Genetic analysis of the nitrogen assimilation control protein from Klebsiella pneumoniae

Journal of Bacteriology

Volumn 192, Issue 19, 2010, Pages 4834-4846

  Rosario, Christopher J ^a,b   Janes, Brian K ^a   Bender, Robert A ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; BACTERIAL PROTEIN; DIMER; DNA; GLUTAMINE; NITROGEN ASSIMILATION CONTROL PROTEIN; POLYPEPTIDE; TETRAMER; UNCLASSIFIED DRUG; TRANSCRIPTION FACTOR;

AMINO ACID SUBSTITUTION; ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; GENETIC ANALYSIS; KLEBSIELLA PNEUMONIAE; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; DNA FOOTPRINTING; GEL CHROMATOGRAPHY; GEL MOBILITY SHIFT ASSAY; GENETICS; METABOLISM; MUTATION; PROTEIN MULTIMERIZATION; SITE DIRECTED MUTAGENESIS;

KLEBSIELLA PNEUMONIAE;

BACTERIAL PROTEINS; CHROMATOGRAPHY, GEL; DNA FOOTPRINTING; ELECTROPHORETIC MOBILITY SHIFT ASSAY; KLEBSIELLA PNEUMONIAE; MUTAGENESIS, SITE-DIRECTED; MUTATION; PROTEIN MULTIMERIZATION; TRANSCRIPTION FACTORS;

EID: 77957374566     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.01114-09     Document Type: Article

References (48)

