The emergence of pathogenic strains of enteric bacteria and their adaptation to unique niches are associated with the acquisition of foreign DNA segments termed 'genetic islands'. We explored these islands for the occurrence of small RNA (sRNA) encoding genes. Previous systematic screens for enteric bacteria sRNAs were mainly carried out using the laboratory strain Escherichia coli K12, leading to the discovery of < 80 new sRNA genes. These searches were based on conservation within closely related members of enteric bacteria and thus, sRNAs, unique to pathogenic strains were excluded. Here we describe the identification and characterization of 19 novel unique sRNA genes encoded within the 'genetic islands' of the virulent strain Salmonella typhimurium. We show that the expression of many of the island-encoded genes is associated with stress conditions and stationary phase. Several of these sRNA genes are induced when Salmonella resides within macrophages. One sRNA, IsrJ, was further examined and found to affect the translocation efficiency of virulence-associated effector proteins into nonphagocytic cells. In addition, we report that unlike the majority of the E. coli sRNAs that are trans regulators, many of the island-encoded sRNAs affect the expression of cis-encoded genes. Our study suggests that the island encoded sRNA genes play an important role within the network that regulates bacterial adaptation to environmental changes and stress conditions and thus controls virulence.
Bibliographical noteFunding Information:
We are grateful to Michael McClelland for generously providing the sequences of the islands of S. typhimurium and to Hilla Giladi for useful comments on the manuscript. We thank Yaniv Baum for technical assistance. Supported by The Israel Science Foundation founded by The Israel Academy of Sciences and Humanities, grant number 663/02, The United States-Israel Binational Science Foundation, grant number 2001032, The Israel Science Foundation-Bikura Program, grant number 1342/05, The Israeli Ministry of Science, grant number 3/2559 and by BACRNAs, a Specific Targeted Research Project supported by European Union’s FP6 Life Science, Genomics and Biotechnology for Health, LSHM-CT-2005-018618. (SA). Funding to pay the Open Access publication charges for this article was provided by BACRNAs, a Specific Targeted Research Project supported by European Union’s FP6 Life Science, Genomics and Biotechnology for Health, LSHM-CT-2005-018618.