Please use this identifier to cite or link to this item: http://hdl.handle.net/11455/22535
標題: 分析高鹽甲烷太古生物鹽逆境反應基因與分子伴護蛋白系統
Identification and analysis the salt stress related genes and molecular chaperone system in Methanohalophilus portucalensis
作者: 施朝仁
Shih, Chao-Jen
關鍵字: 鹽逆境適應
Salt-stress response
差異性表現反轉錄聚合酶連鎖反應
高鹽甲烷太古生物
分子伴護蛋白ClpB
廣泛逆境蛋白USPA
甲烷化反應
緊迫反應
太古生物
高鹽甲烷
逆境反應
Salt-stress adaptation
Differential display reverse transcription-PCR (DDRT-PCR)
Halophilic methanogen
Molecular chaperone ClpB
Universal stress protein USPA
Methanogenesis
Strigent response
Archaea
chaperone
Methanohalophilus
Stress response
出版社: 生命科學系所
引用: Chapter 1 1. Altschul, S. F., T. L. Madden, A. A. Schäffer, 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. Ammendola, R., F. Fiore, F. Esposito, G. Caserta, M. Mesuraca, T. Russo and F. Cimino. 1995. Differentially expressed mRNAs as a consequence of oxidative stress in intact cells. FEBS Lett. 371:209-213. 3. Andersen, G. R., P. Nissen and J. Nyborg. 2003. Elongation factors in protein biosynthesis. Trends Biochem. Sci. 28:434-441. 4. Balch, W. E., G. E. Fox, C. R. Woese and R. S. Wolfe. 1979. Methanogens revaluation of a biological group. Microbiol. Rev. 43:260-296. 5. Bidle, K. A. 2003. Differential expression of genes influenced by changing salinity using RNA arbitrarily primed PCR in the archaeal halophile Haloferax volcanii. Extremophiles 7:1-7. 6. Bohnert. H. J., D. E. Nelson and R. G. Jensen. 1995. Adaptations to environmental stress. Plant cell 7:1099-1111 7. Boone, D. R., I. M. Mathrani, Y. Liu, J. A. G. F. Menaia, R. A. Mah and J. E. Boone. 1993. Isolation and characterization of Methanohalophilus portucalensis sp. nov. and DNA reassociation study of the genus Methanohalophilus. Int. J. Syst. Evol. Microbiol. 43:430-437. 8. Brännvall, M., B. M. F. Peterson and L. A. Kirsebom. 2002. The residue immediately upstream of the RNase P cleavage site is a positive determinant. Biochimie. 84:693-703. 9. Brodersen, D. E. and P. Nissen. 2005. The social life of ribosomal proteins. FEBS J. 272:2098-2108. 10. Burke, S. A. and J. A. Krzycki. 1997. Reconstitution of monomethylamine:coenzyme M methyl transfer with a corrinoid protein and two methyltransferases purified from Methanosarcina barkeri. J. Biol. Chem. 272:16570-16577. 11. Burke, S. A., S. L. Lo and J. A. Krzycki. 1998. Clustered genes encoding the methyltransferases of methanogenesis from monomethylamine. J. Bacteriol. 180:3432-3440. 12. Chang, D. E., D. J. Smalley and T. Conway. 2002. Gene expression profiling of Escherichia coli growth transitions: an expanded stringent response model. Mol. Microbiol. 45:289-306. 13. Chia, J. S., Y. Y. Lee, P. T. Huang and J. Y. Chen. 2001. Identification of stress-responsive genes in Streptococcus mutants by differential display reverse transcription-PCR. Infect. Immun. 69:2493-2501. 14. Crawford, D. R., Y. Wang, G. P. Schools, J. Kochheiser and K. J. A. Davies. 1997. Down-regulation of mammalian mitochondrial RNAs during oxidative stress. Free Rad. Biol. Med. 22:551-559. 15. Csonka, L. N. 1989. Physiological and genetic responses of bacteria to osmotic stress. Microbiol. Rev. 53:121-147. 16. Deppenmeier, U., T. Lienard and G. Gottschalk. 1999. Novel reactions involved in energy conservation by methanogenic archaea. FEBS Lett. 451:291-297. 17. Diez, A., N. Gustavsson and T. Nyström. 2000. The universal stress protein A of Escherichia coli is required for resistance to DNA damaging agents and is regulated by a RecA/FtsK-dependent regulatory pathway. Mol. Microbiol. 36:1394-1503. 18. Donnelly, M. I., J. C. Escalante-Semerena, K. L. Jr Rinehart and R. S. Wolfe. 1985. Methenyl-tetrahydromethanopterin cyclohydrolase in cell extracts of Methanobacterium. Arch. Biochem. Biophys. 242:430-439. 19. Drennan, C. L., S. Huang, J. T. Drummond, R. G. Matthews and M. L. Ludwig. 1994. How a protein binds B12: a 3.0 Å X-ray structure of B12-binding domains of methionine synthase. Science 266:1669-1674. 20. Dzierzbicki, P., P. Koprowski, M. U. Fikus, E. Malc and Z. Ciesla. 2004. Repair of oxidative damage in mitochondrial DNA of Saccharomyces cerevisiae: involvement of the MSH1-dependent pathway. DNA Repair 3:403-411. 21. Earley, M. C. and G. F. Crouse. 1998. The role of mismatch repair in the prevention of base pair mutations in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 95:15487-15491. 22. Freist, W. and D. H. Gauss. 1995. Lysyl-tRNA synthetase. Biol. Chem. Hoppe Seyler 376:451-72. 23. Gardan, R., P. Cossart, The European Listeria Genome Consortium and J. Labadie. 2003. Identification of Listeria monocytogenes genes involved in salt and alkaline-pH tolerance. Appl. Environ. Microbiol. 69:3137-3143. 