ΠΠ½Π°Π»ΠΈΠ· ΡΡΡΡΠΊΡΡΡΠ½ΠΎ-ΡΡΠ½ΠΊΡΠΈΠΎΠ½Π°Π»ΡΠ½ΡΡ ΠΎΡΠΎΠ±Π΅Π½Π½ΠΎΡΡΠ΅ΠΉ Π ΠΠ-ΠΏΠΎΠ»ΠΈΠΌΠ΅ΡΠ°Π·Ρ ΡΠ΅ΡΠΌΠΎΡΠΈΠ»ΡΠ½ΠΎΠΉ Π±Π°ΠΊΡΠ΅ΡΠΈΠΈ Thermus Aquaticus
ΠΠΈΡΡΠ΅ΡΡΠ°ΡΠΈΡ
Π’ΡΠ°Π½ΡΠΊΡΠΈΠΏΡΠΈΡ Π²ΠΊΠ»ΡΡΠ°Π΅Ρ ΡΡΠΈ ΠΎΡΠ½ΠΎΠ²Π½ΡΠ΅ ΡΡΠ°Π΄ΠΈΠΈ: ΠΈΠ½ΠΈΡΠΈΠ°ΡΠΈΡ, ΡΠ»ΠΎΠ½Π³Π°ΡΠΈΡ ΠΈ ΡΠ΅ΡΠΌΠΈΠ½Π°ΡΠΈΡ. ΠΠ½ΠΈΡΠΈΠ°ΡΠΈΡ ΠΏΡΠΎΠΈΡΡ ΠΎΠ΄ΠΈΡ Π² ΡΠΏΠ΅ΡΠΈΡΠΈΡΠ΅ΡΠΊΠΈΡ ΡΡΠ°ΡΡΠΊΠ°Ρ ΠΠΠ — ΠΏΡΠΎΠΌΠΎΡΠΎΡΠ°Ρ , ΠΈ ΡΠ²Π»ΡΠ΅ΡΡΡ ΠΎΠ΄Π½ΠΎΠΉ ΠΈΠ· ΠΎΡΠ½ΠΎΠ²Π½ΡΡ ΠΌΠΈΡΠ΅Π½Π΅ΠΉ Π³Π΅Π½Π΅ΡΠΈΡΠ΅ΡΠΊΠΎΠΉ ΡΠ΅Π³ΡΠ»ΡΡΠΈΠΈ. Π ΠΏΡΠΎΡΠ΅ΡΡΠ΅ ΠΈΠ½ΠΈΡΠΈΠ°ΡΠΈΠΈ Π ΠΠΠ ΡΠ·Π½Π°Π΅Ρ ΠΏΡΠΎΠΌΠΎΡΠΎΡ ΠΈ ΠΏΠ»Π°Π²ΠΈΡ ΠΏΡΠΎΠΌΠΎΡΠΎΡΠ½ΡΡ ΠΠΠ Π² ΡΠΎΡΠΊΠ΅ ΠΈΠ½ΠΈΡΠΈΠ°ΡΠΈΠΈ, ΠΏΠΎΡΠ»Π΅ ΡΠ΅Π³ΠΎ Π½Π°ΡΠΈΠ½Π°Π΅Ρ ΡΠΈΠ½ΡΠ΅Π· Π ΠΠ de novo, Π±Π΅Π· ΠΈΡΠΏΠΎΠ»ΡΠ·ΠΎΠ²Π°Π½ΠΈΡ Π·Π°ΡΡΠ°Π²ΠΊΠΈ. Π£ Π±Π°ΠΊΡΠ΅ΡΠΈΠΉ Π²ΡΠ΅ ΡΡΠ°Π΄ΠΈΠΈ ΠΈΠ½ΠΈΡΠΈΠ°ΡΠΈΠΈ… Π§ΠΈΡΠ°ΡΡ Π΅ΡΡ >
- Π‘ΠΎΠ΄Π΅ΡΠΆΠ°Π½ΠΈΠ΅
- ΠΡΠ΄Π΅ΡΠΆΠΊΠ°
- ΠΠΈΡΠ΅ΡΠ°ΡΡΡΠ°
- ΠΡΡΠ³ΠΈΠ΅ ΡΠ°Π±ΠΎΡΡ
- ΠΠΎΠΌΠΎΡΡ Π² Π½Π°ΠΏΠΈΡΠ°Π½ΠΈΠΈ
Π‘ΠΎΠ΄Π΅ΡΠΆΠ°Π½ΠΈΠ΅
- Π‘ΠΠΠ‘ΠΠ ΠΠ‘ΠΠΠΠ¬ΠΠ£ΠΠΠ«Π₯ Π‘ΠΠΠ ΠΠ©ΠΠΠΠ
- ΠΠΠΠΠ ΠΠΠ’ΠΠ ΠΠ’Π£Π Π«
- I. ΠΡΠ½ΠΎΠ²Π½ΡΠ΅ ΠΌΠ΅Ρ Π°Π½ΠΈΠ·ΠΌΡ ΠΈΠ½ΠΈΡΠΈΠ°ΡΠΈΠΈ ΠΈ ΡΠ»ΠΎΠ½Π³Π°ΡΠΈΠΈ ΡΡΠ°Π½ΡΠΊΡΠΈΠΏΡΠΈΠΈ Π±Π°ΠΊΡΠ΅ΡΠΈΠ°Π»ΡΠ½ΠΎΠΉ Π ΠΠΠ
- 1. ΠΠ΅Ρ Π°Π½ΠΈΠ·ΠΌ ΠΈΠ½ΠΈΡΠΈΠ°ΡΠΈΠΈ ΡΡΠ°Π½ΡΠΊΡΠΈΠΏΡΠΈΠΈ
- 2. ΠΠ΅Ρ
Π°Π½ΠΈΠ·ΠΌ ΡΠΈΠ½ΡΠ΅Π·Π° Π ΠΠ Π½Π° ΡΡΠ°Π΄ΠΈΠΈ ΡΠ»ΠΎΠ½Π³Π°ΡΠΈΠΈ ΡΡΠ°Π½ΡΠΊΡΠΈΠΏΡΠΈΠΈ
- 2. 1. Π‘ΡΡΡΠΊΡΡΡΠ° ΡΠ»ΠΎ/ΡΠ°ΡΠΈΠΎΠ½Π½ΠΎΠ³ΠΎ ΠΊΠΎΠΌΠΏΠ»Π΅ΠΊΡΠ°
- 2. 2. Π Π΅Π°ΠΊΡΠΈΠΈ, ΠΊΠ°ΡΠ°Π»ΠΈΠ·ΠΈΡΡΠ΅ΠΌΡΠ΅ Π ΠΠΠ
- 2. 3. ΠΠ΅Ρ Π°Π½ΠΈΠ·ΠΌ ΠΏΡΠΈΡΠΎΠ΅Π΄ΠΈΠ½Π΅Π½ΠΈΡ NTP Π² Π°ΠΊΡΠΈΠ²Π½ΠΎΠΌ ΡΠ΅Π½ΡΡΠ΅ Π ΠΠΠ
- 2. 4. ΠΠ΅Ρ Π°Π½ΠΈΠ·ΠΌ ΡΡΠ°Π½ΡΠ»ΠΎΠΊΠ°ΡΠΈΠΈ Π ΠΠΠ
- 3. ΠΠ΅ΠΉΡΡΠ²ΠΈΠ΅ Π°Π½ΡΠΈΠ±ΠΈΠΎΡΠΈΠΊΠΎΠ² Π½Π° ΠΊΠ°ΡΠ°Π»ΠΈΡΠΈΡΠ΅ΡΠΊΠΈΠΉ ΡΠΈΠΊΠ» Π ΠΠΠ
- 3. 1. Π‘ΡΡΠ΅ΠΏΡΠΎΠ»ΠΈΠ΄ΠΈΠ³ΠΈΠ½
- 3. 2. Π°-ΠΠΌΠ°Π½ΠΈΡΠΈΠ½
Π‘ΠΏΠΈΡΠΎΠΊ Π»ΠΈΡΠ΅ΡΠ°ΡΡΡΡ
- Acharya, P., Rajakumara, Π., Sankaranarayanan, R., and Rao, N.M. (2004). Structural basis of selection and thermostability of laboratory evolved Bacillus subtilis lipase. J Mol Biol 341, 12 711 281.
- Aniskovitch, L.P., and Winkler, H.H. (1995). Instability of Rickettsia prowazekii RNA polymerase-promoter complexes. J Bacteriol 177, 6301−6303.
- Artsimovitch, I., Chu, C., Lynch, A.S., and Landick, R. (2003). A new class of bacterial RNA polymerase inhibitor affects nucleotide addition. Science 302, 650−654.
