Enzymes from piezophiles

Seminars in Cell & Developmental Biology - Tập 84 - Trang 138-146 - 2018
Toshiko Ichiye1
1Department of Chemistry, Georgetown University, Washington, DC, 20057, United States

Tài liệu tham khảo

Winter, 2005, High pressure effects in molecular bioscience, 29 Meersman, 2013, 607 Fang, 2010, Deep-sea piezosphere and piezophiles: geomicrobiology and biogeochemistry, Trends Microbiol., 18, 413, 10.1016/j.tim.2010.06.006 Prieur, 2009, Piezophilic prokaryotes, 281 Yayanos, 1986, Evolutional and ecological implications of the properties of deep-sea barophilic bacteria, Proc. Natl. Acad. Sci. U. S. A., 83, 9542, 10.1073/pnas.83.24.9542 Picard, 2013, Pressure as an environmental parameter for microbial life - a review, Biophys. Chem., 183, 30, 10.1016/j.bpc.2013.06.019 Kallmeyer, 2012, Global distribution of microbial abundance and biomass in subseafloor sediment, Proc. Natl. Acad. Sci. U. S. A., 109, 16213, 10.1073/pnas.1203849109 Whitman, 1998, Prokaryotes: the unseen majority, Proc. Natl. Acad. Sci. U. S. A., 95, 6578, 10.1073/pnas.95.12.6578 Yayanos, 2001, Deep-sea piezophilic bacteria, Methods Microbiol., 30, 615, 10.1016/S0580-9517(01)30065-X Kato, 2012, Microbiology of piezophiles in deep-sea environments, 233 Yayanos, 1995, Microbiology to 10,500 meters in the deep sea, Ann. Rev. Microbiol., 49, 777, 10.1146/annurev.mi.49.100195.004021 2017 Pal, 2014 Somero, 1995, Proteins and temperature, Ann. Rev. Physiol., 57, 453, 10.1146/annurev.ph.57.030195.000355 Jaenicke, 1990, Proteins under extreme physical conditions, FEBS Lett., 268, 344, 10.1016/0014-5793(90)81283-T D’Amico, 2003, Activity-stability relationships in extremophilic enzymes, J. Biol. Chem., 278, 7891, 10.1074/jbc.M212508200 Závodszky, 1998, Adjustment of conflexibility is a key event in the thermal adaptation of proteins, Proc. Natl. Acad. Sci. U. S. A., 95, 7406, 10.1073/pnas.95.13.7406 Feller, 2003, Psychrophilic enzymes: hot topics in cold adaptation, Nat. Rev. Microbiol., 1, 200, 10.1038/nrmicro773 Georlette, 2004, Some like it cold: biocatalysis at low temperatures, FEMS Microbiol. Rev., 28, 25, 10.1016/j.femsre.2003.07.003 Feller, 2013, Psychrophilic enzymes: from folding to function and biotechnology, Scientifica, 512840 Berezovsky, 2005, Physics and evolution of thermophilic adaptation, Proc. Natl. Acad. Sci. U. S. A., 102, 12742, 10.1073/pnas.0503890102 Nguyen, 2017, High-pressure NMR techniques for the study of protein dynamics, folding and aggregation, J. Magn. Reson., 277, 179, 10.1016/j.jmr.2017.01.009 Boehr, 2010, Millisecond timescale fluctuations in dihydrofolate reductase are equisitely sensitive to the bound ligands, Proc. Natl. Acad. Sci. U. S. A., 107, 1373, 10.1073/pnas.0914163107 Meinhold, 2007, Picosecond fluctuating protein energy landscape mapped by pressure-temperature molecular dynamics simulation, Proc. Natl. Acad. Sci. U. S. A., 104, 17261, 10.1073/pnas.0708199104 Rodgers, 2017, Quasiharmonic analysis of protein energy landscapes from pressure-temperature molecular dynamics simulations, J. Chem. Phys., 147, 125103, 10.1063/1.5003823 Bridgman, 1914, The coagulation of albumen by pressure, J. Biol. Chem., 19, 511, 10.1016/S0021-9258(18)88287-4 Balny, 2006, Review: what lies in the future of high-pressure bioscience?, Biochim. Biophys. Acta, 1764, 632, 10.1016/j.bbapap.2005.10.004 Gross, 1994, Review: