CYP108N12 initiates p-cymene biodegradation in Rhodococcus globerulus

Biodegradation of polystyrene by Spodoptera litura and Spodoptera frugiperda larvae (Lepidoptera: Noctuidae): Insights into the frass characterization and responses of gut microbiomes

Polystyrene (PS) biodegradation by some lepidoptera larvae has been demonstrated, but little is known about the Spodoptera litura and Spodoptera frugiperda (Lepidoptera: Noctuidae). Here we confirmed that PS-fed larvae showed significantly higher survival rates than starvation and antibiotic groups, with S. frugiperda consuming PS more efficiently than S. litura (1.52 vs. 0.56 mg larva⁻¹ day⁻¹). PS-frass characterization revealed oxygen-containing groups (C-O, CO, -OH) with reduced thermal stability and a significant decrease in weight-average molecular weight (S. litura: -6.01 %; S. frugiperda: -8.93 %), evidencing oxidative depolymerization of PS by both species. The gut microbiota (Pedobacter, Achromobacter, Pseudomonas, Acinetobacter, etc.) and functional enzymes (e.g., monooxygenase, dioxygenase, chitinases) were upregulated in PS-fed larvae. Metabolome analysis revealed altered stress responses and reprogrammed metabolic pathways, particularly in lipid and carbohydrate metabolism, which correlated strongly with gut microbiota changes. Overall, we demonstrated the biodegradation of PS by S. litura and S. frugiperda for the first time, and proposed a plausible degradation mechanism mediated by gut microbiota, illustrating both the host and gut microbiomes contributed to PS biodegradation. These findings highlight the feasibility of developing insect-based plastic degradation systems through the isolation of key microbial-enzymatic consortia, offering a sustainable solution for plastic waste management.

Characterisation of the Self-Sufficient Cytochrome P450 CYP116B234 From Rhodococcus globerulus and Its Suggested Native Role in 2-Hydroxyphenylacetic Acid Metabolism

Cytochromes P450 (P450s) are exceptional biocatalysts that enable the selective oxidation of unactivated C-H bonds using molecular oxygen. Typically, auxiliary redox partner proteins deliver electrons from NAD(P)H to the P450, enabling oxygen activation. However, associating native redox partners with P450s can be challenging, particularly when they are genomically separated. Self-sufficient P450s, where the P450 heme domain is naturally fused to redox partners, represent a simpler, single-protein system. Here, we present CYP116B234, a novel self-sufficient P450 from Rhodococcus globerulus, comprising fused heme and phthalate-family oxygenase reductase (PFOR) domains. The gene encoding CYP116B234 was codon-optimised for heterologous expression in E. coli and subsequently purified to homogeneity. Spectroelectrochemical analysis and electron paramagnetic resonance spectroscopy were performed to determine the redox potentials of the heme and associated Fe-S and FMN cofactors of the PFOR domain. CYP116B234 binds and efficiently oxidises the substituted aromatic compound 2-hydroxyphenylacetic acid (2-HPA) to homogentisic acid. Quantitative proteomics revealed the expression of CYP116B234 in R. globerulus grown on 2-HPA, suggesting a role in initiating 2-HPA degradation. This study presents a new addition to the self-sufficient CYP116 family and provides evidence for their native function.

Removal of terpenes in the presence of easily degradable compounds during biofiltration of gas emissions from composting of municipal solid waste

