGOdb supplies a simple user-friendly web-based database for retrieving and exploring relevant information about the proposed SOR families. The database can be queried using an organism name, a locus tag or phylogenetic criteria, and also offers sequence similarity searches using BlastP. Genes encoding SOR have been re-annotated in all available genome sequences (prokaryotic and eukaryotic (complete and in draft) genomes, updated in May 2010). CONCLUSIONS: SORGOdb contains 325 non-redundant and curated SOR, from 274 organisms. It proposes a new classification of SOR into seven different classes and allows biologists to explore and analyze sor in order to establish correlations between the class of SOR and organism phenotypes. SORGOdb is freely available at http://sorgo.genouest.org/index.php.

CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources.

BACKGROUND: The functions of proteins are strongly related to their localization in cell compartments (for example the cytoplasm or membranes) but the experimental determination of the sub-cellular localization of proteomes is laborious and expensive. A fast and low-cost alternative approach is in silico prediction, based on features of the protein primary sequences. However, biologists are confronted with a very large number of computational tools that use different methods that address various localization features with diverse specificities and sensitivities. As a result, exploiting these computer resources to predict protein localization accurately involves querying all tools and comparing every prediction output; this is a painstaking task. Therefore, we developed a comprehensive database, called CoBaltDB, that gathers all prediction outputs concerning complete prokaryotic proteomes. DESCRIPTION: The current version of CoBaltDB integrates the results of 43 localization predictors for 784 complete bacterial and archaeal proteomes (2.548.292 proteins in total). CoBaltDB supplies a simple user-friendly interface for retrieving and exploring relevant information about predicted features (such as signal peptide cleavage sites and transmembrane segments). Data are organized into three work-sets ("specialized tools", "meta-tools" and "additional tools"). The database can be queried using the organism name, a locus tag or a list of locus tags and may be browsed using numerous graphical and text displays. CONCLUSIONS: With its new functionalities, CoBaltDB is a novel powerful platform that provides easy access to the results of multiple localization tools and support for predicting prokaryotic protein localizations with higher confidence than previously possible. CoBaltDB is available at http://www.umr6026.univ-rennes1.fr/english/home/research/basic/software/cobalten.

Membrane Proteocomplexome of Campylobacter jejuni Using 2-D Blue Native/SDS-PAGE Combined to Bioinformatics Analysis.

Campylobacter is the leading cause of the human bacterial foodborne infections in the developed countries. The perception cues from biotic or abiotic environments by the bacteria are often related to bacterial surface and membrane proteins that mediate the cellular response for the adaptation of Campylobacter jejuni to the environment. These proteins function rarely as a unique entity, they are often organized in functional complexes. In C. jejuni, these complexes are not fully identified and some of them remain unknown. To identify putative functional multi-subunit entities at the membrane subproteome level of C. jejuni, a holistic non a priori method was addressed using two-dimensional blue native/Sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) in strain C. jejuni 81-176. Couples of acrylamide gradient/migration-time, membrane detergent concentration and hand-made strips were optimized to obtain reproducible extraction and separation of intact membrane protein complexes (MPCs). The MPCs were subsequently denatured using SDS-PAGE and each spot from each MPCs was identified by mass spectrometry. Altogether, 21 MPCs could be detected including multi homo-oligomeric and multi hetero-oligomeric complexes distributed in both inner and outer membranes. The function, the conservation and the regulation of the MPCs across C. jejuni strains were inspected by functional and genomic comparison analyses. In this study, relatedness between subunits of two efflux pumps, CmeABC and MacABputC was observed. In addition, a consensus sequence CosR-binding box in promoter regions of MacABputC was present in C. jejuni but not in Campylobacter coli. The MPCs identified in C. jejuni 81-176 membrane are involved in protein folding, molecule trafficking, oxidative phosphorylation, membrane structuration, peptidoglycan biosynthesis, motility and chemotaxis, stress signaling, efflux pumps and virulence.

Maternal Linoleic Acid Overconsumption Alters Offspring Gut and Adipose Tissue Homeostasis in Young but Not Older Adult Rats.

Maternal n-6 polyunsaturated fatty acids (PUFA) consumption during gestation and lactation can predispose offspring to the development of metabolic diseases such as obesity later in life. However, the mechanisms underlying the potential programming effect of n-6 PUFA upon offspring physiology are not yet all established. Herein, we investigated the effects of maternal and weaning linoleic acid (LA)-rich diet interactions on gut intestinal and adipose tissue physiology in young (3-month-old) and older (6-month-old) adult offspring. Pregnant rats were fed a control diet (2% LA) or an LA-rich diet (12% LA) during gestation and lactation. At weaning, offspring were either maintained on the maternal diet or fed the other diet for 3 or 6 months. At 3 months of age, the maternal LA-diet favored low-grade inflammation and greater adiposity, while at 6 months of age, offspring intestinal barrier function, adipose tissue physiology and hepatic conjugated linoleic acids were strongly influenced by the weaning diet. The maternal LA-diet impacted offspring cecal microbiota diversity and composition at 3 months of age, but had only few remnant effects upon cecal microbiota composition at 6 months of age. Our study suggests that perinatal exposure to high LA levels induces a differential metabolic response to weaning diet exposure in adult life. This programming effect of a maternal LA-diet may be related to the alteration of offspring gut microbiota.