proteins under pressure: the influence of high hydrostatic pressure on structure, function and assembly of proteins and protein complexes, Eur. J. Biochem., 221, 617, 10.1111/j.1432-1033.1994.tb18774.x Kharakoz, 2000, Protein compressibility, dynamics, and pressure, Biophys. J., 79, 511, 10.1016/S0006-3495(00)76313-2 Wilton, 2008, Pressure-induced changes in the solution structure of the GB1 domain of protein G, Proteins Struc. Funct. Bioinf., 71, 1432, 10.1002/prot.21832 Huang, 2016, A molecular perspective on the limits of life: enzymes under pressure, Condens. Matter Phys., 19, 1, 10.5488/CMP.19.22801 Nagae, 2012, High-pressure-induced water penetration into 3-isopropylmalate dehydrogenase, Acta Crystallogr., D68, 300 Gekko, 2002, Review: compressibility gives new insight into protein dynamics and enzyme function, Biochim. Biophys. Acta, 1595, 382, 10.1016/S0167-4838(01)00358-2 Kamiyama, 2000, Effect of ligand binding on the flexibility of dihydrofolate reductase as revealed by compressibility, Biochim. Biophys. Acta, 1478, 257, 10.1016/S0167-4838(00)00019-4 Huang, 2017, Extreme biophysics: enzymes under pressure, J. Comput. Chem., 38, 1174, 10.1002/jcc.24737 Kundrot, 1987, J. Mol. Biol., 193, 157, 10.1016/0022-2836(87)90634-6 Ascone, 2010, Acta Crystallogr., D66, 654 Heremans, 1982, High pressure effects on proteins and other biomolecules, Annu. Rev. Biophys. Bioeng., 11, 1, 10.1146/annurev.bb.11.060182.000245 Royer, 2002, Review: revisiting volume changes in pressure-induced protein unfolding, Biochim. Biophys. Acta, 1595, 201, 10.1016/S0167-4838(01)00344-2 Silva, 2001, New insights into protein folding, dynamics and structure from high pressure studies, Trends Biochem. Sci., 26, 612, 10.1016/S0968-0004(01)01949-1 Frye, 1998, Probing the contribution of internal cavities to the volume change of protein unfolding under pressure, Protein Sci., 7, 2217, 10.1002/pro.5560071020 Roche, 2012, Cavities determine the pressure unfolding of proteins, Proc. Natl. Acad. Sci. U. S. A., 109, 6945, 10.1073/pnas.1200915109 Collins, 2005, Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation, Proc. Natl. Acad. Sci. U. S. A., 46, 16668, 10.1073/pnas.0508224102 Nucci, 2014, Role of cavities and hydration in the pressure unfolding of T4 lysozyme, Proc. Natl. Acad. Sci. U. S. A., 111, 13846, 10.1073/pnas.1410655111 Mombelli, 2002, Exploring hyperthermophilic proteins under pressure: theoretical aspects and experimental findings, Biochim. Biophys. Acta, 1595, 392, 10.1016/S0167-4838(01)00361-2 Panick, 1998, Structural characterization of the pressure-denatured state and unfolding/refolding kinetics of staphylococcal nuclease by synchrotron small-angle X-ray scattering and Fourier-transform infrared spectroscopy, J. Mol. Biol., 275, 389, 10.1006/jmbi.1997.1454 Hummer, 1998, The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins, Proc. Natl. Acad. Sci. U. S. A., 95, 1552, 10.1073/pnas.95.4.1552 Silva, 1993, Pressure stability of proteins, Annu. Rev. Phys. Chem., 44, 89, 10.1146/annurev.pc.44.100193.000513 Hervé, 2017, Activation of latent dihydroorotase from Aquifex aeolicus by pressure, J. Biol. Chem., 292, 629, 10.1074/jbc.M116.739862 Akasaka, 2001, Low-lying excited states of proteins revealed from nonlinear pressure shifts in 1H and 15N NMR, Biochemistry, 40, 8665, 10.1021/bi010312u Kitahara, 2000, High pressure NMR