-
1
-
-
0031470387
-
Archaea and the prokaryote-to-eukaryote transition
-
An excellent review on the universal tree of life from different biochemical perspectives. The authors review the concept of Archaea, Bacteria and Eukarya, and then present and critically assess phylogenetic trees using a wide variety of protein sequences.
-
Brown JR, Doolittle WF Archaea and the prokaryote-to-eukaryote transition. Microbiol Mol Biol Rev. 61:1997;456-502. An excellent review on the universal tree of life from different biochemical perspectives. The authors review the concept of Archaea, Bacteria and Eukarya, and then present and critically assess phylogenetic trees using a wide variety of protein sequences.
-
(1997)
Microbiol Mol Biol Rev
, vol.61
, pp. 456-502
-
-
Brown, J.R.1
Doolittle, W.F.2
-
2
-
-
0031061411
-
Pyrolobus fumarii, gen. and sp. nov. represents a novel group of Archaea extending the upper temperature limit for life to 113°C
-
This paper describes the most extreme hyperthermophile isolated to date. This organism has novel metabolic properties and can survive autoclaving for one hour at 121°C.
-
Blochl E, Rachel R, Burggraf S, Hafenbrandl D, Jannasch HW, Stetter KO Pyrolobus fumarii, gen. and sp. nov. represents a novel group of Archaea extending the upper temperature limit for life to 113°C. Extemophiles. 1:1997;14-21. This paper describes the most extreme hyperthermophile isolated to date. This organism has novel metabolic properties and can survive autoclaving for one hour at 121°C.
-
(1997)
Extemophiles
, vol.1
, pp. 14-21
-
-
Blochl, E.1
Rachel, R.2
Burggraf, S.3
Hafenbrandl, D.4
Jannasch, H.W.5
Stetter, K.O.6
-
3
-
-
0025300402
-
Towards a natural system of organisms-proposal for the domains Archaea, Bacteria and Eukarya
-
Woese CR, Kandler O, Wheelis ML Towards a natural system of organisms-proposal for the domains Archaea, Bacteria and Eukarya. Proc Natl Acad Sci USA. 87:1990;4576-4579.
-
(1990)
Proc Natl Acad Sci USA
, vol.87
, pp. 4576-4579
-
-
Woese, C.R.1
Kandler, O.2
Wheelis, M.L.3
-
4
-
-
0029970177
-
Identifying microbial diversity in the natural environment: A molecular phylogenetic approach
-
Hugenholtz P, Pace NR Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. Trends Biotechnol. 14:1996;190-197.
-
(1996)
Trends Biotechnol
, vol.14
, pp. 190-197
-
-
Hugenholtz, P.1
Pace, N.R.2
-
5
-
-
0031013145
-
Molecular phylogeny of Archaea from soil
-
Bintrim SB, Donohue TJ, Handelsman J, Roberts GP, Goodman RM Molecular phylogeny of Archaea from soil. Proc Natl Acad Sci USA. 94:1997;277-282.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 277-282
-
-
Bintrim, S.B.1
Donohue, T.J.2
Handelsman, J.3
Roberts, G.P.4
Goodman, R.M.5
-
6
-
-
0029832927
-
Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences
-
Barns SM, Delwiche CF, Palmer JD, Pace NR Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci USA. 93:1996;9188-9193.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 9188-9193
-
-
Barns, S.M.1
Delwiche, C.F.2
Palmer, J.D.3
Pace, N.R.4
-
7
-
-
0030788862
-
Distribution of microorganisms in deep sea hydrothermal vent chimneys investigated by whole-cell hybridization and enrichment culture of thermophilic subpopulations
-
Harmsen HJM, Prieur D, Jeanthon C Distribution of microorganisms in deep sea hydrothermal vent chimneys investigated by whole-cell hybridization and enrichment culture of thermophilic subpopulations. Appl Env Microbiol. 63:1997;2876-2883.
-
(1997)
Appl Env Microbiol
, vol.63
, pp. 2876-2883
-
-
Harmsen, H.J.M.1
Prieur, D.2
Jeanthon, C.3
-
8
-
-
0031912606
-
Novel division level bacterial diversity in a Yellowstone hot spring
-
A culture-independent molecular phylogenetic survey that significantly expands our perception of bacterial diversity and calls into question the commonly held belief that Archaea dominate hydrothermal environments.
-
Hugenholtz P, Pitulle C, Hershberger KL, Pace NR Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol. 180:1998;366-376. A culture-independent molecular phylogenetic survey that significantly expands our perception of bacterial diversity and calls into question the commonly held belief that Archaea dominate hydrothermal environments.
-
(1998)
J Bacteriol
, vol.180
, pp. 366-376
-
-
Hugenholtz, P.1
Pitulle, C.2
Hershberger, K.L.3
Pace, N.R.4
-
9
-
-
0032076707
-
Cloning and expression in Escherichia coli of the gene encoding citrate synthase from the hyperthermophilic Archaeon Sulfolobus solfataricus
-
Connaris H, West SM, Hough DW, Danson MJ Cloning and expression in Escherichia coli of the gene encoding citrate synthase from the hyperthermophilic Archaeon Sulfolobus solfataricus. Extremophiles. 2:1998;61-66.
-
(1998)
Extremophiles
, vol.2
, pp. 61-66
-
-
Connaris, H.1
West, S.M.2
Hough, D.W.3
Danson, M.J.4
-
10
-
-
0032080595
-
Cloning of a thermostable phytase gene (phy) from Bacillus sp. DS11 and its overexpression in Escherichia coli
-
The first reported nucleic acid sequence of a bacterial phytase.