Composting of the organic fraction of municipal solid waste (OFMSW) is accompanied by the emission of large volumes of harmful, hazardous and foul-smelling volatile organic compounds (VOCs). To improve the efficiency of terpenes removal, which constitute a significant part of VOCs, pure cultures of microorganisms dominating in its microbiota were isolated from the microbial community of the biofilter, which has been cleaning such emissions for a long time. Seven pure cultures were isolated and then tested for being able to grow on a mineral medium in the presence of terpene vapor as the only source of carbon and energy. Three of the most actively growing cultures were selected, characterized and identified by the 16S rRNA gene as Rhodococcus erythropolis CA1, Rhodococcus pyridinivorans CA3 and Gordonia sp. CA6. Three identical laboratory biofilters (BF) were inoculated with a mix of these cultures to test the possibility of more complete removal of terpenes. Biofilters were adapting to clearing the model mix of terpineols and geraniol vapors for 45 days. During 45 days the purification efficiency of the model mix reached an average of 91.5% with a contact time (CT) of 3.7 ± 0.2 s and the terpene vapors concentration of 14 ± 2 mg m-3. Then the biofilters number BF2.1 and BF3.1 were connected to real emission from composting OFMSW. The biofilter BF2.1 purified the emission directly, whereas BF3.1 purified similar discharge after the intermediate biofilter of the 1st stage of purification (BF0.0). The BF1.0 was left connected to purification of the model mix as a control. The effectiveness of biofiltration of hard-to-remove terpenes was evaluated by gas chromatography of samples taken at the inlet and outlet of biofilters. The average efficiency of removing terpenes from real emissions by BF2.1 was 93.1 % (CT = 5.5 s). The total efficiency of removing terpenes by (BF0.0 + BF3.1) complex was 93.2 % (total CT = 7.4 s). A study of the microbiota of inoculated biofilters after 60 and 90 days of purification the real emission by cultivation from dilutions, identification by the 16S rRNA gene and fingerprinting showed that in BF2.1 and BF3.1 Rhodococcus erythropolis CA1 and Rhodococcus pyridinivorans CA3 were preserved among living cells at a level of 6.5-12.4 %, and genetically fully corresponded to the original cultures. These results could have a positive impact on improving the results of deodorization of emissions from OFMSW composting by biofiltration, simplifying the design of the biofiltration facility (one stage instead of two) and reducing the total time for effective biofiltration. This, in turn, would contribute to the wider introduction of highly efficient emission purification methods at OFMSW composting facilities in order to create more comfortable and ecologically clean environmental conditions around them.

Bioinformatics Analysis of the Genome of Rhodococcus rhodochrous IEGM 1362, an (-)-Isopulegol Biotransformer

A genome of Rhodococcus rhodochrous IEGM 1362 was sequenced and annotated. This strain can transform monoterpene alcohol (-)-isopulegol with the formation of two novel pharmacologically promising metabolites. Nine genes encoding cytochrome P450, presumably involved in (-)-isopulegol transformation, were found in the genome of R. rhodochrous IEGM 1362. Primers and PCR conditions for their detection were selected. The obtained data can be used for the further investigation of genes encoding enzymes involved in monoterpene biotransformation.

Transformation of Terpenoids and Steroids Using Actinomycetes of the Genus Rhodococcus

Terpenoids and steroids are secondary plant and animal metabolites and are widely used to produce highly effective pharmacologically significant compounds. One of the promising approaches to the transformation of these compounds to form bioactive metabolites is their transformation using microorganisms. Rhodococcus spp. are one of the most developed objects in biotechnology due to their exceptional metabolic capabilities and resistance to extreme environmental conditions. In this review, information on the processes of biotransformation of terpenoid and steroid compounds by actinomycetes of the genus Rhodococcus and their molecular genetic bases are most fully collected and analyzed for the first time. Examples of the use of both native whole-cell catalysts and mutant strains and purified enzyme systems for the production of derivatives of terpenoids and steroids are given.

