School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.
Microb Genom. 2019 Sep;5(9). doi: 10.1099/mgen.0.000291. Epub 2019 Sep 5.
The relationships within a curated set of 112 insertion sequences (ISs) currently assigned to the IS family, here re-named the IS/IS family, in the ISFinder database were examined. The encoded DDE transposases include a helix-helix-turn-helix (H-HTH) potential DNA binding domain N-terminal to the catalytic (DDE) domain, but 10 from include one or two additional N-terminal domains. The transposase phylogeny clearly separated 75 derived from bacteria from 37 from archaea. The longer bacterial transposases also clustered separately. The 65 shorter bacterial transposases, including Tnp26 from IS, formed six clades but share significant conservation in the H-HTH domain and in a short extension at the N-terminus, and several amino acids in the catalytic domain are completely or highly conserved. At the outer ends of these ISs, 14 bp were strongly conserved as terminal inverted repeats (TIRs) with the first two bases (GG) and the seventh base (G) present in all except one IS. The longer bacterial transposases are only distantly related to the short bacterial transposases, with only some amino acids conserved. The TIR consensus was longer and only one IS started with GG. The 37 archaeal transposases are only distantly related to either the short or the long bacterial transposases and different residues were conserved. Their TIRs are loosely related to the bacterial TIR consensus but are longer and many do not begin with GG. As they do not fit well with most bacterial ISs, the inclusion of the archaeal ISs and the longer bacterial ISs in the IS/IS family is not appropriate.
在 ISFinder 数据库中，对当前分配给插入序列家族（IS 家族）的 112 个插入序列（IS）的精选集内的关系进行了研究。所编码的 DDE 转座酶在 N 端包含一个螺旋-转角-螺旋（H-HTH）潜在 DNA 结合结构域，但其 10 个中有一个或两个额外的 N 端结构域。转座酶系统发育明显将 75 个源自细菌的转座酶与 37 个源自古菌的转座酶区分开来。较长的细菌转座酶也单独聚类。较短的 65 个细菌转座酶，包括来自 IS 的 Tnp26，形成了六个分支，但在 H-HTH 结构域和 N 端的短延伸以及催化结构域中的几个氨基酸高度保守。在这些 IS 的外端，14 个碱基强烈保守为末端反向重复（TIR），除一个 IS 外，所有 TIR 都有前两个碱基（GG）和第七个碱基（G）。较长的细菌转座酶与较短的细菌转座酶仅存在远亲关系，只有一些氨基酸保守。TIR 一致序列较长，只有一个 IS 以 GG 开头。37 个古菌转座酶与短或长的细菌转座酶均仅存在远亲关系，并且保守的残基不同。它们的 TIR 与细菌 TIR 一致序列松散相关，但较长，许多不以 GG 开头。由于它们与大多数细菌 IS 不匹配，因此将古菌 IS 和较长的细菌 IS 纳入 IS/IS 家族是不合适的。
