Abstract
The salt-dependent stability of recombinant dimeric isocitrate dehydrogenase [ICDH; isocitrate: NADP oxidoreductase (decarboxylating), EC 1.1.1.42] from the halophilic archaeon Haloferax volcanii (Hv) was investigated in various conditions. Hv ICDH dissociation/deactivation was measured to probe the respective effect of anions and cations on stability. Surprisingly, enzyme stability was found to be mainly sensitive to cations and very little (or not) sensitive to anions. Divalent cations induced a strong shift of the active/inactive transition towards low salt concentration. A high resistance of Hv ICDH to chemical denaturation was also found. The data were analysed and are discussed in the framework of the solvation stability model for halophilic proteins.
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Akoev V, Gogol EP, Barnett ME, Zolkiewski M (2004) Nucleotide-induced switch in oligomerization of the AAA+ATPase ClpB. Protein Sci 13:567–574
Bell GS, Russell RJM, Connaris H, Hough DW, Danson MJ, Taylor GL (2002) Stepwise adaptations of citrate synthase to survival at life’s extremes. From psychrophile to hyperthermophile. Eur J Biochem 269:6250–6260
Bieger B, Essen L-O, Oesterhelt D (2003) Crystal structure of halophilic dodecin. A novel, dodecameric flavin binding protein from Halobacterium salinarum. Structure 11:375–385
Bonete MJ, Perez-Pomares F, Diaz S, Ferrer J, Oren A (2003) Occurrence of two different glutamate dehydrogenase activities in the halophilic bacterium Salinibacter ruber. FEMS Microbiol Lett 226:181–186
Bonneté F, Madern D, Zaccai G (1994) Stability against denaturation mechanisms in halophilic malate dehydrogenase “adapt” to solvent conditions. J Mol Biol 244:436–447
Camacho ML, Brown RA, Bonete MJ, Danson MJ, Hough DW (1995) Isocitrate dehydrogenases from Haloferax volcanii and Sulfolobus solfataricus: enzyme purification, characterisation and N-terminal sequence. FEMS Microbiol Lett 134:85–90
Camacho M, Rodriguez-Arnedo A, Bonete MJ (2002) NADP-dependent isocitrate dehydrogenase from the halophilic archaeon Haloferax volcanii: cloning, sequence determination and overexpression in Escherichia coli. FEMS Microbiol Lett 209:155–160
Collins KD (1997) Charge density-dependent strength of hydration and biological structure. Biophys J 72:65–76
Costenaro L, Zaccai G, Ebel C (2002) Link between protein–solvent and weak protein–protein interactions gives insight into halophilic adaptation. Biochemistry 41:13245–13252
Dill KA (1990) Dominant forces in protein folding. Biochemistry 29:7133–7155
Dym O, Mevarech M, Sussman JL (1995) Structural features that stabilize halophilic malate dehydrogenase from an archaebacterium. Science 267:1344–1346
Ebel C, Faou P, Franzetti B, Kernel B, Madern D, Pascu M, Pfister C, Richard SB, Zaccai G (1999a) Molecular interactions in extreme halophiles. The solvation–stabilisation hypothesis for halophilic proteins. In: Oren A (ed) Microbiology and biogeochemistry of hypersaline environments. CRC, Boca Raton, pp 227–237
Ebel C, Faou P, Kernel B, Zaccai G (1999b) The relative role of anions and cations in the stabilization of halophilic malate dehydrogenase. Biochemistry 38:9039–9047
Ebel C, Costenaro, L, Pascu M, Faou P, Kernel B, Proust-De Martin F, Zaccai G (2002) Solvent interactions of halophilic malate dehydrogenase. Biochemistry 41:13234–13244
Franzetti B, Schoehn G, Ebel C, Gagnon J, Ruigrok RW, Zaccai G (2001) Characterization of a novel complex from halophilic archaebacteria, which displays chaperone-like activities in vitro. J Biol Chem 276:29906–29914
Frolow F, Harel M, Sussman JL, Mevarech M, Shoham M (1996) Protein adaptation to a saturated salt environment: insights from the crystal structure of a halophilic 2Fe–2S ferredoxin. Nat Struct Biol 3:451–457
Hippel P von, Schleich T (1969) The effects of neutral salts on the structure and conformational stability of macromolecules in solution. In: Timasheff SN, Fasman GD (eds) Structure of biological macromolecules. Dekker, New York, pp 417–575
Irimia A, Ebel C, Madern D, Richard SB, Cosenza LW, Zaccai G, Vellieux FMD (2003) The oligomeric state of Haloacrula marismortui malate dehydrogenase are modulated by solvent components as shown by crystallographic and biochemical studies. J Mol Biol 326:859–873
Jaenicke R (2000) Stability and stabilization of globular proteins in solution. J Biotechnol 79:193–203
Jaenicke R, Böhm G (1998) The stability of proteins in extreme environments. Curr Opin Struct Biol 8:738–748
Karshikoff A, Ladenstein R (1998) Proteins from thermophilic and mesophilic organisms essentially do not differ in packing. Protein Eng 11:867–872
Kobayashi T, Kanai H, Aono R, Horikoshi K, Kudo T (1994) Cloning, expression, and nucleotide sequence of the alpha amylase gene of haloalkaliphilic archaeon Natronococcus sp. 3 strain Ah36. J Bacteriol 176:5131–5134
