Role of acinetobacter baylyi crc in catabolite repression of enzymes for aromatic compound catabolism

Journal of Bacteriology

Volumn 191, Issue 8, 2009, Pages 2834-2842

  Zimmermann, Tina ^a   Sorg, Tobias ^b   Siehler, Simone Yasmin ^c   Gerischer, Ulrike ^d  

^a Vifor (International) Inc   (Switzerland)

^b PHILIPPS UNIVERSITY MARBURG   (Germany)

^c UNIVERSITY HOSPITAL ULM   (Germany)

^d UNIVERSITY OF ULM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

4 HYDROXYBENZOATE 3 MONOOXYGENASE; CARBON; MESSENGER RNA; PROTOCATECHUATE 3,4 DIOXYGENASE; ACETIC ACID; AROMATIC HYDROCARBON; BACTERIAL PROTEIN; ENZYME; FRUR PROTEIN, BACTERIA; REPRESSOR PROTEIN; SUCCINIC ACID;

ACINETOBACTER; ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; ENZYME ACTIVITY; ENZYME REPRESSION; GENETIC TRANSCRIPTION; NONHUMAN; OPERON; PRIORITY JOURNAL; PROTEIN DEGRADATION; RNA STABILITY; AMINO ACID SEQUENCE; BIOLOGICAL MODEL; BIOSYNTHESIS; GENE DELETION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; PHYSIOLOGY; SEQUENCE ALIGNMENT;

ACINETOBACTER BAYLYI; BACTERIA (MICROORGANISMS);

4-HYDROXYBENZOATE-3-MONOOXYGENASE; ACETIC ACID; ACINETOBACTER; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CARBON; ENZYME REPRESSION; ENZYMES; GENE DELETION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; HYDROCARBONS, AROMATIC; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; PROTOCATECHUATE-3,4-DIOXYGENASE; REPRESSOR PROTEINS; RNA STABILITY; SEQUENCE ALIGNMENT; SUCCINIC ACID;

EID: 65249143794     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.00817-08     Document Type: Article

References (56)

