Demain AL, Newcomb M, Wu JH: Cellulase, clostridia, and ethanol. Microbiol Mol Biol Rev. 2005, 69 (1): 124-154. 10.1128/MMBR.69.1.124-154.2005.
Article
PubMed
CAS
PubMed Central
Google Scholar
Roberts SB, Gowen CM, Brooks JP, Fong SS: Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production. BMC Syst Biol. 2010, 4 (31):
Alberts B: The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell. 1998, 92 (3): 291-294. 10.1016/S0092-8674(00)80922-8.
Article
PubMed
CAS
Google Scholar
Schagger H, von Jagow G: Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form. Anal Biochem. 1991, 199 (2): 223-231. 10.1016/0003-2697(91)90094-A.
Article
PubMed
CAS
Google Scholar
Stroh A, Anderka O, Pfeiffer K, Yagi T, Finel M, Ludwig B, Schagger H: Assembly of respiratory complexes I, III, and IV into NADH oxidase supercomplex stabilizes complex I in Paracoccus denitrificans. J Biol Chem. 2004, 279 (6): 5000-5007. 10.1074/jbc.M309505200.
Article
PubMed
CAS
Google Scholar
Cruciat CM, Brunner S, Baumann F, Neupert W, Stuart RA: The cytochrome bc1 and cytochrome c oxidase complexes associate to form a single supracomplex in yeast mitochondria. J Biol Chem. 2000, 275 (24): 18093-18098. 10.1074/jbc.M001901200.
Article
PubMed
CAS
Google Scholar
Ciambella C, Roepstorff P, Aro EM, Zolla L: A proteomic approach for investigation of photosynthetic apparatus in plants. Proteomics. 2005, 5 (3): 746-757. 10.1002/pmic.200401129.
Article
PubMed
CAS
Google Scholar
Herranen M, Battchikova N, Zhang P, Graf A, Sirpio S, Paakkarinen V, Aro EM: Towards functional proteomics of membrane protein complexes in Synechocystis sp. PCC 6803. Plant Physiol. 2004, 134 (1): 470-481. 10.1104/pp.103.032326.
Article
PubMed
CAS
PubMed Central
Google Scholar
Pan JY, Li H, Ma Y, Chen P, Zhao P, Wang SY, Peng XX: Complexome of Escherichia coli envelope proteins under normal physiological conditions. J Proteome Res. 2010, 9 (7): 3730-3740. 10.1021/pr100301f.
Article
PubMed
CAS
Google Scholar
Stenberg F, Chovanec P, Maslen SL, Robinson CV, Ilag LL, von Heijne G, Daley DO: Protein complexes of the Escherichia coli cell envelope. J Biol Chem. 2005, 280 (41): 34409-34419. 10.1074/jbc.M506479200.
Article
PubMed
CAS
Google Scholar
Krogh A, Larsson B, von Heijne G, Sonnhammer EL: Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001, 305 (3): 567-580. 10.1006/jmbi.2000.4315.
Article
PubMed
CAS
Google Scholar
Sonnhammer EL, von Heijne G, Krogh A: A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol. 1998, 6: 175-182.
PubMed
CAS
Google Scholar
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV: The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 2001, 29 (1): 22-28. 10.1093/nar/29.1.22.
Article
PubMed
CAS
PubMed Central
Google Scholar
Tatusov RL, Galperin MY, Natale DA, Koonin EV: The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000, 28 (1): 33-36. 10.1093/nar/28.1.33.
Article
PubMed
CAS
PubMed Central
Google Scholar
Lee LK, Stewart AG, Donohoe M, Bernal RA, Stock D: The structure of the peripheral stalk of Thermus thermophilus H(+)-ATPase/synthase. Nat Struct Mol Biol. 2010, 17 (3): 373-378. 10.1038/nsmb.1761.
Article
PubMed
CAS
PubMed Central
Google Scholar
Capaldi RA, Aggeler R: Mechanism of the F(1)F(0)-type ATP synthase, a biological rotary motor. Trends Biochem Sci. 2002, 27 (3): 154-160. 10.1016/S0968-0004(01)02051-5.
Article
PubMed
CAS
Google Scholar
Yokoyama K, Imamura H: Rotation, structure, and classification of prokaryotic V-ATPase. J Bioenerg Biomembr. 2005, 37 (6): 405-410. 10.1007/s10863-005-9480-1.
