Widespread disulfide bonding in proteins from thermophilic archaea

Archaea

Volumn 2011, Issue , 2011, Pages

  Jorda, Julien ^a   Yeates, Todd O ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); CRENARCHAEOTA; EUKARYOTA; EURYARCHAEOTA;

ARCHAEAL PROTEIN; DISULFIDE;

ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CRENARCHAEOTA; EURYARCHAEOTA; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; PROTEIN STABILITY;

ARCHAEAL PROTEINS; COMPUTATIONAL BIOLOGY; CRENARCHAEOTA; DISULFIDES; EURYARCHAEOTA; MODELS, MOLECULAR; PROTEIN STABILITY;

EID: 81555199788     PISSN: 14723646     EISSN: None     Source Type: Journal    
DOI: 10.1155/2011/409156     Document Type: Article

References (54)

1. Stetter K. O., Hyperthermophiles in the history of life Philosophical Transactions of the Royal Society B 2006 361 1474 1837 1842 (Pubitemid 44580387)
2. Creighton T. E., Proteins: Structures and Molecular Properties 1992 W. H. Freeman
3. Jaenicke R., Bhm G., The stability of proteins in extreme environments Current Opinion in Structural Biology 1998 8 6 738 748 (Pubitemid 29004672)
4. Rees D. C., Adams M. W. W., Hyperthermophiles: taking the heat and loving it Structure 1995 3 3 251 254
5. Chakravarty S., Varadarajan R., Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study Biochemistry 2002 41 25 8152 8161 (Pubitemid 34655184)
6. Kumar S., Nussinov R., How do thermophilic proteins deal with heat? Cellular and Molecular Life Sciences 2001 58 9 1216 1233 (Pubitemid 32844095)
7. Petsko G. A., Structural basis of thermostability in hyperthermophilic proteins, or "there's more than one way to skin a cat" Methods in Enzymology 2001 334 469 478 (Pubitemid 32507290)
8. Vieille C., Zeikus G. J., Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability Microbiology and Molecular Biology Reviews 2001 65 1 1 43 (Pubitemid 32204286)
9. Chan M. K., Mukund S., Kletzin A., Adams M. W. W., Rees D. C., Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase Science 1995 267 5203 1463 1469
10. Jaenicke R., Protein stability and molecular adaptation to extreme conditions European Journal of Biochemistry 1991 202 3 715 728
11. Lieph R., Veloso F. A., Holmes D. S., Thermophiles like hot T Trends in Microbiology 2006 14 10 423 426 (Pubitemid 44375019)
12. Yip K. S. P., Britton K. L., Stillman T. J., Lebbink J., De Vos W. M., Robb F. T., Vetriani C., Maeder D., Rice D. W., Insights into the molecular basis of thermal stability from the analysis of ion-pair networks in the glutamate dehydrogenase family European Journal of Biochemistry 1998 255 2 336 346 (Pubitemid 28340241)
13. Hashimoto H., Inoue T., Nishioka M., Fujiwara S., Takagi M., Imanaka T., Kai Y., Hyperthermostable protein structure maintained by infra and inter-helix ion-pairs in archaeal O6-methylguanine-DNA methyltransferase Journal of Molecular Biology 1999 292 3 707 716 (Pubitemid 29457330)
14. Karshikoff A., Ladenstein R., Ion pairs and the thermotolerance of proteins from hyperthermophiles: a 'traffic rule' for hot roads Trends in Biochemical Sciences 2001 26 9 550 556 (Pubitemid 32823440)
15. Thompson M. J., Eisenberg D., Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability Journal of Molecular Biology 1999 290 2 595 604 (Pubitemid 29324842)
16. Mallick P., Boutz D. R., Eisenberg D., Yeates T. O., 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 2002 99 15 9679 9684 (Pubitemid 34831107)
17. Toth E. A., Worby C., Dixon J. E., Goedken E. R., Marqusee S., Yeates T. O., The crystal structure of adenylosuccinate lyase from Pyrobaculum aerophilum reveals an intracellular protein with three disulfide bonds Journal of Molecular Biology 2000 301 2 433 450
