Genome-Based Exploration of Rhodococcus Species for Plastic-Degrading Genetic Determinants Using Bioinformatic Analysis

Abstract

Plastic polymer waste management is an increasingly prevalent issue. In this paper, Rhodococcus genomes were explored to predict new plastic-degrading enzymes based on recently discovered biodegrading enzymes for diverse plastic polymers. Bioinformatics prediction analyses were conducted using 124 gene products deriving from diverse microorganisms retrieved from databases, literature data, omic-approaches, and functional analyses. The whole results showed the plastic-degrading potential of Rhodococcus genus. Among the species with high plastic-degrading potential, R. erythropolis, R. equi, R. opacus, R. qingshengii, R. fascians, and R. rhodochrous appeared to be the most promising for possible plastic removal. A high number of genetic determinants related to polyester biodegradation were obtained from different Rhodococcus species. However, score calculation demonstrated that Rhodococcus species (especially R. pyridinivorans, R. qingshengii, and R. hoagii) likely possess PE-degrading enzymes. The results identified diverse oxidative systems, including multicopper oxidases, alkane monooxygenases, cytochrome P450 hydroxylases, para-nitrobenzylesterase, and carboxylesterase, and they could be promising reference sequences for the biodegradation of plastics with C−C backbone, plastics with heteroatoms in the main chain, and polyesters, respectively. Notably, the results of this study could be further exploited for biotechnological applications in biodegradative processes using diverse Rhodococcus strains and through catalytic reactions.

Polyethylene Degradation by a Rhodococcous Strain Isolated from Naturally Weathered Plastic Waste Enrichment

“…Among the bacterial strains isolated from the 609 day enrichment cultures, a lipase-positive Rhodococcus strain (named A34 strain here) was obtained. Consistent to the existence of potential PE-degrading enzyme genes in Rhodococcus stains based on genome-based exploration, the A34 strain genome had abundant potential PE oxidation and degradation genes. Further time series proteomics data demonstrated the induction and high abundances of extracellular key PE oxidation and depolymerization enzymes such as catalase-peroxidase KatG, multicopper oxidase, lipase, and esterase.…”

“…Transcriptomic analysis of Rhodococcus opacus R7 uncovered the potential key genes involved in depolymerization and oxidation of PE such as alkane monooxygenase and cytochrome P450 hydroxylase . Comparative genomics analysis of Rhodococcus genomes indicated the distribution of these potential key plastic degradation-associated genes in Rhodococcus genomes . Despite these findings, in-depth studies on PE-degrading microorganisms and the underlying plastic degradation mechanisms are still lacking.…”

“…9 Comparative genomics analysis of Rhodococcus genomes indicated the distribution of these potential key plastic degradation-associated genes in Rhodococcus genomes. 10 Despite these findings, in-depth studies on PE-degrading microorganisms and the underlying plastic degradation mechanisms are still lacking.…”

Mechanistic Insights into Cellular and Molecular Basis of Protein‐Nanoplastic Interactions

“…[152,153] The OMICS-level studies have helped in identifying a variety of plastic degrading enzymes (PDEs) associated with the microbes which mediate plastic decomposition utilizing it as a (substrate) source of energy. [154,155] Another critical aspect of protein-PNP interactions is to elucidate the mechanisms of plastic degradation, and the dynamics between plastic degrading enzymes (PDE) and their plastic substrates. Apart from a few studies on PMPs, no other submicron range plastic has been reported as a substrate for the PDEs till date.…”

Computational Exploration of Bio-Degradation Patterns of Various Plastic Types

“…Contemporarily, sequence based analysis is helping in navigating large sequence datasets. Zampolli et al applied sequence-based analysis to determine the genetic determinant of plastic degradation [ 39 ]. Skariyachan et al provided a detailed review about a computational and data driven method applied in the field of plastic degradation [ 40 ].…”