Article
PubMed
CAS
Google Scholar
Takase K, Yamato I, Kakinuma Y: Cloning and sequencing of the genes coding for the A and B subunits of vacuolar-type Na(+)-ATPase from Enterococcus hirae. Coexistence of vacuolar- and F0F1-type ATPases in one bacterial cell. J Biol Chem. 1993, 268 (16): 11610-11616.
PubMed
CAS
Google Scholar
Murata T, Yamato I, Kakinuma Y, Leslie AG, Walker JE: Structure of the rotor of the V-Type Na+-ATPase from Enterococcus hirae. Science. 2005, 308 (5722): 654-659. 10.1126/science.1110064.
Article
PubMed
CAS
Google Scholar
Murata T, Kawano M, Igarashi K, Yamato I, Kakinuma Y: Catalytic properties of Na(+)-translocating V-ATPase in Enterococcus hirae. Biochim Biophys Acta. 2001, 1505 (1): 75-81. 10.1016/S0005-2728(00)00278-4.
Article
PubMed
CAS
Google Scholar
Honer zu Bentrup K, Ubbink-Kok T, Lolkema JS, Konings WN: An Na+-pumping V1V0-ATPase complex in the thermophilic bacterium Clostridium fervidus. J Bacteriol. 1997, 179 (4): 1274-1279.
PubMed
CAS
PubMed Central
Google Scholar
Reid MF, Fewson CA: Molecular characterization of microbial alcohol dehydrogenases. Crit Rev Microbiol. 1994, 20 (1): 13-56. 10.3109/10408419409113545.
Article
PubMed
CAS
Google Scholar
Espinosa A, Yan L, Zhang Z, Foster L, Clark D, Li E, Stanley SL: The bifunctional Entamoeba histolytica alcohol dehydrogenase 2 (EhADH2) protein is necessary for amebic growth and survival and requires an intact C-terminal domain for both alcohol dahydrogenase and acetaldehyde dehydrogenase activity. J Biol Chem. 2001, 276 (23): 20136-20143. 10.1074/jbc.M101349200.
Article
PubMed
CAS
Google Scholar
Habe H, Fukuoka T, Morita T, Kitamoto D, Yakushi T, Matsushita K, Sakaki K: Disruption of the Membrane-Bound Alcohol Dehydrogenase-Encoding Gene Improved Glycerol Use and Dihydroxyacetone Productivity in Gluconobacter oxydans. Biosci Biotechnol Biochem. 2010
Google Scholar
Gomez-Manzo S, Solano-Peralta A, Saucedo-Vazquez JP, Escamilla-Marvan JE, Kroneck PM, Sosa-Torres ME: The membrane-bound quinohemoprotein alcohol dehydrogenase from Gluconacetobacter diazotrophicus PAL5 carries a [2Fe-2S] cluster. Biochemistry. 2010, 49 (11): 2409-2415. 10.1021/bi9015007.
Article
PubMed
CAS
Google Scholar
Moonmangmee D, Fujii Y, Toyama H, Theeragool G, Lotong N, Matsushita K, Adachi O: Purification and characterization of membrane-bound quinoprotein cyclic alcohol dehydrogenase from Gluconobacter frateurii CHM 9. Biosci Biotechnol Biochem. 2001, 65 (12): 2763-2772. 10.1271/bbb.65.2763.
Article
PubMed
CAS
Google Scholar
Choi-Rhee E, Cronan JE: The biotin carboxylase-biotin carboxyl carrier protein complex of Escherichia coli acetyl-CoA carboxylase. J Biol Chem. 2003, 278 (33): 30806-30812. 10.1074/jbc.M302507200.
Article
PubMed
CAS
Google Scholar
Cronan JE, Waldrop GL: Multi-subunit acetyl-CoA carboxylases. Prog Lipid Res. 2002, 41 (5): 407-435. 10.1016/S0163-7827(02)00007-3.
Article
PubMed
CAS
Google Scholar
Diacovich L, Peiru S, Kurth D, Rodriguez E, Podesta F, Khosla C, Gramajo H: Kinetic and structural analysis of a new group of Acyl-CoA carboxylases found in Streptomyces coelicolor A3(2). J Biol Chem. 2002, 277 (34): 31228-31236. 10.1074/jbc.M203263200.
