Divergent Structures of Carbazole DegradativecarOperons Isolated from Gram-negative Bacteria

Abstract

Southern hybridization analysis of the genomes from the newly-isolated 10 carbazole (CAR)-utilizing bacteria revealed that 8 of the isolates carried gene clusters homologous to the CAR-catabolic car operon of Pseudomonas resinovorans strain CA10. Sequencing analysis showed that two car operons and the neighboring regions of Pseudomonas sp. strain K23 are nearly identical to that of strain CA10. In contrast to strains CA10 and K23, carEF genes did not exist downstream of the car gene cluster of Janthinobacterium sp. strain J3. In the car gene clusters, strains CA10, K23 and J3 have Rieske-type ferredoxin as a component of carbazole dioxygenase, although Sphingomonas sp. strain KA1 possesses a putidaredoxin-type ferredoxin. We confirmed that this putidaredoxin-type ferredoxin CarAc can function as an electron mediator to CarAa of strain KA1. In the upstream regions of the carJ3 and carKA1 gene clusters, ORFs whose deduced amino acid sequences showed homology to GntR-family transcriptional regulators were identified.

Properties, environmental fate and biodegradation of carbazole

“…Even though these carbazole degraders are isolated from different sources, comparison of the gene organization and flanking regions of their car gene clusters CB3 (Nojiri and Omori 2007) suggests evolutionary diversity as reflected in differences in copy number of car gene cluster among carbazole degraders (Inoue et al 2004). This phenomenon may arise because car gene clusters are sometimes borne on plasmids or transposons and/or flanked by IS (insertion sequence) elements (Inoue et al 2004). …”

“…GTIN11 (Kilbane II et al 2002) and Sphingomonas sp. (reclassified as Novosphingobium sp) KA1 and the car KA1/GTIN11 gene cluster homolog have been reported to occur in various carbazoledegrading Sphingomonas and related strains (Inoue et al 2004(Inoue et al , 2005.…”

“…Second, though Sphingomonas CarAa exhibits significant homology with CA10 CarAa ([55% identity), its ferredoxin (CarAc) is neither related to CarAc CA10 nor with other Rieske ferredoxins but shows similarity to the putidaredoxin-type ferredoxins. Because the terminal oxygenase of strain KA1 (CarAa KA1 ) can receive electrons from strain KA1 ferredoxin (CarAc KA1 ) and catalyze angular dioxygenation of carbazole, it implies that ferredoxin selectivity differs between strain CarAa CA10 and CarAa KAI/GTIN11 (Inoue et al 2004). Furthermore, two copies of car KA1 gene cluster (car-I KA1 and car-II KA1 ) were found to be domiciled on a [250-kb circular plasmid pCAR3 in Novosphingobium sp.…”

Structural and Molecular Genetic Analyses of the Bacterial Carbazole Degradation System

“…In addition to CA10, we have isolated carbazoledegradative car gene clusters from Janthinobacterium sp. J3, 19) Novosphingobium sp. KA1, 20,21) and Nocardioides aromaticivorans IC177.…”

“…Of these, that of P. resinovorans CA10 is distributed in various carbazole-degrading strains of the genera Pseudomonas, Burkholderia, and Janthinobacterium, 19,22) perhaps because car gene clusters are on mobile genetic elements. In fact, the car gene cluster of CA10 is located on circular plasmid pCAR1.…”