메뉴 건너뛰기




Volumn 18, Issue 1, 2009, Pages 69-79

Exploiting genomic patterns to discover new supramolecular protein assemblies

Author keywords

Bacterial microcompartment; Bacterial ultrastructure; Carboxysome; Homolog; Paralog; Self assembly; Supramolecular assembly

Indexed keywords

HEAT SHOCK PROTEIN;

EID: 58149478360     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.1     Document Type: Article
Times cited : (23)

References (60)
  • 2
    • 58149463566 scopus 로고    scopus 로고
    • Microbiology Monographs
    • Shively JM, editor, Berlin: Springer;
    • Shively JM, editor. Microbiology Monographs, Vol. 2: Complex Intracellular Structures in Prokaryotes. Berlin: Springer; 2006.
    • (2006) Complex Intracellular Structures in Prokaryotes , vol.2
  • 6
    • 0015816557 scopus 로고
    • Functional organelles in prokaryotes: Polyhedral inclusions (carboxysomes) of Thiobacillus neapolitanus
    • Shively JM, Ball F, Brown DH, Saunders RE (1973) Functional organelles in prokaryotes: polyhedral inclusions (carboxysomes) of Thiobacillus neapolitanus. Science 182:584-586.
    • (1973) Science , vol.182 , pp. 584-586
    • Shively, J.M.1    Ball, F.2    Brown, D.H.3    Saunders, R.E.4
  • 8
    • 0018930056 scopus 로고
    • 2 fixing capacity in the obligate chemolithotroph Thiobacillus neapolitanus grown under different limitations in the chemostat
    • 2 fixing capacity in the obligate chemolithotroph Thiobacillus neapolitanus grown under different limitations in the chemostat. Arch Microbiol 124:185-189.
    • (1980) Arch Microbiol , vol.124 , pp. 185-189
    • Buedeker, R.F.1    Cannon, G.C.2    Kuenen, J.G.3    Shively, J.M.4
  • 11
    • 0027934799 scopus 로고
    • The control region of the pdu/cob regulon in Salmonella typhimurium
    • Chen P, Andersson DI, Roth JR (1994) The control region of the pdu/cob regulon in Salmonella typhimurium. J Bacteriol 176:5474-5482.
    • (1994) J Bacteriol , vol.176 , pp. 5474-5482
    • Chen, P.1    Andersson, D.I.2    Roth, J.R.3
  • 12
    • 33645964606 scopus 로고    scopus 로고
    • Conserving a volatile metabolite: A role for carboxysome-like organelles in Salmonella enterica
    • Penrod JT, Roth JR (2006) Conserving a volatile metabolite: a role for carboxysome-like organelles in Salmonella enterica. J Bacteriol 188:2865-2874.
    • (2006) J Bacteriol , vol.188 , pp. 2865-2874
    • Penrod, J.T.1    Roth, J.R.2
  • 13
    • 33645723005 scopus 로고    scopus 로고
    • Polyhedral organelles compartmenting bacterial metabolic processes
    • Bobik TA (2006) Polyhedral organelles compartmenting bacterial metabolic processes. Appl Microbiol Biotechnol 70:517-525.
    • (2006) Appl Microbiol Biotechnol , vol.70 , pp. 517-525
    • Bobik, T.A.1
  • 14
    • 0028301484 scopus 로고
    • Isolation and characterization of a carboxysome shell gene from Thiobacillus neapolitanus
    • English RS, Lorbach SC, Qin X, Shively JM (1994) Isolation and characterization of a carboxysome shell gene from Thiobacillus neapolitanus. Mol Microbiol 12:647-654.
    • (1994) Mol Microbiol , vol.12 , pp. 647-654
    • English, R.S.1    Lorbach, S.C.2    Qin, X.3    Shively, J.M.4
  • 15
    • 43149094164 scopus 로고    scopus 로고
    • Pfam 10 years on: 10,000 families and still growing
    • Sammut SJ, Finn RD, Bateman A (2008) Pfam 10 years on: 10,000 families and still growing. Brief Bioinf 9:210-219.