1. Alting-Mees, M. A., and J. M. Short. 1989. pBluescript II: gene mapping vectors. Nucleic Acids Res. 17:9494.
2. Aranda-Olmedo, I., P. Marin, J. L. Ramos, and S. Marques. 2006. Role of the ptsN gene product in catabolite repression of the Pseudomonas putida TOL toluene degradation pathway in chemostat cultures. Appl. Environ. Microbiol. 72:7418-7421.
3. Aranda-Olmedo, I., J. L. Ramos, and S. Marques. 2005. Integration of signals through Crc and PtsN in catabolite repression of Pseudomonas putida TOL plasmid pWW0. Appl. Environ. Microbiol. 71:4191-4198.
4. Bruckner, R., and F. Titgemeyer. 2002. Carbon catabolite repression in bacteria: choice of the carbon source and autoregulatory limitation of sugar utilization. FEMS Microbiol. Lett. 209:141-148.
5. Brzostowicz, P. C., A. B. Reams, T. J. Clark, and E. L. Neidle. 2003. Transcriptional cross-regulation of the catechol and protocatechuate branches of the beta-ketoadipate pathway contributes to carbon source-dependent expression of the Acinetobacter sp. strain ADP1 pobA gene. Appl. Environ. Microbiol. 69:1598-1606.
6. Buell, C. R., V. Joardar, M. Lindeberg, J. Selengut, I. T. Paulsen, M. L. Gwinn, R. J. Dodson, R. T. Deboy, A. S. Durkin, J. F. Kolonay, R. Madupu, S. Daugherty, L. Brinkac, M. J. Beanan, D. H. Haft, W. C. Nelson, T. Davidsen, N. Zafar, L. Zhou, J. Liu, Q. Yuan, H. Khouri, N. Fedorova, B. Tran, D. Russell, K. Berry, T. Utterback, S. E. Van Aken, T. V. Feldblyum, M. D'Ascenzo, W. L. Deng, A. R. Ramos, J. R. Alfano, S. Cartinhour, A. K. Chatterjee, T. P. Delaney, S. G. Lazarowitz, G. B. Martin, D. J. Schneider, X. Tang, C. L. Bender, O. White, C. M. Fraser, and A. Collmer. 2003. The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc. Natl. Acad. Sci. USA 100:10181-10186.
7. Cases, I., F. Velazquez, and V. de Lorenzo. 2001. Role of ptsO in carbon-mediated inhibition of the Pu promoter belonging to the pWW0 Pseudomonas putida plasmid. J. Bacteriol. 183:5128-5133.
8. Collier, D. N., P. W. Hager, and P. V. Phibbs, Jr. 1996. Catabolite repression control in the Pseudomonads. Res. Microbiol. 147:551-561.
9. Dal, S., I. Steiner, and U. Gerischer. 2002. Multiple operons connected with catabolism of aromatic compounds in Acinetobacter sp. strain ADP1 are under carbon catabolite repression. J. Mol. Microbiol. Biotechnol. 4:389-404.
10. Dal, S., G. Trautwein, and U. Gerischer. 2005. Transcriptional organization of genes for protocatechuate and quinate degradation from Acinetobacter sp. strain ADP1. Appl. Environ. Microbiol. 71:1025-1034.
11. DiMarco, A. A., B. Averhoff, and L. N. Ornston. 1993. Identification of the transcriptional activator pobR and characterization of its role in the expression of pobA, the structural gene for p-hydroxybenzoate hydroxylase in Acinetobacter calcoaceticus. J. Bacteriol. 175:4499-4506.
12. DiMarco, A. A., B. A. Averhoff, E. E. Kim, and L. N. Ornston. 1993. Evolutionary divergence of pobA, the structural gene encoding p-hydroxybenzoate hydroxylase in an Acinetobacter calcoaceticus strain well-suited for genetic analysis. Gene 125:25-33.
13. Dinamarca, M. A., A. Ruiz-Manzano, and F. Rojo. 2002. Inactivation of cytochrome o ubiquinol oxidase relieves catabolic repression of the Pseudo- monas putida GPo1 alkane degradation pathway. J. Bacteriol. 184:3785-3793.
14. +-dependent endonucleases. Trends Biochem. Sci. 25:272-273.
15. Dreyfus, M., and P. Regnier. 2002. The poly(A) tail of mRNAs: bodyguard in eukaryotes, scavenger in bacteria. Cell 111:611-613.
16. Elsemore, D. A., and L. N. Ornston. 1994. The pca-pob supraoperonic cluster of Acinetobacter calcoaceticus contains quiA, the structural gene for quinate- shikimate dehydrogenase. J. Bacteriol. 176:7659-7666.
17. Entsch, B., Y. Nan, K. Weaich, and K. F. Scott. 1988. Sequence and organization of pobA, the gene coding for p-hydroxybenzoate hydroxylase, an inducible enzyme from Pseudomonas aeruginosa. Gene 71:279-291.
18. Finn, R. D., J. Mistry, B. Schuster-Bockler, S. Griffiths-Jones, V. Hollich, T. Lassmann, S. Moxon, M. Marshall, A. Khanna, R. Durbin, S. R. Eddy, E. L. Sonnhammer, and A. Bateman. 2006. Pfam: clans, web tools and services. Nucleic Acids Res. 34:D247-D251.