Article
PubMed
CAS
Google Scholar
Hugler M, Krieger RS, Jahn M, Fuchs G: Characterization of acetyl-CoA/propionyl-CoA carboxylase in Metallosphaera sedula. Carboxylating enzyme in the 3-hydroxypropionate cycle for autotrophic carbon fixation. Eur J Biochem. 2003, 270 (4): 736-744. 10.1046/j.1432-1033.2003.03434.x.
Article
PubMed
CAS
Google Scholar
Santoro N, Brtva T, Roest SV, Siegel K, Waldrop GL: A high-throughput screening assay for the carboxyltransferase subunit of acetyl-CoA carboxylase. Anal Biochem. 2006, 354 (1): 70-77. 10.1016/j.ab.2006.04.006.
Article
PubMed
CAS
Google Scholar
Finlayson SA, Dennis DT: Acetyl-coenzyme A carboxylase from the developing endosperm of Ricinus communis. I. Isolation and characterization. Arch Biochem Biophys. 1983, 225 (2): 576-585. 10.1016/0003-9861(83)90069-3.
Article
PubMed
CAS
Google Scholar
Feldman-Salit A, Wirtz M, Hell R, Wade RC: A Mechanistic Model of the Cysteine Synthase Complex. J Mol Biol. 2009, 386 (1): 37-59. 10.1016/j.jmb.2008.08.075.
Article
PubMed
CAS
Google Scholar
Jurgenson CT, Burns KE, Begley TP, Ealick SE: Crystal structure of a sulfur carrier protein complex found in the cysteine biosynthetic pathway of Mycobacterium tuberculosis. Biochemistry. 2008, 47 (39): 10354-10364. 10.1021/bi800915j.
Article
PubMed
CAS
PubMed Central
Google Scholar
Huang CZ, Lin XM, Wu LN, Zhang DF, Liu D, Wang SY, Peng XX: Systematic identification of the subproteome of Escherichia coli cell envelope reveals the interaction network of membrane proteins and membrane-associated peripheral proteins. J Proteome Res. 2006, 5 (12): 3268-3276. 10.1021/pr060257h.
Article
PubMed
CAS
Google Scholar
de Las Rivas B, Fox GC, Angulo I, Ripoll MM, Rodriguez H, Munoz R, Mancheno JM: Crystal structure of the hexameric catabolic ornithine transcarbamylase from Lactobacillus hilgardii: Structural insights into the oligomeric assembly and metal binding. J Mol Biol. 2009, 393 (2): 425-434. 10.1016/j.jmb.2009.08.002.
Article
PubMed
CAS
Google Scholar
Shi D, Morizono H, Aoyagi M, Tuchman M, Allewell NM: Crystal structure of human ornithine transcarbamylase complexed with carbamoyl phosphate and L-norvaline at 1.9 A resolution. Proteins. 2000, 39 (4): 271-277. 10.1002/(SICI)1097-0134(20000601)39:4<271::AID-PROT10>3.0.CO;2-E.
Article
PubMed
CAS
Google Scholar
Villeret V, Clantin B, Tricot C, Legrain C, Roovers M, Stalon V, Glansdorff N, Van Beeumen J: The crystal structure of Pyrococcus furiosus ornithine carbamoyltransferase reveals a key role for oligomerization in enzyme stability at extremely high temperatures. Proc Natl Acad Sci USA. 1998, 95 (6): 2801-2806. 10.1073/pnas.95.6.2801.
Article
PubMed
CAS
PubMed Central
Google Scholar
Tricot C, Villeret V, Sainz G, Dideberg O, Stalon V: Allosteric regulation in Pseudomonas aeruginosa catabolic ornithine carbamoyltransferase revisited: association of concerted homotropic cooperative interactions and local heterotropic effects. J Mol Biol. 1998, 283 (3): 695-704. 10.1006/jmbi.1998.2133.
Article
PubMed
CAS
Google Scholar
Alam SI, Bansod S, Kumar RB, Sengupta N, Singh L: Differential proteomic analysis of Clostridium perfringens ATCC13124; identification of dominant, surface and structure associated proteins. BMC Microbiol. 2009, 9: 162-10.1186/1471-2180-9-162.