- Artsimovitch, I., Patlan, V., Sekine, S., Vassylyeva, M.N., Hosaka, Π’., Ochi, K., Yokoyama, S., and Vassylyev, D.G. (2004). Structural basis for transcription regulation by alarmone ppGpp. Cell 117, 299−310.
- Artsimovitch, I., Svetlov, V., Anthony, L., Burgess, R.R., and Landick, R. (2000). RNA polymerases from Bacillus subtilis and Escherichia coli differ in recognition of regulatory signals in vitro. J Bacteriol 182, 6027−6035.
- Bae, E., and Phillips, G.N., Jr. (2004). Structures and analysis of highly homologous psychrophilic, mesophilic, and thermophilic adenylate kinases. J Biol Chem 279, 28 202−28 208.
- Bar-Nahum, G., Epshtein, V., Ruckenstein, A.E., Rafikov, R., Mustaev, A., and Nudler, E. (2005). A ratchet mechanism of transcription elongation and its control. Cell 120, 183−193.
- Bar-Nahum, G., and Nudler, E. (2001). Isolation and characterization of sigma (70)-retaining transcription elongation complexes from Escherichia coli. Cell 106, 443−451.
- Barlow, D.J., and Thornton, J.M. (1983). Ion-pairs in proteins. J Mol Biol 168, 867−885.
- Barne, K.A., Bown, J. A., Busby, S.J., and Minchin, S.D. (1997). Region 2.5 of the Escherichia coli RNA polymerase sigma70 subunit is responsible for the recognition of the 'extended-10' motif at promoters. EMBO J 16, 4034−4040.
- Batada, N.N., Westover, K.D., Bushnell, D.A., Levitt, M., and Komberg, R.D. (2004). Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center. Proc Natl Acad Sci U S A101, 17 361−17 364.
- Bell, G.S., Russell, R.J., 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.
- Bigelow, C.C. (1967). On the average hydrophobicity of proteins and the relation between it and protein structure. J Theor Biol 16, 187−211.
- Bismuto, E., Febbraio, F., Limongelli, S., Briante, R., and Nucci, R. (2003). Dynamic fluorescence studies of beta-glycosidase mutants from Sulfolobus solfataricus: effects of single mutations on protein thermostability. Proteins 51, 10−20.
- Bouthier de la Tour, C., Portemer, C., Nadal, M., Stetter, K.O., Forterre, P., and Duguet, M. (1990). Reverse gyrase, a hallmark of the hyperthermophilic archaebacteria. J Bacteriol 172, 68 036 808.
