Complete Genome Sequence of Rhodococcus ruber R1, a Novel Strain Showing a Broad Catabolic Potential toward Lignin-Derived Aromatics

Farkas, Carlos; Donoso, Raúl; Melis-Arcos, Felipe; Gárate-Castro, Carla; Pérez‐Pantoja, Danilo

doi:10.1128/mra.00905-19

Cited by 4 publications

(3 citation statements)

References 12 publications

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“…Results showed that Rhodococcus strains harboring vanAB -like genes similar to R. ruber R1 as R. ruber DSM 43338 T , R. ruber Chol-4 and R. pyridinivorans JCM 10940 T [ 8 , 44 , 45 ], and vanAB genes comparable to R. jostii RHA1 as R. aetherivorans BCP1 [ 46 , 47 ] were able to grow on VA and its O-demethylation product, PCA ( Figure 4 ), suggesting that all these strains contain proficient VanOD-encoded genes and a functional PCA pathway ( Figure 1 D). We also included in our growth profile assays marine-isolated Rhodococcus strains MS13 and H-CA8f as control [ 48 , 49 ], since they apparently do not harbor VanOD-encoded genes, even though they carry the classical PCA pathway [ 50 ], as revealed by BLAST searches and confirmed by growth on PCA as a sole carbon and energy source ( Figure 4 ).…”

Section: Resultsmentioning

confidence: 99%

“…Recently, we isolated a bacterial strain belonging to the Rhodococcus genus from a pulp mill wastewater treatment plant identified as Rhodococcus ruber strain R1, whose genome sequence consisted of one chromosome (~5.3 Mbp) and two plasmids (~179 and ~33 kbp), revealing an extensive catabolic potential [ 8 ]. Strain R1 has the ability to grow on various lignin-derived phenolic monomers, including p -coumarate and 4-hydroxybenzoate [ 8 ], which are typically catabolized via β-ketoadipate through the ring-cleavage intermediate protocatechuate (PCA) in Rhodococcus species [ 9 , 10 ]. Accordingly, we have currently confirmed that strain R1 is capable to grow on vanillate (VA), an additional lignin-derived product generated from the metabolism of ferulate and vanillin [ 10 , 11 ], as a sole carbon and energy source.…”

Section: Introductionmentioning

confidence: 99%

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Identification of a Phylogenetically Divergent Vanillate O-Demethylase from Rhodococcus ruber R1 Supporting Growth on Meta-Methoxylated Aromatic Acids

et al. 2022

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Rieske-type two-component vanillate O-demethylases (VanODs) catalyze conversion of the lignin-derived monomer vanillate into protocatechuate in several bacterial species. Currently, VanODs have received attention because of the demand of effective lignin valorization technologies, since these enzymes own the potential to catalyze methoxy group demethylation of distinct lignin monomers. In this work, we identified a phylogenetically divergent VanOD from Rhodococcus ruber R1, only distantly related to previously described homologues and whose presence, along with a 3-hydroxybenzoate/gentisate pathway, correlated with the ability to grow on other meta-methoxylated aromatics, such as 3-methoxybenzoate and 5-methoxysalicylate. The complementation of catabolic abilities by heterologous expression in a host strain unable to grow on vanillate, and subsequent resting cell assays, suggest that the vanAB genes of R1 strain encode a proficient VanOD acting on different vanillate-like substrates; and also revealed that a methoxy group in the meta position and a carboxylic acid moiety in the aromatic ring are key for substrate recognition. Phylogenetic analysis of the oxygenase subunit of bacterial VanODs revealed three divergent groups constituted by homologues found in Proteobacteria (Type I), Actinobacteria (Type II), or Proteobacteria/Actinobacteria (Type III) in which the R1 VanOD is placed. These results suggest that VanOD from R1 strain, and its type III homologues, expand the range of methoxylated aromatics used as substrates by bacteria.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification of a Phylogenetically Divergent Vanillate O-Demethylase from Rhodococcus ruber R1 Supporting Growth on Meta-Methoxylated Aromatic Acids

et al. 2022

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“…Biodegration of lignin can be observed in nature with enzymes produced by different fungal species and bacterial species [9,10]. Even though, the lignin cannot be digested by cattle and therefore is not suitable for use in animal husbandry as a feed source.…”

