TetR-family transcriptional repressor Thermus thermophilus FadR controls fatty acid degradation

Microbiology

Volumn 157, Issue 6, 2011, Pages 1589-1601

  Agari, Yoshihiro ^a   Agari, Kazuko ^a   Sakamoto, Keiko ^a   Kuramitsu, Seiki ^a,b   Shinkai, Akeo ^a  

^a RIKEN SPring 8 Center   (Japan)

^b OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACYL COENZYME A; PALMITIC ACID; TRANSCRIPTION FACTOR; TRANSCRIPTIONAL REPRESSOR FADR; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM CULTURE; CARBON SOURCE; CRYSTALLIZATION; DNA BINDING; DNA MICROARRAY; DNA TEMPLATE; FATTY ACID METABOLISM; GENE AMPLIFICATION; GENE DISRUPTION; GENE EXPRESSION; GENE TARGETING; GENETIC SCREENING; IN VITRO STUDY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PRIORITY JOURNAL; PROTEIN PURIFICATION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; THERMUS THERMOPHILUS; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; X RAY DIFFRACTION;

ACYL COENZYME A; BACTERIAL PROTEINS; BIOSENSING TECHNIQUES; CRYSTALLOGRAPHY, X-RAY; CULTURE MEDIA; FATTY ACIDS; GENE EXPRESSION REGULATION, BACTERIAL; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRESSOR PROTEINS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; THERMUS THERMOPHILUS;

BACTERIA (MICROORGANISMS); THERMUS THERMOPHILUS;

EID: 79958166755     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.048017-0     Document Type: Article

References (52)