-
Kim YO, Lee JK, Kim HK, Yu JH, Oh TK Cloning of a thermostable phytase gene (phy) from Bacillus sp. DS11 and its overexpression in Escherichia coli. FEMS Microbiol Lett. 162:1998;185-191. The first reported nucleic acid sequence of a bacterial phytase.
-
(1998)
FEMS Microbiol Lett
, vol.162
, pp. 185-191
-
-
Kim, Y.O.1
Lee, J.K.2
Kim, H.K.3
Yu, J.H.4
Oh, T.K.5
-
11
-
-
0030940693
-
If you've got it, flaunt it - rapid screening for microbial biocatalysts
-
Winson MK, Kell DB If you've got it, flaunt it - rapid screening for microbial biocatalysts. Trends Biotechnol. 15:1997;120-122.
-
(1997)
Trends Biotechnol
, vol.15
, pp. 120-122
-
-
Winson, M.K.1
Kell, D.B.2
-
12
-
-
0032496652
-
PCR isolation of catechol 2,3-dioxygenase gene fragments from environmental samples and their assembly into functional genes
-
The central and terminal fragment of the catechol 2,3-dioxygenase gene were amplified from environmental DNA, annealed to form full-length hybrids and expressed in E. coli. A library of functional hybrid genes was created without the need to isolate the parent bacteria.
-
Okuta A, Ohnishi K, Harayama S PCR isolation of catechol 2,3-dioxygenase gene fragments from environmental samples and their assembly into functional genes. Gene. 212:1998;221-228. The central and terminal fragment of the catechol 2,3-dioxygenase gene were amplified from environmental DNA, annealed to form full-length hybrids and expressed in E. coli. A library of functional hybrid genes was created without the need to isolate the parent bacteria.
-
(1998)
Gene
, vol.212
, pp. 221-228
-
-
Okuta, A.1
Ohnishi, K.2
Harayama, S.3
-
13
-
-
16044367245
-
Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii
-
Bult CJ, White O, Olsen GJ, Zhou LX, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JDet al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 273:1996;1058-1073.
-
(1996)
Science
, vol.273
, pp. 1058-1073
-
-
Bult, C.J.1
White, O.2
Olsen, G.J.3
Zhou, L.X.4
Fleischmann, R.D.5
Sutton, G.G.6
Blake, J.A.7
Fitzgerald, L.M.8
Clayton, R.A.9
Gocayne, J.D.10
-
14
-
-
15644383855
-
Complete genome sequence of Methanobacterium thermoautotrophicum delta H: Functional analysis and comparative genomics
-
Smith DR, Doucette Stamm LA, Deloughery C, Lee HM, Dubois J, Aldredge T, Bashirzadeh R, Blakely D, Cook R, Gilbert Ket al. Complete genome sequence of Methanobacterium thermoautotrophicum delta H: functional analysis and comparative genomics. J Bacteriol. 179:1997;7135-7155.
-
(1997)
J Bacteriol
, vol.179
, pp. 7135-7155
-
-
Smith, D.R.1
Doucette Stamm, L.A.2
Deloughery, C.3
Lee, H.M.4
Dubois, J.5
Aldredge, T.6
Bashirzadeh, R.7
Blakely, D.8
Cook, R.9
Gilbert, K.10
-
15
-
-
0031458333
-
The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus
-
Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JDet al. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature. 390:1997;364-370.
-
(1997)
Nature
, vol.390
, pp. 364-370
-
-
Klenk, H.P.1
Clayton, R.A.2
Tomb, J.F.3
White, O.4
Nelson, K.E.5
Ketchum, K.A.6
Dodson, R.J.7
Gwinn, M.8
Hickey, E.K.9
Peterson, J.D.10
-
16
-
-
0032568375
-
The complete genome of the hyperthermophilic bacterium Aquifex aeolicus
-
Deckert G, Warren PV, Gaasterland T, Young WG, Lenox AL, Graham DE, Overbeek R, Snead MA, Keller M, Aujay Met al. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature. 392:1998;353-358.
-
(1998)
Nature
, vol.392
, pp. 353-358
-
-
Deckert, G.1
Warren, P.V.2
Gaasterland, T.3
Young, W.G.4
Lenox, A.L.5
Graham, D.E.6
Overbeek, R.7
Snead, M.A.8
Keller, M.9
Aujay, M.10
-
17
-
-
0032579989
-
Complete sequence and gene organization of the genome of a hyper-thermophilic Archaebacterium, Pyrococcus horikoshii OT3
-
Kawarabayasi Y, Sawada M, Horikawa H, Haikawa Y, Hino Y, Yamamoto S, Sekine M, Baba S, Kosugi H, Hosoyama Aet al. Complete sequence and gene organization of the genome of a hyper-thermophilic Archaebacterium, Pyrococcus horikoshii OT3. DNA Res. 5:1998;55-76.
-
(1998)
DNA Res
, vol.5
, pp. 55-76
-
-
Kawarabayasi, Y.1
Sawada, M.2
Horikawa, H.3
Haikawa, Y.4
Hino, Y.5
Yamamoto, S.6
Sekine, M.7
Baba, S.8
Kosugi, H.9
Hosoyama, A.10
-
18
-
-
0031061532
-
A fosmid-based genomic map and identification of 474 genes of the hyperthermophilic archaeon Pyrobaculum aerophilum
-
FitzGibbon S, Choi AJ, Miller JH, Stetter KO, Simon MI, Swanson R, Kim UJ A fosmid-based genomic map and identification of 474 genes of the hyperthermophilic archaeon Pyrobaculum aerophilum. Extremophiles. 1:1997;36-51.