24. Grabarse, W., M. Vaupel, J. A. Vorholt, S. Shima, R. K. Thauer, A. Wittershagen, G. Bourenkov, H. D. Bartunik and U. Ermler. 1999. The crystal structure of methenyltetrahydro- methanopterin cyclohydrolase from the hyperthermophilic archaeon Methanopyrus kandleri. Structure 7:1257-1268. 25. Grant, W. D. 2004. Life at low water activity. Roy. Society 359:1249-1267. 26. Inagaki, Y., E. Susko and A. J. Roger. 2006. Recombination between elongation factor 1α genes from distantly related archaeal lineages. Proc. Natl. Acad. Sci. USA 103:4528-4533. 27. Jun, S. H., T. G. Kim and C. Ban. 2006. DNA mismatch repair system Classical and fresh roles. FEBS J. 273:1609-1619. 28. Kamekura, M. 1998. Diversity of extremely halophilic bacteria. Extremophiles 2:289-295. 29. Kempf, B. and E. Bremer. 1998. Uptake and synthesis of compatible solutes as microbial stress responses to high-osmolarity environment. Arch. Microbiol. 170:319-330. 30. Kültz, D. and D. Chakravarty. 2001. Hyperosmolarity in the form of elevated NaCl but not urea causes DNA damage in murine kidney. Proc. Natl. Acad. Sci. USA 98:1999-2004. 31. Lai, M. C., K. R. Sowers, D. E. Robertson, M. F. Roberts and R. P. Gunsalus. 1991. Distribution of compatible solutes in the halophilic methanogenic archaebacteria. J. Bacteriol. 173:5352-5358. 32. Lai, M. C. and R. P. Gunsalus. 1992. Glycine betaine and potassium ion are the major compatible solutes in the extremely halophilic methanogen Methanohalophilus strain Z7302. J. Bacteriol. 174:7474-7477. 33. Lai, M. C., D. R. Yang and M. J. Chuang. 1999. Regulatory factors associated with synthesis of the osmolyte glycine betaine in the Halophilic Methanoarchaeon Methanohalophilus portucalensis. Appl. Environ. Microbiol. 65:828-833. 34. Lai, M. C., T. Y. Hong and R. P. Gunsalus. 2000. Glycine Betaine Transport in the Obligate Halophilic Archaeon Methanohalophilus portucalensis. J. Bacteriol. 182:5020-5024. 35. Lai, M. C., S. C. Chen, C. M. Shu, M. S. Chiou, C. C. Wang, M. J. Chuang, T. Y. Hong, C. C. Liu, L. J. Lai and J. J. Hua. 2002. Methanocalculus taiwanensis sp. nov., isolated from an estuarine environment. Int. J. Syst. Evol. Microbiol. 52:1799-1806. 36. Lai, M. C., C. C. Lin, P. H. Yu, Y. F. Huang and S. C. Chen. 2004. Methanocalculus chunghsingensis sp. nov., isolated from an estuary and a marine fishpond in Taiwan. Int. J. Syst. Evol. Microbiol. 54:183-189. 37. Lai, M. C., C. C. Wang, M. J. Chuang, Y. C. Wu and Y. C. Lee. 2006. The Effects of Substrate and Potassium on Betaine Synthesizing Enzyme- Glycine Sarcosine Dimethylglycine N-Methyltransferase from a Halophilic Methanoarchaeon Methanohalophilus portucalensis. Res. Microbiol. 157:948-955. 38. Lee, S., M. E. Sowa, J. M. Choi and F. T. F. Tsai. 2004. The ClpB/Hsp104 molecular chaperone-a protein disaggregating machine. J. Struct. Biol. 146:99-105. 39. Lee, S. and F. T. F. Tsai. 2005. Molecular Chaperones in Protein Quality Control. J. Biochem. Mol. Biol. 38:259-265. 40. Marchler-Bauer, A. and S. H. Bryant. 2004. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 32:327-331. 41. Martin, D. D., R. A. Giulla and M. F. Roberts. 1999. Osmoadaptation in archaea. Appl. Environ. Microbiol. 65:1815-1825. 42. Mascher, T., J. D. Helmann and G. Unden. 2006. Stimulus perception in bacterial signal-transducing histidine kinases. Microbiol. Mol. Biol. Rev. 70:910-938. 43. Mathrani, I. M. and D. R. Boone. 1985. Isolation and Characterization of a Moderately Halophilic Methanogen from a Solar Saltern. Appl. Environ. Microbiol. 50:140-143. 44. Mazurek, A., M. Berardini and R. Fishel. 2002. Activation of human MutS homologs by 8-oxo-guanine DNA damage. J. Biol. Chem. 277:8260-8266. 45. Miura, S., W. Zou, M. Ueda and A. Tanaka. 2000. Screening of genes in isooctane tolerance in Saccharomyces cerevisiae by using mRNA differential display. Appl. Environ. Microbiol. 66:4883-4889. 46. Müller, V., R. Spanheimer and H. Santos. 2005. Stress response by solute accumulation in archaea. Curr. Opin. Microbiol. 8:729-736. 47. Murata, N. and D. A. Los. 2006. Histidine kinase Hik33 is an important participant in cold-signal transduction in cyanobacteria. Physiol. Plant. 126:17-27. 48. Nag, S., S. Das and K. Chaudhuri. 2005. In vivo induced clpB1 gene of Vibrio cholerae is involved in different stress responses and affects in vivo cholera toxin production. Biochem. Biophys. Res. Communic. 331:1365-1373. 49. Nagel, A. C., J. T. Fleming, G. S. Sayler and K. L. Beattie. 2001. Screening for ribosomal-based false positives following prokaryotic mRNA differential display. Biotechniques 30:988-996. 50. Ni, T. T., G. T. Marsischky and R. D. Kolodner. 1999. MSH2 and MSH6 are required for removal of adenine misincorporated opposite 8-oxo-guanine in S. cerevisiae. Mol. Cell 4:439-444. 