    • (2008) Brief Bioinf , vol.9 , pp. 210-219
    • Sammut, S.J.1    Finn, R.D.2    Bateman, A.3
  • 17
    • 0000066404 scopus 로고    scopus 로고
    • 2 concentrating mechanism in several cyanobacterial strains: A review of general physiological characteristics, genes, proteins, and recent advances
    • 2 concentrating mechanism in several cyanobacterial strains: a review of general physiological characteristics, genes, proteins, and recent advances. Can J Bot 76:973-1002.
    • (1998) Can J Bot , vol.76 , pp. 973-1002
    • Price, G.D.1    Sültemeyer, D.2    Klughammer, B.3    Ludwig, M.4    Badger, M.R.5
  • 18
    • 0032851358 scopus 로고    scopus 로고
    • The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins
    • Kofoid E, Rappleye C, Stojiljkovic I, Roth J (1999) The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. J Bacteriol 181:5317-5329.
    • (1999) J Bacteriol , vol.181 , pp. 5317-5329
    • Kofoid, E.1    Rappleye, C.2    Stojiljkovic, I.3    Roth, J.4
  • 19
    • 0028944586 scopus 로고
    • Ethanolamine utilization in Salmonella typhimurium: Nucleotide sequence, protein expression, and mutational analysis of the cchA cchB eutE eutJ eutG eutH gene cluster
    • Stojiljkovic I, Baeumler A, Heffron F (1995) Ethanolamine utilization in Salmonella typhimurium: nucleotide sequence, protein expression, and mutational analysis of the cchA cchB eutE eutJ eutG eutH gene cluster. J Bacteriol 177:1357-1366.
    • (1995) J Bacteriol , vol.177 , pp. 1357-1366
    • Stojiljkovic, I.1    Baeumler, A.2    Heffron, F.3
  • 20
    • 34548276117 scopus 로고    scopus 로고
    • The structure of isolated Synechococcus strain WH8102 carboxysomes as revealed by electron cryotomography
    • Iancu CV, Ding HJ, Morris DM, Dias DP, Gonzales AD, Martino A, Jensen GJ (2007) The structure of isolated Synechococcus strain WH8102 carboxysomes as revealed by electron cryotomography. J Mol Biol 372:764-773.
    • (2007) J Mol Biol , vol.372 , pp. 764-773
    • Iancu, C.V.1    Ding, H.J.2    Morris, D.M.3    Dias, D.P.4    Gonzales, A.D.5    Martino, A.6    Jensen, G.J.7
  • 23
    • 0001542995 scopus 로고
    • The structure of small viruses
    • Klug A, Caspar DL (1960) The structure of small viruses. Adv Virus Res 7:225-325.
    • (1960) Adv Virus Res , vol.7 , pp. 225-325
    • Klug, A.1    Caspar, D.L.2
  • 24
    • 0022409872 scopus 로고
    • Three-dimensional structure of poliovirus at 2.9 Å resolution
    • Hogle JM, Chow M, Filman DJ (1985) Three-dimensional structure of poliovirus at 2.9 Å resolution. Science 229:1358-1365.
    • (1985) Science , vol.229 , pp. 1358-1365
    • Hogle, J.M.1    Chow, M.2    Filman, D.J.3
  • 26
    • 0031588020 scopus 로고    scopus 로고
    • Quasi-equivalent viruses: A paradigm for protein assemblies
    • Johnson JE, Speir JA (1997) Quasi-equivalent viruses: a paradigm for protein assemblies. J Mol Biol 269:665-675.
