Title: Association analysis between Intragenomic Gene Conversions and pathogenicity in genomes of Escherichia coli and Shigella spp.: a scientific workflow approach

Authors: Jamal Alhiyafi, Cavitha Sabesan, Shiyong Lu, Jeffrey L. Ram

Addresses: Department of Computer Science, Wayne State University, 430 State Hall, 5143 Cass Avenue, Detroit, MI 48202, USA. ' Department of Computer Science, Wayne State University, 430 State Hall, 5143 Cass Avenue, Detroit, MI 48202, USA. ' Department of Computer Science, Wayne State University, 430 State Hall, 5143 Cass Avenue, Detroit, MI 48202, USA. ' Department of Physiology, Wayne State University, Detroit, MI 48201 USA

Abstract: The RECOMBFLOW scientific workflow system was used to test a previously suggested hypothesis that pathogenic Escherichia coli have more Intragenomic Gene Conversions (IGC) than non-pathogenic strains. Although some pathogens (O157:H7 and some Urinary Tract Infection (UTI) strains) had high IGC, two UTI strains and six Shigella (pathogens in the E. coli clade) were near non-pathogenic E. coli levels. Functional bacterial gene families with IGC in >4 genomes included efflux pumps, L-serine deaminases, FeS binding subunits of oxidoreductases and glutamate synthase, porins and related membrane proteins, Rhs elements, and L-ribulose-5-phosphate-4-epimerase. Shigella had lower IGCs in these families than non-pathogenic E. coli.

Keywords: bacteria; intragenomic recombination; DNA recombination; genomes; scientific workflows; association analysis; gene conversions; pathogenicity; Escherichia coli; E. coli; Shigella spp; urinary tract infections.

DOI: 10.1504/IJFIPM.2009.022837

International Journal of Functional Informatics and Personalised Medicine, 2009 Vol.2 No.1, pp.57 - 76

Available online: 27 Jan 2009 *

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