Rodionov Dmitry A, Vitreschak Alexey G, Mironov Andrey A, Gelfand Mikhail S
Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny pereulok 19, Moscow 127994, Russia.
Nucleic Acids Res. 2004 Jun 23;32(11):3340-53. doi: 10.1093/nar/gkh659. Print 2004.
Regulation of the methionine biosynthesis and transport genes in bacteria is rather diverse and involves two RNA-level regulatory systems and at least three DNA-level systems. In particular, the methionine metabolism in Gram-positive bacteria was known to be controlled by the S-box and T-box mechanisms, both acting on the level of premature termination of transcription. Using comparative analysis of genes, operons and regulatory elements, we described the methionine metabolic pathway and the methionine regulons in available genomes of Gram-positive bacteria. A large number of methionine-specific RNA elements were identified. S-boxes were shown to be widely distributed in Bacillales and Clostridia, whereas methionine-specific T-boxes occurred mostly in Lactobacillales. A candidate binding signal (MET-box) for a hypothetical methionine regulator, possibly MtaR, was identified in Streptococcaceae, the only family in the Bacillus/Clostridium group of Gram-positive bacteria having neither S-boxes, nor methionine-specific T-boxes. Positional analysis of methionine-specific regulatory sites complemented by genome context analysis lead to identification of new members of the methionine regulon, both enzymes and transporters, and reconstruction of the methionine metabolism in various bacterial genomes. In particular, we found candidate transporters for methionine (MetT) and methylthioribose (MtnABC), as well as new enzymes forming the S-adenosylmethionine recycling pathway. Methionine biosynthetic enzymes in various bacterial species are quite variable. In particular, Oceanobacillus iheyensis possibly uses a homolog of the betaine-homocysteine methyltransferase bhmT gene from vertebrates to substitute missing bacterial-type methionine synthases.
细菌中甲硫氨酸生物合成和转运基因的调控方式相当多样，涉及两个RNA水平的调控系统和至少三个DNA水平的系统。特别是，已知革兰氏阳性菌中的甲硫氨酸代谢受S盒和T盒机制控制，这两种机制均作用于转录提前终止水平。通过对基因、操纵子和调控元件的比较分析，我们描述了革兰氏阳性菌可用基因组中的甲硫氨酸代谢途径和甲硫氨酸调控子。鉴定出了大量甲硫氨酸特异性RNA元件。结果表明，S盒广泛分布于芽孢杆菌目和梭菌目中，而甲硫氨酸特异性T盒主要出现在乳杆菌目中。在链球菌科中鉴定出了一种假定的甲硫氨酸调节因子（可能是MtaR）的候选结合信号（MET盒），链球菌科是革兰氏阳性菌芽孢杆菌/梭菌组中唯一既没有S盒也没有甲硫氨酸特异性T盒的科。对甲硫氨酸特异性调控位点的定位分析辅以基因组背景分析，有助于鉴定甲硫氨酸调控子的新成员，包括酶和转运蛋白，并重建各种细菌基因组中的甲硫氨酸代谢。特别是，我们发现了甲硫氨酸（MetT）和甲基硫代核糖（MtnABC）的候选转运蛋白，以及形成S-腺苷甲硫氨酸循环途径的新酶。不同细菌物种中的甲硫氨酸生物合成酶差异很大。特别是，伊贺海洋芽孢杆菌可能使用脊椎动物中甜菜碱-高半胱氨酸甲基转移酶bhmT基因的同源物来替代缺失的细菌型甲硫氨酸合成酶。
