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

Abstract

Abstract 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.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1]; ORCiD logo [1]
  1. Sandia National Laboratories, Systems Biology Department, Livermore, CA 94551-0969, USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1605044
Grant/Contract Number:  
[NA0003525; HR0011-17-2-0043]
Resource Type:
Published Article
Journal Name:
Nucleic Acids Research
Additional Journal Information:
[Journal Name: Nucleic Acids Research]; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Mageeney, Catherine M., Lau, Britney Y., Wagner, Julian M., Hudson, Corey M., Schoeniger, Joseph S., Krishnakumar, Raga, and Williams, Kelly P. New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements. United Kingdom: N. p., 2020. Web. doi:10.1093/nar/gkaa156.
Mageeney, Catherine M., Lau, Britney Y., Wagner, Julian M., Hudson, Corey M., Schoeniger, Joseph S., Krishnakumar, Raga, & Williams, Kelly P. New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements. United Kingdom. doi:10.1093/nar/gkaa156.
Mageeney, Catherine M., Lau, Britney Y., Wagner, Julian M., Hudson, Corey M., Schoeniger, Joseph S., Krishnakumar, Raga, and Williams, Kelly P. Tue . "New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements". United Kingdom. doi:10.1093/nar/gkaa156.
@article{osti_1605044,
title = {New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements},
author = {Mageeney, Catherine M. and Lau, Britney Y. and Wagner, Julian M. and Hudson, Corey M. and Schoeniger, Joseph S. and Krishnakumar, Raga and Williams, Kelly P.},
abstractNote = {Abstract 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.},
doi = {10.1093/nar/gkaa156},
journal = {Nucleic Acids Research},
number = ,
volume = ,
place = {United Kingdom},
year = {2020},
month = {3}
}

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DOI: 10.1093/nar/gkaa156

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