Article
PubMed
PubMed Central
Google Scholar
Hughes MJ, Moore JC, Lane JD, Wilson R, Pribul PK, Younes ZN, Dobson RJ, Everest P, Reason AJ, Redfern JM, et al: Identification of major outer surface proteins of Streptococcus agalactiae. Infect Immun. 2002, 70 (3): 1254-1259. 10.1128/IAI.70.3.1254-1259.2002.
Article
PubMed
CAS
PubMed Central
Google Scholar
Shi D, Morizono H, Ha Y, Aoyagi M, Tuchman M, Allewell NM: 1.85-A resolution crystal structure of human ornithine transcarbamoylase complexed with N-phosphonacetyl-L-ornithine. Catalytic mechanism and correlation with inherited deficiency. J Biol Chem. 1998, 273 (51): 34247-34254. 10.1074/jbc.273.51.34247.
Article
PubMed
CAS
Google Scholar
Saikawa N, Akiyama Y, Ito K: FtsH exists as an exceptionally large complex containing HflKC in the plasma membrane of Escherichia coli. J Struct Biol. 2004, 146 (1-2): 123-129. 10.1016/j.jsb.2003.09.020.
Article
PubMed
CAS
Google Scholar
Narberhaus F, Obrist M, Fuhrer F, Langklotz S: Degradation of cytoplasmic substrates by FtsH, a membrane-anchored protease with many talents. Res Microbiol. 2009, 160 (9): 652-659. 10.1016/j.resmic.2009.08.011.
Article
PubMed
CAS
Google Scholar
Niwa H, Tsuchiya D, Makyio H, Yoshida M, Morikawa K: Hexameric ring structure of the ATPase domain of the membrane-integrated metalloprotease FtsH from Thermus thermophilus HB8. Structure. 2002, 10 (10): 1415-1423. 10.1016/S0969-2126(02)00855-9.
Article
PubMed
CAS
Google Scholar
Nurmohamed S, Vaidialingam B, Callaghan AJ, Luisi BF: Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly. J Mol Biol. 2009, 389 (1): 17-33. 10.1016/j.jmb.2009.03.051.
Article
PubMed
CAS
PubMed Central
Google Scholar
Chen HW, Koehler CM, Teitell MA: Human polynucleotide phosphorylase: location matters. Trends Cell Biol. 2007, 17 (12): 600-608. 10.1016/j.tcb.2007.09.006.
Article
PubMed
CAS
Google Scholar
Briani F, Del Favero M, Capizzuto R, Consonni C, Zangrossi S, Greco C, De Gioia L, Tortora P, Deho G: Genetic analysis of polynucleotide phosphorylase structure and functions. Biochimie. 2007, 89 (1): 145-157. 10.1016/j.biochi.2006.09.020.
Article
PubMed
CAS
Google Scholar
Lorentzen E, Walter P, Fribourg S, Evguenieva-Hackenberg E, Klug G, Conti E: The archaeal exosome core is a hexameric ring structure with three catalytic subunits. Nat Struct Mol Biol. 2005, 12 (7): 575-581. 10.1038/nsmb952.
Article
PubMed
CAS
Google Scholar
Symmons MF, Jones GH, Luisi BF: A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation. Structure. 2000, 8 (11): 1215-1226. 10.1016/S0969-2126(00)00521-9.
Article
PubMed
CAS
Google Scholar
Taghbalout A, Rothfield L: New insights into the cellular organization of the RNA processing and degradation machinery of Escherichia coli. Mol Microbiol. 2008, 70 (4): 780-782.
PubMed
CAS
Google Scholar
Owen P, Kaback HR: Immunochemical analysis of membrane vesicles from Escherichia coli. Biochemistry. 1979, 18 (8): 1413-1422. 10.1021/bi00575a004.
Article
PubMed
CAS
Google Scholar
Tatur J, Hagen WR, Matias PM: Crystal structure of the ferritin from the hyperthermophilic archaeal anaerobe Pyrococcus furiosus. J Biol Inorg Chem. 2007, 12 (5): 615-630. 10.1007/s00775-007-0212-3.
Article
PubMed
CAS
PubMed Central
Google Scholar
Carrondo MA: Ferritins, iron uptake and storage from the bacterioferritin viewpoint. EMBO J. 2003, 22 (9): 1959-1968. 10.1093/emboj/cdg215.