    • (1997) J Mol Biol , vol.269 , pp. 665-675
    • Johnson, J.E.1    Speir, J.A.2
  • 27
    • 50849120064 scopus 로고    scopus 로고
    • Structure of the PduU shell protein from the Pdu microcompartment of Salmonella
    • Crowley C, Sawaya MR, Bobik TA, Yeates TO (2008) Structure of the PduU shell protein from the Pdu microcompartment of Salmonella. Structure 16:1324-1332.
    • (2008) Structure , vol.16 , pp. 1324-1332
    • Crowley, C.1    Sawaya, M.R.2    Bobik, T.A.3    Yeates, T.O.4
  • 28
    • 1642344759 scopus 로고    scopus 로고
    • Structural/functional homology between the bacterial and eukaryotic cytoskeletons
    • Amos LA, van den Ent F, Löwe J (2004) Structural/functional homology between the bacterial and eukaryotic cytoskeletons. Curr Opin Cell Biol 16:24-31.
    • (2004) Curr Opin Cell Biol , vol.16 , pp. 24-31
    • Amos, L.A.1    van den Ent, F.2    Löwe, J.3
  • 29
    • 38449090921 scopus 로고    scopus 로고
    • Microtubules: An overview
    • Wade RH (2007) Microtubules: an overview. Methods Mol Med 137:1-16.
    • (2007) Methods Mol Med , vol.137 , pp. 1-16
    • Wade, R.H.1
  • 30
    • 0033832615 scopus 로고    scopus 로고
    • Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences
    • Huynen M, Snel B, Lathe W, Bork P (2000) Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res 10:1204-1210.
    • (2000) Genome Res , vol.10 , pp. 1204-1210
    • Huynen, M.1    Snel, B.2    Lathe, W.3    Bork, P.4
  • 31
    • 34147118089 scopus 로고    scopus 로고
    • How electron cryotomography is opening a new window onto prokaryotic ultrastructure
    • Jensen GJ, Briegel A (2007) How electron cryotomography is opening a new window onto prokaryotic ultrastructure. Curr Opin Struct Biol 17:260-267.
    • (2007) Curr Opin Struct Biol , vol.17 , pp. 260-267
    • Jensen, G.J.1    Briegel, A.2
  • 32
    • 33846116032 scopus 로고    scopus 로고
    • Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C (2007) New developments in the Inter-Pro database. Nucleic Acids Res 35:D224-228.
    • Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C (2007) New developments in the Inter-Pro database. Nucleic Acids Res 35:D224-228.
  • 33
    • 34250838686 scopus 로고    scopus 로고
    • Self-assembly in the carboxysome: A viral capsid-like protein shell in bacterial cells
    • Yeates TO, Tsai Y, Tanaka S, Sawaya MR, Kerfeld CA (2007) Self-assembly in the carboxysome: a viral capsid-like protein shell in bacterial cells. Biochem Soc Trans 35:508-11.
    • (2007) Biochem Soc Trans , vol.35 , pp. 508-511
    • Yeates, T.O.1    Tsai, Y.2    Tanaka, S.3    Sawaya, M.R.4    Kerfeld, C.A.5
  • 34
    • 0027489247 scopus 로고
    • Common components in the assembly of type 4 fimbriae, DNA transfer systems, filamentous phage and protein-secretion apparatus: A general system for the formation of surface-associated protein complexes
    • Hobbs M, Mattick JS (1993) Common components in the assembly of type 4 fimbriae, DNA transfer systems, filamentous phage and protein-secretion apparatus: a general system for the formation of surface-associated protein complexes. Mol Microbiol 10:233-43.
    • (1993) Mol Microbiol , vol.10 , pp. 233-243
    • Hobbs, M.1    Mattick, J.S.2
  • 35
    • 0028261412 scopus 로고
    • Gas vesicles
    • Walsby AE (1994) Gas vesicles. Microbiol Rev 58:94-144.
