Selection Acts on DNA Secondary Structures to Decrease Transcriptional Mutagenesis

Single-stranded DNA is more subject to mutation than double stranded. During transcription, DNA is transiently single stranded and therefore subject to higher mutagenesis. However, if local intra-strand secondary structures are formed, some bases will be paired and therefore less sensitive to mutation than unpaired bases. Using complete genome sequences of Escherichia coli, we show that local intra-strand secondary structures can, as a consequence, be used to define an index of transcription-driven mutability. At gene level, we show that natural selection has favoured a reduced transcription-driven mutagenesis via the higher than expected frequency of occurrence of intra-strand secondary structures. Such selection is stronger in highly expressed genes and suggests a sequence-dependent way to control mutation rates and a novel form of selection affecting the evolution of synonymous mutations

aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species

<p>Abstract</p> <p>Background</p> <p>Previous studies have established a correlation between electrophoretic polymorphism of esterase B, and virulence and phylogeny of <it>Escherichia coli</it>. Strains belonging to the phylogenetic group B2 are more frequently implicated in extraintestinal infections and include esterase B₂variants, whereas phylogenetic groups A, B1 and D contain less virulent strains and include esterase B₁variants. We investigated esterase B as a marker of phylogeny and/or virulence, in a thorough analysis of the esterase B-encoding gene.</p> <p>Results</p> <p>We identified the gene encoding esterase B as the acetyl-esterase gene (<it>aes</it>) using gene disruption. The analysis of <it>aes </it>nucleotide sequences in a panel of 78 reference strains, including the <it>E. coli </it>reference (ECOR) strains, demonstrated that the gene is under purifying selection. The phylogenetic tree reconstructed from <it>aes </it>sequences showed a strong correlation with the species phylogenetic history, based on multi-locus sequence typing using six housekeeping genes. The unambiguous distinction between variants B₁and B₂by electrophoresis was consistent with Aes amino-acid sequence analysis and protein modelling, which showed that substituted amino acids in the two esterase B variants occurred mostly at different sites on the protein surface. Studies in an experimental mouse model of septicaemia using mutant strains did not reveal a direct link between <it>aes </it>and extraintestinal virulence. Moreover, we did not find any genes in the chromosomal region of <it>aes </it>to be associated with virulence.</p> <p>Conclusion</p> <p>Our findings suggest that <it>aes </it>does not play a direct role in the virulence of <it>E. coli </it>extraintestinal infection. However, this gene acts as a powerful marker of phylogeny, illustrating the extensive divergence of B2 phylogenetic group strains from the rest of the species.</p

Daily transcriptomes of the copepod Calanus finmarchicus during the summer solstice at high Arctic latitudes

The zooplankter Calanus finmarchicus is a member of the so-called “Calanus Complex”, a group of copepods that constitutes a key element of the Arctic polar marine ecosystem, providing a crucial link between primary production and higher trophic levels. Climate change induces the shift of C. finmarchicus to higher latitudes with currently unknown impacts on its endogenous timing. Here we generated a daily transcriptome of C. finmarchicus at two high Arctic stations, during the more extreme time of Midnight Sun, the summer solstice. While the southern station (74.5 °N) was sea ice-free, the northern one (82.5 °N) was sea ice-covered. The mRNAs of the 42 samples have been sequenced with an average of 126 ± 5 million reads (mean ± SE) per sample, and aligned to the reference transcriptome. We detail the quality assessment of the datasets and the complete annotation procedure, providing the possibility to investigate daily gene expression of this ecologically important species at high Arctic latitudes, and to compare gene expression according to latitude and sea ice-coverage

Widely rhythmic transcriptome in Calanus finmarchicus during the high Arctic summer solstice period

Solar light/dark cycles and seasonal photoperiods underpin daily and annual rhythms of life on Earth. Yet, the Arctic is characterized by severalmonths of permanent illumination (‘‘midnight sun’’). To determine the persistence of 24h rhythms during the midnight sun, we investigated transcriptomic dynamics in the copepod Calanus finmarchicus during the summer solstice period in the Arctic, with the lowest diel oscillation and the highest altitude of the sun’s position. Here we reveal that in these extreme photic conditions, a widely rhythmic daily transcriptome exists, showing that very weak solar cues are sufficient to entrain organisms. Furthermore, at extremely high latitudes and under sea-ice, gene oscillations become re-organized to include <24h rhythms. Environmental synchronization may therefore be modulated to include non-photic signals (i.e. tidal cycles). The ability of zooplankton to be synchronized by extremely weak diel and potentially tidal cycles, may confer an adaptive temporal reorganization of biological processes at high latitudes

Development of an in vitro biofilm model for the study of the impact of fluoroquinolones on sewer biofilm microbiota

