Transcriptional organization and regulatory elements of a pseudomonas sp. strain ADP operon encoding a LysR-Type regulator and a putative solute transport system

Journal of Bacteriology

Volumn 194, Issue 23, 2012, Pages 6560-6573

  Platero, Ana Isabel ^a   GarcÍa Jaramillo, Manuel ^a   Santero, eduardo ^a   Govantes, Fernando ^a  

^a CSIC   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ABC TRANSPORTER; ATZR PROTEIN; ATZS PROTEIN; BACTERIAL PROTEIN; IHF PROTEIN; NITROGEN; NTRC PROTEIN; PATZR PROTEIN; PATZT PROTEIN; REGULATOR PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; BACTERIAL MUTATION; BACTERIAL STRAIN; BINDING ASSAY; CONTROLLED STUDY; GENE MAPPING; IN VITRO STUDY; IN VIVO STUDY; MUTATIONAL ANALYSIS; NONHUMAN; NUCLEOTIDE BINDING SITE; NUTRIENT LIMITATION; OPERON; POINT MUTATION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN FUNCTION; PSEUDOMONAS; REGULATOR GENE; TRANSCRIPTION INITIATION;

DNA MUTATIONAL ANALYSIS; GENE EXPRESSION REGULATION, BACTERIAL; MEMBRANE TRANSPORT PROTEINS; MULTIGENE FAMILY; OPERON; PLASMIDS; POINT MUTATION; PROMOTER REGIONS, GENETIC; PSEUDOMONAS; SEQUENCE DELETION; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

PSEUDOMONAS SP. ADP;

EID: 84871045612     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.01348-12     Document Type: Article

References (55)