Analyzing stochastic transcription to elucidate the nucleoid's organization.

BACKGROUND: The processes of gene transcription, translation, as well as the reactions taking place between gene products, are subject to stochastic fluctuations. These stochastic events are being increasingly examined as it emerges that they can be crucial in the cell's survival. In a previous study we had examined the transcription patterns of two bacterial species (Escherichia coli and Bacillus subtilis) to elucidate the nucleoid's organization. The basic idea is that genes that share transcription patterns, must share some sort of spatial relationship, even if they are not close to each other on the chromosome. We had found that picking any gene at random, its transcription will be correlated with genes at well-defined short - as well as long-range distances, leaving the explanation of the latter an open question. In this paper we study the transcription correlations when the only transcription taking place is stochastic, in other words, no active or "deterministic" transcription takes place. To this purpose we use transcription data of Sinorhizobium meliloti. RESULTS: Even when only stochastic transcription takes place, the co-expression of genes varies as a function of the distance between genes: we observe again the short-range as well as the regular, long-range correlation patterns. CONCLUSION: We explain these latter with a model based on the physical constraints acting on the DNA, forcing it into a conformation of groups of a few successive large and transcribed loops, which are evenly spaced along the chromosome and separated by small, non-transcribed loops. We discuss the question about the link between shared transcription patterns and physiological relationship and come to the conclusion that when genes are distantly placed along the chromosome, the transcription correlation does not imply a physiological relationship.

OxyGene: an innovative platform for investigating oxidative-response genes in whole prokaryotic genomes.

BACKGROUND: Oxidative stress is a common stress encountered by living organisms and is due to an imbalance between intracellular reactive oxygen and nitrogen species (ROS, RNS) and cellular antioxidant defence. To defend themselves against ROS/RNS, bacteria possess a subsystem of detoxification enzymes, which are classified with regard to their substrates. To identify such enzymes in prokaryotic genomes, different approaches based on similarity, enzyme profiles or patterns exist. Unfortunately, several problems persist in the annotation, classification and naming of these enzymes due mainly to some erroneous entries in databases, mistake propagation, absence of updating and disparity in function description. DESCRIPTION: In order to improve the current annotation of oxidative stress subsystems, an innovative platform named OxyGene has been developed. It integrates an original database called OxyDB, holding thoroughly tested anchor-based signatures associated to subfamilies of oxidative stress enzymes, and a new anchor-driven annotator, for ab initio detection of ROS/RNS response genes. All complete Bacterial and Archaeal genomes have been re-annotated, and the results stored in the OxyGene repository can be interrogated via a Graphical User Interface. CONCLUSION: OxyGene enables the exploration and comparative analysis of enzymes belonging to 37 detoxification subclasses in 664 microbial genomes. It proposes a new classification that improves both the ontology and the annotation of the detoxification subsystems in prokaryotic whole genomes, while discovering new ORFs and attributing precise function to hypothetical annotated proteins. OxyGene is freely available at: http://www.umr6026.univ-rennes1.fr/english/home/research/basic/software.

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021.

BACKGROUND: Small untranslated RNAs (sRNAs) seem to be far more abundant than previously believed. The number of sRNAs confirmed in E. coli through various approaches is above 70, with several hundred more sRNA candidate genes under biological validation. Although the total number of sRNAs in any one species is still unclear, their importance in cellular processes has been established. However, unlike protein genes, no simple feature enables the prediction of the location of the corresponding sequences in genomes. Several approaches, of variable usefulness, to identify genomic sequences encoding sRNA have been described in recent years. RESULTS: We used a combination of in silico comparative genomics and microarray-based transcriptional profiling. This approach to screening identified ~60 intergenic regions conserved between Sinorhizobium meliloti and related members of the alpha-proteobacteria sub-group 2. Of these, 14 appear to correspond to novel non-coding sRNAs and three are putative peptide-coding or 5' UTR RNAs (ORF smaller than 100 aa). The expression of each of these new small RNA genes was confirmed by Northern blot hybridization. CONCLUSION: Small non coding RNA (sra) genes can be found in the intergenic regions of alpha-proteobacteria genomes. Some of these sra genes are only present in S. meliloti, sometimes in genomic islands; homologues of others are present in related genomes including those of the pathogens Brucella and Agrobacterium.

Characterization and expression patterns of Sinorhizobium meliloti tmRNA (ssrA).

tmRNA (ssrA) in Sinorhizobium meliloti is a small RNA annotated by homology with the Bradyrhizobium japonicum sra molecule. Here, this molecule is described in Sinorhizobium meliloti as a model for such molecules in Alphaproteobacteria subgroup-2. Northern blot analysis and mapping of both 5' and 3' ends of this tmRNA allow the identification of two pieces: a 214 nt mRNA-like domain and an 82 nt tRNA-like domain, both highly stable, whereas the premature form is unstable. Transcriptional studies reveal that Sinorhizobium meliloti tmRNA is mainly expressed during growth resumption, replication initiation and various stress responses.