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Volume 2011 (2011), Article ID 409156, 9 pages
Widespread Disulfide Bonding in Proteins from Thermophilic Archaea
1UCLA-DOE Institute for Genomics and Proteomics, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
2Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
Received 17 May 2011; Accepted 16 July 2011
Academic Editor: M. Adams
Copyright © 2011 Julien Jorda and Todd O. Yeates. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- K. O. Stetter, “Hyperthermophiles in the history of life,” Philosophical Transactions of the Royal Society B, vol. 361, no. 1474, pp. 1837–1842, 2006.
- T. E. Creighton, Proteins: Structures and Molecular Properties, W. H. Freeman, 1992.
- R. Jaenicke and G. Böhm, “The stability of proteins in extreme environments,” Current Opinion in Structural Biology, vol. 8, no. 6, pp. 738–748, 1998.
- D. C. Rees and M. W. W. Adams, “Hyperthermophiles: taking the heat and loving it,” Structure, vol. 3, no. 3, pp. 251–254, 1995.
- S. Chakravarty and R. Varadarajan, “Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study,” Biochemistry, vol. 41, no. 25, pp. 8152–8161, 2002.
- S. Kumar and R. Nussinov, “How do thermophilic proteins deal with heat?” Cellular and Molecular Life Sciences, vol. 58, no. 9, pp. 1216–1233, 2001.
- G. A. Petsko, “Structural basis of thermostability in hyperthermophilic proteins, or "there's more than one way to skin a cat",” Methods in Enzymology, vol. 334, pp. 469–478, 2001.
- C. Vieille and G. J. Zeikus, “Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability,” Microbiology and Molecular Biology Reviews, vol. 65, no. 1, pp. 1–43, 2001.
- M. K. Chan, S. Mukund, A. Kletzin, M. W. W. Adams, and D. C. Rees, “Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase,” Science, vol. 267, no. 5203, pp. 1463–1469, 1995.
- R. Jaenicke, “Protein stability and molecular adaptation to extreme conditions,” European Journal of Biochemistry, vol. 202, no. 3, pp. 715–728, 1991.
- R. Lieph, F. A. Veloso, and D. S. Holmes, “Thermophiles like hot T,” Trends in Microbiology, vol. 14, no. 10, pp. 423–426, 2006.
- K. S. P. Yip, K. L. Britton, T. J. Stillman et al., “Insights into the molecular basis of thermal stability from the analysis of ion-pair networks in the glutamate dehydrogenase family,” European Journal of Biochemistry, vol. 255, no. 2, pp. 336–346, 1998.
- H. Hashimoto, T. Inoue, M. Nishioka et al., “Hyperthermostable protein structure maintained by infra and inter-helix ion-pairs in archaeal O6-methylguanine-DNA methyltransferase,” Journal of Molecular Biology, vol. 292, no. 3, pp. 707–716, 1999.
- A. Karshikoff and R. Ladenstein, “Ion pairs and the thermotolerance of proteins from hyperthermophiles: a 'traffic rule' for hot roads,” Trends in Biochemical Sciences, vol. 26, no. 9, pp. 550–556, 2001.
- M. J. Thompson and D. Eisenberg, “Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability,” Journal of Molecular Biology, vol. 290, no. 2, pp. 595–604, 1999.
- P. Mallick, D. R. Boutz, D. Eisenberg, and T. O. Yeates, “Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 15, pp. 9679–9684, 2002.
- E. A. Toth, C. Worby, J. E. Dixon, E. R. Goedken, S. Marqusee, and T. O. Yeates, “The crystal structure of adenylosuccinate lyase from Pyrobaculum aerophilum reveals an intracellular protein with three disulfide bonds,” Journal of Molecular Biology, vol. 301, no. 2, pp. 433–450, 2000.
- M. Beeby, B. D. O'Connor, C. Ryttersgaard, D. R. Boutz, L. J. Perry, and T. O. Yeates, “The genomics of disulfide bonding and protein stabilization in thermophiles.,” PLoS Biology, vol. 3, no. 9, article e309, 2005.
- R. Ladenstein and B. Ren, “Reconsideration of an early dogma, saying "there is no evidence for disulfide bonds in proteins from archaea",” Extremophiles, vol. 12, no. 1, pp. 29–38, 2008.