Sewer biofilms are likely to constitute hotspots for selecting and accumulating antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). This study aimed to optimize culture conditions to obtain in vitro biofilms, mimicking the biofilm collected in sewers, to study the impact of fluoroquinolones (FQs) on sewer biofilm microbiota. Biofilms were grown on coupons in CDC Biofilm Reactors®, continuously fed with nutrients and inoculum (1/100 diluted wastewater). Different culture conditions were tested: (i) initial inoculum: diluted wastewater with or without sewer biofilm, (ii) coupon material: concrete vs. polycarbonate, and (iii) time of culture: 7 versus 14 days. This study found that the biomass was highest when in vitro biofilms were formed on concrete coupons. The biofilm taxonomic diversity was not affected by adding sewer biofilm to the initial inoculum nor by the coupon material. Pseudomonadales, Burkholderiales and Enterobacterales dominated in the sewer biofilm composition, whereas in vitro biofilms were mainly composed of Enterobacterales. The relative abundance of qnrA, B, D and S genes was higher in in vitro biofilms than sewer biofilm. The resistome of sewer biofilm showed the highest Shannon diversity index compared to wastewater and in vitro biofilms. A PCoA analysis showed differentiation of samples according to the nature of the sample, and a Procrustes analysis showed that the ARG changes observed were linked to changes in the microbial community. The following growing conditions were selected for in vitro biofilms: concrete coupons, initial inoculation with sewer biofilm, and a culture duration of 14 days. Then, biofilms were established under high and low concentrations of FQs to validate our in vitro biofilm model. Fluoroquinolone exposure had no significant impact on the abundance of qnr genes, but high concentration exposure increased the proportion of mutations in gyrA (codons S83L and D87N) and parC (codon S80I). In conclusion, this study allowed the determination of the culture conditions to develop an in vitro model of sewer biofilm; and was successfully used to investigate the impact of FQs on sewer microbiota. In the future, this setup could be used to clarify the role of sewer biofilms in disseminating resistance to FQs in the environment

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the ∼18,000 families of orthologous genes, we found ∼2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome

The BioMart community portal: an innovative alternative to large, centralized data repositories.

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations

Impact des processus de mutation et de recombinaison sur la diversité génomique au sein de l’espèce Escherichia coli

Escherichia coli represents the major part of commensal aero-anaerobic microbiota of the host’s digestive tract. Though, E. coli is also one of the most frequently encountered species in human and animal pathology. This is one of the most studied and the best known bacterial species. The evolution of genomes within the species is based on two distinct mechanisms: mutation and recombination that generate genetic diversity on which natural selection can operate. In our work, we were interested in those processes and the traces they leave in the genomes. We have at first described a form of variable mutability along the genome which is linked to the existence of local secondary DNA structure: the transcriptional mutability. We were able to quantify this mutagenesis and reveal a selective104response in the genome to limit its effects. Recombination is known to blur the phylogenetic signal significantly. Then, we have shown by a comparative genomics approach that, despite a relatively high recombination rate, the establishment of a robust phylogeny was possible. In addition, we have shown that the many acquisitions and loss of genes occurring in the genomes of different E. coli strains were located preferentially at certain sites. Lastly, we have used the phylogenetic structure of the species to study taxonomic and epidemiologic applications.Escherichia coli constitue la majeure partie de la flore microbienne commensale aéro-anaérobie du tube digestif de l’hôte. Pourtant E. coli est aussi une des espèces les plus fréquemment rencontrées en pathologie humaine et animale. C’est l’une des espèces bactériennes les plus étudiées et les plus connues. L’évolution des génomes au sein de l’espèce repose sur deux mécanismes distincts : la mutation et la recombinaison, qui génèrent une diversité génétique sur laquelle la sélection naturelle peut opérer. Dans notre travail, nous nous sommes intéressés à ces processus et aux traces qu’ils laissent dans les génomes. Nous avons, en premier lieu, décrit une forme de mutabilité variable le long du génome car liée à l‘existence de structure secondaire locale de l’ADN : la mutabilité transcriptionnelle. Nous avons pu d’une part quantifier cette mutagenèse et d’autre part révéler une réponse sélective au sein du génome pour en limiter les effets. La recombinaison, quant à elle, est connue pour brouiller le signal phylogénétique de manière importante. En second lieu, nous avons montré par une approche de génomique comparative que, malgré un taux relativement élevé de recombinaison, l’établissement d’une phylogénie robuste était possible. De plus, nous avons mis en évidence que les nombreuses acquisitions et pertes de gènes dans le génome des différentes souches d’E. coli se situaient préférentiellement à certains sites. Enfin, nous avons utilisé la structure phylogénétique de l’espèce à des applications taxonomiques et épidémiologiques