Autoregulator protein PhaR for biosynthesis of polyhydroxybutyrate [P(3HB)] possibly has two separate domains that bind to the target DNA and P(3HB): Functional mapping of amino acid residues responsible for DNA binding

Journal of Bacteriology

Volumn 189, Issue 3, 2007, Pages 1118-1127

  Yamada, Miwa ^a   Yamashita, Koichi ^b   Wakuda, Akiko ^a   Ichimura, Kazuyoshi ^c   Maehara, Akira ^d   Maeda, Michihisa ^c   Taguchi, Seiichi ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

^b RIKEN   (Japan)

^c MEIJI UNIVERSITY   (Japan)

^d MITSUBISHI GAS CHEMICAL COMPANY INC   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; DNA; GREEN FLUORESCENT PROTEIN; HYDROXYBUTYRIC ACID; PHASIN; POLYESTER; POLYHYDROXYALKANOIC ACID; POLYHYDROXYBUTYRATE; PROTEIN PHAR; REGULATOR PROTEIN; SILICON DIOXIDE; TYROSINE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; AUTOREGULATION; BINDING AFFINITY; BIOSYNTHESIS; CONTROLLED STUDY; DNA BINDING; ESCHERICHIA COLI; GEL MOBILITY SHIFT ASSAY; GENE DELETION; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE REPRESSION; GENETIC ANALYSIS; IN VIVO STUDY; NONHUMAN; PARACOCCUS DENITRIFICANS; POINT MUTATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; QUARTZ CRYSTAL MICROBALANCE; STRUCTURE ACTIVITY RELATION; SURFACE PLASMON RESONANCE;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CIRCULAR DICHROISM; DNA-BINDING PROTEINS; GENE DELETION; GENETIC VECTORS; HYDROXYBUTYRATES; MOLECULAR SEQUENCE DATA; PARACOCCUS DENITRIFICANS; POLYESTERS; POLYMERASE CHAIN REACTION; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; REPRESSOR PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

ESCHERICHIA COLI; PARACOCCUS DENITRIFICANS;

EID: 33846571530     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.01550-06     Document Type: Article

References (49)

