Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440

Abstract

Analysis of the catabolic potential of Pseudomonas putida KT2440 against a wide range of natural aromatic compounds and sequence comparisons with the entire genome of this microorganism predicted the existence of at least four main pathways for the catabolism of central aromatic intermediates, that is, the protocatechuate (pca genes) and catechol (cat genes) branches of the beta-ketoadipate pathway, the homogentisate pathway (hmg/fah/mai genes) and the phenylacetate pathway (pha genes). Two additional gene clusters that might be involved in the catabolism of N-heterocyclic aromatic compounds (nic cluster) and in a central meta-cleavage pathway (pcm genes) were also identified. Furthermore, the genes encoding the peripheral pathways for the catabolism of p-hydroxybenzoate (pob), benzoate (ben), quinate (qui), phenylpropenoid compounds (fcs, ech, vdh, cal, van, acd and acs), phenylalanine and tyrosine (phh, hpd) and n-phenylalkanoic acids (fad) were mapped in the chromosome of P. putida KT2440. Although a repetitive extragenic palindromic (REP) element is usually associated with the gene clusters, a supraoperonic clustering of catabolic genes that channel different aromatic compounds into a common central pathway (catabolic island) was not observed in P. putida KT2440. The global view on the mineralization of aromatic compounds by P. putida KT2440 will facilitate the rational manipulation of this strain for improving biodegradation/biotransformation processes, and reveals this bacterium as a useful model system for studying biochemical, genetic, evolutionary and ecological aspects of the catabolism of aromatic compounds.

Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501

“…Pathways for aromatic degradation through the protocatechuate (pca) and catechol (ben) routes found in the A1501 genome are similar to those found in other Pseudomonas, such as P. entomophila (5) and P. putida (28). Using in vivo expression technology, one of the pca gene was reported to be up-regulated in the rhizosopere of the P. stuzeri A15 (14).…”

Genome‐wide identification of tolerance mechanisms toward p‐coumaric acid in Pseudomonas putida

“…P. putida KT2440 is able to degrade p ‐coumaric acid and use it as carbon source (Figure 2a) (Jiménez, Miñambres, Luis, & Díaz, 2002). In order to investigate the effect of the degradation of p ‐coumaric acid on tolerance, a strain with a deletion of the first gene in the p ‐coumaric acid degradation pathway, fcs , which abolishes p ‐coumaric acid degradation, or conversion to another compound (Calero et al, 2016), was tested in different concentrations of the compound.…”

A Gene Cluster Involved in Degradation of Substituted Salicylates viaorthoCleavage inPseudomonassp. Strain MT1 Encodes Enzymes Specifically Adapted for Transformation of 4-Methylcatechol and 3-Methylmuconate

“…2B). However, a gene encoding a muconolactone isomerase (usually clustered in Pseudomonas strains with genes encoding muconate cycloisomerases and catechol 1,2-dioxygenases (16,17) could not be localized in the sequenced region. In contrast, salC was preceded by ORFs with high homology to genes encoding salicylate 1-hydroxylases (salA) and permeases of the major facilitator subfamily (salB).…”

“…The genetic organization of various catechol gene clusters (cat genes) has been described previously (15,16,36,54). The organization of the cat gene cluster of strain MT1 is identical to the organization characteristic for Pseudomonas strains and shows highest similarity to the cluster identified from an environmental metagenome library constructed from petroleumcontaminated groundwater (57).…”

“…Enzymes for catechol degradation via intradiol cleavage are encoded by the catechol branch of the 3-oxoadipate pathway (15). Pseudomonas strains usually contain a catRBCA gene cluster (16,33,54) comprising genes encoding catechol 1,2-dioxygenase (CatA), muconate cycloisomerase (MCI; CatB), and muconolactone isomerase (CatC), which are controlled by a LysR type regulator (CatR) in response to the inducer muconate (17). However, various permutations with respect to enzyme distribution, regulation, and gene organization have also been observed (15,30,47,55).…”