Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
Antoine, R., et al. 2005. The periplasmic binding protein of a tripartite tricarboxylate transporter is involved in signal transduction. J. Mol. Biol. 351:799-809.
Antoine, R., et al. 2003. Overrepresentation of a gene family encoding extracytoplasmic solute receptors in Bordetella. J. Bacteriol. 185:1470-1474.
Boshoff, H. I. M., and V. Mizrahi. 1998. Purification, gene cloning, targeted knockout, overexpression, and biochemical characterization of the major pyrazinamidase from Mycobacterium smegmatis. J. Bacteriol. 180:5809-5814.
Breugelmans, P., P. J. D'Huys, R. De Mot, and D. Springael. 2007. Characterization of novel linuron-mineralizing bacterial consortia enriched from long-term linuron-treated agricultural soils. FEMS Microbiol. Ecol. 62:374-385.
Breugelmans, P., et al. 2010. Proteomic study of linuron and 3,4-dichloroaniline degradation by Variovorax sp. WDL1: evidence for the involvement of an aniline dioxygenase-related multicomponent protein. Res. Microbiol. 161: 208-218.
Chain, P. S. G., et al. 2006. Burkholderia xenovorans LB400 harbors a multireplicon, 9.73-Mbp genome shaped for versatility. Proc. Natl. Acad. Sci. U. S. A. 103:15280-15287.
Chalupowicz, L., I. Barash, M. Panijel, G. Sessa, and S. Manulis-Sasson. 2009. Regulatory interactions between quorum-sensing, auxin, cytokinin, and the Hrp regulon in relation to gall formation and epiphytic fitness of Pantoea agglomerans pv. gypsophilae. Mol. Plant-Microbe Interact. 22:849-856.
Dejonghe, W. 2003. The importance of genetic and metabolic interactions between bacteria in the degradation of herbicides. Ph.D. thesis. University of Gent, Gent, Belgium.
Dejonghe, W., et al. 2003. Synergistic degradation of linuron by a bacterial consortium and isolation of a single linuron-degrading Variovorax strain. Appl. Environ. Microbiol. 69:1532-1541.
Drummond, A., et al. 2011. Geneious v5.4.4. Biomatters, Ltd., Auckland, New Zealand.
Engelhardt, G., P. Wallnofer, and R. Plapp. 1971. Degradation of linuron and some other herbicides and fungicides by a linuron-inducible enzyme obtained from Bacillus sphaericus. Appl. Microbiol. 22:284-288.
Engelhardt, G., P. Wallnofer, and R. Plapp. 1973. Purification and properties of an aryl acylamidase of Bacillus sphaericus, catalyzing hydrolysis of various phenylamide herbicides and fungicides. Appl. Microbiol. 26:709-718.
Frantz, B., and A. M. Chakrabarty. 1987. Organization and nucleotidesequence determination of a gene cluster involved in 3-chlorocatechol degradation. Proc. Natl. Acad. Sci. U. S. A. 84:4460-4464.
Fukuta, Y., S. Koizumi, H. Komeda, and Y. Asano. 2010. A new aryl acylamidase from Rhodococcus sp. strain Oct1 acting on omega-lactams: its characterization and gene expression in Escherichia coli. Enzyme Microb. Technol. 46:237-245.
Geng, L. Z., et al. 2009. Functional analysis of a putative regulatory gene, tadR, involved in aniline degradation in Delftia tsuruhatensis AD9. Arch. Microbiol. 191:603-614.
Gopalakrishna, K. N., et al. 2004. Mandelamide hydrolase from Pseudomonas putida: characterization of a new member of the amidase signature family. Biochemistry 43:7725-7735.
Gross, R., et al. 2008. The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae. BMC Genomics 9:449.
Guindon, S., and O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
Han, J. I., et al. 2011. Complete genome sequence of the metabolically versatile plant growth-promoting endophyte Variovorax paradoxus S110. J. Bacteriol. 193:1183-1190.
He, Q., and R. A. Sanford. 2002. Induction characteristics of reductive dehalogenation in the ortho-halophenol-respiring bacterium, Anaeromyxobacter dehalogenans. Biodegradation 13:307-316.
Hongpattarakere, T., H. Komeda, and Y. Asano. 2005. Purification, characterization, gene cloning and nucleotide sequencing of D-stereospecific amino acid amidase from soil bacterium: Delftia acidovorans. J. Ind. Microbiol. Biotechnol. 32:567-576.
