User:Jonathan Cline/Notebook/Melaminometer/Related Metabolic Activity

Melamine Formaldehyde

 * Biodegradation of melamine formaldehyde by Micrococcus sp. strain MF-1 isolated from aminoplastic wastewater effluent. International Biodeterioration & Biodegradation Volume 57, Issue 2, March 2006, Pages 75-81 doi:10.1016/j.ibiod.2005.11.006

Atrazine

 * Herbicide
 * Metabolic pathway mostly known
 * Enzymes mostly known
 * Recombination of expressive genes into E. coli successful.


 * [Full Text] Atrazine chlorohydrolase from Pseudomonas sp. strain ADP: gene sequence, enzyme purification, and protein characterization. J Bacteriol. 1996 Aug;178(16):4894-900.  Erratum in:    J Bacteriol 1999 Jan;181(2):695.
 * The most related protein sequence in GenBank was that of TrzA, 41% identity, from Rhodococcus corallinus NRRL B-15444R. TrzA catalyzes the deamination of melamine and the dechlorination of deethylatrazine and desisopropylatrazine but is not active with atrazine. AtzA catalyzes the dechlorination of atrazine, simazine, and desethylatrazine but is not active with melamine, terbutylazine, or desethyldesisopropylatrazine.


 * [Full Text] The atzB gene of Pseudomonas sp. strain ADP encodes the second enzyme of a novel atrazine degradation pathway. Appl Environ Microbiol. 1997 Mar;63(3):916-23.
 * [Full Text] Substrate Specificity of Atrazine Chlorohydrolase and Atrazine-Catabolizing Bacteria. Appl Environ Microbiol. 2000 October; 66(10): 4247¿4252. PMCID: PMC92292
 * For instance, in 1937, melamine (2,4,6-triamino-1,3,5-s-triazine) was reported to be nonbiodegradable. In 1964, however, bacteria capable of slow degradation were isolated. More recently, melamine was reported to be readily biodegraded[8]. [8] = Experientia. 1983 Nov 15;39(11):1191-8, Isolation and cultivation of microbes with biodegradative potential, Cook AM, Grossenbacher H, Hütter R.


 * Microbial aspects of atrazine degradation in natural environments. Biodegradation Volume 13, Number 1 / January, 2002 doi:10.1023/A:1016329628618
 * Biodegradation of atrazine and related s-triazine compounds: from enzymes to field studies. Appl Microbiol Biotechnol. 2002 Jan;58(1):39-45.
 * pADP-1 from Pseudomonas sp. ADP, has been completely sequenced and contains the genes for atrazine catabolism. Insertion sequence elements play a role in constructing different atrazine catabolic plasmids in different bacteria. Atrazine chlorohydrolase has been purified to homogeneity from two sources. Recombinant Escherichia coli strains expressing atrazine chlorohydrolase have been constructed and chemically cross-linked to generate catalytic particles used for atrazine remediation in soil. The method was used for cleaning up a spill of 1,000 pounds of atrazine to attain a level of herbicide acceptable to regulatory agencies.