    • (1994) Microbiol Rev , vol.58 , pp. 94-144
    • Walsby, A.E.1
  • 36
    • 0033593206 scopus 로고    scopus 로고
    • Characterization of a phycoerythrin without alpha-subunits from a unicellular red alga
    • Thomas JC, Passaquet C (1999) Characterization of a phycoerythrin without alpha-subunits from a unicellular red alga. J Biol Chem 274:2472-82.
    • (1999) J Biol Chem , vol.274 , pp. 2472-2482
    • Thomas, J.C.1    Passaquet, C.2
  • 37
    • 34247221579 scopus 로고    scopus 로고
    • The tad locus: Postcards from the widespread colonization island
    • Tomich M, Planet PJ, Figurski DH (2007) The tad locus: postcards from the widespread colonization island. Nat Rev Microbiol 5:363-75.
    • (2007) Nat Rev Microbiol , vol.5 , pp. 363-375
    • Tomich, M.1    Planet, P.J.2    Figurski, D.H.3
  • 38
    • 39649096716 scopus 로고    scopus 로고
    • Structure of the minor pseudopilin EpsH from the Type 2 secretion system of Vibrio cholerae
    • Yanez ME, Korotkov KV, Abendroth J, Hol WG (2008) Structure of the minor pseudopilin EpsH from the Type 2 secretion system of Vibrio cholerae. J Mol Biol 377:91-103.
    • (2008) J Mol Biol , vol.377 , pp. 91-103
    • Yanez, M.E.1    Korotkov, K.V.2    Abendroth, J.3    Hol, W.G.4
  • 39
    • 33749345746 scopus 로고    scopus 로고
    • The TadV protein of Actinobacillus actinomycetemcomitans is a novel aspartic acid prepilin peptidase required for maturation of the Flp1 pilin and TadE and TadF pseudopilins
    • Tomich M, Fine DH, Figurski DH (2006) The TadV protein of Actinobacillus actinomycetemcomitans is a novel aspartic acid prepilin peptidase required for maturation of the Flp1 pilin and TadE and TadF pseudopilins. J Bacteriol 188:6899-914.
    • (2006) J Bacteriol , vol.188 , pp. 6899-6914
    • Tomich, M.1    Fine, D.H.2    Figurski, D.H.3
  • 40
    • 0036195722 scopus 로고    scopus 로고
    • Alpha-crystallin-type heat shock proteins: Socializing minichaperones in the context of a multichaperone network
    • Narberhaus F (2002) Alpha-crystallin-type heat shock proteins: socializing minichaperones in the context of a multichaperone network. Microbiol Mol Biol Rev 66:64-93.
    • (2002) Microbiol Mol Biol Rev , vol.66 , pp. 64-93
    • Narberhaus, F.1
  • 41
    • 0034711315 scopus 로고    scopus 로고
    • Chaperone activity and homo- and hetero-oligomer formation of bacterial small heat shock proteins
    • Studer S, Narberhaus F (2000) Chaperone activity and homo- and hetero-oligomer formation of bacterial small heat shock proteins. J Biol Chem 275:37212-37218.
    • (2000) J Biol Chem , vol.275 , pp. 37212-37218
    • Studer, S.1    Narberhaus, F.2
  • 42
    • 0020394792 scopus 로고
    • Phycobilisomes: Structure and dynamics
    • Glazer AN (1982) Phycobilisomes: structure and dynamics. Annu Rev Microbiol 36:173-198.
    • (1982) Annu Rev Microbiol , vol.36 , pp. 173-198
    • Glazer, A.N.1
  • 43
    • 0022429470 scopus 로고
    • X-ray crystallographic structure of the light-harvesting biliprotein C-phycocyanin from the thermophilic cyanobacterium Mastigocladus laminosus and its resemblance to globin structures
    • Schirmer T, Bode W, Huber R, Sidler W, Zuber H (1985) X-ray crystallographic structure of the light-harvesting biliprotein C-phycocyanin from the thermophilic cyanobacterium Mastigocladus laminosus and its resemblance to globin structures. J Mol Biol 184:257-277.
