Characterization and functional analysis of a novel gene cluster involved in biphenyl degradation in Rhodococcus sp. strain R04

Abstract

Aims: Isolation of the genes relative to PCB biodegradation and identification of the bph gene function in Rhodococcus sp. R04. Methods and Results: A 8·7‐kb fragment carrying the biphenyl catabolic genes bphABCD was isolated from the gene library in Rhodococcus sp. R04. Based on the deduced amino acid sequence homology, seven bph genes, bphA1A2A3A4, bphB, bphC and bphD, were thought to be responsible for the initial four steps of biphenyl degradation. In Escherichia coli, BphA exhibited poor activity for biphenyl transformation, and BphB, BphC and BphD were found to be catalytically active towards 2,3‐dihydro‐2,3‐dihydroxybiphenyl, 2,3‐dihydroxybiphenyl and 2‐hydroxy‐6‐oxo‐6‐phenylhexa‐2,4‐dienoate, respectively (activities of 50, 8·1 and 2·4 μmol l−1 min−1 mg−1). SDS‐PAGE analysis indicated that the sizes of bphA1A2A3A4, bphB, bphC and bphD gene products were 49, 19, 14, 47, 32, 30 and 31 kDa, respectively. After disruption of bph genes, the bphA1 mutants lost the ability to grow on biphenyl, the bphB and bphD mutants were able to transform a little of biphenyl, but hardly grew on biphenyl. Conclusion: The cloned bph genes indeed play an important role in the biphenyl catabolism in this strain. Significance and Impact of the Study: This bph gene organization in Rhodococcus sp. R04 differs from that of other biphenyl degraders reported previously, indicating it is a novel type of bph gene cluster. Analysis of the phylogenetic tree suggested that BphA1 and BphA2 in Rhodococcus sp. R04 had a different evolutionary relationship with those in the other PCB degraders.

Microbial Genes Involved in the Aromatic Compound Degradation Deciphered Through Metagenomics Analysis of Industrial Wastewater.

“…However, strain of R. jostii have multiple pathways like bph and etb gene cluster [36]. Presence of bph, etb and nar gene cluster in CETP metagenome dataset and also identify the bacterial strain according to previous report suggested that the e uent contain chlorinated compounds [36] [37].…”

Cometabolic degradation of mono-chloro benzoic acids by Rhodococcus sp. R04 grown on organic carbon sources

“…R04 during degradation of diverse chlorobiphenyls (Yang et al 2004(Yang et al , 2007. 3-CBA and 4-CBA were, respectively monitored by GC-MS in cultures from strain R04 grown on 3-chlorobiphenyl and 4-chlorobiphenyl (unpublished data).…”

Cloning of three 2,3-dihydroxybiphenyl-1,2-dioxygenase genes from Achromobacter sp. BP3 and the analysis of their roles in the biodegradation of biphenyl

“…strain R04 and Rhodococcus sp. strain K37 [10,12]. Among these gene clusters, the bphC gene encoding 2,3-dihydroxybiphenyl-1,2-dioxygenase is responsible for the ring cleavage of 2,3-dihydroxybiphenyl, which is a critical step in the aerobic degradation of biphenyl by bacteria.…”

“…It is estimated that more than 1.5 million tons of PCBs have been manufactured worldwide [1,2]. PCBs have potential health risks for living organisms due to resulted benzoate and 2-hydroxy-penta-2,4-dienoate are subjected to the downstream pathway and the further metabolism of tricarboxylic acid cycle [8][9][10][11][12]. The genes encoding the enzymes for biphenyl degradation are clustered and termed as bph gene cluster, which could be divided into four types based on its genetic organization.…”