51. Nyström, T. and F. C. Neidhardt. 1993. Isolation and properties of a mutant of Escherichia coli with an insertional inactivation of the uspA gene, which encodes a universal stress protein. J. Bacteriol. 175:3949-3956. 52. Nyström, T. and F. C. Neidhardt. 1994. Expression and role of the universal stress protein, UspA, of Escherichia coli during growth arrest. Mol. Microbiol. 11:537-544. 53. Nyström, T. and F. C. Neidhardt. 1996. Effects of overproducing the universal stress protein, UspA, in Escherichia coli K-12. J Bacteriol. 178:927-930. 54. Obmolova, G., C. Ban, P. Hsieh and W. Yang. 2000. Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA. Nature 407:703-710. 55. Paul, L., D. J. Ferguson, JR. and J. A. Krzycki. 2000. The trimethylamine methyltransferase gene and multiple dimethylamine methyltransferase genes of Methanosarcina barkeri contain in-frame and read-through Amber codons. J. Bacteriol. 182:2520-2529. 56. Persson, B. and P. Argos. 1994. Prediction of transmembrane segments in proteins utilising multiple sequence alignments. J. Mol. Biol. 237:182-192. 57. Queitsch, C., S. W. Hong, E. Vierling and S. Lindquist. 2000. Heat shock protein 101 plays a crucial role in thermotolerance in Arabidopsis. Plant Cell 12:479-492. 58. Rindi, L., N. Lari, M. G. Gil and C. Garzelli. 1998. Oligo(dT)-Primed Synthesis of cDNA by Reverse Transcriptase in Mycobacteria. Biochem. Biophys. Res. Commun. 248:216-218. 59. Rindi, L., N. Lari and C. Garzelli. 1999. Search for Genes Potentially Involved in Mycobacterium tuberculosis Virulence by mRNA Differential Display. Biochem. Biophys. Res. Commun. 258:94-101. 60. Rivera-Marrero, C. A., M. A. Burroughs, R. A. Masse, F. O. Vannberg, D. L. Leimbach, J. Roman and J. J. Murtagh. 1998. Identification of genes differentially expressed in Mycobacterium tuberculosis by differential display PCR. Microb. Pathog. 25:307-316. 61. Roberts, M. F. 2000. Osmoadaptation and osmoregulation in archaea. Front. Biosci. 5:796-812. 62. Roberts, M. F. 2004. Osmoadaptation and osmoregulation in archaea: update 2004. Front. Biosci. 9:1999-2019. 63. Roessner, C. A., H. J. Williams and A. I. Scott. 2005. Genetically engineered production of 1-desmethylcobyrinic acid, 1-desmethylcobyrinic acid a,c-diamide, and cobyrinic acid a,c-diamide in Escherichia coli implies a role for CbiD in C-1 methylation in the anaerobic pathway to cobalamin. J. Biol. Chem. 280:16748-16753. 64. Sambrook, J. and D. W. Russell. 2001. Molecular Cloning: A Laboratory Manual, 3rd ed, Cold Spring Harbor Laboratory, NY: Cold Spring Harbor Laboratory. 65. Sanchez, Y. and S. Lindquist. 1990. Hsp104 required for induced thermotolerance. Science 248:1112-1115. 66. Schlee, S. and J. Reinstein. 2002. The DnaK/ClpB chaperone system from Thermus thermophilus. Cell. Mol. Life. Sci. 59:1598-1606. 67. Shih, C. J. and M. C. Lai. 2007. Analysis of the AAA+ Chaperone ClpB gene and stress-response expression in the halophilic methanogenic archaeon- Methanohalophilus portucalensis. Microbiology (In press). 68. Sleator, R. D. and C. Hill. 2001. Bacterial osmoadaptation: the role of osmolytes in bacterial stress and virulence. FEMS Microbiol. Rev. 26:49-71. 69. Sowers, K. R. 1995. Techniques for monitoring Methanogen cell growth, In Archaea: a Laboratory Manual, vol.2, Methanogens pp.89-95. Edited by K. R. Sowers and H. T. Schreier. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory. 70. Squires, C. L., S. Pedersen, B. M. Ross and C. Squires. 1991. ClpB is the Escherichia coli heat shock protein F84.1. J. Bacteriol. 173:4254-4262. 71. Stanisławska-Sachadyn, A. and P. Sachadyn. 2005) MutS as a tool for mutation detection. Acta Biochim. Polon. 52:575-583. 72. Terada, T., O. Nureki, R. Ishitani, A. Ambrogelly, M. Ibba, D. Söll and S. Yokoyama. 2002. Functional convergence of two lysyl-tRNA synthetases with unrelated topologies. Nat. Struct. Biol. 9:257-262. 73. 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. 74. Tyagi, A. and A. Chandra. 2006. Isolation of stress responsive Psb A gene from rice (Oryza sativa l.) using differential display. Indian J. Biochem. Biophys. 43:244-246. 75. Wang, G., P. Alamuri, M. Z. Humayun, D. E. Taylor and R. J. Maier. 2005. The Helicobacter pylori MutS protein confers protection from oxidative DNA damage. Mol. Microbiol. 58:166-176. 76. Williams, S. B. and V. Stewart. 1999. Functional similarities among two-component sensors and methyl-accepting chemotaxis proteins suggest a role for linker region amphipathic helices in transmembrane signal transduction. Mol. Microbiol. 33:1093-1102. 