19. Gerischer, U. 2002. Specific and global regulation of genes associated with the degradation of aromatic compounds in bacteria. J. Mol. Microbiol. Biotechnol. 4:111-121.
20. Gerischer, U., and P. Dürre. 1992. mRNA analysis of the adc gene region of Clostridium acetobutylicum during the shift to solventogenesis. J. Bacteriol. 174:426-433.
21. Gerischer, U., B. Jerg, and R. Fischer. 2008. Spotlight on the Acinetobacter baylyi ̈-ketoadipate pathway: multiple levels of regulation, p. 203-230. In U. Gerischer (ed.), Acinetobacter molecular biology. Caister Academic Press, Norfolk, United Kingdom.
22. Gerischer, U., A. Segura, and L. N. Ornston. 1998. PcaU, a transcriptional activator of genes for protocatechuate utilization in Acinetobacter. J. Bacteriol. 180:1512-1524.
23. Hanahan, D. 1983. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166:557-580.
24. Hartnett, C., E. L. Neidle, K.-L. Ngai, and L. N. Ornston. 1990. DNA sequences of genes encoding Acinetobacter calcoaceticus protocatechuate 3,4- dioxygenase: evidence indicating shuffling of genes and of DNA sequences within genes during their evolutionary divergence. J. Bacteriol. 172:956-966.
25. Harwood, C. S., and R. E. Parales. 1996. The β-ketoadipate pathway and the biology of self-identity. Annu. Rev. Microbiol. 50:553-590.
26. Hester, K. L., J. Lehman, F. Najar, L. Song, B. A. Roe, C. H. MacGregor, P. W. Hager, P. V. Phibbs, Jr., and J. R. Sokatch. 2000. Crc is involved in catabolite repression control of the bkd operons of Pseudomonas putida and Pseudomonas aeruginosa. J. Bacteriol. 182:1144-1149.
27. Hester, K. L., K. T. Madhusudhan, and J. R. Sokatch. 2000. Catabolite repression control by Crc in 2×YT medium is mediated by posttranscriptional regulation of bkdR expression in Pseudomonas putida. J. Bacteriol. 182:1150-1153.
28. Hoffmann, H., T. Hartsch, and U. Gerischer. 2002. Is the crc gene product involved in catabolite repression in Acinetobacter sp. strain ADP1?, p. 81. VAAM Annual Meeting 2002. Biospektrum Special Issue. Spektrum, Göt- tingen, Germany.
29. Jerg, B., and U. Gerischer. 2008. Relevance of nucleotides of the PcaU binding site from Acinetobacter baylyi. Microbiology 154:756-766.
30. Juni, E., and A. Janik. 1969. Transformation of Acinetobactercalco-aceticus (Bacterium anitratum). J. Bacteriol. 98:281-288.
31. Kanack, K. J., L. J. Runyen-Janecky, E. P. Ferrell, S. J. Suh, and S. E. West. 2006. Characterization of DNA-binding specificity and analysis of binding sites of the Pseudomonas aeruginosa global regulator, Vfr, a homologue of the Escherichia coli cAMP receptor protein. Microbiology 152:3485-3496.
32. Larkin, M. A., G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin, I. M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson, and D. G. Higgins. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
33. MacGregor, C. H., S. K. Arora, P. W. Hager, M. B. Dail, and P. V. Phibbs, Jr. 1996. The nucleotide sequence of the Pseudomonas aeruginosa pyrE-crc- rph region and the purification of the crc gene product. J. Bacteriol. 178: 5627-5635.
34. MacGregor, C. H., J. A. Wolff, S. K. Arora, and P. V. Phibbs, Jr. 1991. Cloning of a catabolite repression control (crc) gene from Pseudomonas aeruginosa, expression of the gene in Escherichia coli, and identification of the gene product in Pseudomonas aeruginosa. J. Bacteriol. 173:7204-7212.
35. Mol, C. D., C. F. Kuo, M. M. Thayer, R. P. Cunningham, and J. A. Tainer. 1995. Structure and function of the multifunctional DNA-repair enzyme exonuclease III. Nature 374:381-386.
36. Molina-Henares, A. J., T. Krell, M. Eugenia Guazzaroni, A. Segura, and J. L. Ramos. 2006. Members of the IclR family of bacterial transcriptional regulators function as activators and/or repressors. FEMS Microbiol. Rev. 30:157-186.
37. Morales, G., J. F. Linares, A. Beloso, J. P. Albar, J. L. Martinez, and F. Rojo. 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.
38. Moreno, R., and F. Rojo. 2008. The target for the Pseudomonas putida Crc global regulator in the benzoate degradation pathway is the BenR transcriptional regulator. J. Bacteriol. 190:1539-1545.
