Tsoy Olga, Ravcheev Dmitry, Mushegian Arcady
Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia.
J Bacteriol. 2009 Dec;191(23):7157-64. doi: 10.1128/JB.00838-09. Epub 2009 Sep 25.
Ethanolamine can be used as a source of carbon and nitrogen by phylogenetically diverse bacteria. Ethanolamine-ammonia lyase, the enzyme that breaks ethanolamine into acetaldehyde and ammonia, is encoded by the gene tandem eutBC. Despite extensive studies of ethanolamine utilization in Salmonella enterica serovar Typhimurium, much remains to be learned about EutBC structure and catalytic mechanism, about the evolutionary origin of ethanolamine utilization, and about regulatory links between the metabolism of ethanolamine itself and the ethanolamine-ammonia lyase cofactor adenosylcobalamin. We used computational analysis of sequences, structures, genome contexts, and phylogenies of ethanolamine-ammonia lyases to address these questions and to evaluate recent data-mining studies that have suggested an association between bacterial food poisoning and the diol utilization pathways. We found that EutBC evolution included recruitment of a TIM barrel and a Rossmann fold domain and their fusion to N-terminal alpha-helical domains to give EutB and EutC, respectively. This fusion was followed by recruitment and occasional loss of auxiliary ethanolamine utilization genes in Firmicutes and by several horizontal transfers, most notably from the firmicute stem to the Enterobacteriaceae and from Alphaproteobacteria to Actinobacteria. We identified a conserved DNA motif that likely represents the EutR-binding site and is shared by the ethanolamine and cobalamin operons in several enterobacterial species, suggesting a mechanism for coupling the biosyntheses of apoenzyme and cofactor in these species. Finally, we found that the food poisoning phenotype is associated with the structural components of metabolosome more strongly than with ethanolamine utilization genes or with paralogous propanediol utilization genes per se.
乙醇胺可被多种进化上不同的细菌用作碳源和氮源。乙醇胺 - 氨裂合酶可将乙醇胺分解为乙醛和氨，该酶由基因串联体eutBC编码。尽管对鼠伤寒沙门氏菌中乙醇胺利用进行了广泛研究，但关于EutBC结构和催化机制、乙醇胺利用的进化起源以及乙醇胺自身代谢与乙醇胺 - 氨裂合酶辅因子腺苷钴胺素之间的调控联系，仍有许多有待了解之处。我们利用对乙醇胺 - 氨裂合酶的序列、结构、基因组背景和系统发育的计算分析来解决这些问题，并评估最近的数据挖掘研究，这些研究表明细菌食物中毒与二醇利用途径之间存在关联。我们发现EutBC的进化包括募集一个TIM桶和一个罗斯曼折叠结构域，并将它们分别与N端α螺旋结构域融合以形成EutB和EutC。这种融合之后，厚壁菌门中辅助乙醇胺利用基因被募集并偶尔丢失，还发生了几次水平转移，最显著的是从厚壁菌门主干转移到肠杆菌科以及从α变形菌转移到放线菌。我们鉴定出一个保守的DNA基序，它可能代表EutR结合位点，并且在几种肠杆菌物种的乙醇胺和钴胺素操纵子中共享，这表明了这些物种中脱辅基酶和辅因子生物合成偶联的一种机制。最后，我们发现食物中毒表型与代谢体的结构成分的关联比与乙醇胺利用基因或与同源丙二醇利用基因本身的关联更强。