Madern D, Zaccai G (1997) Stabilisation of halophilic malate dehydrogenase from Haloarcula marismortui by divalent cations. Effects of temperature, water isotope, cofactor and pH. Eur J Biochem 249:607–611
Madern D, Zaccai G (2004) Molecular adaptation: the malate dehydrogenase from the extreme halophilic bacterium Salinibacter ruber behaves like a non-halophilic protein. Biochimie 86:295–303
Madern D, Pfister C, Zaccai G (1995) Mutation at a single acidic amino acid enhances the halophilic behaviour of malate dehydrogenase from Haloarcula marismortui in physiological salts. Eur J Biochem 230:1088–1095
Madern D, Ebel C, Zaccai G (2000) Halophilic adaptation of enzymes. Extremophiles 4:91–98
Mandrich L, Pezzullo M, Del Vecchio P, Barone G, Rossi M, Manco G (2004) Analysis of thermal adaptation in the HSL enzyme family. J Mol Biol 335:357–369
Mevarech M, Frolow F, Gloss LM (2000) Halophilic enzymes: proteins with a grain of salt. Biophys Chem 86:155–164
Minton AP (2001) The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J Biol Chem 276:10577–10580
Philo JS (2000) A method for directly fitting the time derivative of sedimentation velocity data and an alternative algorithm for calculating sedimentation coefficient distribution functions. Anal Biochem 279:151–163
Pieper U, Kapadia G, Mevarech M, Herzberg O (1998) Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the Dead Sea halophilic archaeon, Haloferax volcanii. Structure 6:75–88
Pundak S, Aloni H, Eisenberg H (1981) Structure and activity of malate dehydrogenase from the extreme halophilic bacteria of the Dead Sea. 2. Inactivation, dissociation and unfolding at NaCl concentrations below 2 M. Salt, salt concentration and temperature dependence of enzyme stability. Eur J Biochem 118:471–477
Richard SB, Madern D, Garcin E, Zaccai G (2000) Halophilic adaptation: novel solvent protein interactions observed in the 2.9 and 2.6 A resolution structures of the wild type and a mutant of malate dehydrogenase from Haloarcula marismortui. Biochemistry 39:992–1000
Scandurra R, Consalvi V, Chiaraluce R, Politi L, Engel PC (2000) Protein stability in extremophilic archaea. Front Biosci 5:787–795
Schellman JA (1987) Selective binding and solvent denaturation. Biopolymers 26:549–559
Solovyova A, Schuck P, Costenaro L, Ebel C (2001) Non-ideality by sedimentation velocity of halophilic malate dehydrogenase in complex solvents. Biophys J 81:1868–1880
Stafford WF III (1992) Boundary analysis in sedimentation transport experiments: a procedure for obtaining sedimentation coefficient distributions using the time derivative of the concentration profile. Anal Biochem 203:295–301
Steen IH, Madern D, Karlstrom M, Lien T, Ladenstein R, Birkeland NK (2001) Comparison of isocitrate dehydrogenase from three hyperthermophiles reveals differences in thermostability, cofactor specificity, oligomeric state, and phylogenetic affiliation. J Biol Chem 276:43924–43931
Taupin CM, Hartlein M, Leberman R (1997) Seryl-tRNA synthetase from the extreme halophile Haloarcula marismortui. Isolation, characterization and sequencing of the gene and its expression in Escherichia coli. Eur J Biochem 243:141–150
Tehei M, Madern D, Pfister C, Zaccai G (2001) Fast dynamics of halophilic malate dehydrogenase and BSA measured by neutron scattering under various solvent conditions influencing protein stability. Proc Natl Acad Sci USA 98:14356–14361
Timasheff SN (1992) Solvent effects on protein stability. Curr Opin Struct Biol 2:35–39
Wright D, Banks D, Lohman J, Hilsenbeck J, Gloss L (2002) The effect of salts on the activity and stability of Escherichia coli and Haloferax volcanii dihydrofolate reductases. J Mol Biol 323:327–344
Yamada Y, Fujiwara T, Sato T, Igarashi N, Tanaka N (2002) The 2.0 A crystal structure of catalase-peroxidase from Haloarcula marismortui. Nat Struct Biol 9:691–695
Zaccai G, Eisenberg H (1990) Halophilic proteins and the influence of solvent on protein stabilisation. Trends Biochem Sci 9:333–337
Zaccai G, Cendrin F, Haik Y, Borochov N, Eisenberg H (1989) Stabilisation of halophilic malate dehydrogenase. J Mol Biol 208:491–500
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Part of this work was financially supported by CICYT (Spain; project number PB98-0969) and by the Programme Interdepartemental GEOMEX du CNRS.
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Madern, D., Camacho, M., Rodríguez-Arnedo, A. et al. Salt-dependent studies of NADP-dependent isocitrate dehydrogenase from the halophilic archaeon Haloferax volcanii . Extremophiles 8, 377–384 (2004). https://doi.org/10.1007/s00792-004-0398-z
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DOI: https://doi.org/10.1007/s00792-004-0398-z