39. Moreno, R., A. Ruiz-Manzano, L. Yuste, and F. Rojo. 2007. The Pseudomonas putida Crc global regulator is an RNA binding protein that inhibits translation of the AlkS transcriptional regulator. Mol. Microbiol. 64:665-675.
40. O'Toole, G. A., K. A. Gibbs, P. W. Hager, P. V. Phibbs, Jr., and R. Kolter. 2000. The global carbon metabolism regulator Crc is a component of a signal transduction pathway required for biofilm development by Pseudomonas aeruginosa. J. Bacteriol. 182:425-431.
41. Paulsen, I. T., C. M. Press, J. Ravel, D. Y. Kobayashi, G. S. Myers, D. V. Mavrodi, R. T. DeBoy, R. Seshadri, Q. Ren, R. Madupu, R. J. Dodson, A. S. Durkin, L. M. Brinkac, S. C. Daugherty, S. A. Sullivan, M. J. Rosovitz, M. L. Gwinn, L. Zhou, D. J. Schneider, S. W. Cartinhour, W. C. Nelson, J. Wei-dman, K. Watkins, K. Tran, H. Khouri, E. A. Pierson, L. S. Pierson III, L. S. Thomashow, and J. E. Loper. 2005. Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat. Biotechnol. 23:873-878.
42. Petruschka, L., G. Burchhardt, C. Müller, C. Weihe, and H. Herrmann. 2001. The cyo operon of Pseudomonas putida is involved in carbon catabolite repression of phenol degradation. Mol. Genet. Genomics 266:199-206.
43. Prentki, P., and H. M. Krisch. 1984. In vitro insertional mutagenesis with a selectable DNA fragment. Gene 29:303-313.
44. Rojo, F., and M. A. Dinamarca. 2004. Catabolite repression and physiological control. In J.-L. Ramos (ed.), Pseudomonas, vol. 2. Kluwer Academic Publishers, New York, NY.
45. Ruiz-Manzano, A., L. Yuste, and F. Rojo. 2005. Levels and activity of the Pseudomonas putida global regulatory protein Crc vary according to growth conditions. J. Bacteriol. 187:3678-3686.
46. Saier, M. H., Jr. 1998. Multiple mechanisms controlling carbon metabolism in bacteria. Biotechnol. Bioeng. 58:170-174.
47. Siehler, S. Y., S. Dal, R. Fischer, P. Patz, and U. Gerischer. 2007. Multiple- level regulation of genes for protocatechuate degradation in Acinetobacter baylyi includes cross-regulation. Appl. Environ. Microbiol. 73:232-242.
48. Smith, M. G., T. A. Gianoulis, S. Pukatzki, J. J. Mekalanos, L. N. Ornston, M. Gerstein, and M. Snyder. 2007. New insights into Acinetobacter bauman- nii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev. 21:601-614.
49. Stover, C. K., X. Q. Pham, A. L. Erwin, S. D. Mizoguchi, P. Warrener, M. J. Hickey, F. S. Brinkman, W. O. Hufnagle, D. J. Kowalik, M. Lagrou, R. L. Garber, L. Goltry, E. Tolentino, S. Westbrock-Wadman, Y. Yuan, L. L. Brody, S. N. Coulter, K. R. Folger, A. Kas, K. Larbig, R. Lim, K. Smith, D. Spencer, G. K. Wong, Z. Wu, I. T. Paulsen, J. Reizer, M. H. Saier, R. E. Hancock, S. Lory, and M. V. Olson. 2000. Complete genome sequence of Pseudomonasaeruginosa PA01, anopportunisticpathogen. Nature406:959-964.
50. Suh, S. J., L. J. Runyen-Janecky, T. C. Maleniak, P. Hager, C. H. MacGregor, N. A. Zielinski-Mozny, P. V. Phibbs, Jr., and S. E. West. 2002. Effect of vfr mutation on global gene expression and catabolite repression control of Pseudomonas aeruginosa. Microbiology 148:1561-1569.
51. Sze, C. C., and V. Shingler. 1999. The alarmone (p)ppGpp mediates physiological-responsive control at the sigma 54-dependent Po promoter. Mol. Microbiol. 31:1217-1228.
52. Titgemeyer, F., and W. Hillen. 2002. Global control of sugar metabolism: a gram-positive solution. Antonie van Leeuwenhoek 82:59-71.
53. Trautwein, G., and U. Gerischer. 2001. Effects exerted by transcriptional regulator PcaU from Acinetobacter sp. strain ADP1. J. Bacteriol. 183:873-881.
54. Tucker, M., R. R. Staples, M. A. Valencia-Sanchez, D. Muhlrad, and R. Parker. 2002. Ccr4p is the catalytic subunit of a Ccr4p/Pop2p/Notp mRNA deadenylase complex in Saccharomyces cerevisiae. EMBO J. 21:1427-1436.
55. Wolff, J. A., C. H. MacGregor, R. C. Eisenberg, and P. V. Phibbs, Jr. 1991. Isolation and characterization of catabolite repression control mutants of Pseudomonas aeruginosa PAO. J. Bacteriol. 173:4700- 4706.
56. Yuste, L., and F. Rojo. 2001. Role of the crc gene in catabolic repression of the Pseudomonas putida GPo1 alkane degradation pathway. J. Bacteriol. 183:6197-6206.