Genome-wide investigation and functional characterization of the β-ketoadipate pathway in the nitrogen-fixing and root-associated bacterium Pseudomonas stutzeriA1501

Danhua Li,Wei Lu,Shuzhen Ping,Wenna Lin,Ming Chen,Yongliang Yan,Lizhao Geng,Min Lin,Wei Zhang,Wei Liu,Liang Li

doi:10.1186/1471-2180-10-36

Abstract

BackgroundSoil microorganisms are mainly responsible for the complete mineralization of aromatic compounds that usually originate from plant products or environmental pollutants. In many cases, structurally diverse aromatic compounds can be converted to a small number of structurally simpler intermediates, which are metabolized to tricarboxylic acid intermediates via the β-ketoadipate pathway. This strategy provides great metabolic flexibility and contributes to increased adaptation of bacteria to their environment. However, little is known about the evolution and regulation of the β-ketoadipate pathway in root-associated diazotrophs.ResultsIn this report, we performed a genome-wide analysis of the benzoate and 4-hydroxybenzoate catabolic pathways of Pseudomonas stutzeri A1501, with a focus on the functional characterization of the β-ketoadipate pathway. The P. stutzeri A1501 genome contains sets of catabolic genes involved in the peripheral pathways for catabolism of benzoate (ben) and 4-hydroxybenzoate (pob), and in the catechol (cat) and protocatechuate (pca) branches of the β-ketoadipate pathway. A particular feature of the catabolic gene organization in A1501 is the absence of the catR and pcaK genes encoding a LysR family regulator and 4-hydroxybenzoate permease, respectively. Furthermore, the BenR protein functions as a transcriptional activator of the ben operon, while transcription from the catBC promoter can be activated in response to benzoate. Benzoate degradation is subject to carbon catabolite repression induced by glucose and acetate in A1501. The HPLC analysis of intracellular metabolites indicated that low concentrations of 4-hydroxybenzoate significantly enhance the ability of A1501 to degrade benzoate.ConclusionsThe expression of genes encoding proteins involved in the β-ketoadipate pathway is tightly modulated by both pathway-specific and catabolite repression controls in A1501. This strain provides an ideal model system for further study of the evolution and regulation of aromatic catabolic pathways.

Highlights

Soil microorganisms are mainly responsible for the complete mineralization of aromatic compounds that usually originate from plant products or environmental pollutants
In A. baylyi ADP1, the b-ketoadipate pathway consists of two parallel branches for the conversion of catechol and protocatechuate, which are derived from benzoate and 4-hydroxybenzoate, respectively [1]
At least 19 genes involved in the peripheral pathways for the catabolism of benzoate and 4-hydroxybenzoate and in the catechol and protocatechuate branches of the b-ketoadipate pathway have been identified in A. baylyi ADP1 [4]

Summary

Introduction

Soil microorganisms are mainly responsible for the complete mineralization of aromatic compounds that usually originate from plant products or environmental pollutants. One of the most abundant classes of natural carbon compounds, accumulate primarily due to the degradation of plant-derived molecules (e.g., lignin) These structurally diverse compounds are independently converted to a small number of structurally simpler common intermediates, such as catechol and protocatechuate, which are subsequently metabolized to tricarboxylic acid intermediates via the b-ketoadipate pathway [1,2,3]. At least 19 genes involved in the peripheral pathways for the catabolism of benzoate (ben) and 4-hydroxybenzoate (pob) and in the catechol (cat) and protocatechuate (pca) branches of the b-ketoadipate pathway have been identified in A. baylyi ADP1 [4]. Further enzymatic studies and amino acid sequence data revealed that the pob, pca, ben and cat gene products are highly conserved in Acinetobacter and Pseudomonas strains These products are usually synthesized in the presence of their respective substrates. BenR-CatR or BenM-CatM regulation may serve as a practical model for complex regulatory circuits involved in the biodegradation of benzoate

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