Article
PubMed
CAS
PubMed Central
Google Scholar
Davidson AL, Dassa E, Orelle C, Chen J: Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol Mol Biol Rev. 2008, 72 (2): 317-364. 10.1128/MMBR.00031-07. table of contents
Article
PubMed
CAS
PubMed Central
Google Scholar
Hvorup RN, Goetz BA, Niederer M, Hollenstein K, Perozo E, Locher KP: Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuF. Science. 2007, 317 (5843): 1387-1390. 10.1126/science.1145950.
Article
PubMed
CAS
Google Scholar
Hollenstein K, Frei DC, Locher KP: Structure of an ABC transporter in complex with its binding protein. Nature. 2007, 446 (7132): 213-216. 10.1038/nature05626.
Article
PubMed
CAS
Google Scholar
Nataf Y, Yaron S, Stahl F, Lamed R, Bayer EA, Scheper TH, Sonenshein AL, Shoham Y: Cellodextrin and laminaribiose ABC transporters in Clostridium thermocellum. J Bacteriol. 2009, 191 (1): 203-209. 10.1128/JB.01190-08.
Article
PubMed
CAS
PubMed Central
Google Scholar
Ferner-Ortner J, Mader C, Ilk N, Sleytr UB, Egelseer EM: High-affinity interaction between the S-layer protein SbsC and the secondary cell wall polymer of Geobacillus stearothermophilus ATCC 12980 determined by surface plasmon resonance technology. J Bacteriol. 2007, 189 (19): 7154-7158. 10.1128/JB.00294-07.
Article
PubMed
CAS
PubMed Central
Google Scholar
Mader C, Huber C, Moll D, Sleytr UB, Sara M: Interaction of the crystalline bacterial cell surface layer protein SbsB and the secondary cell wall polymer of Geobacillus stearothermophilus PV72 assessed by real-time surface plasmon resonance biosensor technology. J Bacteriol. 2004, 186 (6): 1758-1768. 10.1128/JB.186.6.1758-1768.2004.
Article
PubMed
CAS
PubMed Central
Google Scholar
Mesnage S, Fontaine T, Mignot T, Delepierre M, Mock M, Fouet A: Bacterial SLH domain proteins are non-covalently anchored to the cell surface via a conserved mechanism involving wall polysaccharide pyruvylation. EMBO J. 2000, 19 (17): 4473-4484. 10.1093/emboj/19.17.4473.
Article
PubMed
CAS
PubMed Central
Google Scholar
Helaine S, Dyer DH, Nassif X, Pelicic V, Forest KT: 3D structure/function analysis of PilX reveals how minor pilins can modulate the virulence properties of type IV pili. Proc Natl Acad Sci USA. 2007, 104 (40): 15888-15893. 10.1073/pnas.0707581104.
Article
PubMed
CAS
PubMed Central
Google Scholar
Williams TI, Combs JC, Thakur AP, Strobel HJ, Lynn BC: A novel Bicine running buffer system for doubled sodium dodecyl sulfate - polyacrylamide gel electrophoresis of membrane proteins. Electrophoresis. 2006, 27 (14): 2984-2995. 10.1002/elps.200500730.
Article
PubMed
CAS
Google Scholar
Williams TI, Combs JC, Lynn BC, Strobel HJ: Proteomic profile changes in membranes of ethanol-tolerant Clostridium thermocellum. Appl Microbiol Biotechnol. 2007, 74 (2): 422-432. 10.1007/s00253-006-0689-7.
Article
PubMed
CAS
Google Scholar
Bradford MM: A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976, 72: 248-254. 10.1016/0003-2697(76)90527-3.
Article
PubMed
CAS
Google Scholar
Wittig I, Braun HP, Schagger H: Blue native PAGE. Nat Protoc. 2006, 1 (1): 418-428. 10.1038/nprot.2006.62.
Article
PubMed
CAS
Google Scholar
Fernandez-Arenas E, Cabezon V, Bermejo C, Arroyo J, Nombela C, Diez-Orejas R, Gil C: Integrated proteomics and genomics strategies bring new insight into Candida albicans response upon macrophage interaction. Mol Cell Proteomics. 2007, 6 (3): 460-478.
Article
PubMed
CAS
Google Scholar