 * [Full Text] Isolation and characterization of an atrazine-degrading bacterium from industrial wastewater in China. Letters in Applied Microbiology Volume 36 Issue 5, Pages 272 - 276. Published Online: 8 Apr 2003 PMID:12680937 doi:10.1046/j.1472-765X.2003.01307.x
 * Atrazine degradation in anaerobic environment by a mixed microbial consortium. Water Research Volume 38, Issue 9, May 2004, Pages 2277-2284 doi:10.1016/j.watres.2003.10.059
 * Combined metabolic activity within an atrazine-mineralizing community enriched from agrochemical factory soil. International Biodeterioration & Biodegradation Volume 60, Issue 4, 2007, Pages 299-307 doi:10.1016/j.ibiod.2007.05.004
 * [Full Text] Hydroxyatrazine N-ethylaminohydrolase (AtzB): an amidohydrolase superfamily enzyme catalyzing deamination and dechlorination. J Bacteriol. 2007 Oct;189(19):6989-97. Epub 2007 Jul 27.
 * AtzB, therefore, acts to funnel s-triazine metabolites into a common biodegradative pathway, resulting in its eventual transformation to cyanuric acid, which is the central intermediate in s-triazine ring metabolism by many bacteria. [...]  The atzB genes from a variety of hydroxyatrazine-degrading bacteria were previously sequenced and found to have >99% identity to the gene from Pseudomonas sp. strain ADP (8). A GenBank search using BLASTP identified additional bacteria having AtzB homologs with a similar degree of sequence identity in Arthrobacter aurescens TC1, Herbaspirillum sp. strain B601, and Betaproteobacterium strain CDB21. All of these bacteria were isolated for their s-triazine herbicide-degradative ability, and these proteins are considered isofunctional with AtzB from Pseudomonas sp. strain ADP. In addition, BLASTP analysis identified gi86360134 (Rhizobium etli CFN 42) and gi23012454 (Magnetospirillum magnetotacticum MS-1) as having 61% and 59%, respectively, sequence identity to AtzB. These proteins with an intermediate level of sequence identity have unknown functions at this time. All other sequences shared less than 40% sequence identity with AtzB. The highest-scoring proteins with functional assignments from this group included TrzN (Arthrobacter aurescens, gi42558845, 31%), AtzA (Pseudomonas sp. strain ADP, gi3766246, 23%), and guanine deaminase (E. coli K12, gi16130785, 24%). These proteins have been identified as belonging to the amidohydrolase superfamily (27, 32).  [...]  In the case of AtzA and TriA, two proteins that share 98% sequence identity but that have distinct dechlorination and deamination activities, respectively, a single amino acid was identified as being responsible for switching the catalytic activity (29). Triazine hydrolase (TrzA), known to catalyze the deamination of nonalkylated triazines and dechlorination of mono-N-alkylated triazines, has efficiency values that are dependent upon whether or not a substrate is chlorinated. The kcat for the deamination or dechlorination of any chlorinated substrate (0.16 to 0.45 mM¿1 s¿1) was an order of magnitude lower than that seen for the deamination of melamine (2,4,6-triamino-1,3,5-triazine) (4.8 mM¿1 s¿1) (19).

Summary from Wikipedia
Atrazine biodegradation can occur by two known pathways:

1) Atrazine can be dechlorinated followed by removal the other ring substituents via amidohydrolases by the enzymes AtzA, AtzB, and AtzC. The end product is cyanuric acid. The best characterized organism that performs this pathway is Pseudomonas sp. strain ADP.

2) The other pathway involves dealkylation of the amino groups. Subsequent dechlorination yields cyanuric acid. The end result is 2-chloro-4-hydroxy-6-amino-1,3,5-triazine, which currently has no known path to further degradation. This path occurs in Pseudomonas species and a number of bacteria.

[...] The genes for enzymes AtzA-C have been found to be highly conserved in atrazine-degrading organisms worldwide. The prevalence of these genes could be due to the mass transfer of AtzA-C on a global scale. In Pseudomonas sp. ADP, the Atz genes are located non-contiguously on a plasmid with the genes for mercury catabolism. This plasmid is conjugatable to Gram negative bacteria in the laboratory and could lead to the worldwide distribution, in view of the extensive release of of atrazine and mercury. AtzA-C have also been found in a Gram positive bacterium but are chromosomally located.[7] The insertion elements flanking each gene suggests that they are involved in the assembly of this specialized catabolic pathway.

[...] A stable four-member bacterial community, characterized by colony morphology and 16S rDNA sequencing, was rapidly able to mineralize atrazine to CO2 and NH3. Two primary organisms were identified as Arthrobacter species (ATZ1 and ATZ2) and two secondary organisms (CA1 and CA2) belonged to the genera Ochrobactrum and Pseudomonas, respectively. PCR assessment of atrazine-degrading genetic potential of the community, revealed the presence of trzN, trzD, atzB and atzC genes. Isolates ATZ1 and ATZ2 were capable of dechlorinating atrazine to hydroxyatrazine and contained the trzN gene. ATZ2 further degraded hydroxyatrazine to cyanuric acid and contained atzB and atzC genes whereas ATZ1 contained atzC but not atzB. Isolates CA1 and CA2 grew on cyanuric acid and contained the trzD gene. Complete atrazine degradation was a result of the combined metabolic attack on the atrazine molecule, and complex interactions may exist between the community members sharing carbon and nitrogen from atrazine mineralization.