-
(1997)
Extremophiles
, vol.1
, pp. 36-51
-
-
Fitzgibbon, S.1
Choi, A.J.2
Miller, J.H.3
Stetter, K.O.4
Simon, M.I.5
Swanson, R.6
Kim, U.J.7
-
19
-
-
10144228402
-
Organizational characteristics and information content of an archaeal genome: 156 kb of sequence from Sulfolobus solfataricus P2
-
Sensen CW, Klenk HP, Singh RK, Allard G, Chan CCY, Liu QY, Penny SL, Young F, Schenk ME, Gaasterland Tet al. Organizational characteristics and information content of an archaeal genome: 156 kb of sequence from Sulfolobus solfataricus P2. Mol Microbiol. 22:1996;175-191.
-
(1996)
Mol Microbiol
, vol.22
, pp. 175-191
-
-
Sensen, C.W.1
Klenk, H.P.2
Singh, R.K.3
Allard, G.4
Chan, C.C.Y.5
Liu, Q.Y.6
Penny, S.L.7
Young, F.8
Schenk, M.E.9
Gaasterland, T.10
-
20
-
-
0031662567
-
Structure, function and stability of enzymes from the Archaea
-
This is one of the most recent reviews of the structural basis of archaeal enzyme stability, covering thermostability, psychrophily and halophilicity.
-
Danson MJ, Hough DW Structure, function and stability of enzymes from the Archaea. Trends Microbiol. 6:1998;307-314. This is one of the most recent reviews of the structural basis of archaeal enzyme stability, covering thermostability, psychrophily and halophilicity.
-
(1998)
Trends Microbiol
, vol.6
, pp. 307-314
-
-
Danson, M.J.1
Hough, D.W.2
-
21
-
-
0032528267
-
Insights into the molecular basis of thermal stability from the analysis of ion-pair networks in the glutamate dehydrogenase family
-
A homology-based modelling study of glutamate dehydrogenases from species spanning a wide range of growth temperatures. The role of ion-pair networks in hyperstability is emphasised.
-
Yip KSP, Britton KL, Stillman TJ, Lebbink J, de Vos WM, Robb FT, Vetriani C, Maeder D, Rice DW Insights into the molecular basis of thermal stability from the analysis of ion-pair networks in the glutamate dehydrogenase family. Eur J Biochem. 255:1998;336-346. A homology-based modelling study of glutamate dehydrogenases from species spanning a wide range of growth temperatures. The role of ion-pair networks in hyperstability is emphasised.
-
(1998)
Eur J Biochem
, vol.255
, pp. 336-346
-
-
Yip, K.S.P.1
Britton, K.L.2
Stillman, T.J.3
Lebbink, J.4
De Vos, W.M.5
Robb, F.T.6
Vetriani, C.7
Maeder, D.8
Rice, D.W.9
-
22
-
-
0030741375
-
The crystal structure of citrate synthase from the hyperthermophilic Archaeon Pyrococcus furiosus at 1.9 Å resolution
-
Russell RJM, Ferguson JMC, Hough DW, Danson MJ, Taylor GL The crystal structure of citrate synthase from the hyperthermophilic Archaeon Pyrococcus furiosus at 1.9 Å resolution. Biochemistry. 36:1997;9983-9994.
-
(1997)
Biochemistry
, vol.36
, pp. 9983-9994
-
-
Russell, R.J.M.1
Ferguson, J.M.C.2
Hough, D.W.3
Danson, M.J.4
Taylor, G.L.5
-
23
-
-
0016771835
-
Stereochemical basis of heat stability in bacterial ferredoxins and in haemoglobin A2
-
Perutz M, Raidt H Stereochemical basis of heat stability in bacterial ferredoxins and in haemoglobin A2. Nature. 255:1975;256-259.
-
(1975)
Nature
, vol.255
, pp. 256-259
-
-
Perutz, M.1
Raidt, H.2
-
24
-
-
0031564613
-
Crystal structure of glutamate dehydrogenase from the hyperthermophilic eubacterium Thermotoga maritima at 3.0 Å resolution
-
A comparison of the crystal structure of a thermophilic enzyme with hyperthermophilic and mesophilic homologues. Hydrophobic interactions appear to be important in thermophilicity, whereas ionic networks are a common hyperthermophilic feature.
-
Knapp S, de Vos WM, Rice D, Ladenstein R Crystal structure of glutamate dehydrogenase from the hyperthermophilic eubacterium Thermotoga maritima at 3.0 Å resolution. J Mol Biol. 267:1997;916-932. A comparison of the crystal structure of a thermophilic enzyme with hyperthermophilic and mesophilic homologues. Hydrophobic interactions appear to be important in thermophilicity, whereas ionic networks are a common hyperthermophilic feature.
-
(1997)
J Mol Biol
, vol.267
, pp. 916-932
-
-
Knapp, S.1
De Vos, W.M.2
Rice, D.3
Ladenstein, R.4
-
25
-
-
0031554925
-
Crystal structure of the β-glycosidase from the hyperthermophilic Archaeon Sulfolobus solfataricus: Resilience as a key factor in thermostability
-
The paper introduces the novel concept of resilience to thermal denaturation through surface ion-pair and buried solvent networks, and contrasts this with idea of protein thermophilicity being linked to increased rigidity.
-
Aguilar CF, Sanderson I, Moracci M, Ciaramella M, Nucci R, Rossi M, Pearl LH Crystal structure of the β-glycosidase from the hyperthermophilic Archaeon Sulfolobus solfataricus: resilience as a key factor in thermostability. J Mol Biol. 271:1997;789-802. The paper introduces the novel concept of resilience to thermal denaturation through surface ion-pair and buried solvent networks, and contrasts this with idea of protein thermophilicity being linked to increased rigidity.