Section: Introductionmentioning

confidence: 99%

Green Bisphenol A: A High Valued Building Block Isolated from Lignin Biowaste

Shah

Acharige

Kim

et al. 2020

Waste Biomass Valor

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Isolation of high-value chemicals from lignin has been a field of interest over the last few decades driven by growing environmental concerns. This study reports isolation of pyrolysate from the lab scale setup and further purification of it to be used in synthesis of bisphenol A (BPA), a high value building block used in a wide range of plastic materials. Kraft lignin from three different feedstocks were evaluated at different pyrolysis temperature conditions and a correlation between the pyrolysis conditions and yield of phenolics is presented. Phenolics were extracted and purified from the pyrolysate and then used for BPA synthesis. The reaction mixture after the BPA reaction was purified by column chromatography followed by reverse phase high performance liquid chromatography (RP-HPLC). The phenol and BPA were isolated with more than 70% purity. The purified phenolics and BPA were analyzed by gas chromatography-mass spectrometry (GC-MS), HPLC and 1 H nuclear magnetic resonance (NMR) spectroscopy.

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Identification of a self‐sufficient cytochrome P450 monooxygenase from Cupriavidus pinatubonensis JMP134 involved in 2‐hydroxyphenylacetic acid catabolism, via homogentisate pathway

Donoso

Ruiz

Gárate-Castro

et al. 2021

Microbial Biotechnology

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The self-sufficient cytochrome P450 RhF and its homologues belonging to the CYP116B subfamily have attracted considerable attention due to the potential for biotechnological applications based in their ability to catalyse an array of challenging oxidative reactions without requiring additional protein partners. In this work, we showed for the first time that a CYP116B self-sufficient cytochrome P450 encoded by the ohpA gene harboured by Cupriavidus pinatubonensis JMP134, a b-proteobacterium model for biodegradative pathways, catalyses the conversion of 2-hydroxyphenylacetic acid (2-HPA) into homogentisate. Mutational analysis and HPLC metabolite detection in strain JMP134 showed that 2-HPA is degraded through the well-known homogentisate pathway requiring a 2-HPA 5-hydroxylase activity provided by OhpA, which was additionally supported by heterologous expression and enzyme assays. The ohpA gene belongs to an operon including also ohpT, coding for a substrate-binding subunit of a putative transporter, whose expression is driven by an inducible promoter responsive to 2-HPA in presence of a predicted OhpR transcriptional regulator. OhpA homologues can be found in several genera belonging to Actinobacteria and a-, band c-proteobacteria lineages indicating a widespread distribution of 2-HPA catabolism via homogentisate route. These results provide first time evidence for the natural function of members of the CYP116B selfsufficient oxygenases and represent a significant input to support novel kinetic and structural studies to develop cytochrome P450-based biocatalytic processes.

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Complete Genome Sequence of Rhodococcus ruber R1, a Novel Strain Showing a Broad Catabolic Potential toward Lignin-Derived Aromatics

Cited by 4 publications

References 12 publications

Identification of a Phylogenetically Divergent Vanillate O-Demethylase from Rhodococcus ruber R1 Supporting Growth on Meta-Methoxylated Aromatic Acids

Identification of a Phylogenetically Divergent Vanillate O-Demethylase from Rhodococcus ruber R1 Supporting Growth on Meta-Methoxylated Aromatic Acids

Green Bisphenol A: A High Valued Building Block Isolated from Lignin Biowaste

Identification of a self‐sufficient cytochrome P450 monooxygenase from Cupriavidus pinatubonensis JMP134 involved in 2‐hydroxyphenylacetic acid catabolism, via homogentisate pathway

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