Arthrobacter aurescens TC1 Atrazine Catabolism Genes trzN , atzB , and atzC Are Linked on a 160-Kilobase Region and Are Functional in Escherichia coli

Abstract

Arthrobacter aurescens strain TC1 metabolizes atrazine to cyanuric acid via TrzN, AtzB, and AtzC. The complete sequence of a 160-kb bacterial artificial chromosome clone indicated that trzN, atzB, and atzC are linked on the A. aurescens genome. TrzN, AtzB, and AtzC were shown to be functional in Escherichia coli. Hybridization studies localized trzN, atzB, and atzC to a 380-kb plasmid in A. aurescens strain TC1.The complete nucleotide sequences of over 100 bacterial plasmids are now available, but most of these plasmids are relatively small and of interest primarily in microbial pathogenesis (for example, in the context of antibiotic resistance or toxin production). By contrast, only a limited number of large catabolic plasmids or catabolic islands on chromosomes have been sequenced. Examples include plasmids pNL1 from Sphingomonas aromaticivorans strain F199 (23), pAO1 from Arthrobacter nicotinovorans (11), pACR1 from Pseudomonas resinovorans strain CA10 (13), the TOL plasmid pWW0 from Pseudomonas putida (9), pBD2 from Rhodococcus erythropolis BD2 (31), pADP-1 from Pseudomonas sp. strain ADP (16), and the 105-kb catabolic island from Pseudomonas sp. strain B13 (28). Large catabolic plasmids can be difficult to isolate for sequencing. Thus, to facilitate widespread sequencing of large catabolic gene regions, more innovative strategies are needed. For example, plasmids have been identified via whole-genome shotgun sequencing of Deinococcus radiodurans (41) and Enterococcus faecalis (19).A wide variety of bacteria degrading the herbicide atrazine have been reported (2,14,21,22,32,36,37,43), and in all cases examined except one (3) the genes involved are located on plasmids (5,25,36,39). In Pseudomonas sp. strain ADP (14), the six atrazine-catabolic genes (atzA, atzB, atzC, and atzDEF) have been localized to plasmid pADP-1, from which the complete nucleotide sequence is now available (16). The atzA, atzB, and atzC genes have also been localized to different-sized plasmids in the gram-negative bacteria Chelatobacter heintzii, Stenotrophomonas maltophilia, and Pseudaminobacter spp., and hybridization analyses indicate that the atzB and atzC genes reside on a 117-kb plasmid in the gram-positive bacterium Arthrobacter crystallopoietes (25,36). The presence of nearly identical atrazine genes in Agrobacterium, Clavibacter, Rhizobium, Pseudomonas, Alcaligenes, and Ralstonia strains (2,5,22,24,33,39) further suggests that horizontal gene transfer is involved in the dissemination of atrazine-catabolic genes.Some differences have been observed in the gene content of the gram-positive atrazine-degrading bacteria Nocardioides sp. strains C190, SP12, and C157, Arthrobacter crystallopoietes, and Arthrobacter sp. strain AD1 (3,21,24,25,32,37). Nocardioides sp. strain C190 (37) does not contain atzA, atzB, or atzC, and atrazine degradation is initiated by the product of the trzN gene, which has been cloned and sequenced previously (17). A. crystallopoietes was shown to contain trzN, atzB, and atzC (25).The isolation and characteri...

Evolution of Catabolic Pathways: Genomic Insights into Microbial s -Triazine Metabolism

“…Identical insertion sequences have been found flanking the atz genes in other bacteria (76,79), suggesting that mobile gene cassettes have transferred between strains. The linkage of the trzN-atzB-atzC genes on a plasmid element in Arthrobacter aurescens TC1 was established by bacterial artificial chromosome cloning and sequencing (54). This has been corroborated by the complete genome sequencing of A. aurescens TC1 (43), which has also provided the opportunity to analyze s-triazine metabolism in the context of the entire metabolic network of a single bacterium.…”

TraA is required for megaplasmid conjugation in Rhodococcus erythropolis AN12

“…It is unclear whether the traA gene product (Genbank Accession No. AAS20144) from Arthrobacter aurescens also resides on a megaplasmid (Sajjaphan et al, 2004), however, this protein is 29% identical to pREA400 TraA over 1005 residues. The R. equi ATCC33701 traA gene product (Genbank Accession No.…”

Insights learned from pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1 and prevalence of accessory plasmids in other Bradyrhizobium sp. strains

“…Plasmid profiles were obtained using a combination of S1-nuclease digestion and pulsed-field gel electrophoresis (PFGE)-contour clamped homogenous electric field (CHEF) as previously described (Sajjaphan et al, 2006). DNA plugs were incubated at 37 1C for 10 min with 5 U of Aspergillus oryzae S1 nuclease (Invitrogen, Carlsbad, CA, USA) as described (Barton et al, 1995).…”