- D. R. Boutz, D. Cascio, J. Whitelegge, L. J. Perry, and T. O. Yeates, “Discovery of a thermophilic protein complex stabilized by topologically interlinked chains,” Journal of Molecular Biology, vol. 368, no. 5, pp. 1332–1344, 2007.
- J. A. Littlechild, J. E. Guy, and M. N. Isupov, “Hyperthermophilic dehydrogenase enzymes,” Biochemical Society Transactions, vol. 32, no. 2, pp. 255–258, 2004.
- M. Karlström, R. Stokke, I. Helene Steen, N. K. Birkeland, and R. Ladenstein, “Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix: X-ray structure analysis of a ternary enzyme-substrate complex and thermal stability,” Journal of Molecular Biology, vol. 345, no. 3, pp. 559–577, 2005.
- A. Guelorget, M. Roovers, V. Guérineau, C. Barbey, X. Li, and B. Golinelli-Pimpaneau, “Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase,” Nucleic Acids Research, vol. 38, no. 18, Article ID gkq381, pp. 6206–6218, 2010.
- T. Kaper, B. Talik, T. J. Ettema, H. Bos, M. J. E. C. Van Der Maarel, and L. Dijkhuizen, “Amylomaltase of Pyrobaculum aerophilum IM2 produces thermoreversible starch gels,” Applied and Environmental Microbiology, vol. 71, no. 9, pp. 5098–5106, 2005.
- G. Cacciapuoti, S. Forte, M. A. Moretti, A. Brio, V. Zappia, and M. Porcelli, “A novel hyperthermostable 5′-deoxy-5′-methylthioadenosine phosphorylase from the archaeon Sulfolobus solfataricus,” FEBS Journal, vol. 272, no. 8, pp. 1886–1899, 2005.
- G. Cacciapuoti, M. A. Moretti, S. Forte et al., “Methylthioadenosine phosphorylase from the archaeon Pyrococcus furiosus: mechanism of the reaction and assignment of disulfide bonds,” European Journal of Biochemistry, vol. 271, no. 23-24, pp. 4834–4844, 2004.
- H. F. Gilbert, “Molecular and cellular aspects of thiol-disulfide exchange,” Advances in enzymology and related areas of molecular biology, vol. 63, pp. 69–172, 1990.
- U. Jakob, W. Muse, M. Eser, and J. C. A. Bardwell, “Chaperone activity with a redox switch,” Cell, vol. 96, no. 3, pp. 341–352, 1999.
- H. J. Choi, S. J. Kim, P. Mukhopadhyay et al., “Structural basis of the redox switch in the OxyR transcription factor,” Cell, vol. 105, no. 1, pp. 103–113, 2001.
- M. A. Wouters, S. W. Fan, and N. L. Haworth, “Disulfides as redox switches: from molecular mechanisms to functional significance,” Antioxidants and Redox Signaling, vol. 12, no. 1, pp. 53–91, 2010.
- E. Pedone, B. Ren, R. Ladenstein, M. Rossi, and S. Bartolucci, “Functional properties of the protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus: a member of a novel protein family related to protein disulfide-isomerase,” European Journal of Biochemistry, vol. 271, no. 16, pp. 3437–3448, 2004.
- E. Pedone, D. Limauro, and S. Bartolucci, “The machinery for oxidative protein folding in thermophiles,” Antioxidants and Redox Signaling, vol. 10, no. 1, pp. 157–169, 2008.
- A. Becerra, L. Delaye, A. Lazcano, and L. E. Orgel, “Protein disulfide oxidoreductases and the evolution of thermophily: was the last common ancestor a heat-loving microbe?” Journal of Molecular Evolution, vol. 65, no. 3, pp. 296–303, 2007.
- R. Ladenstein and B. Ren, “Protein disulfides and protein disulfide oxidoreductases in hyperthermophiles,” FEBS Journal, vol. 273, no. 18, pp. 4170–4185, 2006.
- E. Pedone, K. D'Ambrosio, G. De Simone, M. Rossi, C. Pedone, and S. Bartolucci, “Insights on a new PDI-like family: structural and functional analysis of a protein disulfide oxidoreductase from the bacterium Aquifex aeolicus,” Journal of Molecular Biology, vol. 356, no. 1, pp. 155–164, 2006.
