The complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870

The catabolism of ethylene glycol by Rhodococcus jostii RHA1 and its dependence on mycofactocin

Ethylene glycol (EG) is a widely used industrial chemical with manifold applications and also generated in the degradation of plastics such as polyethylene terephthalate. Rhodococcus jostii RHA1 (RHA1), a potential biocatalytic chassis, grows on EG. Transcriptomic analyses revealed four clusters of genes potentially involved in EG catabolism: the mad locus, predicted to encode mycofactocin-dependent alcohol degradation, including the catabolism of EG to glycolate; two GCL clusters, predicted to encode glycolate and glyoxylate catabolism; and the mft genes, predicted to specify mycofactocin biosynthesis. Bioinformatic analyses further revealed that the mad and mft genes are widely distributed in mycolic acid-producing bacteria such as RHA1. Neither ΔmadA nor ΔmftC RHA1 mutant strains grew on EG but grew on acetate. In resting cell assays, the ΔmadA mutant depleted glycolaldehyde but not EG from culture media. These results indicate that madA encodes a mycofactocin-dependent alcohol dehydrogenase that initiates EG catabolism. In contrast to some mycobacterial strains, the mad genes did not appear to enable RHA1 to grow on methanol as sole substrate. Finally, a strain of RHA1 adapted to grow ~3× faster on EG contained an overexpressed gene, aldA2, predicted to encode an aldehyde dehydrogenase. When incubated with EG, this strain accumulated lower concentrations of glycolaldehyde than RHA1. Moreover, ecotopically expressed aldA2 increased RHA1's tolerance for EG further suggesting that glycolaldehyde accumulation limits growth of RHA1 on EG. Overall, this study provides insights into the bacterial catabolism of small alcohols and aldehydes and facilitates the engineering of Rhodococcus for the upgrading of plastic waste streams.IMPORTANCEEthylene glycol (EG), a two-carbon (C2) alcohol, is produced in high volumes for use in a wide variety of applications. There is burgeoning interest in understanding and engineering the bacterial catabolism of EG, in part to establish circular economic routes for its use. This study identifies an EG catabolic pathway in Rhodococcus, a genus of bacteria well suited for biocatalysis. This pathway is responsible for the catabolism of methanol, a C1 feedstock, in related bacteria. Finally, we describe strategies to increase the rate of degradation of EG by increasing the transformation of glycolaldehyde, a toxic metabolic intermediate. This work advances the development of biocatalytic strategies to transform C2 feedstocks.

The catabolism of lignin-derived p-methoxylated aromatic compounds by Rhodococcus jostii RHA1

Emergent strategies to valorize lignin, an abundant but underutilized aromatic biopolymer, include tandem processes that integrate chemical depolymerization and biological catalysis. To date, aromatic monomers from C-O bond cleavage of lignin have been converted to bioproducts, but the presence of recalcitrant C-C bonds in lignin limits the product yield. A promising chemocatalytic strategy that overcomes this limitation involves phenol methyl protection and autoxidation. Incorporating this into a tandem process requires microbial cell factories able to transform the p-methoxylated products in the resulting methylated lignin stream. In this study, we assessed the ability of Rhodococcus jostii RHA1 to catabolize the major aromatic products in a methylated lignin stream and elucidated the pathways responsible for this catabolism. RHA1 grew on a methylated pine lignin stream, catabolizing the major aromatic monomers: p-methoxybenzoate (p-MBA), veratrate, and veratraldehyde. Bioinformatic analyses suggested that a cytochrome P450, PbdA, and its cognate reductase, PbdB, are involved in p-MBA catabolism. Gene deletion studies established that both pbdA and pbdB are essential for growth on p-MBA and several derivatives. Furthermore, a deletion mutant of a candidate p-hydroxybenzoate (p-HBA) hydroxylase, ΔpobA, did not grow on p-HBA. Veratraldehyde and veratrate catabolism required both vanillin dehydrogenase (Vdh) and vanillate O-demethylase (VanAB), revealing previously unknown roles of these enzymes. Finally, a ΔpcaL strain grew on neither p-MBA nor veratrate, indicating they are catabolized through the β-ketoadipate pathway. This study expands our understanding of the bacterial catabolism of aromatic compounds and facilitates the development of biocatalysts for lignin valorization.IMPORTANCELignin, an abundant aromatic polymer found in plant biomass, is a promising renewable replacement for fossil fuels as a feedstock for the chemical industry. Strategies for upgrading lignin include processes that couple the catalytic fractionation of biomass and biocatalytic transformation of the resulting aromatic compounds with a microbial cell factory. Engineering microbial cell factories for this biocatalysis requires characterization of bacterial pathways involved in catabolizing lignin-derived aromatic compounds. This study identifies new pathways for lignin-derived aromatic degradation in Rhodococcus, a genus of bacteria well suited for biocatalysis. Additionally, we describe previously unknown activities of characterized enzymes on lignin-derived compounds, expanding their utility. This work advances the development of strategies to replace fossil fuel-based feedstocks with sustainable alternatives.

