The GntR/VanR transcription regulator AlkR represses AlkB2 monooxygenase expression and regulates n‐alkane degradation in Pseudomonas aeruginosa SJTD‐1

TL;DR

This study identifies a new bacterial regulator that controls the breakdown of long-chain alkanes, offering insights for improving oil pollution cleanup.

Contribution

The study reveals a novel GntR/VanR transcription regulator, AlkR, and its role in regulating alkane degradation in Pseudomonas aeruginosa.

Findings

AlkR represses AlkB2 expression and regulates n-alkane degradation in Pseudomonas aeruginosa SJTD-1.

AlkR binds to a conserved DNA motif, and its activity is released by long-chain fatty acyl-CoA compounds.

VanR-AlkB regulatory couples are widely conserved in Pseudomonadaceae, indicating a common regulatory pattern for alkane utilization.

Abstract

Transmembrane alkane monooxygenase (AlkB)‐type monooxygenases, especially AlkB2 monooxygenases, are crucial for aerobic degradation of the medium‐to‐long‐chain n‐alkanes in hydrocarbon‐utilizing microorganisms. In this study, we identified a GntR/VanR transcription regulator AlkR of Pseudomonas aeruginosa SJTD‐1 involved in the negative regulation of AlkB2 and deciphered its nature of DNA binding and ligand release. The deletion of alkR enhanced the transcription levels of the alkB2 gene and the utilization efficiency of the medium‐to‐long‐chain n‐alkanes by strain SJTD‐1. The dimer of AlkR recognizes and binds to a conserved palindromic motif in the promoter of the alkB2 gene, and structural symmetry is vital for DNA binding and transcription repression. The long‐chain fatty acyl coenzyme A compounds can release AlkR and stimulate transcription of alkB2, reflecting the effect of alkane catabolic metabolites. Structural insights unveiled that the arginine residues and scaffold residues of AlkR are critical for DNA binding. Further bioinformatics analysis of AlkR revealed the widespread VanR–AlkB couples distributed in Pseudomonadaceae with high conservation in the sequences of functional genes and intergenic regions, highlighting a conserved regulatory pattern for n‐alkane utilization across this family. These findings demonstrate the regulatory mechanism and structural basis of GntR/VanR transcription regulators in modulating n‐alkane biodegradation and provide valuable insights in improving the bioremediation efficiency of hydrocarbon pollution.

Alkanes are the major components of petroleum hydrocarbon contaminations, and microbial degradation is effective and important for the carbon cycle. Biodegradation efficiency decreases with increasing chain length, and biotransformation of high‐molecular‐weight n‐alkanes is difficult and they persistent in the environment for a long time. How do bacteria precisely regulate the enzyme activities and efficiently catalyze n‐alkane biodegradation? This study reveals a novel GntR/VanR regulator and a universal regulator–enzyme regulation mode widely present in petroleum‐utilizing bacteria, and elucidates the regulatory mechanism and structural basis. The findings formulate the common regulation pattern of n‐alkane biodegradation and offer new insights for hydrocarbon pollution bioremediation.

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