- Brodolin, K.L., Studitsky, V.M., and Mirzabekov, A.D. (1993). Conformational changes in E. coli RNA polymerase during promoter recognition. Nucleic Acids Res 21, 5748−5753.
- Brueckner, F., and Cramer, P. (2008). Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation. Nat Struct Mol Biol 15, 811−818.
- Bushnell, D.A., Cramer, P., and Kornberg, R.D. (2002). Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution. Proc Natl Acad Sci U S A 99, 1218−1222.
- Cambillau, C., and Claverie, J.M. (2000). Structural and genomic correlates of hyperthermostability. J Biol Chem 275, 32 383−32 386.
- Campbell, E.A., Korzheva, N., Mustaev, A., Murakami, K., Nair, S., Goldfarb, A., and Darst, S.A. (2001). Structural mechanism for rifampicin inhibition of bacterial rna polymerase. Cell 104, 901−912.
- Campbell, E.A., Muzzin, O., Chlenov, M., Sun, J.L., Olson, C.A., Weinman, O., Trester-Zedlitz, M.L., and Darst, S.A. (2002). Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Mol Cell 9, 527−539.
- Campbell, E.A., Pavlova, O., Zenkin, N., Leon, F., Irschik, H., Jansen, R., Severinov, K., and Darst, S.A. (2005). Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase. Embo J 24, 674−682.
- Carey, J., Cameron, V., de Haseth, P.L., and Uhlenbeck, O.C. (1983). Sequence-specific interaction of R17 coat protein with its ribonucleic acid binding site. Biochemistry 22, 2601−2610.
- Cech, C.L., and McClure, W.R. (1980). Characterization of ribonucleic acid polymerase-T7 promoter binary complexes. Biochemistry 19, 2440−2447.
- Chafin, D.R., Guo, H., and Price, D.H. (1995). Action of alpha-amanitin during pyrophosphorolysis and elongation by RNA polymerase II. J Biol Chem 270, 19 114−19 119.
- Chakrabartty, A., and Baldwin, R.L. (1995). Stability of alpha-helices. Adv Protein Chem 46, 141 176.
- Chakravarty, S., and Varadarajan, R. (2000). Elucidation of determinants of protein stability through genome sequence analysis. FEBS Lett 470, 65−69.
- Cramer, P., Bushnell, D.A., and Kornberg, R.D. (2001). Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292, 1863−1876.
- Croft, J.E., Love, D.R., and Bergquist, P.L. (1987). Expression of leucine genes from an extremely thermophilic bacterium in Escherichia coli. Mol Gen Genet 210, 490−497.
- Davis, C.A., Capp, M.W., Record, M.T., Jr., and Saecker, R.M. (2005). The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase. Proc Natl Acad Sci USA 102, 285−290.
- Demirjian, D.C., Moris-Varas, F., and Cassidy, C.S. (2001). Enzymes from extremophiles. Curr OpinChemBiol 5,144−151.
- Dill, K.A. (1990). Dominant forces in protein folding. Biochemistry 29, 7133−7155.
- Ederth, J., Artsimovitch, I., Isaksson, L.A., and Landick, R. (2002). The downstream DNA jaw of bacterial RNA polymerase facilitates both transcriptional initiation and pausing. J Biol Chem 277, 37 456−37 463.
- Eichler, J., and Adams, M.W. (2005). Posttranslational protein modification in Archaea. Microbiol Mol Biol Rev 69, 393−425.
- Elcock, A.H. (1998). The stability of salt bridges at high temperatures: implications for hyperthermophilic proteins. J Mol Biol 284, 489−502.
- Epshtein, V., Mustaev, A., Markovtsov, V., Bereshchenko, O., Nikiforov, V., and Goldfarb, A. (2002). Swing-gate model of nucleotide entry into the RNA polymerase active center. Mol Cell 10, 623−634.
- Faraldo, M.M., de Pedro, M.A., and Berenguer, J. (1992). Sequence of the S-layer gene of Thermus thermophilus HB8 and functionality of its promoter in Escherichia coli. J Bacteriol 174, 7458−7462.
- Farias, S.T., and Bonato, M.C. (2003). Preferred amino acids and thermostability. Genet Mol Res 2,383−393.
- Fields, P.A. (2001). Review: Protein function at thermal extremes: balancing stability and flexibility. Comp Biochem Physiol A Mol Integr Physiol 129, 417−431.
- Fields, P.A., and Somero, G.N. (1998). Hot spots in cold adaptation: localized increases in conformational flexibility in lactate dehydrogenase A4 orthologs of Antarctic notothenioid fishes. Proc Natl Acad Sci U S A 95, 11 476−11 481.
- Fitter, J., Herrmann, R., Dencher, N.A., Blume, A., and Hauss, T. (2001). Activity and stability of a thermostable alpha-amylase compared to its mesophilic homologue: mechanisms of thermal adaptation. Biochemistry 40, 10 723−10 731.
- Fukuchi, S., Yoshimune, K., Wakayama, M., Moriguchi, M., and Nishikawa, K. (2003). Unique amino acid composition of proteins in halophilic bacteria. J Mol Biol 327, 347−357.
- Gershenson, A., Schauerte, J.A., Giver, L., and Arnold, F.H. (2000). Tryptophan phosphorescence study of enzyme flexibility and unfolding in laboratory-evolved thermostable esterases. Biochemistry 39, 4658−4665.
- Gianese, G., Bossa, F., and Pascarella, S. (2002). Comparative structural analysis of psychrophilic and meso- and thermophilic enzymes. Proteins 47, 236−249.