1. Aiyar A, Xiang Y, Leis J. 1996. Site-directed mutagenesis using overlap extension PCR. Methods Mol. Biol. 57:177-191.
2. Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
3. 54-dependent promoter sequences. Nucleic Acids Res. 27:4305-4313.
4. N) transcription factor. J. Bacteriol. 182:4129-4136.
5. Burtnick MN, et al. 2007. Insights into the complex regulation of rpoS in Borrelia burgdorferi. Mol. Microbiol. 65:277-293.
6. 54-dependent bacterial promoters. Proc. Natl. Acad. Sci. U. S. A. 94:9568-9572.
7. 54 regulon (sigmulon) of Pseudomonas putida. Environ. Microbiol. 5:1281-1293.
8. de Souza ML, Wackett LP, Sadowsky MJ. 1998. The atzABC genes encoding atrazine catabolism are located on a self-transmissible plasmid in Pseudomonas sp. strain ADP. Appl. Environ. Microbiol. 64:2323-2326.
9. Elliott T, Geiduschek EP. 1984. Defining a bacteriophage T4 late promoter: absence of a "-35" region. Cell 36:211-219.
10. Espinosa-Urgel M, Salido A, Ramos JL. 2000. Genetic analysis of functions involved in adhesion of Pseudomonas putida to seeds. J. Bacteriol. 182:2363-2369.
11. Feng J, Goss TJ, Bender RA, Ninfa AJ. 1995. Repression of the Klebsiella aerogenes nac promoter. J. Bacteriol. 177:5535-5538.
12. Figurski DH, Helinski DR. 1979. Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. Proc. Natl. Acad. Sci. U. S. A. 76:1648-1652.
13. Franklin FC, Bagdasarian M, Bagdasarian MM, Timmis KN. 1981. Molecular and functional analysis of the TOL plasmidpWWOfrom Pseudomonas putida and cloning of genes for the entire regulated aromatic ring meta cleavage pathway. Proc. Natl. Acad. Sci. U. S. A. 78:7458-7462.
14. Friedman DI. 1988. Integration host factor: a protein for all reasons. Cell 55:545-554.
15. García-González V, Govantes F, Shaw LJ, Burns RG, Santero E. 2003. Nitrogen control of atrazine utilization in Pseudomonas sp. strain ADP. Appl. Environ. Microbiol. 69:6987-6993.
16. García-Gonzalez V, Govantes F, Porrua O, Santero E. 2005. Regulation of the Pseudomonas sp. strain ADP cyanuric acid degradation operon. J. Bacteriol. 187:155-167.
17. García-González V, et al. 2009. Distinct roles for NtrC and GlnK in nitrogen regulation of the Pseudomonas sp. strain ADP cyanuric acid utilization operon. FEMS Microbiol. Lett. 300:222-229.
18. Gebendinger N, Radosevich M. 1999. Inhibition of atrazine degradation by cyanazine and exogenous nitrogen in bacterial isolate M91-3. Appl. Microbiol. Biotechnol. 51:375-381.
19. Giladi H, et al. 1998. Participation of IHF and a distant UP element in the stimulation of the phage lambda pL promoter. Mol. Microbiol. 30:443-451.
20. Govantes F, Molina-Lopez JA, Santero E. 1996. Mechanism of coordinated synthesis of the antagonistic regulatory proteins NifL and NifA of Klebsiella pneumoniae. J. Bacteriol. 178:6817-6823.
21. Govantes F, et al. 2010. Regulation of the atrazine-degradative genes in Pseudomonas sp. strain ADP. FEMS Microbiol. Lett. 310:1-8.
22. Govantes F, Porrúa O, García-González V, Santero E. 2009. Atrazine biodegradation in the lab and in the field: enzymatic activities and gene regulation. Microb. Biotechnol. 2:178-185.
23. Hanahan D. 1983. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166:557-580.
24. Hervás AB, Canosa I, Santero E. 2008. Transcriptome analysis of Pseudomonas putida in response to nitrogen availability. J. Bacteriol. 190:416-420.
25. Hervás AB, Canosa I, Little R, Dixon R, Santero E. 2009. NtrCdependent regulatory network for nitrogen assimilation in Pseudomonas putida. J. Bacteriol. 191:6123-6135.
26. Hoover TR, Santero E, Porter S, Kustu S. 1990. The integration host factor stimulates interaction ofRNApolymerase with NIFA, the transcriptional activator for nitrogen fixation operons. Cell 63:11-22.
27. Inoue H, Nojima H, Okayama H. 1990. High efficiency transformation of Escherichia coli with plasmids. Gene 96:23-28.
28. 70-dependent transcription from a nonoverlapping divergent promoter. Mol. Microbiol. 70:709-723.
29. Lane DJ. 1991. 16S/23S rRNA sequencing, p 115-175. In Stackebrandt E, GoodfellowM(ed), Nucleic acid techniques in bacterial systematics. Wiley, Chichester, United Kingdom.
30. Mandelbaum RT, Wackett LP, Allan DL. 1993. Mineralization of the s-triazine ring of atrazine by stable bacterial mixed cultures. Appl. Environ. Microbiol. 59:1695-1701.
31. Mandelbaum RT, Wackett LP, Allan DL. 1995. Isolation and characterization of a Pseudomonas sp. that mineralizes the s-triazine herbicide atrazine. Appl. Environ. Microbiol. 61:1451-1457.
32. Mao XJ, Huo YX, Buck M, Kolb A, Wang YP. 2007. Interplay between CRP-cAMP and PII-Ntr systems forms novel regulatory network between carbon metabolism and nitrogen assimilation in Escherichia coli. Nucleic Acids Res. 35:1432-1440.
33. Marqués S, et al. 1998. Activation and repression of transcription at the double tandem divergent promoters for the xylR and xylS genes of the TOL plasmid of Pseudomonas putida. J. Bacteriol. 180:2889-2894.
34. Martin-Verstraete I, Stulke J, Klier A, Rapoport G. 1995. Two different mechanisms mediate catabolite repression of the Bacillus subtilis levanase operon. J. Bacteriol. 177:6919-6927.
35. Martinez B, Tomkins J, Wackett LP, Wing R, Sadowsky MJ. 2001. Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J. Bacteriol. 183: 5684-5697.
36. Miller JH. 1992. A short course in bacterial genetics: a laboratory manual, p 72-74. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
37. Nash HA, Robertson CA, Flamm E, Weisberg RA, Miller HI. 1987. Overproduction of Escherichia coli integration host factor, a protein with nonidentical subunits. J. Bacteriol. 169:4124-4127.
38. Neumann G, et al. 2004. Simultaneous degradation of atrazine and phenol by Pseudomonas sp. ADP: effects of toxicity and adaptation. Appl. Environ. Microbiol. 70:1907-1912.
39. Ninfa AJ, Reitzer LJ, Magasanik B. 1987. Initiation of transcription at the bacterial glnAp2 promoter by purified E. coli components is facilitated by enhancers. Cell 50:1039-1046.
40. Porrúa O, García-Jaramillo M, Santero E, Govantes F. 2007. The LysRtype regulator AtzR binding site: DNA sequences involved in activation, repression and cyanuric acid-dependent repositioning. Mol. Microbiol. 66:410-427.
41. N-dependent promoter naturally lacking upstream activation sequences. Mol. Microbiol. 73:419-433.
42. Porrúa O, Platero AI, Santero E, Del Solar G, Govantes F. 2010. Complex interplay between the LysR-type regulator AtzR and its binding site mediates atzDEF activation in response to two distinct signals. Mol. Microbiol. 76:331-347.
43. Porter SC, North AK, Wedel AB, Kustu S. 1993. Oligomerization of NTRC at the glnA enhancer is required for transcriptional activation. Genes Dev. 7:2258-2273.
44. Reitzer LJ, Magasanik B. 1986. Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter. Cell 45:785-792.
45. 54-dependent genes in Escherichia coli. Microbiol. Mol. Biol. Rev. 65:422-444.
46. Sambrook J, Russell DW, Russell D. 2000. Molecular cloning, a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
47. Schell MA. 1993. Molecular biology of the LysR family of transcriptional regulators. Annu. Rev. Microbiol. 47:597-626.
48. Shiomi N, et al. 2006. Degradation of cyanuric acid in soil by Pseudomonas sp. NRRL B-12227 using bioremediation with self-immobilization system. J. Biosci. Bioeng. 102:206-209.
49. 54-dependent transcriptional activators. J. Bacteriol. 185:1757-1767.
50. Tropel D, van der Meer JR. 2004. Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol. Mol. Biol. Rev. 68:474-500.
51. Wackett LP, Sadowsky MJ, Martinez B, Shapir N. 2002. Biodegradation of atrazine and related s-triazine compounds: from enzymes to field studies. Appl. Microbiol. Biotechnol. 58:39-45.
52. 54 RNA polymerase and blocks transcriptional activation of the dctA promoter. EMBO J. 17:786-796.
53. Wu SQ, Chai W, Lin JT, Stewart V. 1999. General nitrogen regulation of nitrate assimilation regulatory gene nasR expression in Klebsiella oxytoca M5al. J. Bacteriol. 181:7274-7284.
54. Yanze-Kontchou C, Gschwind N. 1994. Mineralization of the herbicide atrazine as a carbon source by a Pseudomonas strain. Appl. Environ. Microbiol. 60:4297-4302.
55. Zimmer DP, et al. 2000. Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation. Proc. Natl. Acad. Sci. U. S. A. 97:14674-14679.