Suvorova Inna A, Gelfand Mikhail S
Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia.
Faculty of Computer Science, Higher School of Economics, Moscow, Russia.
Front Microbiol. 2019 Mar 29;10:642. doi: 10.3389/fmicb.2019.00642. eCollection 2019.
Aromatic compounds are a common carbon and energy source for many microorganisms, some of which can even degrade toxic chloroaromatic xenobiotics. This comparative study of aromatic metabolism in 32 Betaproteobacteria species describes the links between several transcription factors (TFs) that control benzoate (BenR, BenM, BoxR, BzdR), catechol (CatR, CatM, BenM), chlorocatechol (ClcR), methylcatechol (MmlR), 2,4-dichlorophenoxyacetate (TfdR, TfdS), phenol (AphS, AphR, AphT), biphenyl (BphS), and toluene (TbuT) metabolism. We characterize the complexity and variability in the organization of aromatic metabolism operons and the structure of regulatory networks that may differ even between closely related species. Generally, the upper parts of pathways, rare pathway variants, and degradative pathways of exotic and complex, in particular, xenobiotic compounds are often controlled by a single TF, while the regulation of more common and/or central parts of the aromatic metabolism may vary widely and often involves several TFs with shared and/or dual, or cascade regulation. The most frequent and at the same time variable connections exist between AphS, AphR, AphT, and BenR. We have identified a novel LysR-family TF that regulates the metabolism of catechol (or some catechol derivative) and either substitutes CatR(M)/BenM, or shares functions with it. We have also predicted several new members of aromatic metabolism regulons, in particular, some COGs regulated by several different TFs.
芳香族化合物是许多微生物常见的碳源和能源，其中一些微生物甚至能够降解有毒的氯代芳香族异生物质。这项对32种β-变形菌属物种的芳香族代谢的比较研究描述了几种控制苯甲酸（BenR、BenM、BoxR、BzdR）、儿茶酚（CatR、CatM、BenM）、氯儿茶酚（ClcR）、甲基儿茶酚（MmlR）、2,4-二氯苯氧乙酸（TfdR、TfdS）、苯酚（AphS、AphR、AphT）、联苯（BphS）和甲苯（TbuT）代谢的转录因子（TFs）之间的联系。我们表征了芳香族代谢操纵子组织的复杂性和变异性，以及即使在亲缘关系密切的物种之间也可能不同的调控网络结构。一般来说，途径的上游部分、罕见的途径变体以及外来和复杂的，特别是异生物质的降解途径通常由单个TF控制，而芳香族代谢中更常见和/或核心部分的调控可能差异很大，并且通常涉及几个具有共享和/或双重或级联调控的TF。AphS、AphR、AphT和BenR之间存在最频繁且同时也是可变的联系。我们鉴定出一种新型的LysR家族TF，它调控儿茶酚（或某些儿茶酚衍生物）的代谢，要么替代CatR(M)/BenM，要么与其共享功能。我们还预测了芳香族代谢调控子的几个新成员，特别是一些由几种不同TF调控的COG。