- Gnatt, A.L., Cramer, P., Fu, J., Bushnell, D.A., and Kornberg, R.D. (2001). Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Science 292, 1876−1882.
- Golding, G.B., and Dean, A.M. (1998). The structural basis of molecular adaptation. Mol Biol Evol 15, 355−369.
- Goldman, A. (1995). How to make my blood boil. Structure 3, 1277−1279.
- Gourse, R.L., Gaal, Π’., Aiyar, S.E., Barker, M.M., Estrem, S.T., Hirvonen, C.A., and Ross, W. (1998). Strength and regulation without transcription factors: lessons from bacterial rRNA promoters. Cold Spring Harb Symp Quant Biol 63, 131−139.
- Gross, C.A., Chan, C., Dombroski, A., Gruber, Π’., Sharp, M., Tupy, J., and Young, B. (1998). The functional and regulatory roles of sigma factors in transcription. Cold Spring Harb Symp Quant Biol 63, 141−155.
- Haney, P.J., Stees, M., and Konisky, J. (1999b). Analysis of thermal stabilizing interactions in mesophilic and thermophilic adenylate kinases from the genus Methanococcus. J Biol Chem 274, 28 453−28 458.
- Hartmann, R.K., and Erdmann, V.A. (1989). Thermits thermophilus 16S rRNA is transcribed from an isolated transcription unit. J Bacteriol 171, 2933−2941.
- Hartmann, R.K., Ulbrich, N., and Erdmann, V.A. (1987). An unusual rRNA operon constellation: in Thermus thermophilus HB8 the 23S/5S rRNA operon is a separate entity from the 16S rRNA operon. Biochimie 69, 1097−1104.
- Haslbeck, M., Franzmann, Π’., Weinfurtner, D., and Buchner, J. (2005). Some like it hot: the structure and function of small heat-shock proteins. Nat Struct Mol Biol 12, 842−846.
- Haugen, S.P., Berkmen, M.B., Ross, W., Gaal, Π’., Ward, C., and Gourse, R.L. (2006). rRNA promoter regulation by nonoptimal binding of sigma region 1.2: an additional recognition element for RNA polymerase. Cell 125, 1069−1082.
- Haugen, S.P., Ross, W., and Gourse, R.L. (2008a). Advances in bacterial promoter recognition and its control by factors that do not bind DNA. Nat Rev Microbiol 6, 507−519.
- Haugen, S.P., Ross, W., Manrique, M., and Gourse, R.L. (2008b). Fine structure of the promoter-sigma region 1.2 interaction. Proc Natl Acad Sci USA 105, 3292−3297.
- Hendsch, Z.S., and Tidor, B. (1999). Electrostatic interactions in the GCN4 leucine zipper: substantial contributions arise from intramolecular interactions enhanced on binding. Protein Sci 8, 1381−1392.
- Henne, A., Bruggemann, H., Raasch, C., Wiezer, A., Hartsch, Π’., Liesegang, H., Johann, A., Lienard, Π’., Gohl, O., Martinez-Arias, R., et al. (2004). The genome sequence of the extreme thermophile Thermus thermophilus. Nat Biotechnol 22, 547−553.
- Jaenicke, R. (2000). Do ultrastable proteins from hyperthermophiles have high or low conformational rigidity? Proc Natl Acad Sci U S A 97, 2962−2964.
- Johns, G.C., and Somero, G.N. (2004). Evolutionary convergence in adaptation of proteins to temperature: A4-lactate dehydrogenases of Pacific damselfishes (Chromis spp.). Mol Biol Evol 21, 314−320.
- Jung, Y.H., and Lee, Y. (1997). Escherichia coli rnpB promoter mutants altered in stringent response. Biochem Biophys Res Commun 230, 582−586.
- Kannan, N., and Vishveshwara, S. (2000). Aromatic clusters: a determinant of thermal stability of thermophilic proteins. Protein Eng 13, 753−761.
- Kaplan, C.D., and Kornberg, R.D. (2008). A bridge to transcription by RNA polymerase. J Biology 7,39.31−39.34.
- Kaplan, C.D., Larsson, K.M., and Kornberg, R.D. (2008). The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin. Mol Cell 30, 547−556.
- Karshikoff, A., and Ladenstein, R. (1998). Proteins from thermophilic and mesophilic organisms essentially do not differ in packing. Protein Eng 11, 867−872.
- Kettenberger, H., Armache, K.J., and Cramer, P. (2004). Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol Cell 16, 955−965.
- Komissarova, N., and Kashlev, M. (1997a). RNA polymerase switches between inactivated and activated states By translocating back and forth along the DNA and the RNA. J Biol Chem 272, 15 329−15 338.
- Komissarova, N., and Kashlev, M. (1997b). Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3' end of the RNA intact and extruded. Proc Natl Acad Sci USA 94, 1755−1760.
- Korkegian, A., Black, M.E., Baker, D., and Stoddard, B.L. (2005). Computational thermostabilization of an enzyme. Science 308, 857−860.
- Korndorfer, I., Steipe, Π., Huber, R., Tomschy, A., and Jaenicke, R. (1995). The crystal structure of holo-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima at 2.5 A resolution. J Mol Biol 246, 511−521.
- Korolev, S., Nayal, M., Barnes, W.M., Di Cera, E., and Waksman, G. (1995). Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-A resolution: structural basis for thermostability. Proc Natl Acad Sci U S A 92, 9264−9268.
- Korzheva, N., Mustaev, A., Kozlov, M., Malhotra, A., Nikiforov, V., Goldfarb, A., and Darst, S.A. (2000). A structural model of transcription elongation. Science 289, 619−625.
