Life in extreme environments: Single molecule force spectroscopy as a tool to explore proteins from extremophilic organisms

Biochemical Society Transactions

Volumn 43, Issue , 2015, Pages 179-185

  Tych, Katarzyna M ^a   Hoffmann, Toni ^a   Batchelor, Matthew ^a   Hughes, Megan L ^a   Kendrick, Katherine E ^a   Walsh, Danielle L ^a   Wilson, Michael ^a   Brockwell, David J ^a   Dougan, Lorna ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

Energy landscape; Extreme environments; Hyperthermophile; Mechanical unfolding; Polyprotein; Single molecule

Indexed keywords

PROTEIN;

ACIDOPHILE; ADAPTATION; ARCHAEON; ARTICLE; CONVOLVULACEAE; ENVIRONMENTAL FACTOR; ENVIRONMENTAL TEMPERATURE; GLACIER; HALOPHILE; HYDROGEN BOND; HYPERTHERMOPHILE; NONHUMAN; PACIFIC OCEAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ENGINEERING; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTEIN UNFOLDING; PSYCHROPHILE; ROOM TEMPERATURE; SINGLE MOLECULE FORCE SPECTROSCOPY; SPECTROSCOPY; SULFOLOBUS ACIDOCALDARIUS; THERMAL SPRING; THERMOSTABILITY; THERMOTOGA MARITIMA; CHEMISTRY; ENERGY METABOLISM; ENVIRONMENT; GENETICS; METABOLISM;

ADAPTATION, PHYSIOLOGICAL; ENERGY METABOLISM; ENVIRONMENT; PROTEIN STABILITY; PROTEINS; SPECTRUM ANALYSIS; SULFOLOBUS ACIDOCALDARIUS;

EID: 84934962002     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20140274     Document Type: Article

References (43)

