title: Gene socialization: gene order, GC content and gene silencing in Salmonella.
abstract: BACKGROUND
  Genes of conserved order in bacterial genomes tend to evolve slower than genes whose order is not conserved. In addition, genes with a GC content lower than the GC content of the resident genome are known to be selectively silenced by the histone-like nucleoid structuring protein (H-NS) in Salmonella.
  
  
  RESULTS
  In this study, we use a comparative genomics approach to demonstrate that in Salmonella, genes whose order is not conserved (or genes without homologs) in closely related bacteria possess a significantly lower average GC content in comparison to genes that preserve their relative position in the genome. Moreover, these genes are more frequently targeted by H-NS than genes that have conserved their genomic neighborhood. We also observed that duplicated genes that do not preserve their genomic neighborhood are, on average, under less selective pressure.
  
  
  CONCLUSIONS
  We establish a strong association between gene order, GC content and gene silencing in a model bacterial species. This analysis suggests that genes that are not under strong selective pressure (evolve faster than others) in Salmonella tend to accumulate more AT-rich mutations and are eventually silenced by H-NS. Our findings may establish new approaches for a better understanding of bacterial genome evolution and function, using information from functional and comparative genomics.
authors.affiliation: Division of Medical Sciences, University of Crete Medical School, Heraklion 71110, Crete, Greece. papnikol@med.uoc.gr
authors.forename: Nikolas
authors.initials: N
authors.lastname: Papanikolaou
authors.forename: Kalliopi
authors.initials: K
authors.lastname: Trachana
authors.forename: Theodosios
authors.initials: T
authors.lastname: Theodosiou
authors.forename: Vasilis J
authors.initials: VJ
authors.lastname: Promponas
authors.forename: Ioannis
authors.initials: I
authors.lastname: Iliopoulos
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D001482:Base Composition; D055028:Comparative Genomic Hybridization; D004269:DNA, Bacterial / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D019143:Evolution, Molecular; D023061:Gene Order; D020868:Gene Silencing; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D012475:Salmonella / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; C031908:H-NS protein, bacteria