    • (1985) J Mol Biol , vol.184 , pp. 257-277
    • Schirmer, T.1    Bode, W.2    Huber, R.3    Sidler, W.4    Zuber, H.5
  • 44
    • 2442589577 scopus 로고    scopus 로고
    • Type IV pilus structure and bacterial pathogenicity
    • Craig L, Pique ME, Tainer JA (2004) Type IV pilus structure and bacterial pathogenicity. Nat Rev Microbiol 2:363-378.
    • (2004) Nat Rev Microbiol , vol.2 , pp. 363-378
    • Craig, L.1    Pique, M.E.2    Tainer, J.A.3
  • 45
    • 33748667977 scopus 로고    scopus 로고
    • Characterization of the pilin ortholog of the Helicobacter pylori type IV cag pathogenicity apparatus, a surface-associated protein expressed during infection
    • Andrzejewska J, Lee SK, Olbermann P, Lotzing N, Katzowitsch E, Linz B, Achtman M, Kado CI, Suerbaum S, Josenhans C (2006) Characterization of the pilin ortholog of the Helicobacter pylori type IV cag pathogenicity apparatus, a surface-associated protein expressed during infection. J Bacteriol 188:5865-5877.
    • (2006) J Bacteriol , vol.188 , pp. 5865-5877
    • Andrzejewska, J.1    Lee, S.K.2    Olbermann, P.3    Lotzing, N.4    Katzowitsch, E.5    Linz, B.6    Achtman, M.7    Kado, C.I.8    Suerbaum, S.9    Josenhans, C.10
  • 46
    • 0001522673 scopus 로고
    • Starch-gel electrophoresis - application to the classification of pituitary proteins and polypeptides
    • Ferguson KA (1964) Starch-gel electrophoresis - application to the classification of pituitary proteins and polypeptides. Metab Clin Exp 13:985-1002.
    • (1964) Metab Clin Exp , vol.13 , pp. 985-1002
    • Ferguson, K.A.1
  • 47
    • 0014310082 scopus 로고
    • Size and charge isomer separation and estimation of molecular weights of proteins by disc gel electrophoresis
    • Hedrick JL, Smith AJ (1968) Size and charge isomer separation and estimation of molecular weights of proteins by disc gel electrophoresis. Arch Biochem Biophys 126:155-164.
    • (1968) Arch Biochem Biophys , vol.126 , pp. 155-164
    • Hedrick, J.L.1    Smith, A.J.2
  • 48
    • 5444276327 scopus 로고    scopus 로고
    • The role of the sulfur globule proteins of Allochromatium vinosum: Mutagenesis of the sulfur globule protein genes and expression studies by real-time RT-PCR
    • Prange A, Engelhardt H, Truper HG, Dahl C (2004) The role of the sulfur globule proteins of Allochromatium vinosum: mutagenesis of the sulfur globule protein genes and expression studies by real-time RT-PCR. Arch Microbiol 182:165-174.
    • (2004) Arch Microbiol , vol.182 , pp. 165-174
    • Prange, A.1    Engelhardt, H.2    Truper, H.G.3    Dahl, C.4
  • 49
    • 0031946732 scopus 로고    scopus 로고
    • Molecular genetic evidence for extracytoplasmic localization of sulfur globules in Chromatium vinosum
    • Pattaragulwanit K, Brune DC, Trüper HG, Dahl C (1998) Molecular genetic evidence for extracytoplasmic localization of sulfur globules in Chromatium vinosum. Arch Microbiol 169:434-444.
    • (1998) Arch Microbiol , vol.169 , pp. 434-444
    • Pattaragulwanit, K.1    Brune, D.C.2    Trüper, H.G.3    Dahl, C.4
  • 50
    • 36549036251 scopus 로고    scopus 로고
    • Isolated poly(3-hydroxybutyrate) (PHB) granules are complex bacterial organelles catalyzing formation of PHB from acetyl coenzyme A (CoA) and degradation of PHB to acetyl-CoA
    • Uchino K, Saito T, Gebauer B, Jendrossek D (2007) Isolated poly(3-hydroxybutyrate) (PHB) granules are complex bacterial organelles catalyzing formation of PHB from acetyl coenzyme A (CoA) and degradation of PHB to acetyl-CoA. J Bacteriol 189:8250-8256.