-
(1997)
J Mol Biol
, vol.271
, pp. 789-802
-
-
Aguilar, C.F.1
Sanderson, I.2
Moracci, M.3
Ciaramella, M.4
Nucci, R.5
Rossi, M.6
Pearl, L.H.7
-
26
-
-
0030699980
-
Psychrophilic enzymes: A thermodynamic challenge
-
This is a good review of cold environments, the organisms that grow in them, and the properties of their psychrophilic enzymes. At the time of publication, there were no crystal structures of psychrophilic enzymes and all the structures discussed were generated by homology modelling.
-
Gerday C, Aittaleb M, Arpigny JL, Baise E, Chessa JP, Garsoux G, Petrescu I, Feller G Psychrophilic enzymes: a thermodynamic challenge. Biochim Biophys Acta. 1342:1997;119-131. This is a good review of cold environments, the organisms that grow in them, and the properties of their psychrophilic enzymes. At the time of publication, there were no crystal structures of psychrophilic enzymes and all the structures discussed were generated by homology modelling.
-
(1997)
Biochim Biophys Acta
, vol.1342
, pp. 119-131
-
-
Gerday, C.1
Aittaleb, M.2
Arpigny, J.L.3
Baise, E.4
Chessa, J.P.5
Garsoux, G.6
Petrescu, I.7
Feller, G.8
-
27
-
-
0032521220
-
Structural adaptations of the cold-active citrate synthase from an Antarctic bacterium
-
The first report of a crystal structure of a psychrophilic enzyme, together with an analysis of its structure in terms of the protein's cold activity, thermolability and resistance to cold denaturation.
-
Russell RJM, Gerike U, Danson MJ, Hough DW, Taylor GL Structural adaptations of the cold-active citrate synthase from an Antarctic bacterium. Structure. 6:1998;351-361. The first report of a crystal structure of a psychrophilic enzyme, together with an analysis of its structure in terms of the protein's cold activity, thermolability and resistance to cold denaturation.
-
(1998)
Structure
, vol.6
, pp. 351-361
-
-
Russell, R.J.M.1
Gerike, U.2
Danson, M.J.3
Hough, D.W.4
Taylor, G.L.5
-
28
-
-
0031910806
-
Crystal structures of the psychrophilic alpha-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor
-
A second psychrophilic enzyme structure, although its analysis in terms of its cold-active properties will be the subject of a forthcoming paper.
-
Aghajari I, Feller G, Gerday C, Haser R Crystal structures of the psychrophilic alpha-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor. Protein Sci. 7:1998;564-572. A second psychrophilic enzyme structure, although its analysis in terms of its cold-active properties will be the subject of a forthcoming paper.
-
(1998)
Protein Sci
, vol.7
, pp. 564-572
-
-
Aghajari, I.1
Feller, G.2
Gerday, C.3
Haser, R.4
-
29
-
-
0031195026
-
The structural basis of protein halophilicity
-
This paper reviews the structures of the enzymes malate dehydrogenase, dihydrofolate reductase and dihydrolipoamide dehydrogenase fromhalophilic Archaea and discusses these in the light of models for the structural basis of halophilicity.
-
Danson MJ, Hough DW The structural basis of protein halophilicity. Comp Biochem Physiol A. 117A:1997;307-312. This paper reviews the structures of the enzymes malate dehydrogenase, dihydrofolate reductase and dihydrolipoamide dehydrogenase fromhalophilic Archaea and discusses these in the light of models for the structural basis of halophilicity.
-
(1997)
Comp Biochem Physiol a
, vol.117
, pp. 307-312
-
-
Danson, M.J.1
Hough, D.W.2
-
30
-
-
0028958071
-
Structural features that stabilise halophilic malate dehydrogenase from an Aarchaebacterium
-
Dym O, Mevarech M, Sussman JL Structural features that stabilise halophilic malate dehydrogenase from an Aarchaebacterium. Science. 267:1995;1344-1346.
-
(1995)
Science
, vol.267
, pp. 1344-1346
-
-
Dym, O.1
Mevarech, M.2
Sussman, J.L.3
-
31
-
-
0030010138
-
Insights into protein adaptation to a saturated salt environment from the crystal structure of a halophilic 2Fe-2S ferredoxin
-
Frolow F, Harel M, Sussman JL, Mevarech M, Shoham M Insights into protein adaptation to a saturated salt environment from the crystal structure of a halophilic 2Fe-2S ferredoxin. Nat Struct Biol. 3:1996;452-457.
-
(1996)
Nat Struct Biol
, vol.3
, pp. 452-457
-
-
Frolow, F.1
Harel, M.2
Sussman, J.L.3
Mevarech, M.4
Shoham, M.5
-
32
-
-
0030930383
-
Site-directed mutagenesis and halophilicity of dihydrolipoamde dehydrogenase from the halophilic Archaeon Haloferax volcanii
-
Jolley KA, Russell RJM, Hough DW, Danson MJ Site-directed mutagenesis and halophilicity of dihydrolipoamde dehydrogenase from the halophilic Archaeon Haloferax volcanii. Eur J Biochem. 248:1997;362-368.
-
(1997)
Eur J Biochem
, vol.248
, pp. 362-368
-
-
Jolley, K.A.1
Russell, R.J.M.2
Hough, D.W.3
Danson, M.J.4
-
33
-
-
0031570334
-
Formylmethanofuran: Tetrahydromethanopterin formyltransferase from Methanopyrus kandleri - new insights into salt-dependence and thermostability
-
This paper describes the crystal structure of a formyltransferase from a methanogenic Archaeon that grows optimally at 98°C and has an internal salt concentration of 1.5 M phosphate. The structure is therefore analysed in terms of the enzyme's combined thermophilic and halophilic nature.
