E P Rocha

..A recent report by Drummond et al. suggests that the dominant role of expression levels in slowing the rate of protein evolution stems from selection for translation robustness...

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..Hence, although this method has allowed uncovering some of mechanisms leading to rearrangements, we still ignore the forces that differentially shape selection upon genome stability in different species...

..Efficient natural transformation in Neisseria requires the presence of short DNA uptake sequences (DUSs). Doubts remain whether DUSs propagate by pure selfish molecular drive or are selected for 'safe sex' among conspecifics...

..halodurans. Finally, we propose a more extended model based on the analysis of the substitution asymmetries of CHLAMYDIA: This model fits well with the data provided by bacterial genomes presenting strong strand bias...

..They also indicate that when a control for this variable is included, essentiality plays no significant role in the rate of protein evolution in bacteria, as is the case in eukaryotes...

..Ultimately, the understanding of the interplay between these different elements will allow a better understanding of bacterial genetics and evolution...

..As a result, the clash between elements generating rearrangements and chromosome organization is a classic case of evolutionary conflict...

..The assembly of these results indicates that shortly spaced repeats are key players in the dynamics of genome evolution...

..The presence of PolC is not correlated with compositional strand bias, suggesting that the two biases result from different types of structural asymmetry...

..We suggest that the higher energy cost and limited availability of G and C over A and T/U could be a basis for the understanding of these differences...

..Probably to avoid such events, mycoplasmas strongly avoid inverse repeats, in comparison to co-oriented repeats...

..As a consequence, RMSs constitute a nontrivial third player in the host-parasite relationship between bacteria and phages...

..The correlation of the spatial distribution of repeats and the absence of insertion sequences in a genome may indicate, in the framework of our model, that mechanisms aiming at their avoidance/elimination have been developed...

..subtilis revealed a similar amino acid bias near both termini of proteins consisting of over-representation of hydrophilic residues. This bias near the stop codon is partially release-factor specific...

..These results indicate that essentiality plays a fundamental role in the distribution of genes in most bacterial genomes...

..This may reinforce a recently proposed hypothesis of a selfish gene phenomena in the transfer of restriction/modification systems in bacteria...

..In this article we discuss the various functional and evolutionary roles of these repeats, focusing in particular on their role in terms of genome stability, gene transfer, and antigenic variation...

..They should then be regarded as truly essential genes...

..g., transposases, or the differences in the recombination machinery among bacteria. These results shed light on the challenges imposed on the genome structure by the presence of inverted repeats...

..We use these results to investigate the breakpoint distribution in several prokaryotic genomes...

..AVAILABILITY: http://wwwabi.snv.jussieu.fr/public/RepSeek/..

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..Indeed, IS abundance increases quickly with genome size, which is the exact inverse trend found for the density of genes under strong selection such as essential genes. Hence, for ISs, the bigger the genome the better...

..This suggests a scenario of massive genome reduction through many nearly simultaneous pseudogenization events, leading to a highly specialized pathogen...

..We also refer to programs freely available to analyse strand asymmetry...

..However, genomes harbor two very different categories of genes: those genes present in a majority of organisms - persistent genes - and those present in very few organisms - rare genes...

..AVAILABILITY: http://bioserv.rpbs.jussieu.fr/swelfe. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online...

..This reinforces the need for caution in the interpretation of results derived from closely related taxa...

..pneumoniae and could represent targets for future vaccine development...

..We show that the model is consistent with the asymmetric distribution of highly expressed genes and of stress response genes in Escherichia coli and Bacillus subtilis. The model offers a framework for interpreting data from genomics...

..This suggests the existence of alternative mechanisms contributing to CpG deficiency in bacteria...

..Here we show, however, that in Bacillus subtilis and Escherichia coli, essentiality (the transcript product), not expressiveness (the collision rate), selectively drives the biased gene distribution...

..Adding to its originality, P. haloplanktis further differs from its marine counterparts with recruitment of a plasmid origin of replication for its second chromosome...

..We conclude that, because of the critical effect of time since divergence, inter-taxa comparisons are only possible by comparing trajectories of dN/dS over time and it is not valid to compare taxa on the basis of single time points...

..It also provides new evidence that a selective force for the optimization of the translation machinery is the maximization of growth...

..Together, these results demonstrate that replication-associated gene dosage is an important determinant of chromosome organisation and dynamics, especially among fast-growing bacteria...

..This work reveals that the high plasticity of eukaryotic genomes results from rearrangement rates that vary between lineages but also at different evolutionary times of a given lineage...

..These observations support the hypothesis that recombination occurs between the mgpB gene and MgPar sequences and that the resulting antigenically distinct MgPa variants may contribute to immune evasion and persistence of infection...

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..We further demonstrate that this compartment is associated with the nucleolus, hereby defined for the first time in P.falciparum...