Mittenhuber G
Institut für Mikrobiologie und Molekularbiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany.
J Mol Microbiol Biotechnol. 2001 Oct;3(4):585-600.
In the gram-negative model organism Escherichia coli, the effector molecule of the stringent response, (p)ppGpp, is synthesized by two different enzymes, RelA and SpoT, whereas in the gram-positive model organism Bacillus subtilis only one enzyme named Rel is responsible for this activity. Rel and SpoT also possess (p)ppGpp hydrolase activity. BLAST searches were used to identify orthologous genes in databases. The construction and bootstrapping of phylogenetic trees allowed classification of these orthologs. Four groups could be distinguished: With the exception of Neisseria and Bordetella (beta subdivision), the RelA and SpoT groups are exclusively found in the gamma subdivision of proteobacteria. Two Rel groups representing the actinobacterial and the Bacillus/Clostridium group were also identified. The SpoT proteins are related to the gram positive Rel proteins. RelA proteins carry substitutions in the HD domain (Aravind and Koonin, 1998, TIBS 23: 469-472) responsible for ppGpp degradation. A theory for the evolution of the specialized, paralogous relA and spoT genes is presented: After gene duplication of an ancestral rellike gene, the spoT and relA genes evolved from the duplicated genes. The distribution pattern of the paralogous RelA and SpoT proteins supports a new model of linear bacterial evolution (Gupta, 2000, FEMS Microbiol. Rev. 24: 367-402). This model postulates that the gamma subdivision of proteobacteria represents the most recently evolved bacterial lineage. However, two paralogous, closely related genes of Porphyromonas gingivalis (Cytophaga-Flavobacterium-Bacteroides phylum) encoding proteins with functions probably identical to the RelA and SpoT proteins do not fit in this model. Completely sequenced genomes of several obligately parasitic organisms (Treponema pallidum, Chlamydia species, Rickettsia prowazekii) and the obligate aphid symbiont Buchnera sp. APS as well as archaea do not contain rel-like genes but they are present in the Arabidopsis genome. In crosslinking experiments using different analogs of ppGpp as crosslinking reagents and RNA polymerase preparations of Escherichia coli, binding of ppGpp to distinct regions at the C-terminus of the beta subunit (the RpoB gene product) and/or at the N-terminus of the beta subunit (the RpoC gene product) was observed previously. RpoB and RpoC sequences of the species which do not possess a rel like gene do not exhibit specific insertions or deletions in the ppGpp binding regions.
在革兰氏阴性模式生物大肠杆菌中，严谨反应的效应分子（p）ppGpp由两种不同的酶RelA和SpoT合成，而在革兰氏阳性模式生物枯草芽孢杆菌中，只有一种名为Rel的酶负责此活性。Rel和SpoT也具有（p）ppGpp水解酶活性。利用BLAST搜索在数据库中鉴定直系同源基因。系统发育树的构建和自展分析允许对这些直系同源物进行分类。可区分出四组：除了奈瑟菌属和博德特氏菌属（β亚群）外，RelA和SpoT组仅存在于变形菌门的γ亚群中。还鉴定出代表放线菌和芽孢杆菌/梭菌组的两个Rel组。SpoT蛋白与革兰氏阳性Rel蛋白相关。RelA蛋白在负责ppGpp降解的HD结构域中存在替代（阿拉文德和库宁，1998年，《生物化学趋势》23：469 - 472）。提出了一个关于特化的旁系同源relA和spoT基因进化的理论：在一个祖先rel样基因发生基因复制后，spoT和relA基因从复制的基因进化而来。旁系同源RelA和SpoT蛋白的分布模式支持一种新的线性细菌进化模型（古普塔，2000年，《FEMS微生物学评论》24：367 - 402）。该模型假定变形菌门的γ亚群代表最近进化的细菌谱系。然而，牙龈卟啉单胞菌（噬纤维菌 - 黄杆菌 - 拟杆菌门）的两个旁系同源、密切相关的基因，其编码的蛋白质功能可能与RelA和SpoT蛋白相同，但并不符合该模型。几种专性寄生生物（梅毒螺旋体、衣原体属、普氏立克次体）以及专性蚜虫共生菌布赫纳菌属APS以及古菌的全基因组测序结果表明它们不含rel样基因，但这些基因存在于拟南芥基因组中。在使用不同的ppGpp类似物作为交联试剂和大肠杆菌RNA聚合酶制剂的交联实验中，先前观察到ppGpp与β亚基（RpoB基因产物）C末端和/或β亚基（RpoC基因产物）N末端的不同区域结合。