- Korzheva, N., Mustaev, A., Nudler, E., Nikiforov, V., and Goldfarb, A. (1998). Mechanistic model of the elongation complex of Escherichia coli RNA polymerase. Cold Spring Harb Symp Quant Biol 63, 337−345.
- Kotik, M., and Zuber, H. (1993). Mutations that significantly change the stability, flexibility and quaternary structure of the 1-lactate dehydrogenase from Bacillus megaterium. Eur J Biochem 211, 267−280.
- Kulbachinskiy, A., Bass, I., Bogdanova, E., Goldfarb, A., and Nikiforov, V. (2004). Cold sensitivity of thermophilic and mesophilic RNA polymerases. J Bacteriol 186, 7818−7820.
- Kumar, S., and Nussinov, R. (2001). How do thermophilic proteins deal with heat? Cell Mol Life Sci 58, 1216−1233.
- Kumar, S., Tsai, C.J., and Nussinov, R. (2001). Thermodynamic differences among homologous thermophilic and mesophilic proteins. Biochemistry 40, 14 152−14 165.
- Kuznedelov, K., Lamour, V., Patikoglou, G., Chlenov, M., Darst, S.A., and Severinov, K. (2006). Recombinant Thermus aquaticus RNA polymerase for structural studies. J Mol Biol 359, 110−121.
- Kuznedelov, Π., Minakhin, L., and Severinov, K. (2003). Preparation and characterization of recombinant Thermus aquaticus RNA polymerase. Methods Enzymol 370, 94−108.
- Ma, Π., Kumar, S., Tsai, C.J., and Nussinov, R. (1999). Folding funnels and binding mechanisms. Protein Eng 12, 713−720.
- Macedo-Ribeiro, S., Darimont, Π., Sterner, R., and Huber, R. (1996). Small structural changes account for the high thermostability of l4Fe-4S. ferredoxin from the hyperthermophilic bacterium Thermotoga maritima. Structure 4, 1291−1301.
- Machius, M., Declerck, N., Huber, R., and Wiegand, G. (2003). Kinetic stabilization of Bacillus licheniformis alpha-amylase through introduction of hydrophobic residues at the surface. J Biol Chem 278, 11 546−11 553.
- Madigan, M.T., and Oren, A. (1999). Thermophilic and halophilic extremophiles. Curr Opin Microbiol 2, 265−269.
- Makhatadze, G.I., and Privalov, P.L. (1995). Energetics of protein structure. Adv Protein Chem 47, 307−425.
- Malhotra, A., Severinova, E., and Darst, S.A. (1996). Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase. Cell 87, 127−136.
- Markovtsov, V., Mustaev, A., and Goldfarb, A. (1996). Protein-RNA interactions in the active center of transcription elongation complex. Proc Natl Acad Sci U S A 93, 3221−3226.
- Maseda, H., and Hoshino, T. (1995). Screening and analysis of DNA fragments that show promoter activities in Thermus thermophilus. FEMS Microbiol Lett 128, 127−134.
- Matsui, I., and Harata, K. (2007). Implication for buried polar contacts and ion pairs in hyperthermostable enzymes. FEBS J 274, 4012−4022.
- McClure, W.R. (1985). Mechanism and control of transcription initiation in prokaryotes. Annu Rev Biochem 54, 171−204.
- McDonald, J.H. (2001). Patterns of temperature adaptation in proteins from the bacteria Deinococcus radiodurans and Thermus thermophilus. Mol Biol Evol 18, 741−749.
- McDonald, J.H., Grasso, A.M., and Rejto, L.K. (1999). Patterns of temperature adaptation in proteins from Methanococcus and Bacillus. Mol Biol Evol 16, 1785−1790.
- Meyer, J., Clay, M.D., Johnson, M.K., Stubna, A., Munck, E., Higgins, C., and Wittung-Stafshede, P. (2002). A hyperthermophilic plant-type 2Fe-2S. ferredoxin from Aquifex aeolicus is stabilized by a disulfide bond. Biochemistry 41, 3096−3108.
- Minakhin, L., Nechaev, S., Campbell, E.A., and Severinov, K. (2001). Recombinant Thermus aquaticus RNA polymerase, a new tool for structure- based analysis of transcription. J Bacteriol 183, 71−76.
- Minakhin, L., and Severinov, K. (2003). On the role of the Escherichia coli RNA polymerase sigma 70 region 4.2 and alpha-subunit C-terminal domains in promoter complex formation on the extended -10 galPl promoter. J Biol Chem 278,29 710−29 718.
- Miyazaki, K., Wintrode, P.L., Grayling, R.A., Rubingh, D.N., and Arnold, F.H. (2000). Directed evolution study of temperature adaptation in a psychrophilic enzyme. J Mol Biol 297, 1015−1026.
- Mukhopadhyay, J., Das, K., Ismail, S., Koppstein, D., Jang, M., Hudson, Π., Sarafianos, S., Tuske, S., Patel, J., Jansen, R., et al. (2008). The RNA polymerase «switch region» is a target for inhibitors. Cell 135, 295−307.
- Murakami, K.S., Masuda, S., Campbell, E.A., Muzzin, O., and Darst, S.A. (2002a). Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science 296, 12 851 290.
- Murakami, K.S., Masuda, S., and Darst, S.A. (2002b). Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution. Science 296, 1280−1284.
- Muslin, E.H., Clark, S.E., and Henson, C.A. (2002). The effect of proline insertions on the thermostability of a barley alpha-glucosidase. Protein Eng 15, 29−33.
- Nagi, A.D., and Regan, L. (1997). An inverse correlation between loop length and stability in a four-helix-bundle protein. Fold Des 2, 67−75.