- S. Bartolucci, D. De Pascale, and M. Rossi, “Protein disulfide oxidoreductase from Pyrococcus furiosus: biochemical properties,” Methods in Enzymology, vol. 334, pp. 62–73, 2001.
- K. D'Ambrosio, E. Pedone, E. Langella et al., “A novel member of the protein disulfide oxidoreductase family from Aeropyrum pernix K1: structure, function and electrostatics,” Journal of Molecular Biology, vol. 362, no. 4, pp. 743–752, 2006.
- W. P. Inskeep, D. B. Rusch, Z. J. Jay et al., “Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function,” PloS one, vol. 5, no. 3, article e9773, 2010.
- R. J. Dutton, D. Boyd, M. Berkmen, and J. Beckwith, “Bacterial species exhibit diversity in their mechanisms and capacity for protein disulfide bond formation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 33, pp. 11933–11938, 2008.
- R. Daniels, P. Mellroth, A. Bernsel et al., “Disulfide bond formation and cysteine exclusion in gram-positive bacteria,” Journal of Biological Chemistry, vol. 285, no. 5, pp. 3300–3309, 2010.
- T. Iwasaki, “Iron-sulfur world in aerobic and hyperthermoacidophilic archaea sulfolobus,” Archaea, vol. 2010, Article ID 842639, 14 pages, 2010.
- L. Aravind, R. L. Tatusov, Y. I. Wolf, D. R. Walker, and E. V. Koonin, “Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles,” Trends in Genetics, vol. 14, no. 11, pp. 442–444, 1998.
- F. G. Pearce, M. A. Perugini, H. J. McKerchar, and J. A. Gerrard, “Dihydrodipicolinate synthase from Thermotoga maritima,” Biochemical Journal, vol. 400, no. 2, pp. 359–366, 2006.
- T. Toyooka, T. Awai, T. Kanai, T. Imanaka, and H. Hori, “Stabilization of tRNA (m1G37) methyltransferase [TrmD]from Aquifex aeolicus by an intersubunit disulfide bond formation,” Genes to Cells, vol. 13, no. 8, pp. 807–816, 2008.
- K. F. Jarrell, “Extreme oxygen sensitivity in methanogenic archaebacteria,” Bioscience, vol. 35, pp. 298–302, 1985.
- E. T. Larson, B. Eilers, S. Menon et al., “A winged-helix protein from sulfolobus turreted icosahedral virus points toward stabilizing disulfide bonds in the intracellular proteins of a hyperthermophilic virus,” Virology, vol. 368, no. 2, pp. 249–261, 2007.
- E. T. Larson, B. J. Eilers, D. Reiter, A. C. Ortmann, M. J. Young, and C. M. Lawrence, “A new DNA binding protein highly conserved in diverse crenarchaeal viruses,” Virology, vol. 363, no. 2, pp. 387–396, 2007.
- S. K. Menon, W. S. Maaty, G. J. Corn et al., “Cysteine usage in Sulfolobus spindle-shaped virus 1 and extension to hyperthermophilic viruses in general,” Virology, vol. 376, no. 2, pp. 270–278, 2008.
- J. A. Littlechild, “Thermophilic archaeal enzymes and applications in biocatalysis,” Biochemical Society Transactions, vol. 39, no. 1, pp. 155–158, 2011.
- J. Moult, K. Fidelis, A. Kryshtafovych, B. Rost, and A. Tramontano, “Critical assessment of methods of protein structure prediction-Round VIII,” Proteins: Structure, Function and Bioformatics, vol. 77, no. 9, pp. 1–4, 2009.
- K. Hiller, A. Grote, M. Scheer, R. Münch, and D. Jahn, “PrediSi: prediction of signal peptides and their cleavage positions,” Nucleic Acids Research, vol. 32, pp. W375–W379, 2004.
- P. W. Rose, B. Beran, C. Bi et al., “The RCSB Protein Data Bank: redesigned web site and web services,” Nucleic Acids Research, vol. 39, supplement 1, pp. D392–D401, 2011.
- S. B. Needleman and C. D. Wunsch, “A general method applicable to the search for similarities in the amino acid sequence of two proteins,” Journal of Molecular Biology, vol. 48, no. 3, pp. 443–453, 1970.
- I. Letunic and P. Bork, “Interactive Tree of Life v2: online annotation and display of phylogenetic trees made easy,” Nucleic Acids Research, vol. 39, supplement 2, pp. W475–W478, 2011.