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of DNA and protein sequences. Brief Bioinform 2008,9(4):299–306.PubMedCrossRef Authors’ contributions J.C., A.H. and R.R.C. designed research; T.S.B., D.C.B., J.C.D., C.S.H., N.A.H. performed research; J.C., C.J.G., N.A.H., B.J.H., and #Selleck JPH203 randurls[1|1|,|CHEM1|]# S.Y.C. analyzed data; B.J.H. and R.R.C. wrote the paper. All authors have read and approved the manuscript.”
“Background The acquisition of horizontally transferred genes plays an important role in prokaryotic evolution [1]. The colonization of Selleck MK5108 new ecological niches is often enabled by the acquisition of foreign genes, which can be transmitted by a large variety of mobile genetic elements (MGE) present in individual members of the microbial community. In terms of evolutionary success, it is thus interesting to understand how different mobile DNA elements control their mobility and may adapt to their bacterial host [2]. Various classes of MGE are known, the most well-studied

of which are plasmids and bacteriophages [3, 4]. Plasmids, apart from certain exceptions such as the F-episome in Escherichia coli, generally occur as extrachromosomal DNA in the bacterial cell. An important aspect of their life-style, therefore, is to ensure replication, stability and maintenance in the host cell [5], and a variety of control

mechanisms have evolved hereto 4��8C [6]. Conjugative plasmids encode and orchestrate specific machineries to produce the transfer system dedicated to their own distribution (e.g., type IV secretion system) [7]. By contrast, temperate bacteriophages insert into the host’s chromosome, where they can remain silent and are co-replicated with the host’s DNA for many generations, or are eventually genetically defunctionalized. Feedback regulatory systems silence phage behaviour in the temperate form, but can very rapidly induce the lytic phase (e.g., upon SOS response), upon which thousands of phage particles are produced to commence a new infection cycle [8, 9]. More recently, a large new class of DNA elements has been recognized that contributes importantly to bacterial genome evolution via horizontal gene transfer. Most of these have been detected by comparative genome sequencing and have in general been named ‘genomic islands’ (GEI) to portray their foreign character within the host genome [10]. Often, according to the functions encoded by the GEI, they were classified as pathogenicity, symbiosis, metabolic, secretion or resistance islands [11, 12].