BIOINFORMATIC ANALYSIS OF ACCELERATED SEQUENCE EVOLUTION OF SPECIFIC EUBACTERIA

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目及 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 这项工作的两个具体目标是确定和定量一组四个快速进化的RNA聚合酶（RNAP）基因，构成抗生素治疗的目标之间的序列变异水平，并确定高度保守的结构基序在四个RNAP核心复合物亚基蛋白，可能是新的抗生素开发的合适候选人。 RNA聚合酶亚基通常以相对缓慢的速率进化，但在一个开花植物家族中，天竺葵科，叶绿体中的蓝细菌型RNAP以高得多的速率进化。核苷酸和推导的氨基酸序列分析的全长和部分（约。从天竺葵属的几个物种中获得的8 a（rpoA）、19 beta（rpoB）、16 beta <$（rpoC 1）和1 beta <$（rpoC 2）亚基基因的基因组序列揭示了序列进化的梯度，其中rpoA（编码装配或支架蛋白）进化最快，其次是rpoC 1、rpoC 2和rpoB （编码参与RNAP和DNA模板之间的催化和接触的亚基）。 这些基因似乎是最迅速演变的RNAP基因测序。 值得注意的是，这一属植物中的rpo基因（代表了大约2000万年的进化）之间的序列差异与代表了至少20亿年进化的远缘真细菌群体中的rpo基因之间的序列差异一样多。 因此，来自这些生物体的rpo基因可能代表了饱和诱变的自然实验，并可能有助于定义RNAP结构的不可变部分。 所有基因中的几个核心基序被发现是高度保守的，并且可能代表针对真细菌RNAP同源物的智能药物设计的合适靶标。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The two specific aims of this effort are to identify and quantitate the level of sequence variation among a set of four rapidly evolving RNA polymerase (RNAP) genes that constitute targets for antibiotic therapy, and to identify highly conserved structural motifs in the four RNAP core complex subunit proteins that could be suitable candidates for new antibiotic development. RNA polymerase subunits normally evolve at comparatively slow rates, but in one family of flowering plants, the Geraniaceae, the cyanobacterial-type RNAP in chloroplasts are evolving at a much higher rate. Nucleotide and deduced-amino acid sequence analysis of full length and partial (ca. 1 kb) genomic sequences of 8 a (rpoA), 19 beta (rpoB), 16 beta¿ (rpoC1) and one beta¿ (rpoC2) subunit genes from several species of the genus Pelargonium revealed a gradient of sequence evolution, with rpoA (encoding an assembly or scaffolding protein) evolving most rapidly, followed by rpoC1 , rpoC2, and rpoB (encoding subunits involved in catalysis and contact between the RNAP and the DNA template). These genes appear to be the most rapidly evolving RNAP genes yet sequenced. Remarkably, there is as much sequence divergence between rpo genes in this genus of plants (representing about 20 million years of evolution) as between rpo genes from distantly-related groups of eubacteria representing at least 2 billion years of evolution. As such, the rpo genes from these organisms might represent a natural experiment in saturation mutagenesis, and may help define immutable portions of the RNAP structure. Several core motifs in all genes were found to be highly conserved, and may represent suitable targets for ¿smart drug¿ design against the eubacterial RNAP homologues.