1. Agari, Y., Kashihara, A., Yokoyama, S., Kuramitsu, S. & Shinkai, A. (2008). Global gene expression mediated by Thermus thermophilus SdrP, a CRP/FNR family transcriptional regulator. Mol Microbiol 70, 60-75.
2. Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. (2001). Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 98, 10037-10041.
3. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M. & other authors (1998). Crystallography & NMR System: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54, 905-921.
4. Campbell, J. W. & Cronan, J. E., Jr (2001). Escherichia coli FadR positively regulates transcription of the fabB fatty acid biosynthetic gene. J Bacteriol 183, 5982-5990.
5. Cho, B. K., Knight, E. M. & Palsson, B. O. (2006). Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA. Microbiology 152, 2207-2219.
6. Cronan, J. E., Jr & Subrahmanyam, S. (1998). FadR, transcriptional co-ordination of metabolic expediency. Mol Microbiol 29, 937-943.
7. Crooks, G. E., Hon, G., Chandonia, J. M. & Brenner, S. E. (2004). WebLogo: a sequence logo generator. Genome Res 14, 1188-1190.
8. DiRusso, C. C. & Nyström, T. (1998). The fats of Escherichia coli during infancy and old age: regulation by global regulators, alarmones and lipid intermediates. Mol Microbiol 27, 1-8.
9. DiRusso, C. C., Heimert, T. L. & Metzger, A. K. (1992). Characterization of FadR, a global transcriptional regulator of fatty acid metabolism in Escherichia coli. Interaction with the fadB promoter is prevented by long chain fatty acyl coenzyme A. J Biol Chem 267, 8685-8691.
10. Emsley, P. & Cowtan, K. (2004). Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60, 2126-2132.
11. Feng, Y. & Cronan, J. E. (2010). Overlapping repressor binding sites result in additive regulation of Escherichia coli FadH by FadR and ArcA. J Bacteriol 192, 4289-4299.
12. Fujita, Y., Matsuoka, H. & Hirooka, K. (2007). Regulation of fatty acid metabolism in bacteria. Mol Microbiol 66, 829-839.
13. Gouet, P., Robert, X. & Courcelle, E. (2003). ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res 31, 3320-3323.
14. Grkovic, S., Brown, M. H., Roberts, N. J., Paulsen, I. T. & Skurray, R. A. (1998). QacR is a repressor protein that regulates expression of the Staphylococcus aureus multidrug efflux pump QacA. J Biol Chem 273, 18665-18673.
15. Hashimoto, Y., Yano, T., Kuramitsu, S. & Kagamiyama, H. (2001). Disruption of Thermus thermophilus genes by homologous recombination using a thermostable kanamycin-resistant marker. FEBS Lett 506, 231-234.
16. Haydon, D. J. & Guest, J. R. (1991). A new family of bacterial regulatory proteins. FEMS Microbiol Lett 63, 291-295.
17. Henry, M. F. & Cronan, J. E., Jr (1991). Escherichia coli transcription factor that both activates fatty acid synthesis and represses fatty acid degradation. J Mol Biol 222, 843-849.
18. Henry, M. F. & Cronan, J. E., Jr (1992). A new mechanism of transcriptional regulation: release of an activator triggered by small molecule binding. Cell 70, 671-679.
19. Higashitani, A., Nishimura, Y., Hara, H., Aiba, H., Mizuno, T. & Horiuchi, K. (1993). Osmoregulation of the fatty acid receptor gene fadL in Escherichia coli. Mol Gen Genet 240, 339-347.
20. Hisanaga, Y., Ago, H., Nakagawa, N., Hamada, K., Ida, K., Yamamoto, M., Hori, T., Arii, Y., Sugahara, M. & other authors (2004). Structural basis of the substrate-specific two-step catalysis of long chain fatty acyl-CoA synthetase dimer. J Biol Chem 279, 31717-31726.
21. Holm, L. & Sander, C. (1998). Touring protein fold space with Dali/ FSSP. Nucleic Acids Res 26, 316-319.
22. Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.
23. Kuramitsu, S., Hiromi, K., Hayashi, H., Morino, Y. & Kagamiyama, H. (1990). Pre-steady-state kinetics of Escherichia coli aspartate aminotransferase catalyzed reactions and thermodynamic aspects of its substrate specificity. Biochemistry 29, 5469-5476.
24. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A. & other authors (2007). CLUSTAL W and CLUSTAL X version 2.0. Bioinformatics 23, 2947-2948.
25. 15N heteronuclear NMR studies of Escherichia coli thioredoxin in samples isotopically labeled by residue type. Biochemistry 24, 7263-7268.
26. Marchler-Bauer, A., Panchenko, A. R., Shoemaker, B. A., Thiessen, P. A., Geer, L. Y. & Bryant, S. H. (2002). CDD: a database of conserved domain alignments with links to domain threedimensional structure. Nucleic Acids Res 30, 281-283.
27. Marrakchi, H., Zhang, Y. M. & Rock, C. O. (2002). Mechanistic diversity and regulation of type II fatty acid synthesis. Biochem Soc Trans 30, 1050-1055.
