Open Access Research article

Gene socialization: gene order, GC content and gene silencing in Salmonella

Nikolas Papanikolaou1, Kalliopi Trachana2, Theodosios Theodosiou3, Vasilis J Promponas4* and Ioannis Iliopoulos1*

Author Affiliations

1 Division of Medical Sciences, University of Crete Medical School, Heraklion 71110, Crete, Greece

2 EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany

3 Department of Informatics, School of Natural Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece

4 Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, CY 1678, Nicosia, Cyprus

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BMC Genomics 2009, 10:597  doi:10.1186/1471-2164-10-597

Published: 11 December 2009



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.


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.


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.