77. Zarembinski, T. I., L. W. Hung, H. J. Mueller-Dieckmann, K. K. Kim, H. Yokota, R. Kim and S. H. Kim. 1998. Structure-based assignment of the biochemical function of a hypothetical protein: A test case of structural genomics. Proc. Natl. Acad. Sci. USA 95:15189-15193. Chapter 2 1. Albers, S.-V., van de Vossenberg, J. L. C. M., Driessen A. J. M. & Konings, W. N. (2000) Adaptations of the archaeal cell membrane to heat stress. Front. Biosci. 5, 813-820. 2. Balch, W. E., Fox, G. E., Woese, C. R. & Wolfe. R. S. (1979) Methanogens revaluation of a biological group. Microbiol. Rev. 43, 260-296. 3. Barnett, M. E., Zolkiewska, A. & Zolkiewski M. (2000) Structure and activity of ClpB from Escherichia coli: Role of the amino-and carboxyl terminal domains. J. Biol. Chem. 275, 37565-37571. 4. Ben-Zvi, A. P. & Goloubinoff, P. (2001) Mechanism of disaggregation and refolding of stable protein aggregates by molecular chaperone. J. Struct. Biol. 135, 84-93. 5. Boone, D. R., Mathrani, I. M., Liu, Y., Menaia, J. A. G. F., Mah, R. A. & Boone, J. E. (1993) Isolation and characterization of Methanohalophilus portucalensis sp. nov. and DNA reassociation study of the genus Methanohalophilus. Int. J. Syst. Evol. Microbiol. 43, 430-437. 6. Boonyaratanakornkit, B. B., Simpson, A. J., Whitehead, T. A., Fraser, C. M., El-Sayed, N. M. A. & Clark, D. S. (2005) Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock. Environ. Microbiol. 7, 789-797. 7. Cannio, R., Fiorentino, G., Morana, A., Rossi M. & Bartolucci, S. (2000) Oxygen: friend or foe? Archaeal superoxide dismutases in the protection of intra- and extracellular oxidative stress. Front. Biosci. 5, 768-779. 8. Celerin, M., Gilpin, A. A., Schisler, N. J., Ivanov, A. G., E. Miskiewicz, Krol, M. & Laudenbach, D. E. (1998) ClpB in a cyanobacterium: Predicted structure, phylogenetic relationships, and regulation by light and temperature. J. Bacteriol. 180, 5173-5182. 9. Conway de Macario, E., Maeder, D. L. & Macario, A. J. L. (2003) Breaking the mould: Archaea with all four chaperoning systems. Biochem. Biophys. Res. Commun. 301, 811-812. 10. Deppenmeier, U., Johann, A., Hartsch, T., Merkl, R., Schmitz, R. A., Martinez-Arias, R., Henne, A., Wiezer, A., Bäumer, S., Jacobi, C., Brüggemann, H., Lienard, T., Christmann, A., Bömeke, M., Steckel, S., Bhattacharyya, A., Lykidis A., Overbeek, R., Klenk, H.-P., Gunsalus, R. P., Fritz, H.-J. & Gottschalk, G. (2002) The genome of Methanosarcina mazei: Evidence for lateral gene transfer between bacteria and archaea. J. Mol. Microbiol. Biotechnol. 4, 453-461. 11. Diamant, S., Eliahu, N., Rosenthal, D. & Goloubinoff, P. (2001) Chemical chaperones regulate molecular chaperones in vitro and in cells under combined salt and heat stresses. J. Biol. Chem. 276, 39586-39591. 12. Diamant, S., Rosenthal, D., Azem, A., Eliahu, N., Ben-Zvi, A. P. & Goloubinoff, P. (2003) Dicarboxylic amino acids and glycine-betaine regulate chaperone-mediated protein-disaggregation under stress. Mol. Microbiol. 49, 401-410. 13. Dougan, D. A., Mogk, A., Zeth, K., Turgay, K., & Bukau, B. (2002) AAA+ proteins and substrate recognition, it all depends on their partner in crime. FEBS Lett. 529, 6-10. 14. Galagan, J. E., Nusbaum, C., Roy, A., Endrizzi, M. G., Macdonald, P., FitzHugh, W., Calvo, S., Engels, R., Smirnov, S., Atnoor, D., Brown, A., Allen, N., Naylor, J., Stange-Thomann, N., DeArellano, K., Johnson, R., Linton, L., McEwan, P., McKernan, K., Talamas, J., Tirrell, A., Ye, W., Zimmer, A., Barber, R. D., Cann, I., Graham, D. E., Grahame, D. A., Guss, A., Hedderich, M., Ingram-Smith, R. C., Kuettner, H. C., Krzycki, J. A., Leigh, J. A., Li, W., Liu, J., Mukhopadhyay, B., Reeve, J. N., Smith, K., Springer, T. A., Umayam, L. A., White, O., White, R. H., Conway de Macario, E., Ferry, J. G., Jarrell, K. F., Jing, H., Macario, A. J. L., Paulsen, I., Pritchett, M., Sowers, K. R., Swanson, R. V., Zinder, S. H., Lander, E., Metcalf, W. W. & Birren, B. (2002) The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 12, 532-542. 15. Jarrell, K. F., Faguy, D., Hebert, A. M. & Kalmokoff, M. L. (1992) A general method of isolating high molecular weight DNA from methanogenic archaea (archaebacteria). Can. J. Microbiol. 38, 65-68. 16. Johnson, J. L. (1985) DNA reassociation and DNA hybridization of bacterial nucleic acids. Methods Microbiol. 18, 33-74. 17. Kagawa, H. K., Osipiuk, J., Maltsev, N., Overbeek, R., Quaite-Randall, E., Joachimiak, A. & Trent, J. D. (1995) The 60 kDa heat shock proteins in the hyperthermophilic archaeon Sulfolobus shibatae. J. Mol. Biol. 253, 712-725. 18. Klunker, D., Haas, B., Hirtreiter, A., Figueiredo, L., Naylor, G D., Pfeifer, J., Müller, V., Deppenmeier, U., Gottschalk, G., Hartl, F. U. & Hayer-Hartl, M. (2003) Coexistence of Group I and Group II Chaperonins in the Archaeon Methanosarcina mazei. J. Biol. Chem. 278, 33256-33267. 