Involvement of the global crp regulator in cyclic amp-dependent utilization of aromatic amino acids by pseudomonas putida

Journal of Bacteriology

Volumn 194, Issue 2, 2012, Pages 406-412

  Herrera, M Carmen ^b   Daddaoua, Abdelali ^a   Ana, Fernández Escamilla ^a   Ramos, Juan Luis ^a  

^a CSIC   (Spain)

^b MRC CLINICAL SCIENCES CENTRE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC AMINO ACID; C REACTIVE PROTEIN; CYCLIC AMP; DEOXYRIBONUCLEASE I; INTEGRATION HOST FACTOR; NUCLEOPROTEIN; PHENYLALANINE; PHENYLALANINE 4 MONOOXYGENASE; RNA POLYMERASE; SIGMA FACTOR RPON; TYROSINE;

ARTICLE; BINDING SITE; CONTROLLED STUDY; DNA FOOTPRINTING; GEL MOBILITY SHIFT ASSAY; GENETIC TRANSCRIPTION; NONHUMAN; OPERON; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PSEUDOMONAS PUTIDA; REGULATORY MECHANISM;

AMINO ACIDS, AROMATIC; BACTERIAL PROTEINS; CONDITIONING, OPERANT; CYCLIC AMP; CYCLIC AMP RECEPTOR PROTEIN; GENE EXPRESSION REGULATION, BACTERIAL; MODELS, MOLECULAR; PHENYLALANINE; PSEUDOMONAS PUTIDA; TYROSINE;

PSEUDOMONAS PUTIDA;

EID: 84855870411     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.06353-11     Document Type: Article

References (50)