1. Bencini, D. A., G. A. O'Donovan, and J. R. Wild. 1984. Rapid chemical degradation sequencing. Biotechniques 2:4-5.
2. Best, E. A., and R. A. Bender. 1990. Cloning of the Klebsiella aerogenes nac gene, which encodes a factor required for nitrogen regulation of the histidine utilization (hut) operons in Salmonella typhimurium. J. Bacteriol. 172:7043-7048.
3. Blauwkamp, T. A., and A. J. Ninfa. 2002. Nac-mediated repression of the serA promoter of Escherichia coli. Mol. Microbiol. 45:351-363.
4. Blauwkamp, T. A., and A. J. Ninfa. 2002. Physiological role of the GlnK signal transduction protein of Escherichia coli: survival of nitrogen starvation. Mol. Microbiol. 46:203-214.
5. Busby, S., and R. H. Ebright. 1999. Transcription activation by catabolite activator protein (CAP). J. Mol. Biol. 293:199-213.
6. Choi, H., S. Kim, P. Mukhopadhyay, S. Cho, J. Woo, G. Storz, and S. Ryu. 2001. Structural basis of the redox switch in the OxyR transcription factor. Cell 105:103-113.
7. Ezezika, O. C., S. Haddad, T. J. Clark, E. L. Neidle, and C. Momany. 2007. Distinct effector-binding sites enable synergistic transcriptional activation by BenM, a LysR-type regulator. J. Mol. Biol. 367:616-629.
8. Feng, J., T. J. Goss, R. A. Bender, and A. J. Ninfa. 1995. Activation of transcription initiation from the nac promoter of Klebsiella aerogenes. J. Bacteriol. 177:5523-5534.
9. Feng, J., T. J. Goss, R. A. Bender, and A. J. Ninfa. 1995. Repression of the Klebsiella aerogenes nac promoter. J. Bacteriol. 177:5535-5538.
10. Frisch, R. L., and R. A. Bender. 2010. Properties of the NAC (nitrogen assimilation control protein)-binding site within the ureD promoter of Klebsiella pneumoniae. J. Bacteriol. 192:4821-4826.
11. Frisch, R. L., and R. A. Bender. 2010. Expanded role for the nitrogen assimilation control protein in the response of Klebsiella pneumoniae to nitrogen stress. J. Bacteriol. 192:4812-4820.
12. Goss, T. J. 2008. The ArgP protein stimulates the Klebsiella pneumoniae gdhA promoter in a lysine-sensitive manner. J. Bacteriol. 190:4351-4359.
13. Goss, T. J., and R. A. Bender. 1995. The nitrogen assimilation control protein, NAC, is a DNA binding transcription activator in Klebsiella aerogenes. J. Bacteriol. 177:3546-3555.
14. Goss, T. J., B. K. Janes, and R. A. Bender. 2002. Repression of glutamate dehydrogenase formation in Klebsiella aerogenes requires two binding sites for the nitrogen assimilation control protein, NAC. J. Bacteriol. 184:6966-6975.
15. Irwin, N., and M. Ptashne. 1987. Mutants of the catabolite activator protein of Escherichia coli that are specifically deficient in the gene-activation function. Proc. Natl. Acad. Sci. U. S. A. 84:8315-8319.
16. Janes, B. K., and R. A. Bender. 1998. Alanine catabolism in Klebsiella aerogenes: molecular characterization of the dadAB operon and its regulation by the nitrogen assimilation control protein. J. Bacteriol. 180:563-570.
17. Janes, B. K., P. J. Pomposiello, A. Perez-Matos, D. J. Najarian, T. J. Goss, and R. A. Bender. 2001. Growth inhibition caused by overexpression of the structural gene for glutamate dehydrogenase (gdhA) from Klebsiella aerogenes. J. Bacteriol. 183:2709-2714.
18. Janes, B. K., C. J. Rosario, and R. A. Bender. 2003. Isolation of a negative control mutant of the nitrogen assimilation control protein, NAC, in Klebsiella aerogenes. J. Bacteriol. 185:688-692.
19. Jourdan, A. D., and G. V. Stauffer. 1998. Mutational analysis of the transcriptional regulator GcvA: amino acids important for activation, repression, and DNA binding. J. Bacteriol. 180:4865-4871.
20. Liu, Q., and R. A. Bender. 2007. Complex regulation of urease formation from the two promoters of the ure operon of Klebsiella pneumoniae. J. Bacteriol. 189:7593-7599.
21. Lochowska, A., R. Iwanicka-Nowicka, D. Plochocka, and M. M. Hryniewicz. 2001. Functional dissection of the LysR-type CysB transcriptional regulator. Regions important for DNA binding, inducer response, oligomerization, and positive control. J. Biol. Chem. 276:2098-2107.
22. Lochowska, A., R. Iwanicka-Nowicka, J. Zaim, M. Witkowska-Zimny, K. Bolewska, and M. M. Hryniewicz. 2004. Identification of activating region (AR) of Escherichia coli LysR-type transcription factor CysB and CysB contact site on RNA polymerase alpha subunit at the cysP promoter. Mol. Microbiol. 53:791-806.
23. Lorenz, E., and G. V. Stauffer. 1996. MetR-mediated repression of the glyA gene in Escherichia coli. FEMS Microbiol. Lett. 144:229-233.
24. Lowry, O. H., N. J. Rosebrough, A. L. Farr, and R. J. Randall. 1951. Protein measurement with the Folin phenol reagent. J. Biol. Chem. 193:265-275.
25. Macaluso, A., E. A. Best, and R. A. Bender. 1990. Role of the nac gene product in the nitrogen regulation of some NTR-regulated operons of Klebsiella aerogenes. J. Bacteriol. 172:7249-7255.
26. MacPhee, D. G., I. W. Sutherland, and J. F. Wilkinson. 1969. Transduction in Klebsiella. Nature 221:475-476.