- Nardmann, J., and Messer, W. (2000). Identification and characterization of the dnaA upstream region of Thermus thermophilus. Gene 261, 299−303.
- Naryshkina, Π’., Kuznedelov, K., and Severinov, K. (2006). The role of the largest RNA polymerase subunit lid element in preventing the formation of extended RNA-DNA hybrid. J Mol Biol 361, 634−643.
- Nikiforov, V.G. (1971). Hybrid RNA polymerases formed from core enzymes and sigma factors of E. coli and thermophilic B. megaterium. FEBS Lett 16, 74−76.
- Nudler, E., Kashlev, M., Nikiforov, V., and Goldfarb, A. (1995). Coupling between transcription termination and RNA polymerase inchworming. Cell 81, 351−357.
- Opalka, N., Chlenov, M., Chacon, P., Rice, W.J., Wriggers, W., and Darst, S.A. (2003). Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase. Cell 114, 335−345.
- Orlova, M., Newlands, J., Das, A., Goldfarb, A., and Borukhov, S. (1995). Intrinsic transcript cleavage activity of RNA polymerase. Proc Natl Acad Sci USA 92, 4596−4600.
- Osipiuk, J., and Joachimiak, A. (1997). Cloning, sequencing, and expression of dnaK-operon proteins from the thermophilic bacterium Thermus thermophilus. Biochim Biophys Acta 1353, 253 265.
- Pack, S.P., and Yoo, Y.J. (2004). Protein thermostability: structure-based difference of amino acid between thermophilic and mesophilic proteins. J Biotechnol 111, 269−277.
- Pack, S.P., and Yoo, Y.J. (2005). Packing-based difference of structural features between thermophilic and mesophilic proteins. Int J Biol Macromol 35, 169−174.
- Pemberton, I.K., Muskhelishvili, G., Travers, A.A., and Buckle, M. (2000). The G+C-rich discriminator region of the tyrT promoter antagonises the formation of stable preinitiation complexes. J Mol Biol 299, 859−864.
- Perederina, A., Svetlov, V., Vassylyeva, M.N., Tahirov, Π’.Π., Yokoyama, S., Artsimovitch, I., and Vassylyev, D.G. (2004). Regulation through the secondary channel—structural framework for ppGpp-DksA synergism during transcription. Cell 118, 297−309.
- Perutz, M.F., and Raidt, H. (1975). Stereochemical basis of heat stability in bacterial ferredoxins and in haemoglobin A2. Nature 255, 256−259.
- Ramirez-Romero, M.A., Masulis, I., Cevallos, M.A., Gonzalez, V., and Davila, G. (2006). The Rhizobium etli sigma70 (SigA) factor recognizes a lax consensus promoter. Nucleic Acids Res 34, 1470−1480.
- Razvi, A., and Scholtz, J.M. (2006). Lessons in stability from thermophilic proteins. Protein Sci 15, 1569−1578.
- Ring, B.Z., Yarnell, W.S., and Roberts, J.W. (1996). Function of E. coli RNA polymerase sigma factor sigma 70 in promoter-proximal pausing. Cell 86, 485−493.
- Roberts, C.W., and Roberts, J.W. (1996). Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase. Cell 86, 495−501.
- Roberts, J.W., Yarnell, W., Bartlett, E., Guo, J., Marr, M., ΠΠΎ, D.C., Sun, H., and Roberts, C.W. (1998). Antitermination by bacteriophage lambda Q protein. Cold Spring Harb Symp Quant Biol 63, 319−325.
- Robinson, C.R., and Sauer, R.T. (1998). Optimizing the stability of single-chain proteins by linker length and composition mutagenesis. Proc Natl Acad Sci USA 95, 5929−5934.
- Ross, W., Gosink, K.K., Salomon, J., Igarashi, K., Zou, C., Ishihama, A., Severinov, K., and Gourse, R.L. (1993). A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science 262, 1407−1413.
- Ross, W., and Gourse, R.L. (2005). Sequence-independent upstream DNA-alphaCTD interactions strongly stimulate Escherichia coli RNA polymerase-lacUV5 promoter association. Proc Natl Acad Sci USA 102, 291−296.
- Rozovskaya, T.A., Chenchik, A.A., and Beabealashvilli, R. (1982). Processive pyrophosphorolysis of RNA by Escherichia coli RNA polymerase. FEBS Lett 137, 100−104.
- Rudd, M.D., Izban, M.G., and Luse, D.S. (1994). The active site of RNA polymerase II participates in transcript cleavage within arrested ternary complexes. Proc Natl Acad Sci U S A 91, 8057−8061.
- Rudd, M.D., and Luse, D.S. (1996). Amanitin greatly reduces the rate of transcription by RNA polymerase II ternary complexes but fails to inhibit some transcript cleavage modes. J Biol Chem 271, 21 549−21 558.
- Russell, R.J., Hough, D.W., Danson, M.J., and Taylor, G.L. (1994). The crystal structure of citrate synthase from the thermophilic archaeon, Thermoplasma acidophilum. Structure 2, 1157−1167.
- Sadeghi, M., Naderi-Manesh, H., Zarrabi, M., and Ranjbar, B. (2006). Effective factors in thermostability of thermophilic proteins. Biophys Chem 119, 256−270.
- Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989). Molecular cloning. (Cold Spring Harbour Press.).
- Sanchez, R., Roovers, M., and Glansdorff, N. (2000). Organization and expression of a Thermus thermophilus arginine cluster: presence of unidentified open reading frames and absence of a Shine-Dalgarno sequence. J Bacteriol 182, 5911−5915.