Khurana, J. L., et al. 2009. Characterization of the phenylurea hydrolases A and B: founding members of a novel amidohydrolase subgroup. Biochem. J. 418:431-441.
Ko, H. J., et al. 2010. Molecular characterization of a novel bacterial aryl acylamidase belonging to the amidase signature enzyme family. Mol. Cells 29:485-492.
Krieg, L., H. Slusarczyk, S. Verseck, and M. R. Kula. 2005. Identification and characterization of a novel D-amidase gene from Variovorax paradoxus and its expression in Escherichia coli. Appl. Microbiol. Biotechnol. 66:542-550.
Lavrov, K. V., I. A. Zalunin, E. K. Kotlova, and A. S. Yanenko. 2010. A new acylamidase from Rhodococcus erythropolis TA37 can hydrolyze N-substituted amides. Biochemistry (Moscow) 75:1006-1013.
Leroy, B., et al. 2010. Differential proteomic analysis using isotope-coded protein-labeling strategies: comparison, improvements, and application to simulated microgravity effect on Cupriavidus metallidurans CH34. Proteomics 10:2281-2291.
Mayaux, J. F., et al. 1991. Purification, cloning, and primary structure of a new enantiomer-selective amidase from a Rhodococcus strain: structural evidence for a conserved genetic coupling with nitrile hydratase. J. Bacteriol. 173:6694-6704.
Muller, T. A., S. A. Byrde, C. Werlen, J. R. van der Meer, and H. P. E. Kohler. 2004. Genetic analysis of phenoxyalkanoic acid degradation in Sphingomonas herbicidovorans MH. Appl. Environ. Microbiol. 70:6066-6075.
Neumann, S., and M. R. Kula. 2002. Gene cloning, overexpression, and biochemical characterization of the peptide amidase from Stenotrophomonas maltophilia. Appl. Microbiol. Biotechnol. 58:772-780.
Ogawa, N., K. Miyashita, and A. M. Chakrabarty. 2003. Microbial genes and enzymes in the degradation of chlorinated compounds. Chem. Rec. 3:158-171.
Ohtaki, A., et al. 2010. Structure and characterization of amidase from Rhodococcus sp. N-771: insight into the molecular mechanism of substrate recognition. Biochim. Biophys. Acta Prot. Proteom. 1804:184-192.
Parke, D. 1993. Positive regulation of phenolic catabolism in Agrobacterium tumefaciens by the pcaQ gene in response to beta-carboxy-cis,cis-muconate. J. Bacteriol. 175:3529-3535.
Pease, H. L. 1962. Separation and colorimetric determination of monuron and diuron residues. J. Agric. Food Chem. 10:279-281.
Pohlmann, A., et al. 2006. Genome sequence of the bioplastic-producing "Knallgas" bacterium Ralstonia eutropha H16. Nat. Biotechnol. 24:1257-1262.
Potrawfke, T., J. Armengaud, and R. M. Wittich. 2001. Chlorocatechols substituted at positions 4 and 5 are substrates of the broad-spectrum chlorocatechol 1,2-dioxygenase of Pseudomonas chlororaphis RW71. J. Bacteriol. 183:997-1011.
Rose, T. M., J. G. Henikoff, and S. Henikoff. 2003. CODEHOP (COnsensus- DEgenerate hybrid oligonucleotide primer) PCR primer design. Nucleic Acids Res. 31:3763-3766.
Sambrook, J., and D. W. Russell. 2001. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
Satsuma, K. 2010. Mineralization of the herbicide linuron by Variovorax sp. strain RA8 isolated from Japanese river sediment using an ecosystem model (microcosm). Pest Manag. Sci. 66:847-852.
Schmidt, R., V. Battaglia, K. Scow, S. Kane, and K. R. Hristova. 2008. Involvement of a novel enzyme, MdpA, in methyl tert-butyl ether degradation in Methylibium petroleiphilum PM1. Appl. Environ. Microbiol. 74:6631-6638.
Shamsuzzaman, K. M., and E. A. Barnsley. 1974. Regulation of naphtalene oxygenase in Pseudomonas. J. Gen. Microbiol. 83:165-170.
Shapir, N., G. Cheng, M. J. Sadowsky, and L. P. Wackett. 2006. Purification and characterization of TrzF: biuret hydrolysis by allophanate hydrolase supports growth. Appl. Environ. Microbiol. 72:2491-2495.