27. Maddocks, S. E., and P. C. Oyston. 2008. Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins. Microbiology 154:3609-3623.
28. Monferrer, D., T. Tralau, M. A. Kertesz, I. Dix, M. Sola, and I. Uson. 2010. Structural studies on the full-length LysR-type regulator TsaR from Comamonas testosteroni T-2 reveal a novel open conformation of the tetrameric LTTR fold. Mol. Microbiol. 75:1199-1214.
29. Muraoka, S., R. Okumura, N. Ogawa, T. Nonaka, K. Miyashita, and T. Senda. 2003. Crystal structure of a full-length LysR-type transcriptional regulator, CbnR: unusual combination of two subunit forms and molecular bases for causing and changing DNA bend. J. Mol. Biol. 328:555-566.
30. Muse, W. B., and R. A. Bender. 1998. The nac (nitrogen assimilation control) gene from Escherichia coli. J. Bacteriol. 180:1166-1173.
31. Muse, W. B., and R. A. Bender. 1999. The amino-terminal 100 residues of the nitrogen assimilation control protein (NAC) encode all known properties of NAC from Klebsiella aerogenes and Escherichia coli. J. Bacteriol. 181:934-940.
32. Muse, W. B., C. J. Rosario, and R. A. Bender. 2003. Nitrogen regulation of the codBA (cytosine deaminase) operon from Escherichia coli by the nitrogen assimilation control protein, NAC. J. Bacteriol. 185:2920-2926.
33. Osuna, R., A. Schwacha, and R. A. Bender. 1994. Identification of the hutUH operator (hutUo) from Klebsiella aerogenes by DNA deletion analysis. J. Bacteriol. 176:5525-5529.
34. Pomposiello, P. J., and R. A. Bender. 1995. Activation of the Escherichia coli lacZ promoter by the Klebsiella aerogenes nitrogen assimilation control protein (NAC), a LysR family transcription factor. J. Bacteriol. 177:4820-4824.
35. Pomposiello, P. J., B. K. Janes, and R. A. Bender. 1998. Two roles for the DNA recognition site of the Klebsiella aerogenes nitrogen assimilation control protein. J. Bacteriol. 180:578-585.
36. Rosario, C. J. 2005. The importance of tetramer formation by the nitrogen assimilation control protein (NAC) for DNA binding and repression at the gdhA promoter in Klebsiella pneumoniae. Ph.D. thesis. University of Michian, Ann Arbor, MI.
37. Rosario, C. J., R. L. Frisch, and R. A. Bender. 2010. The LysR-type nitrogen assimilation control protein forms complexes with both long and short DNA binding sites in the absence of coeffectors. J. Bacteriol. 192:4827-4833.
38. Rosario, C. J., and R. A. Bender. 2005. Importance of tetramer formation by the nitrogen assimilation control protein for strong repression of glutamate dehydrogenase formation in Klebsiella pneumoniae. J. Bacteriol. 187:8291-8299.
39. Schell, M. A. 1993. Molecular biology of the LysR family of transcriptional regulators. Annu. Rev. Microbiol. 47:597-626.
40. Schwacha, A., and R. A. Bender. 1993. The nac (nitrogen assimilation control) gene from Klebsiella aerogenes. J. Bacteriol. 175:2107-2115.
41. Schwacha, A., and R. A. Bender. 1993. The product of the Klebsiella aerogenes nac (nitrogen assimilation control) gene is sufficient for activation of the hut operons and repression of the gdh operon. J. Bacteriol. 175:2116-2124.
42. Smirnova, I. A., C. Dian, G. A. Leonard, S. McSweeney, D. Birse, and P. Brzezinski. 2004. Development of a bacterial biosensor for nitrotoluenes: the crystal structure of the transcriptional regulator DntR. J. Mol. Biol. 340:405-418.
43. Sonnhammer, E. L., S. R. Eddy, and R. Durbin. 1997. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28:405-420.
44. Stec, E., M. Witkowska-Zimny, M. M. Hryniewicz, P. Neumann, A. J. Wilkinson, A. M. Brzozowski, C. S. Verma, J. Zaim, S. Wysocki, and G. D. Bujacz. 2006. Structural basis of the sulphate starvation response in E. coli: crystal structure and mutational analysis of the cofactor-binding domain of the Cbl transcriptional regulator. J. Mol. Biol. 364:309-322.
45. Toledano, M. B., I. Kullik, F. Trinh, P. T. Baird, T. D. Schneider, and G. Storz. 1994. Redox-dependent shift of OxyR-DNA contacts along an extended DNA-binding site: a mechanism for differential promoter selection. Cell 78:897-909.
46. Tyrrell, R., K. H. Verschueren, E. J. Dodson, G. N. Murshudov, C. Addy, and A. J. Wilkinson. 1997. The structure of the cofactor-binding fragment of the LysR family member, CysB: a familiar fold with a surprising subunit arrangement. Structure 5:1017-1032.
47. Wang, L., and S. C. Winans. 1995. High angle and ligand-induced low angle DNA bends incited by OccR lie in the same plane with OccR bound to the interior angle. J. Mol. Biol. 253:32-38.
48. Zhou, X., Z. Lou, S. Fu, A. Yang, H. Shen, Z. Li, Y. Feng, M. Bartlam, H. Wang, and Z. Rao. 2010. Crystal structure of ArgP from Mycobacterium tuberculosis confirms two distinct conformations of full-length LysR transcriptional regulators and reveals its function in DNA binding and transcriptional regulation. J. Mol. Biol. 396:1012-1024.