The effect of methylation on some biological parameters in Salmonella enterica serovar Typhimurium.

International audienceCell growth is tightly coupled to DNA replication and its methylation [Proc Natl Acad Sci U S A 93 (1996) 12206-12211]. In a culture medium, growing of Salmonella  Typhimurium (S. Typhimurium) mutant cells (dam(-)) decreased (2.5 fold) relative to the wild type strain (dam(+)). In this study, we show that the reason for this growth deficiency is due to the DNA methylation. The absence of a Dam methyltransferase protein results in poor growth efficiency and disturbs the synchrony of replication initiation in vivo, as evaluated by flow cytometry. On the other hand, we show that lack of methylation could increase the DNA response to thermal stress (decreasing the DNA melting temperature, T(m)), and the reason for this effect is due to the methylation status and not to the number of guanine and cytosine bases (G+C) in the duplex DNA. Our results show that methylation is an epigenetic factor that may play a key role in the cell growth, the synchrony of DNA replication [C R Biologies 330 (2007) 576-580] and the stress protection

Mutant phenotypes for thousands of bacterial genes of unknown function.

One-third of all protein-coding genes from bacterial genomes cannot be annotated with a function. Here, to investigate the functions of these genes, we present genome-wide mutant fitness data from 32 diverse bacteria across dozens of growth conditions. We identified mutant phenotypes for 11,779 protein-coding genes that had not been annotated with a specific function. Many genes could be associated with a specific condition because the gene affected fitness only in that condition, or with another gene in the same bacterium because they had similar mutant phenotypes. Of the poorly annotated genes, 2,316 had associations that have high confidence because they are conserved in other bacteria. By combining these conserved associations with comparative genomics, we identified putative DNA repair proteins; in addition, we propose specific functions for poorly annotated enzymes and transporters and for uncharacterized protein families. Our study demonstrates the scalability of microbial genetics and its utility for improving gene annotations