- Sanderova, H., Hulkova, M., Malon, P., Kepkova, M., and Jonak, J. (2004). Thermostability of multidomain proteins: elongation factors EF-Tu from Escherichia coli and Bacillus stearothermophilus and their chimeric forms. Protein Sci 13, 89−99.
- Sandman, K., Krzycki, J.A., Dobrinski, Π., Lurz, R., and Reeve, J.N. (1990). HMf, a DNA-binding protein isolated from the hyperthermophilic archaeon Methanothermus fervidus, is most closely related to histones. Proc Natl Acad Sci U S A 87, 5788−5791.
- Sato, S., Nakada, Y., Kanaya, S., and Tanaka, T. (1988). Molecular cloning and nucleotide sequence of Thermus thermophilus HB8 trpE and trpG. Biochim Biophys Acta 950, 303−312.
- Serrano, L., Bycroft, M., and Fersht, A.R. (1991). Aromatic-aromatic interactions and protein stability. Investigation by double-mutant cycles. J Mol Biol 218, 465−475.
- Shiraki, K., Nishikori, S., Fujiwara, S., Hashimoto, H., Kai, Y., Takagi, M., and Imanaka, T. (2001). Comparative analyses of the conformational stability of a hyperthermophilic protein and its mesophilic counterpart. Eur J Biochem 268, 4144−4150.
- Siddhikol, C., Erbstoeszer, J.W., and Weisblum, B. (1969). Mode of action of streptolydigin. J Bacteriol 99, 151−155.
- Singer, G.A., and Hickey, D.A. (2003). Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content. Gene 317, 39−47.
- Sosunov, V., Sosunova, E., Mustaev, A., Bass, I., Nikiforov, V., and Goldfarb, A. (2003). Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase. EMBO J 22, 22 342 244.
- Sosunova, E., Sosunov, V., Kozlov, M., Nikiforov, V., Goldfarb, A., and Mustaev, A. (2003). Donation of catalytic residues to RNA polymerase active center by transcription factor Gre. Proc Natl Acad Sci USA 100, 15 469−15 474.
- Steitz, T.A. (1998). A mechanism for all polymerases. Nature 391, 231−232.
- Sterner, R., and Liebl, W. (2001). Thermophilic adaptation of proteins. Crit Rev Biochem Mol Biol 36, 39−106.
- Stetter, K.O. (1999). Extremophiles and their adaptation to hot environments. FEBS Lett 452, 2225.
- Struck, J.C., Toschka, H.Y., and Erdmann, V.A. (1988). Nucleotide sequence of the 4.5S RNA gene from Thermus thermophilus HB8. Nucleic Acids Res 16, 9042.
- Suhre, K., and Claverie, J.M. (2003). Genomic correlates of hyperthermostability, an update. J Biol Chem 278, 17 198−17 202.
- Svetlov, V., Belogurov, G.A., Shabrova, E., Vassylyev, D.G., and Artsimovitch, I. (2007). Allosteric control of the RNA polymerase by the elongation factor RfaH. Nucleic Acids Res 35, 56 945 705.
- Svetlov, V., Vassylyev, D.G., and Artsimovitch, I. (2004). Discrimination against deoxyribonucleotide substrates by bacterial RNA polymerase. J Biol Chem 279, 38 087−38 090.
- Svingor, A., Kardos, J., Hajdu, I., Nemeth, A., and Zavodszky, P. (2001). A better enzyme to cope with cold. Comparative flexibility studies on psyclirotrophic, mesophilic, and thermophilic IPMDHs. J Biol Chem 276, 28 121−28 125.
- Szilagyi, A., and Zavodszky, P. (2000). Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey. Structure 8, 493−504.
- Tan, L., Wiesler, S., Trzaska, D., Carney, H.C., and Weinzierl, R.O. (2008). Bridge helix and trigger loop perturbations generate superactive RNA polymerases. J Biol 7, 40.
- Tanner, J.J., Hecht, R.M., and Krause, K.L. (1996). Determinants of enzyme thermostability observed in the molecular structure of Thermus aquaticus D-glyceraldehyde-3-phosphate dehydrogenase at 25 Angstroms Resolution. Biochemistry 35, 2597−2609.
- Temiakov, D., Zenkin, N., Vassylyeva, M.N., Perederina, A., Tahirov, Π’.Π., Kashkina, E., Savkina, M., Zorov, S., Nikiforov, V., Igarashi, N., et al. (2005). Structural basis of transcription inhibition by antibiotic streptolydigin. Mol Cell 19, 655−666.
- Thompson, M.J., and Eisenberg, D. (1999). Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability. J Mol Biol 290, 595−604.
- Tomazic, S.J., and Klibanov, A.M. (1988). Mechanisms of irreversible thermal inactivation of Bacillus alpha-amylases. J Biol Chem 263, 3086−3091.
- Toulokhonov, I., and Landick, R. (2006). The role of the lid element in transcription by E. coli RNA polymerase. J Mol Biol 361, 644−658.
- Toulokhonov, I., Zhang, J., Palangat, M., and Landick, R. (2007). A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing. Mol Cell 27, 406 419.
- Travers, A.A. (1980). Promoter sequence for stringent control of bacterial ribonucleic acid synthesis. J Bacteriol 141, 973−976.
- Trivedi, S., Gehlot, H.S., and Rao, S.R. (2006). Protein thermostability in Archaea and Eubacteria. Genet Mol Res 5,816−827.
- Unsworth, L.D., van der Oost, J., and Koutsopoulos, S. (2007). Hyperthermophilic enzymes-stability, activity and implementation strategies for high temperature applications. FEBS J 274, 40 444 056.
- Van de Casteele, M., Chen, P., Roovers, M., Legrain, C., and Glansdorff, N. (1997). Structure and expression of a pyrimidine gene cluster from the extreme thermophile Thermus strain Z05. J Bacteriol 179, 3470−3481.