-
Ermler U, Merckel MC, Thauer RK, Shima S Formylmethanofuran: tetrahydromethanopterin formyltransferase from Methanopyrus kandleri - new insights into salt-dependence and thermostability. Structure. 5:1997;635-646. This paper describes the crystal structure of a formyltransferase from a methanogenic Archaeon that grows optimally at 98°C and has an internal salt concentration of 1.5 M phosphate. The structure is therefore analysed in terms of the enzyme's combined thermophilic and halophilic nature.
-
(1997)
Structure
, vol.5
, pp. 635-646
-
-
Ermler, U.1
Merckel, M.C.2
Thauer, R.K.3
Shima, S.4
-
34
-
-
0032054520
-
Engineering of a stable mutant malic enzyme by introducing an extra ion-pair to the protein
-
A double mutant of pigeon liver malic enzyme was designed to introduce an additional ion-pair. The mutant was much more stable to thermal or urea-induced denaturation but was less active than the wild type enzyme.
-
Huang S-H, Chou W-Y, Lin S-I Chang G-G Engineering of a stable mutant malic enzyme by introducing an extra ion-pair to the protein. Proteins. 31:1998;61-73. A double mutant of pigeon liver malic enzyme was designed to introduce an additional ion-pair. The mutant was much more stable to thermal or urea-induced denaturation but was less active than the wild type enzyme.
-
(1998)
Proteins
, vol.31
, pp. 61-73
-
-
Huang, S.-H.1
Chou, W.-Y.2
Lin S-I, C.G.-G.3
-
35
-
-
0031565980
-
Disruption of an ionic network leads to accelerated thermal denaturation of D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima
-
One of the most lucid accounts of analysing the changes in kinetics and thermodynamics of protein thermostability after site-directed mutagenesis.
-
Pappenberger G, Schurig H, Jaenicke R Disruption of an ionic network leads to accelerated thermal denaturation of D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima. J Mol Biol. 274:1997;676-683. One of the most lucid accounts of analysing the changes in kinetics and thermodynamics of protein thermostability after site-directed mutagenesis.
-
(1997)
J Mol Biol
, vol.274
, pp. 676-683
-
-
Pappenberger, G.1
Schurig, H.2
Jaenicke, R.3
-
37
-
-
0032560505
-
Adjustment of conformational flexibility is a key event in the thermal adaption of proteins
-
Isopropylmalate dehydrogenase from Thermus thermophilus has optimum activity at 22-25°C above the E. coli enzyme and a 17°C higher melting temperature. H-D exchange showed that the Thermus enzyme is significantly more rigid at room temperature, whereas both enzymes have similar flexibility at their respective optimum temperatures.
-
Zavodsky P, Kardos J, Svingor A, Petsko G Adjustment of conformational flexibility is a key event in the thermal adaption of proteins. Proc Nat Acad Sci USA. 95:1998;7406-7411. Isopropylmalate dehydrogenase from Thermus thermophilus has optimum activity at 22-25°C above the E. coli enzyme and a 17°C higher melting temperature. H-D exchange showed that the Thermus enzyme is significantly more rigid at room temperature, whereas both enzymes have similar flexibility at their respective optimum temperatures.
-
(1998)
Proc Nat Acad Sci USA
, vol.95
, pp. 7406-7411
-
-
Zavodsky, P.1
Kardos, J.2
Svingor, A.3
Petsko, G.4
-
38
-
-
0032573217
-
Directed evolution of a thermostable esterase
-
Directed evolution of p-nitrobenzyl esterase from Bacillus subtilis produced a mutant with a 14°C increase in melting temperature with no reduction in catalytic activity at lower temperatures. This suggests that these properties are not necessarily inversely correlated, although mutations that increased stability without compromising activity were rare.
-
Giver L, Gershenson A, Freskgard P-O, Arnold FH Directed evolution of a thermostable esterase. Proc Natl Acad Sci USA. 95:1998;12809-12813. Directed evolution of p-nitrobenzyl esterase from Bacillus subtilis produced a mutant with a 14°C increase in melting temperature with no reduction in catalytic activity at lower temperatures. This suggests that these properties are not necessarily inversely correlated, although mutations that increased stability without compromising activity were rare.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 12809-12813
-
-
Giver, L.1
Gershenson, A.2
Freskgard, P.-O.3
Arnold, F.H.4
-
39
-
-
0032478082
-
Engineering an enzyme to resist boiling
-
One of the most impressive examples of enzyme engineering that combines rationally designed mutations with changes based on sequence comparisons with thermostable homologues. A protease is produced that is able to function at 100°C but which retains wild type activity at 37°C.
-
Van den Burg B, Vriend G, Veltman OR, Venema G, Eijsink VGH Engineering an enzyme to resist boiling. Proc Natl Acad Sci USA. 95:1998;2056-2060. One of the most impressive examples of enzyme engineering that combines rationally designed mutations with changes based on sequence comparisons with thermostable homologues. A protease is produced that is able to function at 100°C but which retains wild type activity at 37°C.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 2056-2060
-
-
Van Den Burg, B.1
Vriend, G.2
Veltman, O.R.3
Venema, G.4
Eijsink, V.G.H.5
-
40
-
-
0031935580
-
Serial increase in the thermal stability of 3-isopropylmalate dehydrogenase from Bacillus subtilis by experimental evolution
-
An excellent example of in vivo evolutionary engineering to increase the thermostability of an enzyme while at the same time improving the catalytic activity.
-
Akanuma S, Yamagishi A, Tanaka N, Oshima T Serial increase in the thermal stability of 3-isopropylmalate dehydrogenase from Bacillus subtilis by experimental evolution. Protein Sci. 7:1998;698-705. An excellent example of in vivo evolutionary engineering to increase the thermostability of an enzyme while at the same time improving the catalytic activity.