28. Matsuoka, H., Hirooka, K. & Fujita, Y. (2007). Organization and function of the YsiA regulon of Bacillus subtilis involved in fatty acid degradation. J Biol Chem 282, 5180-5194.
29. Orth, P., Schnappinger, D., Hillen, W., Saenger, W. & Hinrichs, W. (2000). Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system. Nat Struct Biol 7, 215-219.
30. Oshima, T. & Imahori, K. (1974). Description of Thermus thermophilus (Yoshida and Oshima) com. nov., a non-sporulating thermophilic bacterium from a Japanese thermal spa. Int J Syst Bacteriol 24, 102-112.
31. Oshima, M. & Miyagawa, A. (1974). Comparative studies on the fatty acid composition of moderately and extremely thermophilic bacteria. Lipids 9, 476-480.
32. Otwinowski, Z. & Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276, 307-326.
33. Pauli, G., Ehring, R. & Overath, P. (1974). Fatty acid degradation in Escherichia coli: requirement of cyclic adenosine monophosphate and cyclic adenosine monophosphate receptor protein for enzyme synthesis. J Bacteriol 117, 1178-1183.
34. Pepper, S. D., Saunders, E. K., Edwards, L. E., Wilson, C. L. & Miller, C. J. (2007). The utility of MAS5 expression summary and detection call algorithms. BMC Bioinformatics 8, 273.
35. Perrakis, A., Harkiolaki, M., Wilson, K. S. & Lamzin, V. S. (2001). ARP/wARP and molecular replacement. Acta Crystallogr D Biol Crystallogr 57, 1445-1450.
36. Rock, C. O. & Cronan, J. E. (1996). Escherichia coli as a model for the regulation of dissociable (type II) fatty acid biosynthesis. Biochim Biophys Acta 1302, 1-16.
37. Sakamoto, K., Agari, Y., Agari, K., Kuramitsu, S. & Shinkai, A. (2010). Structural and functional characterization of the transcriptional repressor CsoR from Thermus thermophilus HB8. Microbiology 156, 1993-2005.
38. Sanger, F., Nicklen, S. & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74, 5463-5467.
39. Schneider, T. D. & Stephens, R. M. (1990). Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18, 6097-6100.
40. Schujman, G. E., Paoletti, L., Grossman, A. D. & de Mendoza, D. (2003). FapR, a bacterial transcription factor involved in global regulation of membrane lipid biosynthesis. Dev Cell 4, 663-672.
41. Schujman, G. E., Guerin, M., Buschiazzo, A., Schaeffer, F., Llarrull, L. I., Reh, G., Vila, A. J., Alzari, P. M. & de Mendoza, D. (2006). Structural basis of lipid biosynthesis regulation in Gram-positive bacteria. EMBO J 25, 4074-4083.
42. Schumacher, M. A., Miller, M. C., Grkovic, S., Brown, M. H., Skurray, R. A. & Brennan, R. G. (2001). Structural mechanisms of QacR induction and multidrug recognition. Science 294, 2158-2163.
43. Shinkai, A., Kira, S., Nakagawa, N., Kashihara, A., Kuramitsu, S. & Yokoyama, S. (2007). Transcription activation mediated by a cyclic AMP receptor protein from Thermus thermophilus HB8. J Bacteriol 189, 3891-3901.
44. Siristova, L., Melzoch, K. & Rezanka, T. (2009). Fatty acids, unusual glycophospholipids and DNA analyses of thermophilic bacteria isolated from hot springs. Extremophiles 13, 101-109.
45. Storey, J. D. (2002). A direct approach to false discovery rates. J R Stat Soc, B 64, 479-498.
46. Storey, J. D. & Tibshirani, R. (2003). Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100, 9440-9445.
47. Subrahmanyam, S. & Cronan, J. E., Jr (1998). Overproduction of a functional fatty acid biosynthetic enzyme blocks fatty acid synthesis in Escherichia coli. J Bacteriol 180, 4596-4602.
48. Terwilliger, T. C. & Berendzen, J. (1999). Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr 55, 849-861.
49. Ueno, G., Kanda, H., Hirose, R., Ida, K., Kumasaka, T. & Yamamoto, M. (2006). RIKEN structural genomics beamlines at the SPring-8; high throughput protein crystallography with automated beamline operation. J Struct Funct Genomics 7, 15-22.
50. van Aalten, D. M., DiRusso, C. C. & Knudsen, J. (2001). The structural basis of acyl coenzyme A-dependent regulation of the transcription factor FadR. EMBO J 20, 2041-2050.
51. Willems, A. R., Tahlan, K., Taguchi, T., Zhang, K., Lee, Z. Z., Ichinose, K., Junop, M. S. & Nodwell, J. R. (2008). Crystal structures of the Streptomyces coelicolor TetR-like protein ActR alone and in complex with actinorhodin or the actinorhodin biosynthetic precursor (S)-DNPA. J Mol Biol 376, 1377-1387.
52. Zhang, Y. M., Marrakchi, H. & Rock, C. O. (2002). The FabR (YijC) transcription factor regulates unsaturated fatty acid biosynthesis in Escherichia coli. J Biol Chem 277, 15558-15565.