Abridgement of Microbial Esterases and Their Eminent Industrial Endeavors

Esterases are hydrolases that contribute to the hydrolysis of ester bonds into both water-soluble acyl esters and emulsified glycerol-esters containing short-chain acyl groups. They have garnered significant attention from biotechnologists and organic chemists due to their immense commercial value. Esterases, with their diverse and significant properties, have become highly sought after for various industrial applications. Synthesized ubiquitously by a wide range of living organisms, including animals, plants, and microorganisms, these enzymes have found microbial esterases to be the preferred choice in industrial settings. The cost-effective production of microbial esterases ensures higher yields, unaffected by seasonal variations. Their applications span diverse sectors, such as food manufacturing, leather tanneries, paper and pulp production, textiles, detergents, cosmetics, pharmaceuticals, biodiesel synthesis, bioremediation, and waste treatment. As the global trend shifts toward eco-friendly and sustainable practices, industrial processes are evolving with reduced waste generation, lower energy consumption, and the utilization of biocatalysts derived from renewable and unconventional raw materials. This review explores the background, structural characteristics, thermostability, and multifaceted roles of bacterial esterases in crucial industries, aiming to optimize and analyze their properties for continued successful utilization in diverse industrial processes. Additionally, recent advancements in esterase research are overviewed, showcasing novel techniques, innovations, and promising areas for further exploration.

Draft Genome Sequence of Rhodococcus rhodochrous Strain G38GP, Isolated from the Madagascar Hissing Cockroach

Rhodococcus rhodochrous is a bacterial species with applications in biocatalysis and bioremediation. Here, we report the draft genome sequence of strain G38GP, isolated from the gut of the cockroach Gromphadorhina portentosa. The genome consists of 76 contigs, with a total length of 6,256,198 bp and a GC content of 67.82%.

Complete Genome Sequence of Rhodococcus sp. Strain M8, a Platform Strain for Acrylic Monomer Production

We report a 6.27-Mbp complete genome of Rhodococcus sp. strain M8, an originally discovered strain that is now under investigation for production of acrylic monomers. The genome consists of a 6.1-Mbp circular chromosome and a 173.2-kbp plasmid.

We report a 6.27-Mbp complete genome of Rhodococcus sp. strain M8, an originally discovered strain that is now under investigation for production of acrylic monomers. The genome consists of a 6.1-Mbp circular chromosome and a 173.2-kbp plasmid.

Characterization of a novel carbendazim-degrading strain Rhodococcus sp. CX-1 revealed by genome and transcriptome analyses

The persistence and ecotoxicity of carbendazim residues pose a potential risk to environmental ecology and human health. Here, a novel and highly efficient carbendazim-degrading bacterium Rhodococcus sp. CX-1, capable of utilizing carbendazim as its sole source of carbon and energy, was isolated from contaminated soil. The biodegradation characteristics and metabolic pathways were studied by mass spectrometry, genomic annotation, and transcriptome analysis. The degradation rate of carbendazim by strain CX-1 was 3.98-9.90 mg/L/h under different conditions, and the optimum degradation conditions were 40 °C and pH 7.0. The addition of carbon sources (glucose, fructose, and sucrose, 100 mg/L) could accelerate carbendazim degradation. HPLC-MS/MS identification suggested that carbendazim is first hydrolyzed into 2-aminobenzimidazole and then to 2-hydroxybenzimidazole, and is ultimately mineralized to carbon dioxide. The genome of strain CX-1 contained 6,511,628 bp nucleotides, 2 linear plasmids, 2 circular plasmids, and 6437 protein coding genes. Genome annotation and transcriptome analysis indicated that carbendazim degradation may be regulated by the degradation genes harbored in the chromosome and in plasmid 2, and two different degradation pathways of carbendazim by imidazole ring cleavage or benzene ring cleavage were predicted. This study provided new insight to reveal the biodegradation mechanism of carbendazim; furthermore, strain CX-1 is a promising bioresource for carbendazim bioremediation.

Functional Expression and Characterization of a Panel of Cobalt and Iron-Dependent Nitrile Hydratases

Nitrile hydratases (NHase) catalyze the hydration of nitriles to the corresponding amides. We report on the heterologous expression of various nitrile hydratases. Some of these enzymes have been investigated by others and us before, but sixteen target proteins represent novel sequences. Of 21 target sequences, 4 iron and 16 cobalt containing proteins were functionally expressed from Escherichia coli BL21 (DE3) Gold. Cell free extracts were used for activity profiling and basic characterization of the NHases using the typical NHase substrate methacrylonitrile. Co-type NHases are more tolerant to high pH than Fe-type NHases. A screening for activity on three structurally diverse nitriles was carried out. Two novel Co-dependent NHases from Afipia broomeae and Roseobacter sp. and a new Fe-type NHase from Gordonia hydrophobica were very well expressed and hydrated methacrylonitrile, pyrazine-carbonitrile, and 3-amino-3-(p-toluoyl)propanenitrile. The Co-dependent NHases from Caballeronia jiangsuensis and Microvirga lotononidis, as well as two Fe-dependent NHases from Pseudomonades, were—in addition—able to produce the amide from cinnamonitrile. Summarizing, seven so far uncharacterized NHases are described to be promising biocatalysts.