-
(1998)
Protein Sci
, vol.7
, pp. 698-705
-
-
Akanuma, S.1
Yamagishi, A.2
Tanaka, N.3
Oshima, T.4
-
41
-
-
0031747102
-
An autonomously replicating transforming vector for Sulfolobus solfataricus
-
A plasmid shuttle vector able to transform and to be stably maintained both in S. solfataricus and in E. coli was constructed. The vector suffered no rearrangement and/or chromosome integration, and its copy number in Sulfolobus was increased by exposure of the cells to mitomycin C.
-
Cannio R, Contursi P, Rossi M, Bartolucci S An autonomously replicating transforming vector for Sulfolobus solfataricus. J Bacteriol. 180:1998;3237-3240. A plasmid shuttle vector able to transform and to be stably maintained both in S. solfataricus and in E. coli was constructed. The vector suffered no rearrangement and/or chromosome integration, and its copy number in Sulfolobus was increased by exposure of the cells to mitomycin C.
-
(1998)
J Bacteriol.
, vol.180
, pp. 3237-3240
-
-
Cannio, R.1
Contursi, P.2
Rossi, M.3
Bartolucci, S.4
-
42
-
-
0031543435
-
Directed evolution of enzyme catalysts
-
Reviews the directed evolution approach to engineering biocatalysts, including techniques for creating and screening combinatorial enzyme libraries. Examples include the evolution of thermostability, resistance to organic solvents, substrate specificity and enantioselectivity.
-
Kuchner O, Arnold FH Directed evolution of enzyme catalysts. Trends Biotechnol. 15:1997;523-530. Reviews the directed evolution approach to engineering biocatalysts, including techniques for creating and screening combinatorial enzyme libraries. Examples include the evolution of thermostability, resistance to organic solvents, substrate specificity and enantioselectivity.
-
(1997)
Trends Biotechnol
, vol.15
, pp. 523-530
-
-
Kuchner, O.1
Arnold, F.H.2
-
43
-
-
0031046956
-
Cold adaptation of a mesophilic serine protease, subtilisin, by in vitro random mutagenesis
-
Random mutagenesis of subtilisin BPN′ resulted in the isolation of a mutant with increased activity at low temperature (1-10°C). The thermostability of the mutant was similar to the wild type enzyme.
-
Kano H, Taguchi S, Momose H Cold adaptation of a mesophilic serine protease, subtilisin, by in vitro random mutagenesis. Appl Microbiol Biotechnol. 47:1997;46-51. Random mutagenesis of subtilisin BPN′ resulted in the isolation of a mutant with increased activity at low temperature (1-10°C). The thermostability of the mutant was similar to the wild type enzyme.
-
(1997)
Appl Microbiol Biotechnol
, vol.47
, pp. 46-51
-
-
Kano, H.1
Taguchi, S.2
Momose, H.3
-
44
-
-
0030737949
-
Generation of large libraries of random mutants in Bacillus subtilis by PCR-based plasmid multimerization
-
Shafikhani S, Siegel RA, Ferrari E, Schellenberger V Generation of large libraries of random mutants in Bacillus subtilis by PCR-based plasmid multimerization. Biotechniques. 23:1997;304-310.
-
(1997)
Biotechniques
, vol.23
, pp. 304-310
-
-
Shafikhani, S.1
Siegel, R.A.2
Ferrari, E.3
Schellenberger, V.4
-
45
-
-
0031587291
-
Stategies for the in vitro evolution of protein function: Enzyme evolution by random recombination of improved sequences
-
This paper describes an enhancement of the direct evolution approach in order to produce further improvements in the properties of enzyme biocatalysts. Following initial rounds of random mutagenesis, the benefits of random recombination of gene fragments in vitro (DNA shuffling) are compared with additional rounds of random mutagenesis.
-
Moore JC, Jin H-M, Kuchner O, Arnold FH Stategies for the in vitro evolution of protein function: enzyme evolution by random recombination of improved sequences. J Mol Biol. 272:1997;336-347. This paper describes an enhancement of the direct evolution approach in order to produce further improvements in the properties of enzyme biocatalysts. Following initial rounds of random mutagenesis, the benefits of random recombination of gene fragments in vitro (DNA shuffling) are compared with additional rounds of random mutagenesis.
-
(1997)
J Mol Biol
, vol.272
, pp. 336-347
-
-
Moore, J.C.1
Jin, H.-M.2
Kuchner, O.3
Arnold, F.H.4
-
46
-
-
0032518266
-
DNA shuffling of a family of genes from diverse species accelerates directed evolution
-
Reviews the DNA shuffling approach, by which libraries of chimaeric genes can be generated by random fragmentation of a pool of related genes, followed by reassembly of the fragments in a self-priming polymerase reaction.
-
Crameri A, Raillard SA, Bermudez E, Stemmer WP DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature. 391:1997;288-291. Reviews the DNA shuffling approach, by which libraries of chimaeric genes can be generated by random fragmentation of a pool of related genes, followed by reassembly of the fragments in a self-priming polymerase reaction.
-
(1997)
Nature
, vol.391
, pp. 288-291
-
-
Crameri, A.1
Raillard, S.A.2
Bermudez, E.3
Stemmer, W.P.4
-
47
-
-
0030951186
-
Molecular evolution of an arsenate detoxification pathway DNA shuffling
-
This paper describes the functional evolution of an arsenic resistance operon by DNA shuffling and homologous recombination. It demonstrates how DNA shuffling can improve the function of a pathway by complex and unexpected mutational mechanisms that are likely to be overlooked by rational design.
