Complete Nucleotide Sequence and Organization of the Atrazine Catabolic Plasmid pADP-1 from Pseudomonas sp . Strain ADP

Abstract

The complete 108,845-nucleotide sequence of catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP was determined. Plasmid pADP-1 was previously shown to encode AtzA, AtzB, and AtzC, which catalyze the sequential hydrolytic removal of s-triazine ring substituents from the herbicide atrazine to yield cyanuric acid. Computational analyses indicated that pADP-1 encodes 104 putative open reading frames (ORFs), which are predicted to function in catabolism, transposition, and plasmid maintenance, transfer, and replication. Regions encoding transfer and replication functions of pADP-1 had 80 to 100% amino acid sequence identity to pR751, an IncP␤ plasmid previously isolated from Enterobacter aerogenes. pADP-1 was shown to contain a functional mercury resistance operon with 99% identity to Tn5053. Complete copies of transposases with 99% amino acid sequence identity to TnpA from IS1071 and TnpA from Pseudomonas pseudoalcaligenes were identified and flank each of the atzA, atzB, and atzC genes, forming structures resembling nested catabolic transposons. Functional analyses identified three new catabolic genes, atzD, atzE, and atzF, which participate in atrazine catabolism. Crude extracts from Escherichia coli expressing AtzD hydrolyzed cyanuric acid to biuret. AtzD showed 58% amino acid sequence identity to TrzD, a cyanuric acid amidohydrolase, from Pseudomonas sp. strain NRRLB-12227. Two other genes encoding the further catabolism of cyanuric acid, atzE and atzF, reside in a contiguous cluster adjacent to a potential LysR-type transcriptional regulator. E. coli strains bearing atzE and atzF were shown to encode a biuret hydrolase and allophanate hydrolase, respectively. atzDEF are cotranscribed. AtzE and AtzF are members of a common amidase protein family. These data reveal the complete structure of a catabolic plasmid and show that the atrazine catabolic genes are dispersed on three disparate regions of the plasmid. These results begin to provide insight into how plasmids are structured, and thus evolve, to encode the catabolism of compounds recently added to the biosphere.

Biodegradation of melamine and its hydroxy derivatives by a bacterial consortium containing a novel Nocardioides species

“…3a). To completely decompose the melamine, a batch co-culture of strain ATD6 and strain CDB21, which has the atzD, E, and F genes for catabolizing cyanuric acid (Martinez et al 2001), was examined. The co-culture degraded melamine more rapidly than strain ATD6 alone.…”

The sulfonated osmolyte N-methyltaurine is dissimilated by Alcaligenes faecalis and by Paracoccus versutus with release of methylamine

“…Alternatively, the reaction might proceed by hydrolytic removal of the methylamino moiety to yield sulfoacetaldehyde, analogous to reactions (e.g. AtzB and AtzC) observed in the degradation of N-alkylated triazines (Cook, 1987;Martinez et al, 2001). …”

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“…The complete nucleotide sequencing of pADP-1 (the atrazine gene-containing plasmid of Pseudomonas ADP) revealed the arrangement and composition of atrazine degradation genes (Martinez et al, 2001). Many studies indicated that many gram-negative (Topp et al, 2000;Wackett et al, 2002) as well as gram positive atrazine-degrading bacteria contain large molecular weight plasmids containing atrazine degradation genes (Behki et al, 1993;Cai et al, 2003;Rousseaux et al, 2001;Strong et al, 2002;Vaishampayan et al, 2007).…”

“…AtzE identified as a biuret amidohydrolase hydrolyze biuret to produce allophanate. AtzF, a protein involved in the last step in atrazine biodegradation converts allophanate to CO2 and NH4 (Martinez et al, 2001).The trzB gene has been identified as the ammeline aminohydrolase involved in the conversion of ammeline to ammelide. The gene encodes the ammelide aminohydrolase enzyme known as trzC.…”

“…AtrA gene in Rhodococcus strain TE1 involved in N-dealkylation of atrazine and forms DIA and DEA (Shao et al, 1995). AtzB (hydroxyatrazine ethylaminohydrolase) catalyzes hydroxyatrazine and form Nisopropylammelide which further catalyzed by AtzC (N-isopropylammelide isopropylamino hydrolase), forming a cyanuric acid (Martinez et al, 2001;Shapir et al, 2007). converts cyanuric acid into biurate.…”