1. Abril MA, Michán C, Timmis KN, Ramos JL. 1989. Regulator and enzyme specificities of the TOL plasmid-encoded upper pathway for degradation of aromatic hydrocarbons and expansion of the substrate range of the pathway. J. Bacteriol. 171:6782-6790.
2. Aranda-Olmedo I, Ramos JL, Marqués S. 2005. Integration of signals through Crc and PtsN in catabolite repression of Pseudomonas putidaTOL plasmid pWW0. Appl. Environ. Microbiol. 71:4191-4198.
3. Bai Q, Somerville RL. 1998. Integration host factor and cyclic AMP receptor protein are required for TyrR-mediated activation of tpl in Citrobacter freundii. J. Bacteriol. 180:6173-6186.
4. Crr phosphorylation, and intracellular cyclic AMP levels in Escherichia coli K-12. J. Bacteriol. 189:6891-6900.
5. Botsford JL, Harman JG. 1992. Cyclic AMP in prokaryotes. Microbiol. Rev. 56:100-122.
6. Busby S, Kolb A. 1996. The CAP modulon, p 255-270. In Lin ECC, Lynch AS (ed), Regulation of gene expression in Escherichia coli. Chapman & Hall, Austin, TX.
7. Busby S, Ebright RH. 1999. Transcription activation by catabolite activator protein (CAP). J. Mol. Biol. 293:199-213.
8. Daniels C, et al. 2010. Global regulation of food supply by Pseudomonas putida DOT-T1E. J. Bacteriol. 192:2169-2181.
9. Duque E, et al. 2007. Towards a genome-wide mutant library of Pseudomonas putida strains KT2440, p 227-254. In Ramos JL (ed), Pseudomonas, vol V. Kluwer, London, United Kingdom.
10. Fillet S, et al. 2009. TtgV represses two different promoters by recognizing different sequences. J. Bacteriol. 191:1901-1909.
11. Franklin FCH, Bagdasarian M, Bagdasarian MM, Timmis KN. 1981. Molecular and functional analysis of the TOL plasmid pWW0 from 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.
12. Gill SC, von Hippel PH. 1989. Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182:319-326.
13. González-Pérez MM, Ramos JL, Gallegos MT, Marqués S. 1999. Critical nucleotides in the upstream region of the XylS-dependent TOL metacleavage pathway operon promoter as deduced from analysis of mutants. J. Biol. Chem. 274:2286-2290.
14. Gosh T, Bose D, Zhang X. 2010. Mechanisms for activating bacterial RNA polymerase. FEMS Microbiol. Rev. 34:611-622.
15. Gosset G, Zhang Z, Nayyar S, Cuevas WA, Saier MJ. 2004. Transcriptome analysis of Crp-dependent catabolite control of gene expression in Escherichia coli. J. Bacteriol. 186:3516-3524.
16. Gralla JD, Collado-Vides J. 1996. Organization and function of transcription regulatory elements, p 1232-1245. In Neidhardt FC, et al (ed), Escherichia coli and Salmonella: cellular and molecular biology. ASM Press, Washington, DC.
17. Herrera MC, Duque E, Rodríguez-Herva JJ, Ramos JL. 2010. PhhR controls a regulon including two phenylalanine degradation pathways and the MexEF/OprN system in Pseudomonas putida. Environ. Microbiol. 12: 1427-1438.
18. Herrera MC, Krell T, Zhang X, Ramos JL. 2009. PhhR binds to target sequences at different distances with respect to RNA polymerase in order to activate transcription. J. Mol. Biol. 394:576-586.
19. 70. J. Mol. Biol. 366:1374-1386.
20. Ishihama A. 2010. Prokaryotic genome regulation: multifactor promoters, multitarget regulators and hierarchic networks. FEMS Microbiol. Rev. 34:628-645.
21. Jeong HS, Kim SM, Lim MS, Kim KS, Choi SH. 2010. Direct interaction between quorum-sensing regulator SmcR and RNA polymerase is mediated by integration host factor to activate vvpE encoding elastase in Vibrio vulnificus. J. Biol. Chem. 285:9357-9366.
22. Jeong HS, Lee MH, Lee KH, Park SJ, Choi SH. 2003. SmcR and cyclic AMP receptor protein coactivate Vibrio vulnificus vvpE encoding elastase through the RpoS-dependent promoter in a synergistic manner. J. Biol. Chem. 278:45072-45081.
23. Kennedy N, Brodie E, Connolly J, Clipson N. 2004. Impact of lime, nitrogen and plant species on bacterial community structure in grassland microcosm. Environ. Microbiol. 6:1070-1080.
24. Kim CM, Shim SH. 2010. Regulation of the Vibrio vulnificus vvpE expression by cyclic AMP-receptor protein and quorum-sensing regulator SmcR. Microb. Pathog. 49:348-353.
25. Matilla MA, Espinosa-Urgel M, Rodríguez-Herva JJ, Ramos JL, Ramos-González MA. 2007. Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere. Genome Biol. 8:R179.
