Sandia National Laboratories, Systems Biology Department, Livermore, CA 94551-0969, USA.
Nucleic Acids Res. 2020 May 7;48(8):4052-4065. doi: 10.1093/nar/gkaa156.
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.
整合遗传元件 (IGE) 是一种可移动的多基因 DNA 单元，可整合到宿主细菌基因组中并从其中切除。每个 IGE 通常针对宿主基因内的特定保守位点，以保留靶基因功能的方式进行整合。然而，已知少数细菌基因在 IGE 整合后失活，在切除后重新激活，从而调节多细胞细菌的毒力、突变率和末端分化等表型。由于难以精确和全面地定位基因组中的 IGE，因此受调控基因完整性 (RGI) 案例的数量增长缓慢。我们提出了一种软件 (TIGER)，该软件可以以前所未有的精度和没有 attB 位点偏差的方式定位 IGE。TIGER 使用基于比较基因组学的乒乓 BLAST 方法，基于 IGE 整合模块（即其 int-attP 区域）具有凝聚力的原理。从 2168 个基因组中获得的 IGE 及其整合酶系统发育分析和基因失活测试，揭示了 19 个新的 RGI 案例（包括 dut、eccCa1、gntT、hrpB、merA、ompN、prkA、tqsA、traG、yifB、yfaT 和 ynfE），以及恢复了先前已知的案例（在 sigK、spsM、comK、mlrA 和 hlb 基因中）。它还恢复了已知的位点混杂整合酶的聚类，并确定了可能的新聚类。