reveals active-site hinge motion of folate-bound Escherichia coli dihydrofolate reductase, Biochemistry, 39, 12789, 10.1021/bi0009993 Ohmae, 2008, Effects of pressure on enzyme functiion of Escherichia coli dihydrofolate reductase, Biochim. Biophys. Acta, 1784, 1115, 10.1016/j.bbapap.2008.04.005 Kitahara, 2005, NMR snapshots of a fluctuating protein structure: ubiquitin at 30 bar–3 kbar, J. Mol. Biol., 347, 277, 10.1016/j.jmb.2005.01.052 Meinhold, 2005, Pressure-dependent transition in protein dynamics at about 4 kbar revealed by molecular dynamics simulations, Phys. Rev. E, 72, 061908, 10.1103/PhysRevE.72.061908 Kitahara, 2003, Close identity of a pressure-stabilized intermediate with a kinetic intermediate in protein folding, Proc. Natl. Acad. Sci. U. S. A., 100, 3167, 10.1073/pnas.0630309100 Li, 2006, Conformational fluctuations of proteins revealed by variable pressure NMR, Biochim. Biophys. Acta, 1764, 331, 10.1016/j.bbapap.2005.12.014 Boonyaratanakornkit, 2002, Review: pressure effects on intra- and intermolecular interactions within proteins, Biochim. Biophys. Acta, 1595, 235, 10.1016/S0167-4838(01)00347-8 Ohmae, 2007, Review: pressure effects on enzyme functions, J. Biol. Macromol., 7, 23 Ohmae, 2012, Pressure dependence of activity and stability of dihydrofolate reductases of the deep-sea bacterium Moritella profunda and Escherichia coli, Biochim. Biophys. Acta, 1824, 511, 10.1016/j.bbapap.2012.01.001 Northrop, 2002, Review: effects of high pressure on enzymatic activity, Biochim. Biophys. Acta, 1595, 71, 10.1016/S0167-4838(01)00335-1 Barstow, 2008, Alteration of citrine structure by hydrostatic pressure explains the accompanying spectral shift, Proc. Natl. Acad. Sci. U. S. A., 105, 13362, 10.1073/pnas.0802252105 Kasahara, 2009, Piezo-adapted 3-isopropylmalate dehydrogenase of the obligate piezophile Shewanella benthica DB21MT-2 isolated from the 11,000-m depth of the Mariana Trench, Biosci. Biotechnol. Biochem., 73, 2541, 10.1271/bbb.90448 Bartlett, 2002, Review: pressure effects on in vivo microbial processes, Biochim. Biophys. Acta, 1595, 367, 10.1016/S0167-4838(01)00357-0 Eloe, 2011, Going deeper: metagenome of a hadopelagic microbial community, Plos One, 6, e20388, 10.1371/journal.pone.0020388 Zhang, 2015, Current developments in marine microbiology: high-pressure biotechnology and the genetic engineering of piezophiles, Curr. Opin. Biotechnol., 33, 157, 10.1016/j.copbio.2015.02.013 Harrison, 2013, The limits for life under multiple extremes, Trends Microbiol., 21, 204, 10.1016/j.tim.2013.01.006 Kaye, 2004, Synchronous effects of temperature, hydrostatic pressure, and salinity on growth, phospholipid profiles, and protein patterns of four Halomonas species from deep-sea hydrothermal vent and sea surface environments, Appl. Environ. Microbiol., 70, 6220, 10.1128/AEM.70.10.6220-6229.2004 Martin, 2002, Solute accumulation in the deep-sea bacterium Photobacterium profundum, Extremophiles, 6, 507, 10.1007/s00792-002-0288-1 Amrani, 2014, Transcriptomics reveal several gene expression patterns in the piezophile Desulfovibrio hydrothermalis in response to hydrostatic pressure, Plos One, 9, e106831, 10.1371/journal.pone.0106831 Ohmae, 2013, Solvent environments significantly affect the enzymatic function of Escherichia coli dihydrofolate reductase: comparison of wild-type protein and the active-site mutant