19. Kumar, S., Tamura, K. & Nei, M. (2004) MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5, 150-163. 20. Lai, M.-C., Chen, S.-C., Shu, C.-M., Chiou, M.-S., Wang, C.-C., Chuang, M.-J., Hong, T.-Y., Liu, C.-C., Lai, L.-J. & Hua, J. J. (2002) Methanocalculus taiwanensis sp. nov., isolated from an estuarine environment. Int. J. Syst. Evol. Microbiol. 52, 1799-1806. 21. Lai, M.-C., Lin, C.-C., Yu, P.-H., Huang, Y.-F. & Chen, S.-C. (2004) Methanocalculus chunghsingensis sp. nov., isolated from an estuary and a marine fishpond in Taiwan. Int. J. Syst. Evol. Microbiol. 54, 183-189. 22. Lai, M.-C., Hong, T.-Y. & Gunsalus, R. P. (2000) Glycine betaine transport in halophilic methanogenic Archaea, Methanohalophilus portucalensis. J. Bacteriol. 182, 5020-5024. 23. Lai, M.-C., Yang, D.-R. & Cuang, M.-J. (1999) Regulatory factors associated with synthesis of the osmolyte glycine betaine in the Halophilic Methanoarchaeon Methanohalophilus portucalensis. Appl. Environ. Microbiol. 65, 828-833. 24. Lai, M.-C., Wang, C.-C., Chuang, M.-J., Wu, Y.-C. & Lee, Y.-C. (2006) The effects of substrate and potassium on betaine synthesizing enzyme- Glycine Sarcosine Dimethylglycine N-Methyltransferase from a Halophilic Methanoarchaeon Methanohalophilus portucalensis. Res. Microbiol. 157, 948-955. 25. Lai, M.-C., Sowers, K. R., Robertson, D. E., Roberts, M. F. & Gunsalus, R. P. (1991) Distribution of compatible solutes in the halophilic methanogenic archaebacteria. J. Bacteriol. 173, 5352-5358. 26. Laksanalamai, P., Whitehead, T. A. & Robb, F. T. (2004) Minimal protein-folding systems in hyperthermophilic archaea. Nature reviews. 2, 315-324. 27. Lee, S., Sowa, M. E., Choi, J.-M. & Tsai, F. T. F. (2004) The ClpB/Hsp104 molecular chaperone-a protein disaggregating machine. J. Struct. Biol. 146, 99-105. 28. Lee, S., Sowa, M. E., Watanabe, Y.-H., Sigler, P. B., Chiu W., Yoshida, M. & Tsai, F. T. F. (2003) The structure of ClpB: A molecular chaperone that rescues proteins from an aggregated state. Cell. 115, 229-240. 29. Lee., S. & Tsai, F. T. F. (2005) Molecular Chaperones in Protein Quality Control. J. Biochem. Mol. Biol. 38, 259-265. 30. Lupas, A. (1996) Coiled coils: new structures and new functions. Trends Biochem. Sci. 21, 375-382. 31. Macario, A. J. L., Lange, M., Ahring, B. K. & Conway de Macario, E. (1999) Stress genes and proteins in the Archaea. Microbiol. Mol. Biol. Reviews. 63, 923-967. 32. Macario, A. J. L., Malz, M. & Conway de Macario, E. (2004) Evolution of assisted protein folding: The distribution of the main chaperoning systems within the phylogenetic domain archaea. Front. Biosci. 9, 1318-1332. 33. Macario, A. J. L., Brocchieri, L., Shenoy, A. R. & Conway de Macario, E. (2006) Evolution of a protein-folding machine: genomic and evolutionary analyses reveal three lineages of the archaeal hsp70(dnaK) gene. J. Mol. Evol. 63, 74-86. 34. Martin, J., Gruber, M. & Lupas, A. N. (2004) Coiled coils meet the chaperone world. Trends Biochem. Sci. 29, 455-458. 35. Maruyama, T. & Furutani, M. (2000) Archaeal peptidyl prolyl cis-trans isomerases (PPIases). Front. Biosci. 5, 821-836. 36. Mathrani, I. M., & Boone, D. R. (1985) Isolation and Characterization of a Moderately Halophilic Methanogen from a Solar Saltern. Appl. Environ. Microbiol. 50, 140-143. 37. Neuwald, A. F., Aravind, L., Spouge, J. L. & Koonin, E. V. (1999) AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res. 9, 27-43. 38. Ogura, T. & Wilkinson, A. J. (2001) AAA+ superfamily ATPases: Common structure- diverse function. Genes Cells 6, 575-597. 39. Osipiuk, J. & Joachimiak, A. (1997) Cloning, sequencing, and expression of dnaK-operon proteins from the thermophilic bacterium Thermus thermophilus. Biochim. Biophys. Acta. 1353, 253-265. 40. Quaite-Randall, E., Trent, J. D., Josephs, R. & Joachimiak, A. (1995) Conformational cycle of the archaeosome, a TCP1-like chaperonin from Sulfolobus shibatae. J. Biol. Chem. 270, 28818-28823. 41. Queitsch, C., Hong, S. W., Vierling, E. & Lindquist, S. (2000) Heat shock protein 101 plays a crucial role in thermotolerance in Arabidopsis. Plant Cell 12, 479-492. 42. Roberts, M. F. (2000) Osmoadaptation and osmoregulation in Archaea. Front. Biosci. 5, 796-812. 43. Sambrook, J. & Russell, D. W. (2001) Molecular Cloning: A Laboratory Manual, 3rd ed, Cold Spring Harbor Laboratory, NY: Cold Spring Harbor Laboratory. 44. Sanchez, Y. & Lindquist, S. (1990) Hsp104 required for induced thermotolerance. Science 248, 1112-1115. 