Please use this identifier to cite or link to this item: https://doi.org/10.1128/mSphere.00693-18
Title: Comprehensive identification of Fim-mediated inversions in uropathogenic Escherichia coli with structural variation detection using relative entropy
Authors: Russell, C.W. 
Sukumaran, R. 
Liow, L.T. 
Periaswamy, B. 
Rafee, S. 
Chee, Y.C. 
Chen, S.L. 
Keywords: Genomics
Information theory
Phase variation
Structural variations
Type 1 pili
Uropathogenic Escherichia coli
Issue Date: 2019
Publisher: American Society for Microbiology
Citation: Russell, C.W., Sukumaran, R., Liow, L.T., Periaswamy, B., Rafee, S., Chee, Y.C., Chen, S.L. (2019). Comprehensive identification of Fim-mediated inversions in uropathogenic Escherichia coli with structural variation detection using relative entropy. mSphere 4 (2) : e00693-18. ScholarBank@NUS Repository. https://doi.org/10.1128/mSphere.00693-18
Rights: Attribution 4.0 International
Abstract: Most urinary tract infections (UTIs) are caused by uropathogenic Escherichia coli (UPEC), which depends on an extracellular organelle (type 1 pili) for adherence to bladder cells during infection. Type 1 pilus expression is partially regulated by inversion of a piece of DNA referred to as fimS, which contains the promoter for the fim operon encoding type 1 pili. fimS inversion is regulated by up to five recombinases collectively known as Fim recombinases. These Fim recombinases are currently known to regulate two other switches: the ipuS and hyxS switches. A longstanding question has been whether the Fim recombinases regulate the inversion of other switches, perhaps to coordinate expression for adhesion or virulence. We answered this question using whole-genome sequencing with a newly developed algorithm (structural variation detection using relative entropy [SVRE]) for calling structural variations using paired-end short-read sequencing. SVRE identified all of the previously known switches, refining the specificity of which recombinases act at which switches. Strikingly, we found no new inversions that were mediated by the Fim recombinases. We conclude that the Fim recombinases are each highly specific for a small number of switches. We hypothesize that the unlinked Fim recombinases have been recruited to regulate fimS, and fimS only, as a secondary locus; this further implies that regulation of type 1 pilus expression (and its role in gastrointestinal and/or genitourinary colonization) is important enough, on its own, to influence the evolution and maintenance of multiple additional genes within the accessory genome of E. coli. © 2019 Russell et al.
Source Title: mSphere
URI: https://scholarbank.nus.edu.sg/handle/10635/212319
ISSN: 23795042
DOI: 10.1128/mSphere.00693-18
Rights: Attribution 4.0 International
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