An analysis of the IS6/IS26 family of insertion sequences: is it a single family?
An analysis of the IS6/IS26 family of insertion sequences: is it a single family?
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DOI：
10.1099/mgen.0.000291
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发表时间：
2019-09-01
影响因子：
3.9
通讯作者：
Hall, Ruth M.
中科院分区：
文献类型：
--
作者：
Harmer, Christopher J.;Hall, Ruth M.
检查了ISTRY数据库中目前分配给IS 6家族（此处重新命名为IS 6/IS 26家族）的112个插入序列（IS）的策展集内的关系。编码的DDE转座酶包括螺旋-螺旋-转角-螺旋（H-HTH）潜在的DNA结合结构域N-末端至催化（DDE）结构域，但来自梭菌的10种转座酶包括一个或两个额外的N-末端结构域。转座酶同源性分析清楚地将75个来源于细菌的转座酶与37个来源于古细菌的转座酶分开。较长的细菌转座酶也分开聚集。65个较短的细菌转座酶，包括来自IS 26的Tnp 26，形成6个进化枝，但在H-HTH结构域和N-末端的短延伸中具有显著的保守性，并且催化结构域中的几个氨基酸是完全或高度保守的。在这些IS的外端，14 bp作为末端反向重复序列（TIR）高度保守，其中前两个碱基（GG）和第七个碱基（G）存在于除一个IS外的所有IS中。较长的细菌转座酶仅与短的细菌转座酶远亲，仅具有一些氨基酸保守。TIR共识较长，只有一个IS以GG开头。37个古细菌转座酶与细菌的短转座酶或长转座酶都是远亲，并且不同的残基是保守的。它们的TIR与细菌TIR共有序列松散相关，但更长，并且许多不以GG开始开始。由于它们与大多数细菌IS不匹配，因此将古细菌IS和较长的细菌IS纳入IS 6/IS 26家族是不合适的。
The relationships within a curated set of 112 insertion sequences (ISs) currently assigned to the IS6 family, here re-named the IS6/IS26 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 Clostridia 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 IS26, 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 IS6/IS26 family is not appropriate.