A Novel Gene Cluster Is Involved in the Degradation of Lignin-Derived Monoaromatics in Thermus oshimai JL-2

Abstract

A novel gene cluster involved in the degradation of lignin-derived monoaromatics such as p-hydroxybenzoate, vanillate, and ferulate has been identified in the thermophilic nitrate reducer Thermus oshimai JL-2. Based on conserved domain analyses and metabolic pathway mapping, the cluster was classified into upper and peripheral pathway operons. The upper pathway genes, responsible for the degradation of p-hydroxybenzoate and vanillate, are located on a 0.27 Mb plasmid, whereas the peripheral pathway genes, responsible for the transformation of ferulate, are spread throughout the plasmid and the chromosome. In addition, a lower pathway operon was also identified in the plasmid that corresponds to the meta-cleavage pathway of catechol. Spectrophotometric and gene induction data suggest that the upper and lower operons are induced by p-hydroxybenzoate, which the strain can degrade completely within 4 days of incubation, whereas the peripheral genes are expressed constitutively. The upper degradation pathway follows a less common route, proceeding via the decarboxylation of protocatechuate to form catechol, and involves a novel thermostable γ-carboxymuconolactone decarboxylase homolog, identified as protocatechuate decarboxylase based on gene deletion experiments. This gene cluster is conserved in only a few Thermales and shows traces of vertical expansion of catabolic pathways in these organisms toward lignoaromatics. IMPORTANCE High-temperature steam treatment of lignocellulosic biomass during the extraction of cellulose and hemi-cellulose fractions leads to the release of a wide array of lignin-derived aromatics into the natural ecosystem, some of which can have detrimental effects on the environment. Not only will identifying organisms capable of using such aromatics aid in environmental cleanup, but thermostable enzymes, if characterized, can be used for efficient lignin valorization. However, no thermophilic lignin degraders have been reported thus far. The present study reports T. oshimai JL-2 as a thermophilic bacterium with the potential to use lignin-derived aromatics. The identification of a novel thermostable protocatechuate decarboxylase gene in the strain further adds to its significance, as such an enzyme can be efficiently used in the biosynthesis of cis,cis-muconate, an important intermediate in the commercial production of plastics.

Elucidation of 4-Hydroxybenzoic Acid Catabolic Pathways in Pseudarthrobacter phenanthrenivorans Sphe3

“…A thorough in silico analysis of the Sphe3 genome failed to come up with a PCA decarboxylase sequence. However, Chakraborty et al recently discovered that in the thermophilus bacterium Thermus oshimai JL-2, the PCA decarboxylation to catechol is catalyzed by a 4-carboxymuconolactone decarboxylase [45]. 4-carboxymuconolactone is a metabolite of the PCA 3,4-cleavage pathway and the Sphe3 genome harbors a gene coding for this carboxylase (locus tag Asphe3_38820).…”

A highly explicit electrochemical biosensor for catechol detection in real samples based on copper-polypyrrole

“…The introduction of catechol into aquatic systems can originate from natural or artificial sources. 9 Primary sources include the large-scale decomposition of natural material, industrial wastewater, the degradation of lignin in wood pulp, 10 and oil processing units. 11 Because molecular catechol has the propensity to interact with H 2 N- and HS-proteins, it is more vulnerable to being absorbed by animals and plants.…”