1. Rothschild, L.J. and Mancinelli, R.L. (2001) Life in extreme environments. Nature 409, 1092-1101 CrossRef PubMed
2. Stroud, M. (2004) The biology of human survival: Life and death in extreme environments. Nature 431, 510-512 CrossRef
3. Schafer, G. (2004) Extremophilic archaea and bacteria -introduction. J. Bioenerg. Biomembr. 36, 3-4 CrossRef PubMed
4. Horikoshi, K. and Grant, W.D. (1998) Extremophiles: Microbial Life in Extreme Environments, Wiley
5. Nisbet, E.G. and Sleep, N.H. (2001) The habitat and nature of early life. Nature 409, 1083-1091 CrossRef PubMed
6. Elleuche, S., Schro, C., Sahm, K. and Antranikian, G. (2014) Extremozymes -biocatalysts with unique properties from extremophilic microorganisms. Curr. Opin. Biotech. 29, 116-123 CrossRef
7. Siddiqui, K.S. and Thomas, T. (2008) Protein Adaptation in Extremophiles, Nova BiomecialBooks, New York
8. Sterner, R. and Liebl, W. (2001) Thermophilic adaptation of proteins. Crit. Rev. Biochem. Mol. 36, 39-106 CrossRef
9. Brock, T.D. and Brock, M.L. (1968) Relationship between environmental temperature and optimum temperature of bacteria along a hot spring thermal gradient. J. Appl. Bacteriol. 31, 54-58 CrossRef
10. Brock, T.D., Brock, M.L., Bott, T.L. and Edwards, M.R. (1971) Microbial Life at 90 C -sulfur bacteria of boulder spring. J. Bacteriol. 107, 303-314 PubMed
11. Stetter, K.O. (2011) History of Discovery of Extremophiles, Springer, Tokyo
12. Majhi, M.C., Behera, A.K., Kulshreshtha, N.M., Mahmooduzafar, Kumar, R. and Kumar, A. (2013) ExtremeDB: A unified web repository of extremophilic archaea and bacteria. PLoS ONE 8, e63083 CrossRef PubMed
13. Cavicchioli, R., Siddiqui, K.S., Andrews, D. and Sowers, K.R. (2002) Low-temperature extremophiles and their applications. Curr. Opin. Biotech. 13, 253-261 CrossRef
14. Baker-Austin, C. and Dopson, M. (2007) Life in acid: PH homeostasis in acidophiles. Trends Microbiol 15, 165-171 CrossRef PubMed
15. Bowers, K.J. and Wiegel, J. (2011) Temperature and pH optima of extremely halophilic archaea: A mini-review. Extremophiles 15, 119-128 CrossRef PubMed
16. Das Sharma, S. and Das Sharma, P. (1995) Archaea: A Laboratory Manual -Halophiles, Cold Spring Harbor Laboratory Press, New York
17. Abe, F. and Horikoshi, K. (2001) The biotechnological potential of piezophiles. Trends Biotechnol 19, 102-108 CrossRef PubMed
18. Brock, T.D. and Freeze, H. (1969) Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophile. J. Bacteriol. 98, 289-297 PubMed
19. Saiki, R.K., Gelfand, D.H., Stoffel, S., Scharf, S.J., Higuchi, R., Horn, G.T., Mullis, K.B. and Erlich, H.A. (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA-polymerase. Science 239, 487-491 CrossRef PubMed
20. Margesin, R. and Feller, G. (2010) Biotechnological applications of psychrophiles. Environ. Technol. 31, 835-844 CrossRef PubMed
21. Perl, D., Welker, C., Schindler, T., Schroder, K., Marahiel, M.A., Jaenicke, R. and Schmid, F.X. (1998) Conservation of rapid two-state folding in mesophilic, thermophilic and hyperthermophilic cold shock proteins. Nat. Struct. Mol. Biol. 5, 229-235 CrossRef
22. Russell, R.J. M. and Taylor, G.L. (1995) Engineering thermostability -lessons from thermophilic proteins. Curr. Opin. Biotech. 6, 370-374 CrossRef
23. Bell, G.S., Russell, R.J. M., Connaris, H., Hough, D.W., Danson, M.J. and Taylor, G.L. (2002) Stepwise adaptations of citrate synthase to survival at life's extremes -from psychrophile to hyperthermophile. Eur. J. Biochem. 269, 6250-6260 CrossRef PubMed
24. Fraser, J.S., Clarkson, M.W., Degnan, S.C., Erion, R., Kern, D. and Alber, T. (2009) Hidden alternative structures of proline isomerase essential for catalysis. Nature 462, 669-U149 CrossRef PubMed
25. Nettels, D., Hoffmann, A. and Schuler, B. (2008) Unfolded protein and peptide dynamics investigated with single-molecule FRET and correlation spectroscopy from picoseconds to seconds. J. Phys. Chem. B 112, 6137-6146 CrossRef PubMed
26. Hoffmann, T. and Dougan, L. (2012) Single molecule force spectroscopy using polyproteins. Chem. Soc. Rev. 41, 4781-4796 CrossRef PubMed
27. Scholl, Z.N., Li, Q. and Marszalek, P.E. (2014) Single molecule mechanical manipulation for studying biological properties of proteins, DNA, and sugars. Wires Nanomed. Nanobi. 6, 211-229 CrossRef
28. Zoldak, G. and Rief, M. (2013) Force as a single molecule probe of multidimensional protein energy landscapes. Curr. Opin. Struct. Biol. 23, 48-57 CrossRef PubMed
29. Brockwell, D.J., Paci, E., Zinober, R.C., Beddard, G.S., Olmsted, P.D., Smith, D.A., Perham, R.N. and Radford, S.E. (2003) Pulling geometry defines the mechanical resistance of a beta-sheet protein. Nat. Struct. Biol. 10, 731-737 CrossRef PubMed
30. Carrion-Vazquez, M., Li, H., Lu, H., Marszalek, P.E., Oberhauser, A.F. and Fernandez, J.M. (2003) The mechanical stability of ubiquitin is linkage dependent. Nat. Struct. Mol. Biol. 10, 738-743 CrossRef
31. Dietz, H. and Rief, M. (2008) Elastic bond network model for protein unfolding mechanics. Phys. Rev. Lett. 100
32. Sadler, D.P., Petrik, E., Taniguchi, Y., Pullen, J.R., Kawakami, M., Radford, S.E. and Brockwell, D.J. (2009) Identification of a mechanical rheostat in the hydrophobic core of protein L. J. Mol. Biol. 393, 237-248 CrossRef PubMed
33. Ng, S.P., Billings, K.S., Ohashi, T., Allen, M.D., Best, R.B., Randles, L.G., Erickson, H.P. and Clarke, J. (2007) Designing an extracellular matrix protein with enhanced mechanical stability. Proc. Natl. Acad. Sci. U.S.A. 104, 9633-9637 CrossRef PubMed
34. Guzmá n, D.L., Randall, A., Baldi, P. and Guan, Z. (2010) Computational and single-molecule force studies of a macro domain protein reveal a key molecular determinant for mechanical stability. Proc. Natl. Acad. Sci. U.S.A. 107, 1989-1994 CrossRef PubMed
35. Sharma, D., Perisic, O., Peng, Q., Cao, Y., Lam, C., Lu, H. and Li, H.B. (2007) Single-molecule force spectroscopy reveals a mechanically stable protein fold and the rational tuning of its mechanical stability. Proc. Natl. Acad. Sci. U.S.A. 104, 9278-9283 CrossRef PubMed
36. Tych, K.M., Hoffmann, T., Brockwell, D.J. and Dougan, L. (2013) Single molecule force spectroscopy reveals the temperature-dependent robustness and malleability of a hyperthermophilic protein. Soft Matter 9, 9016-9025 CrossRef
37. Hoffmann, T., Tych, K.M., Brockwell, D.J. and Dougan, L. (2013) Single-molecule force spectroscopy identifies a small cold shock protein as being mechanically robust. J. Phys. Chem. B 117, 1819-1826 CrossRef PubMed
38. Horn, G., Hofweber, R., Kremer, W. and Kalbitzer, H. (2007) Structure and function of bacterial cold shock proteins. Cell Mol. Life Sci. 64, 1457-1470 CrossRef PubMed
39. Wassenberg, D., Welker, C. and Jaenicke, R. (1999) Thermodynamics of the unfolding of the cold-shock protein from Thermotoga maritima. J. Mol. Biol. 289, 187-193 CrossRef PubMed
40. Kremer, W., Schuler, B., Harrieder, S., Geyer, M., Gronwald, W., Welker, C., Jaenicke, R. and Kalbitzer, H.R. (2001) Solution NMR structure of the cold-shock protein from the hyperthermophilic bacterium Thermotoga maritima. Eur. J. Biochem. 268, 2527-2539 CrossRef PubMed
41. Fang, J., Mehlich, A., Koga, N., Huang, J.Q., Koga, R., Gao, X.Y., Hu, C.G., Jin, C., Rief, M., Kast, J. et al. (2013) Forced protein unfolding leads to highly elastic and tough protein hydrogels. Nat. Commun. 4, 1-10 PubMed
42. Li, H.B. and Cao, Y. (2010) Protein mechanics: From single molecules to functional biomaterials. Acc. Chem. Res. 43, 1331-1341 CrossRef PubMed
43. Lv, S., Dudek, D.M., Cao, Y., Balamurali, M.M., Gosline, J. and Li, H. (2010) Designed biomaterials to mimic the mechanical properties of muscles. Nature 465, 69-73 CrossRef PubMed