-
Crameri A, Dawes G, Rodriguez E, Silver S, Stemmer WPC Molecular evolution of an arsenate detoxification pathway DNA shuffling. Nat Biotechnol. 15:1997;436-438. This paper describes the functional evolution of an arsenic resistance operon by DNA shuffling and homologous recombination. It demonstrates how DNA shuffling can improve the function of a pathway by complex and unexpected mutational mechanisms that are likely to be overlooked by rational design.
-
(1997)
Nat Biotechnol
, vol.15
, pp. 436-438
-
-
Crameri, A.1
Dawes, G.2
Rodriguez, E.3
Silver, S.4
Stemmer, W.P.C.5
-
48
-
-
0032142727
-
Alkaline detergent enzymes from alkaliphiles: Enzymatic properties, genetics and structures
-
Ito S, Kobayashi T, Ara K, Ozaki K, Kawai S, Hatada Y Alkaline detergent enzymes from alkaliphiles: enzymatic properties, genetics and structures. Extremophiles. 2:1998;185-190.
-
(1998)
Extremophiles
, vol.2
, pp. 185-190
-
-
Ito, S.1
Kobayashi, T.2
Ara, K.3
Ozaki, K.4
Kawai, S.5
Hatada, Y.6
-
50
-
-
0030826555
-
Cloning, sequencing, and expression of the gene encoding extracellular alpha-amylase from Pyrococcus furiosus and biochemical characterization of the recombinant enzyme
-
The expressed enzyme (α-amylase) has optimal activity at 100°C and is much more thermostable than commercially available amylases.
-
Dong GQ, Vieille C, Savchenko A, Zeikus JG Cloning, sequencing, and expression of the gene encoding extracellular alpha-amylase from Pyrococcus furiosus and biochemical characterization of the recombinant enzyme. Appl Environ Microbiol. 63:1997;3569-3576. The expressed enzyme (α-amylase) has optimal activity at 100°C and is much more thermostable than commercially available amylases.
-
(1997)
Appl Environ Microbiol
, vol.63
, pp. 3569-3576
-
-
Dong, G.Q.1
Vieille, C.2
Savchenko, A.3
Zeikus, J.G.4
-
51
-
-
0030910823
-
Cloning, sequencing, characterization and expression of an extracellular alpha-amylase from the hyperthermophilic Archaeon Pyrococcus furiosus in Escherichia coli and Bacillus subtilis
-
Jorgensen S, Vorgias CE, Antranikian G Cloning, sequencing, characterization and expression of an extracellular alpha-amylase from the hyperthermophilic Archaeon Pyrococcus furiosus in Escherichia coli and Bacillus subtilis. J Biol Chem. 272:1997;16335-16342.
-
(1997)
J Biol Chem
, vol.272
, pp. 16335-16342
-
-
Jorgensen, S.1
Vorgias, C.E.2
Antranikian, G.3
-
52
-
-
0030803307
-
Cloning, sequencing, and expression of the gene encoding amylopullulanase from Pyrococcus furiosus and biochemical characterization of the recombinant enzyme
-
Dong GQ, Vieille C, Zeikus JG Cloning, sequencing, and expression of the gene encoding amylopullulanase from Pyrococcus furiosus and biochemical characterization of the recombinant enzyme. Appl Environ Microbiol. 63:1997;3577-3584.
-
(1997)
Appl Environ Microbiol
, vol.63
, pp. 3577-3584
-
-
Dong, G.Q.1
Vieille, C.2
Zeikus, J.G.3
-
53
-
-
0032485355
-
Molecular cloning of extremely thermostable esterase gene from hyperthermophilic archaeon Pyrococcus furiosus in Escherichia coli
-
A thermophilic esterase was identified by screening a genomic library of P. furiosus. The enzyme has the highest temperature optimum and thermal stability of all esterases reported to date.
-
Ikeda M, Clark DS Molecular cloning of extremely thermostable esterase gene from hyperthermophilic archaeon Pyrococcus furiosus in Escherichia coli. Biotechnol Bioeng. 57:1998;624-629. A thermophilic esterase was identified by screening a genomic library of P. furiosus. The enzyme has the highest temperature optimum and thermal stability of all esterases reported to date.
-
(1998)
Biotechnol Bioeng
, vol.57
, pp. 624-629
-
-
Ikeda, M.1
Clark, D.S.2
-
54
-
-
0030061364
-
Catalytical potency of beta-glucosidase from the extremophile Pyrococcus furiosus in glucoconjugate synthesis
-
Fischer L, Bromann R, Kengen SWM, de Vos WM, Wagner F Catalytical potency of beta-glucosidase from the extremophile Pyrococcus furiosus in glucoconjugate synthesis. Biotechnology. 14:1996;88-91.
-
(1996)
Biotechnology
, vol.14
, pp. 88-91
-
-
Fischer, L.1
Bromann, R.2
Kengen, S.W.M.3
De Vos, W.M.4
Wagner, F.5
-
55
-
-
0031127645
-
Detoxification of synthetic pyrethroid insecticides by thermophilic microorganisms
-
Maloney SE, Marks TS, Sharp RJ Detoxification of synthetic pyrethroid insecticides by thermophilic microorganisms. J Chem Technol Biotechnol. 68:1997;357-360.
-
(1997)
J Chem Technol Biotechnol
, vol.68
, pp. 357-360
-
-
Maloney, S.E.1
Marks, T.S.2
Sharp, R.J.3
-
56
-
-
0030610935
-
Degradation of 3-chlorobenzoate by thermophilic microorganisms
-
Maloney SE, Marks TS, Sharp RJ Degradation of 3-chlorobenzoate by thermophilic microorganisms. Lett Appl Microbiol. 24:1997;441-444.
