Transcriptomic analysis of Rhodococcus opacus R7 grown on polyethylene by RNA-seq. 2021

Jessica Zampolli, and Alessandro Orro, and Andrea Manconi, and Diletta Ami, and Antonino Natalello, and Patrizia Di Gennaro
Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.

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.

UI MeSH Term Description Entries
D000081246 RNA-Seq High-throughput nucleotide sequencing techniques developed for determining and analyzing the composition of the TRANSCRIPTOME of a sample. Whole Transcriptome Shotgun Sequencing
D001673 Biodegradation, Environmental Elimination of ENVIRONMENTAL POLLUTANTS; PESTICIDES and other waste using living organisms, usually involving intervention of environmental or sanitation engineers. Bioremediation,Phytoremediation,Natural Attenuation, Pollution,Environmental Biodegradation,Pollution Natural Attenuation
D012240 Rhodococcus A bacterial genus of the order ACTINOMYCETALES.
D017550 Spectroscopy, Fourier Transform Infrared A spectroscopic technique in which a range of wavelengths is presented simultaneously with an interferometer and the spectrum is mathematically derived from the pattern thus obtained. FTIR,Fourier Transform Infrared Spectroscopy,Spectroscopy, Infrared, Fourier Transform
D020869 Gene Expression Profiling The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell. Gene Expression Analysis,Gene Expression Pattern Analysis,Transcript Expression Analysis,Transcriptome Profiling,Transcriptomics,mRNA Differential Display,Gene Expression Monitoring,Transcriptome Analysis,Analyses, Gene Expression,Analyses, Transcript Expression,Analyses, Transcriptome,Analysis, Gene Expression,Analysis, Transcript Expression,Analysis, Transcriptome,Differential Display, mRNA,Differential Displays, mRNA,Expression Analyses, Gene,Expression Analysis, Gene,Gene Expression Analyses,Gene Expression Monitorings,Gene Expression Profilings,Monitoring, Gene Expression,Monitorings, Gene Expression,Profiling, Gene Expression,Profiling, Transcriptome,Profilings, Gene Expression,Profilings, Transcriptome,Transcript Expression Analyses,Transcriptome Analyses,Transcriptome Profilings,mRNA Differential Displays
D020959 Polyethylene A vinyl polymer made from ethylene. It can be branched or linear. Branched or low-density polyethylene is tough and pliable but not to the same degree as linear polyethylene. Linear or high-density polyethylene has a greater hardness and tensile strength. Polyethylene is used in a variety of products, including implants and prostheses. HDPE,High-Density Polyethylene,Polythene,LDPE,Low-Density Polyethylene,High Density Polyethylene,Low Density Polyethylene,Polyethylene, High-Density,Polyethylene, Low-Density

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