26. McLeod SM, Xu J, Johnson RC. 2000. Coactivation of the RpoSdependent proP P2 promoter by Fis and cyclic AMP receptor protein. J. Bacteriol. 182:4180-4187.
27. Milanesio P, et al. 2011. Regulatory exaptation of the catabolite repression protein (Crp)-cAMP system in Pseudomonas putida. Environ. Microbiol. 13:324-339.
28. Miller JH. 1972. Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
29. Molina-Henares AM, et al. 2009. Functional analysis of aromatic biosynthetic pathways in Pseudomonas putida KT2440. Microb. Biotechnol. 2:91-100.
30. Morales G, et al. 2004. The Pseudomonas putida Crc global regulator controls the expression of genes from several chromosomal catabolic pathways for aromatic compounds. J. Bacteriol. 186:1337-1344.
31. Morales G, Ugidos A, Rojo F. 2006. Inactivation of the Pseudomonas putida cytochrome o ubiquinol oxidase leads to a significant change in the transcriptome and to increased expression of the CIO and cbb3-1 terminal oxidases. Environ. Microbiol. 8:1764-1774.
32. Moreno R, Fonseca P, Rojo F. 2010. The Crc global regulator inhibits the Pseudomonas putida pWW0 toluene/xylene assimilation pathway by repressing the translation of regulatory and structural genes. J. Biol. Chem. 285:24412-24419.
33. Moreno R, Martinez-Gomariz M, Yuste L, Gil C, Rojo F. 2009. The Pseudomonas putida Crc global regulator controls the hierarchical assimilation of amino acids in a complete medium: evidence from proteomic and genomic analyses. Proteomics 9:2910-2928.
34. Moreno R, Marzi S, Romby P, Rojo F. 2009. The Crc global regulator binds to an unpaired A-rich motif at the Pseudomonas putida alkS mRNA coding sequence and inhibits translation. Nucleic Acids Res. 37: 7678-7690.
35. Nagaich AK, Appella E, Harrington RE. 1997. DNA bending is essential for the site-specific recognition of DNA response elements by the DNA binding domain of the tumor suppressor protein p53. J. Biol. Chem. 272: 14842-14849.
36. Parkinson G, et al. 1996. Structure of the CAP-DNA complex at 2.5 angstroms resolution: a complete picture of the protein-DNA interface. J. Mol. Biol. 260:395-408.
37. Pérez-Martín J, de Lorenzo V. 1997. Clues and consequences of DNA bending in transcription. Annu. Rev. Microbiol. 51:593-628.
38. Rhodius VA, Busby SJ. 1998. Positive activation of gene expression. Curr. Opin. Microbiol. 1:152-159.
39. Richet E, Vidal-Ingigliardi D, Raibaud O. 1991. A new mechanism for coaction of transcription: repositioning of an activator triggered by the binding of a second activator. Cell 66:1185-1195.
40. Robertson CA, Nash H. 1988. Bending of the bacteriophage X attachment site by Escherichia coli integration host factor. J. Biol. Chem. 263: 3554-3557.
41. Rojo F. 2010. Carbon catabolite repression in Pseudomonas: optimizing metabolic versatility and interactions with the environment. FEMS Microbiol. Rev. 34:658-684.
42. Rojo F, Dinamarca A. 2004. Catabolic repression and physiological control, p 365-387. In Ramos JL (ed), Pseudomonas. Kluwer Academic/ Plenum Publishers, London, United Kingdom.
43. Saier MH, Jr. 1989. Protein phosphorylation and allosteric control of inducer exclusion and catabolite repression by the bacterial phosphoenolpyruvate: sugar phosphotransferase system. Microbiol. Rev. 53:109-120.
44. Schultz SC, Shields GC, Steitz TA. 1991. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 235:1001-1007.
45. Spaink HP, Okker JH, Wijffelman CSA, Pees E, Lugtemberg BJJ. 1987. Promoters in the nodulation region of the Rhizobium leguminosarum Sym plasmids pRL1JL. Plant Mol. Biol. 9:27-39.
46. Suh SJ, Runyen-Janecky LJ, et al. 2002. Effect of vfr mutation on global gene expression and catabolite repression control of Pseudomonas aeruginosa. Microbiology 148:1561-1569.
47. Thompson JF, Landy S. 1988. Empirical estimation of protein-induced DNA bending angles: application to lambda site-specific recombination complexes. Nucleic Acids Res. 16:9687-9705.
48. van Dijk M, Bonvin AM. 2009. 3D-DART: a DNA structure modelling server. Nucleic Acids Res. 37:W235-W239.
49. Wu H-M, Crothers DM. 1984. The locus of sequence-directed and protein-induced DNA bending. Nature 308:509-513.
50. Young H, Koh J, Roberts GP. 2008. Two-state allosteric modeling suggests protein equilibrium as an integral component for cyclic AMP (cAMP) specificity in the cAMP receptor protein of Escherichia coli. J. Bacteriol. 190:4532-4540.