-
(1997)
Lett Appl Microbiol
, vol.24
, pp. 441-444
-
-
Maloney, S.E.1
Marks, T.S.2
Sharp, R.J.3
-
57
-
-
0030438856
-
Biotransformation of halophenols by a thermophilic Bacillus sp
-
Reinscheid UM, Bauer MP, Muller R Biotransformation of halophenols by a thermophilic Bacillus sp. Biodegradation. 7:1997;445-461.
-
(1997)
Biodegradation
, vol.7
, pp. 445-461
-
-
Reinscheid, U.M.1
Bauer, M.P.2
Muller, R.3
-
58
-
-
0031279683
-
Thermophiles and fermentation technology
-
This paper describes methods to overcome the problems associated with the growth of thermophiles to high cell density in a fermentor by the use of gas-lift fermentors, dialysis fermentors or cell recycling systems.
-
Holst O, Manelius Å, Krahe M, Märkl H, Raven N, Sharp R Thermophiles and fermentation technology. Comp Biochem Physiol. 118A:1997;415-422. This paper describes methods to overcome the problems associated with the growth of thermophiles to high cell density in a fermentor by the use of gas-lift fermentors, dialysis fermentors or cell recycling systems.
-
(1997)
Comp Biochem Physiol
, vol.118
, pp. 415-422
-
-
Holst, O.1
Manelius, Å.2
Krahe, M.3
Märkl, H.4
Raven, N.5
Sharp, R.6
-
59
-
-
0031814109
-
Thermotoga neapolitana homotetrameric xylose isomerase is expressed as a catalytically active and thermostable dimer in Escherichia coli
-
Expression of the T. neapolitana xylose isomerase gene in E. coli produced a dimeric recombinant with similar stability and biocatalytic properties to the native, tetrameric enzyme.
-
Hess JM, Tchernajenko V, Vieille C, Zeikus JG, Kelly RM Thermotoga neapolitana homotetrameric xylose isomerase is expressed as a catalytically active and thermostable dimer in Escherichia coli. Appl Environ Microβiol. 64:1998;2357-2360. Expression of the T. neapolitana xylose isomerase gene in E. coli produced a dimeric recombinant with similar stability and biocatalytic properties to the native, tetrameric enzyme.
-
(1998)
Appl Environ Microβiol
, vol.64
, pp. 2357-2360
-
-
Hess, J.M.1
Tchernajenko, V.2
Vieille, C.3
Zeikus, J.G.4
Kelly, R.M.5
-
60
-
-
0030789078
-
Sequencing and expression of the gene encoding a cold-active citrate synthase from an Antarctic bacterium, strain DS2-3R
-
One of the first reports of the expression of a psychrophilic enzyme in E. coli, highlighting the need to grow the host at low (27°C) temperatures to get maximum yields of active recombinant protein.
-
Gerike U, Danson MJ, Russell NJ, Hough DW Sequencing and expression of the gene encoding a cold-active citrate synthase from an Antarctic bacterium, strain DS2-3R. Eur J Biochem. 248:1997;49-57. One of the first reports of the expression of a psychrophilic enzyme in E. coli, highlighting the need to grow the host at low (27°C) temperatures to get maximum yields of active recombinant protein.
-
(1997)
Eur J Biochem
, vol.248
, pp. 49-57
-
-
Gerike, U.1
Danson, M.J.2
Russell, N.J.3
Hough, D.W.4
-
61
-
-
0031887070
-
Expression of psychrophilic genes in mesophilic hosts: Assessment of the folding state of a recombinant alpha-amylase
-
Feller G, LeBussy O, Gerday C Expression of psychrophilic genes in mesophilic hosts: assessment of the folding state of a recombinant alpha-amylase. Appl Environ Microbiol. 64:1998;1163-1165.
-
(1998)
Appl Environ Microbiol
, vol.64
, pp. 1163-1165
-
-
Feller, G.1
Lebussy, O.2
Gerday, C.3
-
62
-
-
0027195301
-
Cloning, sequencing and expression in Escherichia coli of the gene coding for malate dehydrogenase of the extremely halophilic archaebacterium Haloarcula marismortui
-
Cendrin F, Chroboczek J, Zaccai G, Eisenberg H, Mevarech M Cloning, sequencing and expression in Escherichia coli of the gene coding for malate dehydrogenase of the extremely halophilic archaebacterium Haloarcula marismortui. Biochemistry. 32:1993;4308-4313.
-
(1993)
Biochemistry
, vol.32
, pp. 4308-4313
-
-
Cendrin, F.1
Chroboczek, J.2
Zaccai, G.3
Eisenberg, H.4
Mevarech, M.5
-
63
-
-
0027272686
-
High expression in Escherichia coli of the gene encoding for dihydrofolate reductase of the extremely halophilic archaebacterium Haloferax volcanii
-
Blecher O, Goldman S, Mevarech M High expression in Escherichia coli of the gene encoding for dihydrofolate reductase of the extremely halophilic archaebacterium Haloferax volcanii. Eur J Biochem. 216:1993;199-203.
-
(1993)
Eur J Biochem
, vol.216
, pp. 199-203
-
-
Blecher, O.1
Goldman, S.2
Mevarech, M.3
-
64
-
-
0031030713
-
Seryl-tRNA synthetase from the extreme halophile Haloarcula marismortui; Isolation, characterization and sequencing of the gene and its expression in Escherichia coli
-
Taupin CM-J, Hartlein M, Leberman R 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. 243:1997;141-150.
-
(1997)
Eur J Biochem
, vol.243
, pp. 141-150
-
-
Taupin, C.-J.1
Hartlein, M.2
Leberman, R.3
|