Transcriptomic analysis of Rhodococcus opacus R7 grown on polyethylene by RNA-seq

Abstract

Plastic waste management has become a global issue. Polyethylene (PE) is the most abundant synthetic plastic worldwide, and one of the most resistant to biodegradation. Indeed, few bacteria can degrade polyethylene. In this paper, the transcriptomic analysis unveiled for the first time Rhodococcus opacus R7 complex genetic system based on diverse oxidoreductases for polyethylene biodegradation. The RNA-seq allowed uncovering genes putatively involved in the first step of oxidation. In-depth investigations through preliminary bioinformatic analyses and enzymatic assays on the supernatant of R7 grown in the presence of PE confirmed the activation of genes encoding laccase-like enzymes. Moreover, the transcriptomic data allowed identifying candidate genes for the further steps of short aliphatic chain oxidation including alkB gene encoding an alkane monooxygenase, cyp450 gene encoding cytochrome P450 hydroxylase, and genes encoding membrane transporters. The PE biodegradative system was also validated by FTIR analysis on R7 cells grown on polyethylene.

Enzymes’ Power for Plastics Degradation

“…Rhodococcus ruber C208 (DSM 45332) was cultivated for 3 days with 0.6% of various Rhodococcus opacus R7 grown on PE powder, prepared at 1.2% as only carbon and energy source was also analyzed by transcriptomics. 612 It confirmed the activation of genes encoding laccase-like enzymes. LMCO1 that was described as a laccase-like multicopper oxidase (LMCO) was upregulated by 19.5-fold.…”

Mycobacteriaceae Mineralizes Micropolyethylene in Riverine Ecosystems

“…56 Notably, 7 MAGs, which were all 13 C-mPE as a solo carbon source confirmed their ability to mineralize mPE (Figure 4). Significant higher δ 13 C in the headspace of the cultures amended by both 13 C-mPE and pure isolates was observed compared to the cultures amended by the isolates only or the killed control, suggesting that the production of 13 S1), were analyzed to assess the completeness of the proposed mPE mineralization pathway 21,57,58 (Figure 5).…”

“…mPE12, both are belonging to the family Mycobacteriaceae , a pangenomic analysis was performed to investigate whether mPE degradation is a common function shared by members of Mycobacteriaceae . A total of eight MAGs associated with putative mPE-degrading Mycobacteriaceae identified in this study (five Mycobacterium MAGs, two Nocardia MAGs, and one Jongsikchunia MAG), together with publicly available genomes/MAGs of Mycobacteriaceae including 35 Mycobacterium , 8 Nocardia , and 1 Jongsikchunia (Table S1), were analyzed to assess the completeness of the proposed mPE mineralization pathway ,, (Figure ).…”

Microbial enzymes will offer limited solutions to the global plastic pollution crisis

“…However, the recent study is so far the only one that linked enzymatic activities to high-molecularweight PE-degradation. The possible involvement in the initial breakdown of long-chain alkanes was further supported by transcriptome studies using Rhodobacter opacus R7 (Zampolli et al, 2021). Rhodobacter opacus R7 grown on PE and RNA sequencing (RNAseq) analyses implied that at least one multicopper oxidase was 19.5-fold induced under these conditions.…”

“…In combination with omics‐analyses and sophisticated analytical technologies, smart enrichments can deliver polymer‐active enzymes. Using RNAseq, metabolomics and proteomics in these multispecies consortia will further give us clues on key genes involved in polymer degradation (Tesei et al, 2020 ; Zampolli et al, 2021 ).…”