1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Anderson, A. J., and E. A. Dawes. 1990. Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates. Microbiol. Rev. 54:450-472.
3. Cabrera, J. E., G. Panzetta-Dutari, J. L. Pruneda, and S. Genti-Raimondi. 1997. A new Comamonas testosteroni steroid-inducible gene: cloning and sequence analysis. J. Steroid Biochem. Mol. Biol. 63:91-98.
4. Doi, Y. 1990. Microbial polyesters. VCH, New York, NY.
5. Encarnación, S., M. del Carmen Vargas, M. F. Dunn, A. Dávalos, G. Mendoza, Y. Mora, and J. Mora. 2002. AniA regulates reserve polymer accumulation and global protein expression in Rhizobium etli. J. Bacteriol. 184:2287-2295.
6. Franco, I. S., L. J. Mota, C. M. Soares, and I. de Sá-Nogueria. 2006. Functional domains of the Bacillus subtilis transcription factor AraR and identification of amino acids important for nucleoprotein complex assembly and effector binding. J. Bacteriol. 188:3024-3036.
7. Fukui, T., T. Kichise, T. Iwata, and Y. Doi. 2001. Characterization of 13 kDa granule-associated protein in Aeromonas caviae and biosynthesis of polyhydroxyalkanoate with altered molar composition by recombinant bacteria. Biomacromolecules 2:148-153.
8. Gao, D., A. Maehara, T. Yamane, and S. Ueda. 2001. Identification of the intracellular polyhydroxyalkanoate depolymerase gene of Paracoccus denitrificans and some properties of the gene product. FEMS Microbiol. Lett. 196:159-164.
9. Hanley, S. Z., D. J. C. Pappin, D. Rahman, A. J. White, K. M. Elborough, and A. R. Slabas. 1999. Re-evaluation of the primary structure of Ralstonia eutropha phasin and implications for polyhydroxyalkanoic acid granule binding. FEBS Lett. 447:99-105.
10. Hiraishi, T., Y. Hirahara, Y. Doi, M. Maeda, and S. Taguchi. 2006. Effects of mutations in the substrate-binding domain of poly[(R)-3- hydoxybutyrate] (PHB) depolymerase from Ralstonia pickettii T1 on PHB degradation. Appl. Environ. Microbiol. 72:7331-7338.
11. Hisano, T., K. Kasuya, Y. Tezuka, N. Ishii, T. Kobayashi, M. Shiraki, E. Oroudjev, H. Hansma, T. Iwata, Y. Doi, T. Saito, and K. Miki. 2006. The crystal structure of polyhydroxybutyrate depolymerase from Penicillium funiculosum provides insights into the recognition and degradation of biopolyesters. J. Mol. Biol. 356:993-1004.
12. Höök, F., and B. Kasemo. 2001. Variations in coupled water, viscoelastic properties, and film thickness of a Mefp-1 protein film during adsorption and cross-linking: a quartz crystal microbaJance with dissipation monitoring, ellipsometry, and surface plasmon resonance study. Anal. Chem. 73:5796-5804.
13. Jossek, R., R. Reichelt, and A. Steinbüchel. 1998. In vitro biosynthesis of poly(3-hydroxybutyric acid) by using purified poly(hydroxyalkanoic acid) synthase of Chromatium vinosum. Appl. Microbiol. Biotechnol. 49:258-266.
14. Kawaguchi, Y., and Y. Doi. 1990. Structure of native poly(3-hydroxybutyrate) granules characterized by X-ray diffraction. FEMS Microbiol. Lett. 79:151-156.
15. Kim, H. S., M. A. Schell, Y. Yu, R. L. Ulrich, and S. H. Sarria. 2005. Bacterial genome adaptation to niches: divergence of the potential virulence genes in three Burkholderia species of different survival strategies. BMC Genomics 6:174-187.
16. Kojima, T., T. Yamane, and H. Nakano. 2006. In vitro selection of DNA binding sites for transcription factor, PhaR, from Paracoccus denitrificans using genetic library on microbeads and flow cytometry. J. Biosci. Bioeng. 101:440-444.
17. 2 compounds in the methylotroph Methylobacterium extorquera AM1. J. Bacteriol. 183:1038-1046.
18. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.
19. Lee, S. Y. 1996. Plastic bacteria? Progress and prospects for polyhydroxyalkanoate production in bacteria. Trends Biotechnol. 14:431-438.
20. Lenz, R. W., and R. H. Marchessault. 2005. Bacterial polyesters: biosynthesis, biodegradable plastics and biotechnology. Biomacromolecules 6:1-8.
21. Liebergesell, M., and A. Steinbüchel. 1993. Cloning and molecular analysis of the poly(3-hydroxybutyric acid) biosynthetic genes of Thiocystis violacea. Appl. Microbiol. Biotechnol. 38:493-501.
22. Madison, L. L., and G. W. Huisman. 1999. Metabolic engineering of poly(3-hydroxyalkanoates): from DNA to plastic. Microbiol. Mol. Biol. Rev. 63:21-53.
23. Maehara, A., S. Taguchi, T. Nishiyama, T. Yamane, and Y. Doi. 2002. A repressor protein, PhaR, regulates polyhydroxyalkanoate (PHA) synthesis via its direct interaction with PHA. J. Bacteriol. 184:3992-1002.
24. Maehara, A., Y. Doi, T. Nishiyama, Y. Takagi, S. Ueda, H. Nakano, and T. Yamane. 2001. PhaR, a protein of unknown function conserved among short-chain-length polyhydroxyalkanoic acid-producing bacteria, is a DNA binding protein and represses Paracoccus denitrificans phaP expression in vitro. FEMS Microbiol. Lett. 200:9-15.