CYP108N14: A Monoterpene Monooxygenase from Rhodococcus globerulus

Rhodococcus globerulus (R. globerulus) was isolated from the soil beneath a Eucalypt tree. Metabolic growth studies revealed that R. globerulus was capable of living on certain monoterpenes, including 1,8-cineole and p-cymene, as sole sources of carbon and energy. Multiple P450 genes were identified in the R. globerulus genome that shared homology to known bacterial, monoterpene hydroxylating P450s. To date, two of these P450s have been expressed and characterised as 1,8-cineole (CYP176A1) and p-cymene (CYP108N12) monooxygenases that are believed to initiate the biodegradation of these terpenes. In this work, another putative P450 gene (CYP108N14) was identified in R. globerulus genome. Given its amino acid sequence identity to other monoterpene hydroxylating P450s it was hypothesised to catalyse monoterpene hydroxylation. These include CYP108A1 from Pseudomonas sp. (47 % identity, 68 % similarity) which hydroxylates α-terpineol, and CYP108N12 also from R. globerulus (62 % identity, 77 % similarity). Also present in the operon containing CYP108N14 were putative ferredoxin and ferredoxin reductase genes, suggesting a typical Class I P450 system. CYP108N14 was successfully over-expressed heterologously and purified, resulting in a good yield of CYP108N14 holoprotein. However, neither the ferredoxin nor ferredoxin reductase could be produced heterologously. Binding studies with CYP108N14 revealed a preference for the monoterpenes p-cymene, (R)-limonene, (S)-limonene, (S)-α-terpineol and (S)-4-terpineol. An active catalytic system was reconstituted with the non-native redox partners cymredoxin (from the CYP108N12 system) and putidaredoxin reductase (from the CYP101A1 system). CYP108N14 when supported by these redox partners was able to catalyse the hydroxylation of the five aforementioned substrates selectively at the methyl benzylic/allylic positions.

Synthesis of substituted norcaranes for use as probes of enzyme mechanisms

Norcarane is a mechanistic probe of monooxygenase enzymes that is able to detect the presence of cationic or radical intermediates. The addition of substituents around the bicycloheptane ring of the norcarane scaffold can assist in improving enzyme binding affinity and thus improve the regioselectivity of oxidation. Here we prepare in three-step, diastereoselective syntheses, ten norcaranes monosubstituted α to the cyclopropane as advanced probes. Four of these compounds were examined in enzyme binding experiments to evaluate their potential as probe substrates. Additionally, 19 potential products of enzymatic oxidation were generated via two additional synthetic steps for use as product standards in future studies.

Cymredoxin, a [2Fe-2S] ferredoxin, supports catalytic activity of the p-cymene oxidising P450 enzyme CYP108N12

Rhodococcus globerulus is a metabolically active organism that has been shown to utilise eucalypt oil as its sole source of carbon and energy. This oil includes 1,8-cineole, p-cymene and limonene. Two identified and characterised cytochromes P450 (P450s) from this organism initiate the biodegradation of the monoterpenes 1,8-cineole (CYP176A1) and p-cymene (CYP108N12). Extensive characterisation has been completed for CYP176A1 and it has been successfully reconstituted with its immediate redox partner, cindoxin, and E. coli flavodoxin reductase. Two putative redox partner genes are encoded in the same operon as CYP108N12 and here the isolation, expression, purification, and characterisation of its specific [2Fe-2S] ferredoxin redox partner, cymredoxin is presented. Reconstitution of CYP108N12 with cymredoxin in place of putidaredoxin, a [2Fe-2S] redox partner of another P450, improves both the rate of electron transfer (from 13 ± 2 to 70 ± 1 μM NADH/min/μM CYP108N12) and the efficiency of NADH utilisation (the so-called coupling efficiency increases from 13% to 90%). Cymredoxin improves the catalytic ability of CYP108N12 in vitro. Aldehyde oxidation products of the previously identified substrates p-cymene (4-isopropylbenzaldehyde) and limonene (perillaldehyde) were observed in addition to major hydroxylation products 4-isopropylbenzyl alcohol and perillyl alcohol respectively. These further oxidation products had not previously been seen with putidaredoxin supported oxidation. Furthermore, when supported by cymredoxin CYP108N12 is able to oxidise a wider range of substrates than previously reported. These include o-xylene, α-terpineol, (-)-carveol and thymol yielding o-tolylmethanol, 7-hydroxyterpineol, (4R)-7-hydroxycarveol and 5-hydroxymethyl-2-isopropylphenol, respectively. Cymredoxin is also capable of supporting CYP108A1 (P450_terp) and CYP176A1 activity, allowing them to catalyse the hydroxylation of their native substrates α-terpineol to 7-hydroxyterpineol and 1,8-cineole to 6β-hydroxycineole respectively. These results indicate that cymredoxin not only improves the catalytic capability of CYP108N12 but can also support the activity of other P450s and prove useful for their characterisation.