Genome Sequencing and Comparative Transcriptomics Provide a Holistic View of 4-Nitrophenol Degradation and Concurrent Fatty Acid Catabolism by Rhodococcus sp. Strain BUPNP1

Abstract

Rhodococcus sp.strain BUPNP1 can utilize the priority environmental pollutant 4-nitrophenol (4-NP) as its sole source of carbon and energy. In this study, genome and transcriptome sequencing were used to gain mechanistic insights into 4-NP degradation. The draft BUPNP1 genome is 5.56 Mbp and encodes 4,963 proteins, which are significantly enriched in hypothetical proteins compared to other Rhodococcus sp. A novel 4-NP catabolic 43 gene cluster “nph” was identified that encodes all the genes required for the conversion of 4-NP into acetyl-CoA and succinate, via 4-nitrocatechol. The cluster also encodes pathways for the catabolism of other diverse aromatic compounds. Comparisons between BUPN1 growing on either 4-NP or glucose resulted in significant changes in the expression of many nph cluster genes, and, during 4-NP growth, a loss of lipid inclusions. Moreover, fatty acid degradation/synthesis genes were found within the nph cluster, suggesting fatty acids may be concurrently catabolised with 4-NP. A holistic model for the action of the nph gene cluster is proposed which incorporates genetic architecture, uptake and metabolism of aromatic compounds, enzymatic activities and transcriptional regulation. The model provides testable hypotheses for further biochemical investigations into the genes of the nph cluster, for potential exploitation in bioremediation.

Catabolism of Alkylphenols in Rhodococcus via a Meta-Cleavage Pathway Associated With Genomic Islands

“…The length of the acyl-CoA produced depends on the alkyl side chain of the growth substrate. This is in contrast to the Phe and Nph pathways that catabolize phenol and 4-NP, respectively, via ortho- cleavage (Takeo et al, 2008; Szoköl et al, 2014; Sengupta et al, 2019).…”

“…More specifically, PheA EP4 and AphA EP4 clustered most closely, respectively, with NphA1 from Rhodococcus sp. BUBNP1 (WP_059382681.1; Sengupta et al, 2019) and NphA1 from Rhodococcus sp. PN1 (Q8RQQ0; Takeo et al, 2003).…”

“…Rhodococcus is a genus of mycolic acid-producing Actinobacteria that catabolize a wide variety of aromatic compounds (Yam et al, 2010), including phenols (Kolomytseva et al, 2007; Gröning et al, 2014). These bacteria also have considerable potential as biocatalysts for the industrial production of compounds ranging from nitriles to steroids and high-value lipids (Alvarez et al, 1996; Round et al, 2017; Shields-Menard et al, 2017; Sengupta et al, 2019). In Rhodococcus , phenol catabolism is initiated by a two-component flavin-dependent monooxygenase (PheA1A2; Saa et al, 2010) to generate a catechol.…”

Microbial Degradation of Pyridine by Co-culture of Two Newly Isolated Strains, Arthrobacter sp. Strain PDC-1 and Rhodococcus sp. Strain HPD-2

“…The two isolates were mixed to form bacterial consortium CoPD. Both Arthrobacter and Rhodococcus were widely studied because of their properties of degradation for recalcitrant aromatic and pyridinic compounds (Arora and Sharma, 2015;Presentato et al, 2018;Ren et al, 2018;Sengupta et al, 2019;Sun et al, 2011;Yao et al, 2012;Zefirov et al, 1994). Compared with reported Arthrobacter and Rhodococcus, the co-culture CoPD showed more excellent pyridine degradation capacity.…”

Catabolism of alkylphenols inRhodococcusvia ameta-cleavage pathway associated with genomic islands

“…More specifically, 303PheAEP4 and AphAEP4 clustered most closely, respectively, with NphA1 from Rhodococcus sp. 304 BUBNP1 (WP_059382681.1)(Sengupta et al, 2019) and NphA1 from Rhodococcus sp. PN1 305 (Q8RQQ0)(Takeo et al, 2003).…”