45. Saunders, N. F. W., Thomas, T., Curmi, P. M. G., Mattick, J. S., Kuczek, E., Slade, R., Davis, J., Franzmann, P. D., Boone, D., Rusterholtz, K. Feldman, R., Gates, C., Bench, S., Sowers, K., Kadner, K., Aerts, A., Dehal, P., Detter, C., Glavina, T., Lucas, S., Richardson, P., Larimer, F., Hauser, L., Land M. & Cavicchioli. R. (2003) Mechanisms of thermal adaptation revealed from the genomes of the antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res. 13, 1580-1588. 46. Scandurra, R., Consalvi, V., Chiaraluce, R., Politi, L. & Engel, P. C. (2000) Protein stability in extremophilic archaea. Front. Biosci. 5, 787-795. 47. Schirmer, E. C., Glover, J. R., Singer, M. A. & Lindquist, S. (1996) HSP100/Clp proteins: a common mechanism explains diverse functions. Trends Biochem. Sci. 21, 289-296. 48. Schlieker, C., Weibezahn, J., Patzelt, H., Tessarz, P., Strub, C., Zeth, K., Erbse, A., Schneider-Mergener, J., Chin, J. W., Schultz, P. G. & Mogk, A. (2004) Substrate recognition by the AAA+ chaperone ClpB. Nature Struct. Mol. Biol. 11, 607-615. 49. Singh, S. K., Rozycki, J., Ortega, J., Ishikawa, T., Lo, J. , Steven, A. C. & Maurizi, M. R. (2001) Functional domains of the ClpA and ClpX molecular chaperones identified by limited proteolysis and deletion analysis. J. Biol. Chem. 276, 29420-29429. 50. Singh, S. K., Grimaud, R., Hoskins, J. R., Wickner, S. & Maurizi, M. R. (2000) Unfolding and internalization of proteins by ATP-dependent protease ClpXP and ClpAP. Proc. Natl. Acad. Sci. USA. 97, 8898-8903. 51. Squires, C. L., Pedersen, S., Ross, B. M. & Squires, C. (1991) ClpB is the Escherichia coli heat shock protein F84.1. J. Bacteriol. 173, 4254-4262. 52. Squires, C. & Squires, C. L. (1992) The Clp proteins: Proteolysis regulators or molecular chaperones? J. Bacteriol. 174, 1081-1085. 53. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (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. 54. Waldmann, T., Lupas, A. N., Kellermann, J., Peters, J. & Baumeister, W. (1995) Primary structure of the thermosome from Thermoplasma acidophilum. Biol. Chem. Hoppe Seyler 376, 119-126. 55. Woo, K. M., Kim, K. I., Goldberg, A. L., Ha, D. B. & Chung, C. H. (1992) The heat-shock protein ClpB in Escherichia coli is a protein-activated ATPase. J. Biol. Chem. 267, 20429-20434. 56. Zolkiewski, M. (1999) ClpB cooperates with DnaK, DnaJ, and GrpE in suppressing protein aggregation. A novel multi-chaperone system from Escherichia coli. J. Biol. Chem. 274, 28083-28086. Chapter 3 1. Babst, M., T. K. Sato, L. M. Banta and S. D. Emr. 1997. Endosomal transport function in yeast requires a novel AAA-type ATPase, Vps4p. EMBO J. 16:1820-1831. 2. Barnett, M. E. and M. Zolkiewski. 2002. Site-directed mutagenesis of conserved charged amino acid residues in ClpB from Escherichia coli. Biochem. 2002:11277-11283. 3. Barnett, M. E., A. Zolkiewska and M. Zolkiewski. 2000. Structure and activity of ClpB from Escherichia coli: Role of the amino- and carboxylterminal domains. J. Biol. Chem. 275:37565-37571. 4. Barnett, M. E., M. Nagy, S. Kedzierska and M. Zolkiewski. 2005. The amino-terminal domain of ClpB supports binding to strongly aggregated proteins. J. Biol. Chem. 280:34940-34945. 5. Dougan, D. A., A. Mogk, K. Zeth, K. Turgay and B. Bukau. 2002. AAA+ proteins and substrate recognition, it all depends on their partner in crime. FEBS Lett. 529:6-10. 6. Hess, H. H. and J. E. Derr. 1975. Assay of inorganic and organic phosphorus in the 0.1-5 nanomole range. Anal. Biochem. 63:607-613. 7. Lanzetta, P. A., L. J. Alvarez, P. S. Reinach and O. A. Candia. 1979. An improved assay for nanomole amounts of inorganic phosphate. Anal. Biochem. 100:95-97. 8. Lee, S., M. E. Sowa, J.-M. Choi and F. F. T. Tsai. 2004. The ClpB/Hsp104 molecular chaperone-a protein disaggregating machine. J. Struct. Biol. 146:99-105. 9. Lee, S., M. E. Sowa, Y.-H. Watanabe, P. B. Sigler, W. Chiu, M. Yoshida and F. T. F. Tsai. 2003. The structure of ClpB: A molecular chaperone that rescues proteins from an aggregated state. Cell. 115:229-240. 10. Mogk, A., T. Tomoyasu, P. Goloubinoff, S. Rüdiger, D. Röder, H. Langen and B. Bukau. 1999. Identification of thermolabile Escherichia coli proteins: prevention and reversion of aggregation by DnaK and ClpB. EMBO J. 18:6934-6949. 11. Mogk, A., C. Schlieker, C. Strub, W. Rist, J. Weibezahn and B. Bukau. 2003. Roles of individual domains and conserved motifs of the AAA+ chaperone ClpB in oligomerization, ATP hydrolysis, and chaperone activity. J. Biol. Chem. 278:17615-17624. 12. Parsell, D. A., A. S. Kowal, M. A. Singer, S. Lindquist. 1994. Protein disaggregation mediated by heat-shock protein HSP104. Nature. 372:475-478. 13. Peters, J. M., M. J. Walsh and W. W. Franke. 1990. An abundant and ubiquitous homo-oligomeric ring-shaped ATPase particle related to the putative vesicle fusion proteins Sec18p and NSF. EMBO J. 9:1757-1767. 