D27E, Biochim. Biophys. Acta, 1834, 2782, 10.1016/j.bbapap.2013.09.024 Herberhold, 2004, Effects of chaotropic and kosmotropic cosolvents on the pressure-induced unfolding and denaturation of proteins: an FT-IR study on staphylococcal nuclease, Biochemistry, 43, 3336, 10.1021/bi036106z Reed, 2013, Review: protein adaptations in archaeal extremophiles, Archaea, 2013, 373275, 10.1155/2013/373275 Ohmae, 2013, Thermodynamic and functional characteristics of deep-sea enzymes revealed by pressure effects, Extremophiles, 17, 701, 10.1007/s00792-013-0556-2 Meersman, 2002, Comparative Fourier transform infrared spectroscopy study of cold-, pressure-, and heat-induced unfolding and aggregation of myoglobin, Biophys. J., 82, 2635, 10.1016/S0006-3495(02)75605-1 Hammes, 2011, Flexibility, diversity, and cooperativity: pillars of enzyme catalysis, Biochemistry, 50, 10422, 10.1021/bi201486f Berman, 2000, The Protein Data Bank, Nucleic Acids Res., 28, 235, 10.1093/nar/28.1.235 Sawaya, 1997, Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence, Biochemistry, 36, 586, 10.1021/bi962337c Hay, 2009, Are the catalytic properties of enzymes from piezophilic organisms pressure adapted?, ChemBioChem, 10, 2348, 10.1002/cbic.200900367 Xu, 2003, Moritella profunda sp. nov. and Moritella abyssi sp. nov., two psychropiezophilic organisms isolated from deep Atlantic sediments, Int. J. Sys. Evol. Microbiol., 53, 533, 10.1099/ijs.0.02228-0 Nagae, 2012, Structural analysis of 3-isopropylmalate dehydrogenase from the obligate piezophile Shewanella benthica DB21MT-2 and the nonpiezophile Shewanella oneidensis MR-1, Acta Crysta., F68, 265 Kato, 1998, Extremely barophilic bacteria isolated from the Mariana Trench, Challenger Deep, at a depth of 11,000 meters, Appl. Environ. Microbiol., 64, 1510, 10.1128/AEM.64.4.1510-1513.1998 Abboud, 2005, Low-temperature growth of Shewanella oneidensis MR-1, Appl. Environ. Microbiol., 71, 811, 10.1128/AEM.71.2.811-816.2005 Murakami, 2010, Cloning and characterization of dihydrofolate reductases from deep-sea bacteria, J. Biochem. Tokyo, 147, 591, 10.1093/jb/mvp206 Murakami, 2011, Comparative study on dihydrofolate reductases from Shewanella species living in deep-sea and ambient atmospheric-pressure environments, Extremophiles, 15, 165, 10.1007/s00792-010-0345-0 Evans, 2010, Catalysis by dihydrofolate reductase from the psychropiezophile Moritella profunda, ChemBioChem, 11, 2010, 10.1002/cbic.201000341 Xu, 2003, Moritella cold-active dihydrofolate reductase: are there natural limits to optimization of catalytic efficiency at low temperature?, J. Bacteriol., 185, 5519, 10.1128/JB.185.18.5519-5526.2003 Loveridge, 2011, The role of large-scale motions in catalysis by dihydrofolate reductase, J. Am. Chem. Soc., 113, 20561, 10.1021/ja208844j Hamajima, 2016, Pressure adaptation of 3-isopropylmalate dehydrogenase from an extemely piezophilic bacterium is attributed to a single amino acid substitution, Extremophiles, 20, 177, 10.1007/s00792-016-0811-4 Huang, Q., Q.A. Do, J.M. Rodgers, R.J. Hemley, and T. Ichiye. Quasi-harmonic analysis of the energy landscapes of dihydrofolate reductase from piezophiles and mesophiles. unpublished. DOI: 10.1002/jcc.24737. Schnell, 2004, Structure, dynamics, and catalytic function of dihydrofolate reductase, Annu. Rev. Biophys. Biomol. Struc., 33, 119, 10.1146/annurev.biophys.33.110502.133613