Abstract
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.
Highlights
Aromatic compounds such as phenol, toluene, xylene, benzoate are the second most abundant class of organic compounds after carbohydrates and a common carbon and energy source for many microorganisms (Arai et al, 1999; López Barragán et al, 2004; Gescher et al, 2005; Carmona et al, 2009; Li et al, 2010; Marín et al, 2010; Valderrama et al, 2012)
Nucleotide position weight matrices (PWMs) for each transcription factors (TFs) were constructed by the SignalX program as previously described (Gelfand et al, 2000), using training sets of upstream regions of genes presumably belonging to the respective regulons
AphS and BphS are very close homologs and their binding motifs have a similar structure. Here these TFs have been assigned names AphS or BphS according to the branching of the phylogenetic tree (Supplementary Figure S1) and co-localization of the regulatory genes with either phenol or biphenol metabolic genes
Summary
Aromatic compounds such as phenol, toluene, xylene, benzoate are the second most abundant class of organic compounds after carbohydrates and a common carbon and energy source for many microorganisms (Arai et al, 1999; López Barragán et al, 2004; Gescher et al, 2005; Carmona et al, 2009; Li et al, 2010; Marín et al, 2010; Valderrama et al, 2012) In natural habitats, they are accumulated mainly due to the degradation of plant-derived molecules (e.g., lignin) (Li et al, 2010). Bacterial metabolism of aromatic compounds and its regulation is an important research object
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