New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements

Mageeney, Catherine M.; Lau, Britney Y.; Wagner, Julian M.; Hudson, Corey M.; Schoeniger, Joseph S.; Krishnakumar, Raga; Williams, Kelly P.

doi:10.1093/nar/gkaa156

Title: New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements

Journal Article · 17 March 2020 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkaa156 · OSTI ID:1605044

Mageeney, Catherine M. ^[1]; Lau, Britney Y. ^[1]; Wagner, Julian M. ^[1]; Hudson, Corey M. ^[1]; Schoeniger, Joseph S. ^[1]; Krishnakumar, Raga ^[1];

^[1]

Sandia National Lab. (SNL-CA), Livermore, CA (United States). Systems Biology Dept.

Integrative genetic elements (IGEs) are mobile multigene DNA units that integrate into and excise from host bacterial genomes. Each IGE usually targets a specific site within a conserved host gene, integrating in a manner that preserves target gene function. However, a small number of bacterial genes are known to be inactivated upon IGE integration and reactivated upon excision, regulating phenotypes of virulence, mutation rate, and terminal differentiation in multicellular bacteria. The list of regulated gene integrity (RGI) cases has been slow-growing because IGEs have been challenging to precisely and comprehensively locate in genomes. We present software (TIGER) that maps IGEs with unprecedented precision and without attB site bias. TIGER uses a comparative genomic, ping-pong BLAST approach, based on the principle that the IGE integration module (i.e. its int-attP region) is cohesive. The resultant IGEs from 2168 genomes, along with integrase phylogenetic analysis and gene inactivation tests, revealed 19 new cases of genes whose integrity is regulated by IGEs (including dut, eccCa1, gntT, hrpB, merA, ompN, prkA, tqsA, traG, yifB, yfaT and ynfE), as well as recovering previously known cases (in sigK, spsM, comK, mlrA and hlb genes). It also recovered known clades of site-promiscuous integrases and identified possible new ones.

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Research Organization:: Sandia National Lab. (SNL-CA), Livermore, CA (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); USDOE Laboratory Directed Research and Development (LDRD) Program; Defense Advanced Research Projects Agency (DARPA)

Grant/Contract Number:: NA0003525; HR0011-17-2-0043

OSTI ID:: 1605044

Alternate ID(s):: OSTI ID: 1815571

Journal Information:: Nucleic Acids Research, Vol. 48, Issue 8; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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