14. Queitsch, C., S. W. Hong, E. Vierling and S. Lindquist. 2000. Heat shock protein 101 plays a crucial role in thermotolerance in Arabidopsis. Plant Cell. 12:479-492. 15. Sambrook, J. and D. W. Russell. 2001. Molecular Cloning: A Laboratory Manual, 3rd ed, Cold Spring Harbor Laboratory, NY: Cold Spring Harbor Laboratory. 16. Sanchez, Y. and S. Lindquist, S. 1990. Hsp104 required for induced thermotolerance. Science. 248:1112-1115. 17. Schirmer, E. C., J. R. Glover, M. A. Singer and S. Lindquist. 1996. HSP100/Clp proteins: a common mechanism explains diverse functions. Trends Biochem. Sci. 21:289-296. 18. Shih, C. J. and M. C. Lai. 2007. Analysis of the AAA+ Chaperone ClpB gene and stress-response expression in the halophilic methanogenic archaeon- Methanohalophilus portucalensis. Microbiology. 153:2572-2583. 19. Tek, V. and M. Zolkiewski. 2002. Stability and interactions of the amino-terminal domain of ClpB from Escherichia coli. Protein Sci. 11:1192-1198. 20. Tomoyasu, T., A. Mogk, H. Langen, P. Goloubinnoff and B. Bukau. 2001. Genetic dissection of the roles of chaperones and proteases in protein folding and degradation in the Escherichia coli cytosol. Mol. Microbiol. 40:397-413. 21. Watanabe, Y.-H., M. Takano and M. Yoshida. 2005. ATP binding to nucleotide binding domain (NBD) 1 of the ClpB chaperone induces motion of the long coiled-coil, stabilizes the hexamer, and activates NBD2. J. Biol. Chem. 280:24562-24567. 22. Whiteheart, S. W., K. Rossnagel, S. A. Buhrow, M. Brunner, R. Jaenicke and J. E. Rothman. 1994. N-ethylmaleimide-sensitive fusion protein: a trimeric ATPase whose hydrolysis of ATP is required for membrane fusion. J. Cell Biol. 126:945-954. 23. Zolkiewski, M. 1999. ClpB cooperates with DnaK, DnaJ, and GrpE in suppressing protein aggregation. J. Biol. Chem. 274:28083-28086. Chapter 4 1. Altschul, S. F., T. L. Madden, A. A. Schäffer, 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. Braig, K., Z. Otwinowski, R. Hegde, D. C. Boisvert, A. Joachimiak, A. L. Horwich and P. B. Sigler. 1994. The crystal structure of the bacterial chaperonin GroEL at 2.8 Å. Nature. 371:578-586. 3. Fenton, W. A., Y. Kashi, K. Furtak and A. L. Horwich. 1994. Residues in chaperonin GroEL required for polypeptide binding and release. Nature. 371:614-619. 4. Galagan, J. E., C. Nusbaum, A. Roy, M. G. Endrizzi, P. Macdonald, W. FitzHugh, S. Calvo, R. Engels, S. Smirnov, D. Atnoor, A. Brown, N. Allen, J. Naylor, N. Stange-Thomann, K. DeArellano, R. Johnson, L. Linton, P. McEwan, K. McKernan, J. Talamas, A. Tirrell, W. Ye, A. Zimmer, R. D. Barber, I. Cann, D. E. Graham, D. A. Grahame, A. Guss, M. Hedderich, R. C. Ingram-Smith, H. C. Kuettner, J. A. Krzycki, J. A. Leigh, W. Li, J. Liu, B. Mukhopadhyay, J. N. Reeve, K. Smith, T. A. Springer, L. A. Umayam, O. White, R. H. White, E. Conway de Macario, J. G. Ferry, K. F. Jarrell, H. Jing, A. J. L. Macario, I. Paulsen, M. Pritchett, K. R. Sowers, R. V. Swanson, S. H. Zinder, E. Lander, W. W. Metcalf and B. Birren. 2002. The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 12:532-542. 5. Hartl, F. U. and M. Hayer-Hartl. 2002. Molecular chaperones in the cytosol: from nascent chain to fold protein. Science 295:1852-1858. 6. Hunt, J. F., A. J. Weaver, S. J. Landry, L. Gierasch and J. Beisenhofer. 1996. The crystal structure of GroES co-chaperonin at 2.8 Å resolution. Nature 379:37-45. 7. Koike-Takeshita, A., T Shimamura, K. Yokoyama, M. Yoshida and H. Taguchi. 2006. Leu309 plays a critical role in the encapsulation of substrate protein into the internal cavity of GroEL. J. Biol. Chem. 8. Kumar, S., K. Tamura and M. Nei. 2004. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief. Bioinform. 5:150-163. 9. Lai, M.-C., C.-C. Lin, P.-H. Yu, Y.-F. Huang and S.-C. Chen. 2004. Methanocalculus chunghsingensis sp. nov., isolated from an estuary and a marine fishpond in Taiwan. Int. J. Syst. Evol. Microbiol. 54:183-189. 10. Lund, P. A., A. T. Large and G. Kapatai. 2003. The chaperonins: perspectiv