- Van den Burg, Π., Vriend, G., Veltman, O.R., Venema, G., and Eijsink, V.G. (1998). Engineering an enzyme to resist boiling. Proc Natl Acad Sci U S A 95, 2056−2060.
- Vassylyev, D.G., Sekine, S., Laptenko, O., Lee, J., Vassylyeva, M.N., Borukhov, S., and Yokoyama, S. (2002). Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature 417, 712−719.
- Vassylyev, D.G., Svetlov, V., Vassylyeva, M.N., Perederina, A., Igarashi, N., Matsugaki, N., Wakatsuki, S., and Artsimovitch, I. (2005). Structural basis for transcription inhibition by tagetitoxin. Nat Struct Mol Biol 12, 1086−1093.
- Vassylyev, D.G., Vassylyeva, M.N., Perederina, A., Tahirov, Π’.Π., and Artsimovitch, I. (2007a). Structural basis for transcription elongation by bacterial RNA polymerase. Nature 448, 157−162.
- Vassylyev, D.G., Vassylyeva, M.N., Zhang, J., Palangat, M., Artsimovitch, I., and Landick, R. (2007b). Structural basis for substrate loading in bacterial RNA polymerase. Nature 448, 163−168.
- Vassylyeva, M.N., Svetlov, V., Dearborn, A.D., Klyuyev, S., Artsimovitch, I., and Vassylyev, D.G. (2007). The carboxy-terminal coiled-coil of the RNA polymerase beta'-subunit is the main binding site for Gre factors. EMBO Rep 8, 1038−1043.
- Vetriani, C., Maeder, D.L., Tolliday, N., Yip, K.S., Stillman, T.J., Britton, K.L., Rice, D.W., Klump, Π.Π., and Robb, F.T. (1998). Protein thermostability above 100 degreesC: a key role for ionic interactions. Proc Natl Acad Sci U S A 95, 12 300−12 305.
- Vieille, C., and Zeikus, G.J. (2001). Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol Mol Biol Rev 65, 1−43.
- Villbrandt, Π., Sobek, H., Frey, Π., and Schomburg, D. (2000). Domain exchange: chimeras of Thermus aquaticus DNA polymerase, Escherichia coli DNA polymerase I and Thermotoga neapolitana DNA polymerase. Protein Eng 13, 645−654.
- Vogt, G., Woell, S., and Argos, P. (1997). Protein thermal stability, hydrogen bonds, and ion pairs. J Mol Biol 269, 631−643.
- Wang, D., Bushnell, D.A., Westover, K.D., Kaplan, C.D., and Kornberg, R.D. (2006). Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 127, 941−954.
- Wang, D., and Hawley, D.K. (1993). Identification of a 3'—>5' exonuclease activity associated with human RNA polymerase II. Proc Natl Acad Sci U S A 90, 843−847.
- Weisburg, W.G., Giovannoni, S.J., and Woese, C.R. (1989). The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction. Syst Appl Microbiol 11, 128 134.
- Westover, K.D., Bushnell, D.A., and Kornberg, R.D. (2004). Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center. Cell 119, 481−489.
- Wieland, Π’., and Faulstich, H. (1991). Fifty years of amanitin. Experientia 47, 1186−1193.
- Wintrode, P.L., Miyazaki, K., and Arnold, F.H. (2001). Patterns of adaptation in a laboratory evolved thermophilic enzyme. Biochim Biophys Acta 1549, 1−8.
- Wooll, J.O., Wrabl, J.O., and Hilser, V.J. (2000). Ensemble modulation as an origin of denaturant-independent hydrogen exchange in proteins. J Mol Biol 301, 247−256.
- Xiao, L., and Honig, B. (1999). Electrostatic contributions to the stability of hyperthermophilic proteins. J Mol Biol 289, 1435−1444.
- Xue, Y., Hogan, B.P., and Erie, D.A. (2000). Purification and initial characterization of RNA polymerase from Thermus thermophilus strain HB8. Biochemistry 39, 14 356−14 362.
- Yang, X., and Price, C.W. (1995). Streptolydigin resistance can be conferred by alterations to either the beta or beta' subunits of Bacillus subtilis RNA polymerase. J Biol Chem 270, 23 930−23 933.
- Zaccai, G. (2000). How soft is a protein? A protein dynamics force constant measured by neutron scattering. Science 288, 1604−1607.
- Zavodszky, P., Kardos, J., Svingor, and Petsko, G.A. (1998). Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins. Proc Natl Acad Sci USA 95, 74 067 411.
- Zaychikov, E., Martin, E., Denissova, L., Kozlov, M., Markovtsov, V., Kashlev, M., Heumann, H., Nikiforov, V., Goldfarb, A., and Mustaev, A. (1996). Mapping of catalytic residues in the RNA polymerase active center. Science 273, 107−109.
- Zenkin, N., Naryshkina, Π’., Kuznedelov, K., and Severinov, K. (2006a). The mechanism of DNA replication primer synthesis by RNA polymerase. Nature 439, 617−620.
- Zenkin, N., Yuzenkova, Y., and Severinov, K. (2006b). Transcript-assisted transcriptional proofreading. Science 313, 518−520.
- Zhang, G., Campbell, E.A., Minakhin, L., Richter, C., Severinov, K., and Darst, S.A. (1999). Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution. Cell 98, 811−824.
- Zhou, X.X., Wang, Y.B., Pan, Y.J., and Li, W.F. (2008). Differences in amino acids composition and coupling patterns between mesophilic and thermophilic proteins. Amino Acids 34, 25−33.