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Updated: Dec 9, 2025

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Transcriptomic Analysis of Rhodococcus opacus R7 Grown on o-Xylene by RNA-Seq.

Jessica Zampolli¹, Alessandra Di Canito¹, Andrea Manconi²

¹Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.

Frontiers in Microbiology

|September 9, 2020

Summary

Rhodococcus opacus R7 utilizes a unique pathway for o-xylene degradation, identified using RNA sequencing. This study reveals key genes and enzymes involved in breaking down this environmental contaminant.

Keywords:

RNA-seq Rhodococcus opacus environmental contamination o-xylene oxygenases stress response

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Last Updated: Dec 9, 2025

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Measuring mRNA Levels Over Time During the Yeast S. cerevisiae Hypoxic Response

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Published on: August 10, 2017

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing

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Published on: August 7, 2021

Area of Science:

Environmental Microbiology
Molecular Biology
Biochemistry

Background:

Xylenes are significant environmental pollutants, with o-xylene oxidation being less understood than biodegradation.
Rhodococcus opacus R7 is a known degrader of aromatic hydrocarbons, including o-xylene as a sole carbon source.

Purpose of the Study:

To elucidate the genetic underpinnings of o-xylene degradation in Rhodococcus opacus R7 using RNA sequencing.
To identify novel enzymes and pathways involved in o-xylene metabolism.

Main Methods:

RNA sequencing (RNA-seq) was employed to analyze gene expression changes in R. opacus R7.
Gene ontology (GO) enrichment and KEGG pathway analyses were performed on transcriptomic data.

Main Results:

542 differentially expressed genes were identified, linked to aromatic hydrocarbon oxidation, stress response, and metabolism.
The akb gene cluster, encoding the ethylbenzene dioxygenase system, showed the highest upregulation.
Candidate enzymes potentially involved in o-xylene degradation and metabolite formation were identified.

Conclusions:

R. opacus R7 possesses redundant genetic systems for o-xylene metabolism, utilizing a unique degradation pathway.
This research provides valuable insights into o-xylene metabolism and identifies potential molecular tools for enhanced bioremediation.