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

Abstract

Xylenes are considered one of the most common hazardous sources of environmental contamination. The biodegradation of these compounds has been often reported, rarer the ability to oxidize the ortho-isomer. Among few o-xylene-degrading bacteria, Rhodococcus opacus R7 is well known for its capability to degrade diverse aromatic hydrocarbons and toxic compounds, including o-xylene as only carbon and energy source. This work shows for the first time the RNA-seq approach to elucidate the genetic determinants involved in the o-xylene degradation pathway in R. opacus R7. Transcriptomic data showed 542 differentially expressed genes that are associated with the oxidation of aromatic hydrocarbons and stress response, osmotic regulation and central metabolism. Gene ontology (GO) enrichment and KEGG pathway analysis confirmed significant changes in aromatic compound catabolic processes, fatty acid metabolism, beta-oxidation, TCA cycle enzymes, and biosynthesis of metabolites when cells are cultured in the presence of o-xylene. Interestingly, the most up-regulated genes belong to the akb gene cluster encoding for the ethylbenzene (Akb) dioxygenase system. Moreover, the transcriptomic approach allowed identifying candidate enzymes involved in R7 o-xylene degradation for their likely participation in the formation of the metabolites that have been previously identified. Overall, this approach supports the identification of several oxidative systems likely involved in o-xylene metabolism confirming that R. opacus R7 possesses a redundancy of sequences that converge in o-xylene degradation through R7 peculiar degradation pathway. This work advances our understanding of o-xylene metabolism in bacteria belonging to Rhodococcus genus and provides a framework of useful enzymes (molecular tools) that can be fruitfully targeted for optimized o-xylene consumption.

Study on the antifungal mechanism of Chinese herbal extract on Botryosphaeria dothidea

“…The number of genes was varied greatly in the two groups, indicating that the inhibitory effect of the CHEC on B. dothidea was very strong. This result was similar to that of the experiment conducted by Zampolli et al (2020). The total number of differential genes was 20,510 (included genes expressed in the control group and those not expressed in the treatment group), of which the number of down‐regulated genes reached 19,139, while the number of up‐regulated genes was only 1371.…”

“…The number of genes was varied greatly in the two groups, indicating that the inhibitory effect of the CHEC on B. dothidea was very strong. This result was similar to that of the experiment conducted by Zampolli et al (2020). The total number of differential genes was 20,510 (included genes expressed in the The different color curves correspond to different experimental results of samples in (Figure 8a).…”

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

“…Abnormal LogFC values were shown by 19 differentially expressed genes (DEGs) due to the switch-off/-on effect 48 , thus they were corrected with a min-value approximation resulting in an approximated LogFC varying from − 20 to 21. Among the 19 DEGs with corrected LogFC, 5 were up-regulated genes, 14 were down-regulated genes, and 11 genes were preliminary annotated as hypothetical proteins (Table S1 ).…”

Combined Omics Approach Reveals Key Differences between Aerobic and Microaerobic Xylene-Degrading Enrichment Bacterial Communities: Rhodoferax─A Hitherto Unknown Player Emerges from the Microbial Dark Matter

“…Members of the genus Rhodococcus are often reported as effective o-xylene degraders, 1−3 and their o-xylene metabolism has been deeply studied. 4 Nevertheless, results of a recent enrichment study suggested that members of the genus Rhodococcus prefer clear aerobic conditions for the degradation of petroleum hydrocarbons and are marginalized under microaerobic conditions. 5 Since subsurface environments are naturally oxygen-limited, we sought to determine which bacterial lineages play a role in the aerobic degradation of xylene under limited oxygen availability.…”

“…Although m -xylene- and p -xylene-degrading bacteria are frequently reported, those bacteria which can use the ortho isomer of xylene as their sole source of carbon and energy are seemingly much rarer. Members of the genus Rhodococcus are often reported as effective o -xylene degraders, − and their o -xylene metabolism has been deeply studied . Nevertheless, results of a recent enrichment study suggested that members of the genus Rhodococcus prefer clear aerobic conditions for the degradation of petroleum hydrocarbons and are marginalized under microaerobic conditions .…”