Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

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

For all author emails, please log on.

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

Published: 11 December 2009

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.