Shapir, N., M. J. Sadowsky, and L. P. Wackett. 2005. Purification and characterization of allophanate hydrolase (AtzF) from Pseudomonas sp. strain ADP. J. Bacteriol. 187:3731-3738.
Shin, K. A., and J. C. Spain. 2009. Pathway and evolutionary implications of diphenylamine biodegradation by Burkholderia sp. strain JS667. Appl. Environ. Microbiol. 75:2694-2704.
Shin, S., et al. 2003. Characterization of a novel Ser-cisSer-Lys catalytic triad in comparison with the classical Ser-His-Asp triad. J. Biol. Chem. 278:24937-24943.
Sorensen, S. R., et al. 2005. Elucidating the key member of a linuronmineralizing bacterial community by PCR and reverse transcription-PCR denaturing gradient gel electrophoresis 16S rRNA gene fingerprinting and cultivation. Appl. Environ. Microbiol. 71:4144-4148.
Sorensen, S. R., A. Simonsen, and J. Aamand. 2009. Constitutive mineralization of low concentrations of the herbicide linuron by a Variovorax sp. strain. FEMS Microbiol. Lett. 292:291-296.
Thiel, M., S. Kaschabek, J. Groning, M. Mau, and M. Schlomann. 2005. Two unusual chlorocatechol catabolic gene clusters in Sphingomonas sp. TFD44. Arch. Microbiol. 183:80-94.
Top, E. M., and D. Springael. 2003. The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Curr. Opin. Biotechnol. 14:262-269.
Trefault, N., et al. 2004. Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways. Environ. Microbiol. 6:655-668.
Tropel, D., and J. R. van der Meer. 2004. Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol. Mol. Biol. Rev. 68:474-500.
Turnbull, G. A., M. Ousley, A. Walker, E. Shaw, and J. A. W. Morgan. 2001. Degradation of substituted phenylurea herbicides by Arthrobacter globiformis strain D47 and characterization of a plasmid-associated hydrolase gene, puhA. Appl. Environ. Microbiol. 67:2270-2275.
Vallenet, D., et al. 2006. MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res. 34:53-65.
Vandermeer, J. R. 1997. Evolution of novel metabolic pathways for the degradation of chloroaromatic compounds. Antonie Van Leeuwenhoek Int. J. Gen. Mol. Microbiol. 71:159-178.
Vandermeer, J. R., R. I. L. Eggen, A. J. B. Zehnder, and W. M. Devos. 1991. Sequence analysis of the Pseudomonas sp. strain P51 tcb gene cluster, which encodes metabolism of chlorinated catechols: evidence for specialization of catechol 1,2-dioxygenases for chlorinated substrates. J. Bacteriol. 173:2425-2434.
Vedler, E., V. Koiv, and A. Heinaru. 2000. Analysis of the 2,4-dichlorophenoxyacetic acid-degradative plasmid pEST4011 of Achromobacter xylosoxidans subsp denitrificans strain EST4002. Gene 255:281-288.
Yamada, T., C. J. Palm, B. Brooks, and T. Kosuge. 1985. Nucleotide sequences of the Pseudomonas savastanoi indoleacetic acid genes show homology with Agrobacterium tumefaciens T-DNA. Proc. Natl. Acad. Sci. U. S. A. 82:6522-6526.
Yamamoto, K., et al. 1996. Production of R-(-)-ketoprofen from an amide compound by Comamonas acidovorans KPO-2771-4. Appl. Environ. Microbiol. 62:152-155.
Yasuhira, K., et al. 2009. X-ray crystallographic analysis of the 6-aminohexanoate cyclic dimer hydrolase: catalytic mechanism and evolution of an enzyme responsible for nylon-6 by-product degradation. J. Biol. Chem. 285: 1239-1248.
Yun, S. H., et al. 2008. Proteomic analysis of outer membrane proteins from Acinetobacter baumannii DU202 in tetracycline stress condition. J. Microbiol. 46:720-727.
Zhang, T., J. L. Zhang, S. J. Liu, and Z. P. Liu. 2008. A novel and complete gene cluster involved in the degradation of aniline by Delftia sp. AN3. J. Environ. Sci. China 20:717-724.
Zhang, X., et al. 2011. The R-R-type MYB-like transcription factor, At-MYBL, is involved in promoting leaf senescence and modulates an abiotic stress response in Arabidopsis. Plant Cell Physiol. 52:138-148.