摘要: 高鹽甲烷太古生物Methanohalophilus portucalensis FDF1能生長在胞外鹽濃度1.2 M-2.9 M的環境中,並以methanol及trimethylamine做為甲烷反應的基質。為了克服高鹽環境滲透壓力的波動,細胞能運送betaine或自體生合成betaine、β-glutamine、以及Nε-acetyl-β-lysine做為相容質。以55組引子進行差異性表現逆轉錄聚合酶連鎖反應,用以比較細胞在高鹽逆境與低鹽逆境下基因表現的差異性。結果共偵測到14個在高鹽或低鹽逆境表現具差異的基因並完成選殖與定序。其中幾個基因與甲烷菌特有的甲烷化反應基因相關,分別是膜蛋白MttP (SU11312),cobalamin生合成蛋白 (SU34312),methenyl-H4MPT cyclohydrolase (SD44094) 以及monomethylamine 甲基轉移酶 (SU26311)。在高鹽逆境下有鑑別出一個與訊息傳遞有關的histidine kinase (SU37311)。另外有三個已知的逆境反應基因也在此實驗中被偵測到,包括DNA 修復蛋白 Muts (SU25311),universal stress protein UspA (SD38092) 以及分子伴護蛋白系統的ClpB (SU12312)。從轉錄分析發現,能量代謝基因會受瞬間高鹽逆境而降低轉錄量。最值得一提的是,核糖體蛋白基因 (SU37311)、lysyl tRNA合成酶 (SD44093)、nitrite及sulfite還原酶以及translation elongation factor 1 alpha (SD17092) 則是第一次發現與鹽逆境反應有關。 ClpB和GroES及GroEL都屬於分子伴護蛋白系統,能促使蛋白進行去凝集化以及重新摺疊。此論文中我們提出了Methanohalophilus portucalensis的ClpB、GroES及GroEL基因。Methanohalophilus portucalensis ClpB基因序列全長2610 bp及其上游的GroEL (1611 bp) 與GroES (276 bp) 基因是利用inverse PCR及南方墨點法所得並完成定序。ClpB預測的多肽鏈包含869個胺基酸並含有一個會形成coiled coil的中間區域及兩個ATP結合區 (NBD1和NBD2)。NBD1有一個Walker A及兩個Walker B motif而NBD1則只有各一個Walker motif。在ClpB的N端則有兩個重複的Clp amino-terminal domain motifs (ClpN)。GroES和GroEL的多肽鏈分別為91及536個胺基酸。根據初步的系統演化分析則可發現MpClpB與革蘭氏陽性菌的ClpB演化距離較為接近而太古生物的GroES與GroEL則是自成一群且與細菌的該蛋白演化距離較遠。以北方墨點法分析發現clpB在瞬間高鹽逆境 (NaCL從2.1 M提高至3.1 M NaCl) 及低鹽逆境 (NaCl從2.1 M降至0.9 M) 的轉錄量均會提升約1.5倍。ClpB與GroEL/ES基因的轉錄量都會隨溫度上升 (37°C-55°C)而提升。在熱逆境下添加1 mM的betaine則會降低clpB的轉錄量。總結來說,本論文為第一次鑑別並分析高鹽甲烷太古生物與溫度、鹽濃度及相容質betaine波動反應相關的AAA+ chaperone ClpB基因。
Methanohalophilus portucalensis FDF1, a member of the halophilic genus of methanoarchaea, can grow over a range of external NaCl concentrations from 1.2 to 2.9 M and utilize methanol and trimethylamine as substrates for methanogenesis. To encounter the changing osmotic stress in hypersaline environment, cell could transport betaine or de novo synthesize betaine, β-glutamine, and Nε-acetyl-β-lysine as compatible solutes. Differential gene expression in response to long term hyper-salt stress (3.1 M NaCl) and hypo-salt stress (0.9 M NaCl) were analyzed and compared by differential display reverse transcription-PCR with fifty five primer sets. Fourteen differentially expressed genes respond to long term hyper-salt stress or hypo-salt stress were detected, cloned and sequenced. Several of differentially expressed genes were related to the unique energy-acquiring methanogenesis of methanogen as transmembrane protein MttP (SU11312), cobalamin biosynthesis protein (SU24312), methenyl-H4MPT cyclohydrolase (SD44094) and monomethylamine methyltransferase (SU26311). One signal transduction histidine kinase (SU12317) was identified from hyper-salt stress culture. Moreover, three known stress responsive gene homologues: the DNA mismatch repair protein Muts (SU25311), the universal stress protein UspA (SD38092), and the member of protein-disaggregating multichaperone system ClpB (SU12312) were also detected. The transcript analysis of the immediately expression indicated the energy metabolism was arrested during hyper-salt shock while the chaperone clpB gene was stimulated in both hypo and hyper salt shock. Notably, genes for ribosomal proteins (SU37311), lysyl tRNA synthetase (SD44093), nitrite and sulfite reductase (SD18092) and translation elongation factor 1 alpha (SD17092) were the first time to identified associated with salt stress. ClpB, GrpEL and GroES promote protein disaggregation and refolding and belong to the molecular chaperone system. Here, we describe a new ClpB gene and the group I chaperonin GroEL/ES genes from the halophilic methanoarchaeon Methanohalophilus portucalensis (Mp). The complete clpB sequence (2610 nt) and its up stream genes encoding the type I chaperonin GroEL/ES (1611 bp/276 bp) were obtained through the inverse PCR, southern hybridization, and sequencing. The predicted polypeptide of ClpB contains 869 amino acids and posses a long central domain, a predicted distinctly discontinuous coiled-coil motif separating two ATP-binding sites (NBD1 and NBD2). NBD1 has a single Walker A and two Walker B motifs and NBD2 has only one of each Walker motifs. Two repeated Clp amino-terminal domain motifs (ClpN) were identified in ClpB. The predicted polypeptide of GroES and GroEL contain 91 and 536 amino acids, respectively. The predicted mobile loop in GroES and the putative ATP-Mg2+ binding domains, GxxLE region in GroEL were identified. Preliminary phylogenetic analysis clustered MpClpB with the low G+C gram-positive bacteria while the archaeal GroES and GroEL formed a distinguish group distant from bacterial ones. The stress response analysis of clpB by Northern blot showed up to 1.5 fold increased transcriptional level in response to both salt upshock (from 2.1 M NaCl to 3.1 M NaCl) and downshock (from 2.1 M NaCl to 0.9 M NaCl). Both clpB and groEL/ES transcript levels increased while temperature shifted from 37°C to 55°C. Under heat stress clpB transcription was repressed with the addition of osmolyte betaine (1 mM). In conclusion, a novel AAA+ chaperone ClpB gene that responded to the fluctuation of temperature, salt concentrations, and osmolyte betaine from a halophilic methanogen was identified and analyzed for the first time.
URI: http://hdl.handle.net/11455/22535
其他識別: U0005-1708200714361000
文章連結: http://www.airitilibrary.com/Publication/alDetailedMesh1?DocID=U0005-1708200714361000
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