The structure-function relationship of bacterial transcriptional regulators as a target for enhanced biodegradation of aromatic hydrocarbons

Abstract

The sheer persistence and dissemination of xenobiotic aromatic hydrocarbons contaminants demand sustainable solutions for degradation. Therefore, major pathways of microbial catabolism of aromatic hydrocarbons under aerobic conditions are reviewed and analysed to elicit enhanced biodegradation of aromatic hydrocarbons, via the structure-function relationship of bacterial transcriptional regulators. The initial step of the catabolism occurs via the incorporation of molecular oxygen into the aromatic ring by a multicomponent aromatic ring-hydroxylating-dioxygenase (RHD) enzyme system or monooxygenase system forming different central intermediates such as catechols, protocatechuates, gentisates, and (hydroxy)benzoquinols. The central or lower pathways involve the ring cleavage of central intermediates to tricarboxylic acids. These metabolic pathways are tightly regulated, where the inducer or substrate-specific transcriptional regulation of aromatic catabolic pathways depend on the specific regulatory proteins that acts on a specific promoter in response to a respective inducer signal. These regulatory systems have been grouped according to the regulatory proteins and their families, and identified based on their conserved motifs and their modes of DNA binding. Different regulators from protein families like AraC/XylS, LysR, XylR/NtrC, IclR, etc. have been identified, that are involved in aromatic hydrocarbon regulation. These regulatory proteins have different structures and have different mechanisms of regulation. The proteins of the XylS/AraC family have two domains structure: a highly conserved C-terminus that contains two HTH motifs and the N-terminus end containing the regulatory domain. The LysR type regulatory proteins (LTTRs) act as tetramers that have a helix-turn-helix (HTH) domain at the N terminus and a regulatory binding domain at the C terminus. The IclR regulatory proteins also have a helix-turn-helix DNA binding motif in the N-terminus domain-like LTTRs but include an effector binding motif in the C-terminus domain that is also involved in subunit multimerization. In contrast, the XylR-like regulatory proteins have three domain structures; one for effector sensing, another for ATP binding and hydrolysis, and a domain for DNA binding which contains an HTH motif. This review describes in depth and critical assessment of the aerobic bacterial degradation pathways of aromatic hydrocarbon pollutants with state of art information, underscores areas that are viable and others that require further development, with particular reference to metabolic engineering and synthetic biology applications.

Keywords: Aromatic hydrocarbon; Biodegradation; Catabolic pathways; Transcriptional regulation.