18. Beeby M., O'Connor B. D., Ryttersgaard C., Boutz D. R., Perry L. J., Yeates T. O., The genomics of disulfide bonding and protein stabilization in thermophiles. PLoS Biology 2005 3 9, article e309
19. Ladenstein R., Ren B., Reconsideration of an early dogma, saying "there is no evidence for disulfide bonds in proteins from archaea" Extremophiles 2008 12 1 29 38
20. Boutz D. R., Cascio D., Whitelegge J., Perry L. J., Yeates T. O., Discovery of a thermophilic protein complex stabilized by topologically interlinked chains Journal of Molecular Biology 2007 368 5 1332 1344 (Pubitemid 46621191)
21. Littlechild J. A., Guy J. E., Isupov M. N., Hyperthermophilic dehydrogenase enzymes Biochemical Society Transactions 2004 32 2 255 258 (Pubitemid 38582102)
22. Karlstrm M., Stokke R., Helene Steen I., Birkeland N. K., Ladenstein R., Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix: X-ray structure analysis of a ternary enzyme-substrate complex and thermal stability Journal of Molecular Biology 2005 345 3 559 577 (Pubitemid 39575925)
23. Guelorget A., Roovers M., Guérineau V., Barbey C., Li X., Golinelli-Pimpaneau B., Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase Nucleic Acids Research 2010 38 18 6206 6218
24. Kaper T., Talik B., Ettema T. J., Bos H., Van Der Maarel M. J. E. C., Dijkhuizen L., Amylomaltase of Pyrobaculum aerophilum IM2 produces thermoreversible starch gels Applied and Environmental Microbiology 2005 71 9 5098 5106 (Pubitemid 41338236)
25. Cacciapuoti G., Forte S., Moretti M. A., Brio A., Zappia V., Porcelli M., A novel hyperthermostable 5′-deoxy-5′-methylthioadenosine phosphorylase from the archaeon Sulfolobus solfataricus FEBS Journal 2005 272 8 1886 1899 (Pubitemid 40547246)
26. Cacciapuoti G., Moretti M. A., Forte S., Brio A., Camardella L., Zappia V., Porcelli M., Methylthioadenosine phosphorylase from the archaeon Pyrococcus furiosus: mechanism of the reaction and assignment of disulfide bonds European Journal of Biochemistry 2004 271 23-24 4834 4844 (Pubitemid 40065586)
27. Gilbert H. F., Molecular and cellular aspects of thiol-disulfide exchange Advances in enzymology and related areas of molecular biology 1990 63 69 172
28. Jakob U., Muse W., Eser M., Bardwell J. C. A., Chaperone activity with a redox switch Cell 1999 96 3 341 352 (Pubitemid 29077588)
29. Choi H. J., Kim S. J., Mukhopadhyay P., Cho S., Woo J. R., Storz G., Ryu S. E., Structural basis of the redox switch in the OxyR transcription factor Cell 2001 105 1 103 113 (Pubitemid 32323920)
30. Wouters M. A., Fan S. W., Haworth N. L., Disulfides as redox switches: from molecular mechanisms to functional significance Antioxidants and Redox Signaling 2010 12 1 53 91
31. Pedone E., Ren B., Ladenstein R., Rossi M., Bartolucci S., 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 2004 271 16 3437 3448 (Pubitemid 39120343)
32. Pedone E., Limauro D., Bartolucci S., The machinery for oxidative protein folding in thermophiles Antioxidants and Redox Signaling 2008 10 1 157 169 (Pubitemid 350115988)
33. Becerra A., Delaye L., Lazcano A., Orgel L. E., Protein disulfide oxidoreductases and the evolution of thermophily: was the last common ancestor a heat-loving microbe? Journal of Molecular Evolution 2007 65 3 296 303 (Pubitemid 47561684)
34. Ladenstein R., Ren B., Protein disulfides and protein disulfide oxidoreductases in hyperthermophiles FEBS Journal 2006 273 18 4170 4185 (Pubitemid 44326498)
35. Pedone E., D'Ambrosio K., De Simone G., Rossi M., Pedone C., Bartolucci S., 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 2006 356 1 155 164 (Pubitemid 43069734)
36. Bartolucci S., De Pascale D., Rossi M., Protein disulfide oxidoreductase from Pyrococcus furiosus: biochemical properties Methods in Enzymology 2001 334 62 73 (Pubitemid 32507264)
