Under-representation of intrinsic terminators across bacterial genomic islands: Rho as a principal regulator of xenogenic DNA expression

Mitra, Anirban and Nagaraja, Valakunja (2012) Under-representation of intrinsic terminators across bacterial genomic islands: Rho as a principal regulator of xenogenic DNA expression. In: GENE, 508 (2). pp. 221-228.

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Abstract

Two transcription termination mechanisms - intrinsic and Rho-dependent - have evolved in bacteria. The Rho factor occurs in most bacterial lineages, and has been hypothesized to play a global regulatory role. Genome-wide studies using microarray, 2D-gel electrophoresis and ChIP-chip provided evidence that Rho serves to silence transcription from horizontally acquired genes and prophages in Escherichia coli K-12, implicating the factor to be a part of the ``cellular immune mechanism'' protecting against deleterious phages and aberrant gene expression from acquired xenogenic DNA. We have investigated this model by adopting an alternate in silico approach and have extended the study to other species. Our analysis shows that several genomic islands across diverse phyla have under-representation of intrinsic terminators, similar to that experimentally observed in E. coli K-12. This implies that Rho-dependent termination is the predominant process operational in these islands and that silencing of foreign DNA is a conserved function of Rho. From the present analysis, it is evident that horizontally acquired islands have lost intrinsic terminators to facilitate Rho-dependent termination. These results underscore the importance of Rho as a conserved, genome-wide sentinel that regulates potentially toxic xenogenic DNA. (C) 2012 Elsevier B.V. All rights reserved.

Item Type:	Journal Article
Publication:	GENE
Publisher:	ELSEVIER SCIENCE BV
Additional Information:	Copyright for this article belongs to Elsevier
Keywords:	Horizontal gene transfer; Intrinsic termination; Hairpin; RNA polymerase; Pathogenicity
Department/Centre:	Division of Biological Sciences > Microbiology & Cell Biology
Date Deposited:	31 Jan 2013 12:45
Last Modified:	31 Jan 2013 12:45
URI:	http://eprints.iisc.ac.in/id/eprint/45338

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