Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer
Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer
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DOI：
10.1016/j.gene.2004.03.017
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发表时间：
2004-06-23
期刊：
影响因子：
3.5
通讯作者：
Aravind, L
中科院分区：
文献类型：
--
作者：
Iyer, LM;Koonin, EV;Aravind, L
细菌dna依赖性RNA聚合酶（DdRp）的β、β′和sigma（70）亚基结构域结构的比较分析，结合基于序列的系统发育分析，揭示了细菌之间的基本分裂。第一类的dna依赖RNA聚合酶亚基，包括变形菌门、水蛭门、衣原体、螺旋体、细胞噬菌-绿藻和植物菌，其特征在于三个不同的插入，即β亚基上的三明治桶杂交Motif结构域，β亚基上的β - β '模块（BBM） I结构域，以及sigma亚基上独特的螺旋模块。其余细菌的DdRp亚基，包括第11群，缺乏这些插入结构域，尽管在个别谱系中存在一些额外的插入结构域。细菌分为第I类和第11类，与DdRp亚基保守区和连接核糖体蛋白的系统发育树的拓扑结构基本一致，可能代表了细菌进化的主要分支。这一进化模式的一个显著偏差是Aquifex，其DdRp亚基属于第1组，而核糖体蛋白的系统发育分析将Aquifex与另一种超嗜热细菌Thermotoga属于第2组。DdRp亚基的演化过程包括结构域增生和重排，以及一些可能的水平转移事件。尽管细菌DdRp的进化似乎普遍以垂直遗传为主，但所有或部分亚基的完整基因的水平转移，导致祖先基因的位移，可能在一些谱系中发挥作用，如aqufex， Thermotoga和Fusobacterium。(C) 2004 Elsevier B.V.版权所有
Comparative analysis of the domain architectures of the, beta, beta', and sigma(70) subunits of bacterial DNA-dependent RNA polymerases (DdRp), combined with sequence-based phylogenetic analysis, revealed a fundamental split among bacteria. DNA-dependent RNA polymerase subunits of Group I, which includes Proteobacteria, Aquifex, Chlamydia, Spirochaetes, Cytophaga-Chlorobium, and Planctomycetes, are characterized by three distinct inserts, namely a Sandwich Barrel Hybrid Motif domain in the beta subunit, a beta - beta' module (BBM) I domain in the beta' subunit, and a distinct helical module in the sigma subunit. The DdRp subunits of remaining bacteria, which comprise Group 11, lack these inserts, although some additional inserted domains are present in individual lineages. The separation of bacteria into Group I and Group 11 is generally compatible with the topologies of phylogenetic trees of the conserved regions of DdRp subunits and concatenated ribosomal proteins and might represent the primary bifurcation in bacterial evolution. A striking deviation from this evolutionary pattern is Aquifex whose DdRp subunits cluster within Group 1, whereas phylogenetic analysis of ribosomal proteins identifies Aquifex as grouping with Thermotoga another bacterial hyperthemophile belonging to Group II. The inferred evolutionary scenario for the DdRp subunits includes domain accretion and rearrangement, with some likely horizontal transfer events. Although evolution of bacterial DdRp appeared to be generally dominated by vertical inheritance, horizontal transfer of complete genes for all or some of the,subunits, resulting in displacement of the ancestral genes, might have played a role in several lineages, such as Aquifex, Thermotoga, and Fusobacterium. (C) 2004 Elsevier B.V. All rights reserved.