25. Maehara, A., S. Ueda, H. Nakano, and T. Yamane. 1999. Analyses of a polyhydroxyalkanoic acid granule-associated 16-kilodalton protein and its putative regulator in the pha locus of Paracoccus denitrificans. J. Bacteriol. 181:2914-2921.
26. McCool, G. J., and M. C. Cannon. 1999. Polyhydroxyalkanoate inclusion body-associated proteins and coding region in Bacillus megaterium. J. Bacteriol. 181:585-592.
27. Pettinari, M. J., L. Chaneton, G. Vazquez, A. Steinbüchel, and B. S. Méndeza. 2003. Insertion sequence-like elements associated with putative polyhydroxybutyrate regulatory genes in Azotobacter sp. FA8. Plasmid 50:36-44.
28. Pieper-Fürst, U., M. H. Madkour, F. Mayer, and A. Steinbüchel. 1995. Identification of the region of a 14-kilodalton protein of Rhodococcus ruber that is responsible for the binding of this phasin to polyhydroxyalkanoic acid granules. J. Bacteriol. 177:2513-2523.
29. Pieper-Fürst, U., M. H. Madkour, F. Mayer, and A. Steinbüchel. 1994. Purification and characterization of a 14-kilodalton protein that is bound to the surface of polyhydroxyalkanoic acid granules in Rhodococcus ruber. J. Bacteriol. 176:4328-4337.
30. Pötter, M., H. Müller, and A. Steinbüchel. 2005. Influence of homologous phasins (PhaP) on PHA accumulation and regulation of their expression by the transcriptional repressor PhaR in Ralstonia eutropha H16. Microbiology 151:825-833.
31. Pötter, M., H. Müller, F. Reinecke, R. Wieczorek, F. Fricke, B. Bowien, B. Friendrich, and A. Steinbüchel. 2004. The complex structure of polyhydroxybutyrate (PHB) granules: four orthologous and paralogous phasins occur in Ralstonia eutropha. Microbiology 150:2301-2311.
32. Pötter, M., M. H. Madkour, F. Mayer, and A. Steinbüchel. 2002. Regulation of phasin expression and polyhydroxyalkanoate (PHA) granule formation in Ralstonia eutropha H16. Microbiology 148:2413-2426.
33. Rigali, S., A. Derouaux, F. Giannotta, and J. Dusart. 2002. Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies. J. Biol. Chem. 227:12507-12515.
34. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
35. Sauerbrey, Z. 1959. Verwendung von Schwingquarzen zur Wägung dünner Schichten und zur Mikrowägung. Z. Physik. 155:206-222.
36. Slater, S., K. L. Houmiel, M. Tran, T. A. Mitsky, N. B. Taylor, S. R. Padgette, and K. J. Gruys. 1998. Multiple β-ketothiolases mediate poly(β-hydroxyalkanoate) copolymer synthesis in Ralstonia eutropha. J. Bacteriol. 180:1979-1987.
37. Steinbüchel, A., E. Hustede, M. Libergesell, U. Piper, A. Timm, and H. Valentin. 1992. Molecular basis for biosynthesis and accumulation of polyhydroxyalkanoic acids in bacteria. FEMS Microbiol. Rev. 9:217-230.
38. Steinbüchel, A., K. Aerts, W. Babel, C. Follner, M. Liebergesell, M. H. Madkour, F. Mayer, U. Pieper-Fürst, A. Pries, H. E. Valentin, and R. Wieczorek. 1995. Consideration on the structure and biochemistry of bacterial polyhydroxyalkanoic acid inclusions. Can. J. Microbiol. 41:94-105.
39. Sudesh, K., H. Abe, and Y. Doi. 2000. Synthesis, structure and properties of polyhydroxyalkanoates: biological polyesters. Prog. Polym. Sci. 25:1503-1555.
40. Taguchi, S., K. Kuwasako, A. Suenaga, M. Okada, and H. Momose. 2000. Functional mapping against Escherichia coli for the broad-spectrum antimicrobial peptide, thanatin, based on an in vivo monitoring assay system. J. Biochem. 128:745-754.
41. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
42. Tombolini, R., S. Povolo, A. Buson, A. Squartini, and M. P. Nuti. 1995. Poly-β-hydroxybutyrate (PHB) biosynthetic genes in Rhizobium meliloti 41. Microbiology 141:2553-2559.
43. Ueda, S., T. Yabutani, A. Maehara, and T. Yamane. 1996. Molecular analysis of the poly(3-hydroxyalkanoate) synthase gene from a methylotrophic bacterium, Paracoccus denitrificans. J. Bacteriol. 178:774-779.
44. Yabutani, T., A. Maehara, S. Ueda, and T. Yamane. 1995. Analysis of β-ketothiolase and acetoacetyl-CoA reductase genes of a methylotrophic bacterium, Paracoccus denitrificans. FEMS Microbiol. Lett. 133:85-90.
45. Yamane, T., X. F. Chen, and S. Ueda. 1996. Growth-associated production of poly(3-hydroxyvalerate) from n-pentanol by a methylotrophic bacterium, Paracoccus denitrificans. Appl. Environ. Microbiol. 62:380-384.
46. Yamane, T., X. F. Chen, and S. Ueda. 1996. Polyhydroxyalkanoate synthesis from alcohols during the growth of Paracoccus denitrificans. FEMS Microbiol. Lett. 135:207-211.
47. Yamashita, K., M. Yamada, K. Numata, and S. Taguchi. 2006. Nonspecific hydrophobic interactions of a repressor protein, PhaR, with poly[(R)-3-hydroxybutyrate] film studied with a quartz crystal microbalance. Biomacromolecules 8:2449-2454.
48. York, G. M., J. Stubbe, and A. J. Sinskey. 2002. The Ralstonia eutropha PhaR protein couples synthesis of the PhaP phasin to the presence of polyhydroxybutyrate production. J. Bacteriol. 184:59-66.
49. York, G. M., J. Stubbe, and A. J. Sinskey. 2001. New insight into the role of the PhaP phasin of Ralstonia eutropha in promoting synthesis of polyhydroxybutyrate. J. Bacteriol. 183:2394-2397.