This study gives the first picture of whole RNA-Sequencing analysis of a PCB-degrading microbe, Rhodococcus jostii RHA1. Genes that were highly expressed in biphenyl-grown cells, compared with pyruvate-grown cells, were chosen based on the Reads Per Kilobase Million (RPKM) value and were summarized based on the criteria of RPKM ≥100 and fold change ≥2.0. Consequently, 266 total genes were identified as genes expressed particularly for the degradation of biphenyl. After comparison with previous microarray data that identified highly-expressed genes, based on a fold change ≥2.0 and p-value ≤0.05, 62 highly-expressed genes from biphenyl-grown cells were determined from both analytical platforms. As these 62 genes involve known PCB degradation genes, such as bph, etb, and ebd, the genes identified in this study can be considered as essential genes for PCB/biphenyl degradation. In the 62 genes, eleven genes encoding hypothetical proteins were highly expressed in the biphenyl-grown cells. Meanwhile, we identified several highly-expressed unannotated DNA regions on the opposite strand. In order to verify the encoded proteins, two regions were cloned into an expression vector. A protein was successfully obtained from one region at approximately 25 kDa from the unannotated strand. Thus, the genome sequence with transcriptomic analysis gives new insight, considering re-annotation of the genome of R. jostii RHA1, and provides a clearer picture of PCB/biphenyl degradation in this strain.
The coral reefs of the Persian Gulf are the most diverse systems of life in the marine environment of the Middle East. Unfortunately, they are highly threatened by local and global stressors, particularly oil pollutants. This is the first quantitative and qualitative study aimed at assessing the concentration and sources of n-alkanes and POPs (PAHs, PCBs and PCNs) in coral tissues, symbiotic algae (zooxanthellae), reef sediments and seawaters in coral reefs of Lark and Kharg in the Persian Gulf, Iran. This work was conducted on eight species of six genera and three families of hard corals and one family of soft coral. A significant variation in the concentration of ∑30n-alkanes and POPs (∑40PAHs, ∑22PCBs and 20PCNs) was found in the decreasing order: zooxanthellae > coral tissue > skeleton > reef sediment > seawater. The bioaccumulation of these compounds was 2-times higher in ahermatypic than in hermatypic corals, among which significant variations were observed in both sites. In Kharg, Porites lutea had the highest mean concentration of ∑30n-alkanes and ∑40PAHs in soft tissue, whereas the lowest values were in Platygyra daedalea. A contrasting trend was documented for ∑22PCBs and 20PCNs, with the highest level reported in soft tissue of P. daedalea and the lowest in P. lutea at Kharg. Compositional pattern of AHs and PAHs demonstrated the predominance of LMW-PAHs and n-alkanes. In skeleton and reef sediments, tetra, penta and tri-CBs were the most abundant PCBs congeners followed by di-CB > hexa-CB > hepta-CB > octa-CB,whiletri-CB > di-CB > tetra-CB > penta-CB > hexa-CB > hepta-CB > octa-CB was observed for soft tissue, zooxanthellae and seawater. The results of RAD test indicated significantly negative correlation between total concentration of these compounds with zooxanthellae density, the chlorophyll-a and C2 in corals at both reefs. This is the first report on levels, health assessment and source apportionments of POPs in zooxanthellae and a first step in the implementation of specific coral reef management measures.
Rhodococcus jostii RHA1 (RHA1) degrades polychlorinated biphenyl (PCB) via co-metabolism with biphenyl. To identify the novel open reading frames (ORFs) that contribute to PCB/biphenyl metabolism in RHA1, we compared chromatin immunoprecipitation chip and transcriptomic data. Six novel ORFs involved in PCB/biphenyl metabolism were identified. Gene deletion mutants of these 6 ORFs were made and were tested for their ability to grow on biphenyl. Interestingly, only the ro10225 deletion mutant showed deficient growth on biphenyl. Analysis of Ro10225 protein function showed that growth of the ro10225 deletion mutant on biphenyl was recovered when exogenous recombinant Ro10225 protein was added to the culture medium. Although Ro10225 protein has no putative secretion signal sequence, partially degraded Ro10225 protein was detected in conditioned medium from wild-type RHA1 grown on biphenyl. This Ro10225 fragment appeared to form a complex with another PCB/biphenyl oxidation enzyme. These results indicated that Ro10225 protein is essential for the formation of the PCB/biphenyl dioxygenase complex in RHA1.