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. 2022 Sep 15;10(9):1846.
doi: 10.3390/microorganisms10091846.

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

Jessica Zampolli  1 , Alessandro Orro  2 , Daniele Vezzini  1 , Patrizia Di Gennaro  1
Affiliations

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

Jessica Zampolli et al. Microorganisms. .

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.

Keywords: PET-hydrolase; Rhodococcus genus; depolymerase; esterase; genome analyses; hydroxylase/monooxygenase; oxidase; plastic; plastic-degrading enzymes; polymer biodegradation.

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Conflict of interest statement

All other authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Clusterization tree of unique input gene products belonging to different microorganisms (retrieved from PlasticDB database, literature data, omic studies, and functional analyses for the capability of degrading at least one type of plastic) divided into fifteen clades: cutinase I (clade I), polyester-hydrolase/PET-hydrolase (clade II), depolymerase (clade III), oxygenase (clade IV), multicopper oxidase (clade V), cytochrome P450 hydroxylase (clade VI), PLA-depolymerase (clade VII), esterase (clade VIII), PU esterase (clade IX), membrane transporters (clade X), carboxylesterase (clade XI), PHB-depolymerase I (clade XII), polyurethanase (clade XIII), cutinase II (clade XIV), and PHB-depolymerase II (clade XV).
Figure 2
Figure 2
Total number of unique HIT sequences, deriving from the comparison of 124-input degrading-genes against Rhodococcus genomes, were classified into three main polymer categories: polyesters, C−C backbone plastics, and heteroatomic backbone plastics.
Figure 3
Figure 3
Total number of unique HIT sequences identified in Rhodococcus genomes for each polymer material.
Figure 4
Figure 4
Total number of unique HIT sequences identified in Rhodococcus species genomes for each polymer category: polyesters, heteroatomic backbone plastics, and C−C backbone plastics.
Figure 5
Figure 5
Normalized number of unique HIT sequences identified in Rhodococcus species genomes for each polymer category: polyesters, heteroatomic backbone plastics, and C−C backbone plastics.
Figure 6
Figure 6
Number of unique HIT sequences identified in Rhodococcus genomes for different enzyme categories putatively related to C−C backbone plastic degradation.
Figure 7
Figure 7
Subtree clusterization of HIT sequences identified by oxidase input genes putatively involved in C-C backbone plastic degradation. Marked boxes evidence the reference input genes.
Figure 8
Figure 8
Subtree clusterization of HIT sequences identified by alkane monooxygenase input genes putatively involved in C-C backbone plastic degradation. Marked box evidences the reference input gene.
Figure 9
Figure 9
Subtree clusterization of HIT sequences identified by cytochrome P450 hydroxylase input gene putatively involved in C-C backbone plastic degradation. Marked box evidences the reference input gene.
Figure 10
Figure 10
Number of unique HIT sequences identified in Rhodococcus genomes for different enzyme categories putatively related to heteroatomic backbone plastic degradation.
Figure 11
Figure 11
Subtree clusterization of HIT sequences identified by PU esterase and polyurethanase input gene putatively involved in heteroatomic backbone plastic degradation. Marked boxes evidence the reference input genes.
Figure 12
Figure 12
Number of unique HIT sequences identified in Rhodococcus genomes for different enzyme categories putatively related to polyester degradation.
Figure 13
Figure 13
Score values for the most prominent Rhodococcus species for each class of diverse polymer materials.
Figure 14
Figure 14
Score values for the most prominent Rhodococcus species for the main enzymatic categories involved in C-C backbone plastic degradation.
Figure 15
Figure 15
Score values for the most prominent Rhodococcus species for the main enzymatic categories involved in PET, PU, and polyesters degradation.
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