THE PHYLOGENY OF RNA-DEPENDENT RNA-POLYMERASES OF POSITIVE-STRAND RNA VIRUSES
THE PHYLOGENY OF RNA-DEPENDENT RNA-POLYMERASES OF POSITIVE-STRAND RNA VIRUSES
复制标题
DOI：
10.1099/0022-1317-72-9-2197
复制
发表时间：
1991-09-01
影响因子：
3.8
通讯作者：
KOONIN, EV
中科院分区：
文献类型：
--
作者：
KOONIN, EV
对所有正链RNA病毒依赖于RNA的RNA聚合酶的代表性氨基酸序列进行了层级比对，从关系最密切的开始。这导致了三个大的超群的划分。在每个超基团中，来自聚合酶中心和/或C-末端部分的大约300个氨基酸残基的片段序列可以与统计上显著的分数比对。每个超群的保守氨基酸残基的特定共识模式被推导出来。聚合酶超群的组成如下。I.Picorna-、Noda-、COMO-、NEPO-、POTY-、BYMO-、SOBEMEMO病毒和黄体病毒的一个子集(甜菜西部黄化病毒和马铃薯卷叶病毒)。二、Carmo病毒、Tombus病毒、黄花病毒、黄体病毒(大麦黄矮病病毒)的另一个子集、鼠疫病毒、丙型肝炎病毒(丙型肝炎病毒)、黄病毒以及出人意料的单链RNA噬菌体。Tabamo-、Tobra-、Hordei-、Tricorna-病毒、甜菜黄化病毒、α-、Rubi-、FuroVirus、HEV、Potex-、Carla-、TymoVirus和苹果褪绿叶斑病毒。冠状和环状病毒聚合酶显示出一种不寻常的结构，其N末端区域与超群I的各自结构域有关，C末端区域与超群III聚合酶的结构域相关。三个聚合酶超群的比对被叠加以产生一个全面的最终比对，包括八个不同的保守基序。用三种独立的树构建方法进行的系统发育分析证实了正链RNA病毒聚合酶被分成三个超群，并揭示了超群中一些意想不到的集群。其中包括丙型肝炎病毒和鼠疫病毒与卡莫病毒和相关植物病毒在超组II中的分组，以及HEV和Rubiv病毒与FuroVirus在超组III中的分组。
Representative amino acid sequences of the RNA-dependent RNA polymerases of all groups of positive-strand RNA viruses were aligned hierarchically, starting with the most closely related ones. This resulted in delineation of three large supergroups. Within each of the supergroups, the sequences of segments of approximately 300 amino acid residues originating from the central and/or C-terminal portions of the polymerases could be aligned with statistically significant scores. Specific consensus patterns of conserved amino acid residues were derived for each of the supergroups. The composition of the polymerase supergroups was as follows. I. Picorna-, noda-, como-, nepo-, poty-, bymo-, sobemoviruses, and a subset of luteoviruses (beet western yellows virus and potato leafroll virus). II. Carmo-, tombus-, dianthoviruses, another subset of luteoviruses (barley yellow dwarf virus), pestiviruses, hepatitis C virus (HCV), flaviviruses and, unexpectedly, single-stranded RNA bacteriophages. III. Tobamo-, tobra-, hordei-, tricorna-viruses, beet yellows virus, alpha-, rubi-, furoviruses, hepatitis E virus (HEV), potex-, carla-, tymoviruses, and apple chlorotic leaf spot virus. An unusual organization was shown for corona- and torovirus polymerases whose N-terminal regions were found to be related to the respective domains of supergroup I, and the C-terminal regions to those of the supergroup III polymerases. The alignments of the three polymerase supergroups were superimposed to produce a comprehensive final alignment encompassing eight distinct conserved motifs. Phylogenetic analysis using three independent methods of tree construction confirmed the separation of the positive-strand RNA viral polymerases into three supergroups and revealed some unexpected clusters within the supergroups. These included the grouping of HCV and the pestiviruses with carmoviruses and related plant viruses in supergroup II, and the grouping of HEV and rubiviruses with furoviruses in supergroup III.