    • (2007) J Bacteriol , vol.189 , pp. 8250-8256
    • Uchino, K.1    Saito, T.2    Gebauer, B.3    Jendrossek, D.4
  • 51
    • 4344627575 scopus 로고    scopus 로고
    • The complex structure of polyhydroxybutyrate (PHB) granules: Four orthologous and paralogous phasins occur in Ralstonia eutropha
    • Potter M, Muller H, Reinecke F, Wieczorek R, Fricke F, Bowien B, Friedrich B, Steinbuchel A (2004) The complex structure of polyhydroxybutyrate (PHB) granules: four orthologous and paralogous phasins occur in Ralstonia eutropha. Microbiology 150:2301-2311.
    • (2004) Microbiology , vol.150 , pp. 2301-2311
    • Potter, M.1    Muller, H.2    Reinecke, F.3    Wieczorek, R.4    Fricke, F.5    Bowien, B.6    Friedrich, B.7    Steinbuchel, A.8
  • 53
    • 0031748312 scopus 로고    scopus 로고
    • Structural characteristics of halobacterial gas vesicles
    • Offner S, Ziese U, Wanner G, Typke D, Pfeifer F (1998) Structural characteristics of halobacterial gas vesicles. Microbiology 144 (Pt 5):1331-1342.
    • (1998) Microbiology , vol.144 , Issue.PART 5 , pp. 1331-1342
    • Offner, S.1    Ziese, U.2    Wanner, G.3    Typke, D.4    Pfeifer, F.5
  • 54
    • 2342660728 scopus 로고    scopus 로고
    • Complexity of gas vesicle biogenesis in Halobacterium sp. strain NRC-1: Identification of five new proteins
    • Shukla HD, DasSarma S (2004) Complexity of gas vesicle biogenesis in Halobacterium sp. strain NRC-1: identification of five new proteins. J Bacteriol 186:3182-3186.
    • (2004) J Bacteriol , vol.186 , pp. 3182-3186
    • Shukla, H.D.1    DasSarma, S.2
  • 56
    • 16844368450 scopus 로고    scopus 로고
    • The small heat shock protein IbpA of Escherichia coli cooperates with IbpB in stabilization of thermally aggregated proteins in a disaggregation competent state
    • Matuszewska M, Kuczynska-Wisnik D, Laskowska E, Liberek K (2005) The small heat shock protein IbpA of Escherichia coli cooperates with IbpB in stabilization of thermally aggregated proteins in a disaggregation competent state. J Biol Chem 280:12292-12298.
    • (2005) J Biol Chem , vol.280 , pp. 12292-12298
    • Matuszewska, M.1    Kuczynska-Wisnik, D.2    Laskowska, E.3    Liberek, K.4
  • 57
    • 0032169688 scopus 로고    scopus 로고
    • PQS: A protein quaternary structure file server
    • Henrick K, Thornton JM (1998) PQS: a protein quaternary structure file server. Trends Biochem Sci 23:358-361.
    • (1998) Trends Biochem Sci , vol.23 , pp. 358-361
    • Henrick, K.1    Thornton, J.M.2
  • 58
  • 59
    • 33748092050 scopus 로고    scopus 로고
    • Genome reviews: Standardizing content and representation of information about complete genomes
    • Sterk P, Kersey PJ, Apweiler R (2006) Genome reviews: standardizing content and representation of information about complete genomes. OMICS 10:114-118.
    • (2006) OMICS , vol.10 , pp. 114-118
    • Sterk, P.1    Kersey, P.J.2    Apweiler, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.