37. D'Ambrosio K., Pedone E., Langella E., De Simone G., Rossi M., Pedone C., Bartolucci S., A novel member of the protein disulfide oxidoreductase family from Aeropyrum pernix K1: structure, function and electrostatics Journal of Molecular Biology 2006 362 4 743 752 (Pubitemid 44332421)
38. Inskeep W. P., Rusch D. B., Jay Z. J., Herrgard M. J., Kozubal M. A., Richardson T. H., Macur R. E., Hamamura N., Jennings R., Fouke B. W., Reysenbach A. L., Roberto F., Young M., Schwartz A., Boyd E. S., Badger J. H., Mathur E. J., Ortmann A. C., Bateson M., Geesey G., Frazier M., Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function PloS one 2010 5 3, article e9773
39. Dutton R. J., Boyd D., Berkmen M., Beckwith J., 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 2008 105 33 11933 11938
40. Daniels R., Mellroth P., Bernsel A., Neiers F., Normark S., Von Heijne G., Henriques-Normark B., Disulfide bond formation and cysteine exclusion in gram-positive bacteria Journal of Biological Chemistry 2010 285 5 3300 3309
41. Iwasaki T., Iron-sulfur world in aerobic and hyperthermoacidophilic archaea sulfolobus Archaea 2010 2010 14
42. Aravind L., Tatusov R. L., Wolf Y. I., Walker D. R., Koonin E. V., Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles Trends in Genetics 1998 14 11 442 444 (Pubitemid 28508919)
43. Pearce F. G., Perugini M. A., McKerchar H. J., Gerrard J. A., Dihydrodipicolinate synthase from Thermotoga maritima Biochemical Journal 2006 400 2 359 366 (Pubitemid 44852048)
44. Toyooka T., Awai T., Kanai T., Imanaka T., Hori H., Stabilization of tRNA (m1G37) methyltransferase [TrmD]from Aquifex aeolicus by an intersubunit disulfide bond formation Genes to Cells 2008 13 8 807 816
45. Jarrell K. F., Extreme oxygen sensitivity in methanogenic archaebacteria Bioscience 1985 35 298 302
46. Larson E. T., Eilers B., Menon S., Reiter D., Ortmann A., Young M. J., Lawrence C. M., A winged-helix protein from sulfolobus turreted icosahedral virus points toward stabilizing disulfide bonds in the intracellular proteins of a hyperthermophilic virus Virology 2007 368 2 249 261 (Pubitemid 350016222)
47. Larson E. T., Eilers B. J., Reiter D., Ortmann A. C., Young M. J., Lawrence C. M., A new DNA binding protein highly conserved in diverse crenarchaeal viruses Virology 2007 363 2 387 396 (Pubitemid 46764946)
48. Menon S. K., Maaty W. S., Corn G. J., Kwok S. C., Eilers B. J., Kraft P., Gillitzer E., Young M. J., Bothner B., Lawrence C. M., Cysteine usage in Sulfolobus spindle-shaped virus 1 and extension to hyperthermophilic viruses in general Virology 2008 376 2 270 278
49. Littlechild J. A., Thermophilic archaeal enzymes and applications in biocatalysis Biochemical Society Transactions 2011 39 1 155 158
50. Moult J., Fidelis K., Kryshtafovych A., Rost B., Tramontano A., Critical assessment of methods of protein structure prediction-Round VIII Proteins: Structure, Function and Bioformatics 2009 77 9 1 4
51. Hiller K., Grote A., Scheer M., Mnch R., Jahn D., PrediSi: prediction of signal peptides and their cleavage positions Nucleic Acids Research 2004 32 W375 W379
52. Rose P. W., Beran B., Bi C., Bluhm W. F., Dimitropoulos D., Goodsell D. S., Prli A., Quesada M., Quinn G. B., Westbrook J. D., Young J., Yukich B., Zardecki C., Berman H. M., Bourne P. E., The RCSB Protein Data Bank: redesigned web site and web services Nucleic Acids Research 2011 39 supplement 1 D392 D401
53. Needleman S. B., Wunsch C. D., A general method applicable to the search for similarities in the amino acid sequence of two proteins Journal of Molecular Biology 1970 48 3 443 453
54. Letunic I., Bork P., Interactive Tree of Life v2: online annotation and display of phylogenetic trees made easy Nucleic Acids Research 2011 39 supplement 2 W475 W478