Proteome Organization in a Genome-Reduced Bacterium

被引:357
作者
Kuehner, Sebastian [1 ]
van Noort, Vera [1 ]
Betts, Matthew J. [1 ]
Leo-Macias, Alejandra [1 ]
Batisse, Claire [1 ]
Rode, Michaela [1 ]
Yamada, Takuji [1 ]
Maier, Tobias [2 ]
Bader, Samuel [1 ]
Beltran-Alvarez, Pedro [1 ]
Castano-Diez, Daniel [1 ]
Chen, Wei-Hua [1 ]
Devos, Damien [1 ]
Gueell, Marc [2 ]
Norambuena, Tomas [3 ]
Racke, Ines [1 ]
Rybin, Vladimir [1 ]
Schmidt, Alexander [4 ]
Yus, Eva [2 ]
Aebersold, Ruedi [4 ]
Herrmann, Richard [5 ]
Boettcher, Bettina [1 ]
Frangakis, Achilleas S. [1 ]
Russell, Robert B. [1 ]
Serrano, Luis [2 ,6 ]
Bork, Peer [1 ]
Gavin, Anne-Claude [1 ]
机构
[1] European Mol Biol Lab, D-69117 Heidelberg, Germany
[2] Univ Pompeu Fabra, Ctr Regulac Genom, Barcelona 08003, Spain
[3] Pontificia Univ Catolica Chile, Santiago, Chile
[4] ETH, CH-8093 Zurich, Switzerland
[5] Univ Heidelberg, Zentrum Mol Biol, D-69120 Heidelberg, Germany
[6] ICREA, Barcelona 08010, Spain
基金
欧洲研究理事会;
关键词
TRANSFER-RNA SYNTHETASES; MYCOPLASMA-PNEUMONIAE; ESCHERICHIA-COLI; INTERACTION MAP; HELICOBACTER-PYLORI; COMPLEX-FORMATION; CELL-CYCLE; PROTEINS; SEQUENCE; DNA;
D O I
10.1126/science.1176343
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
The genome of Mycoplasma pneumoniae is among the smallest found in self-replicating organisms. To study the basic principles of bacterial proteome organization, we used tandem affinity purification-mass spectrometry (TAP-MS) in a proteome-wide screen. The analysis revealed 62 homomultimeric and 116 heteromultimeric soluble protein complexes, of which the majority are novel. About a third of the heteromultimeric complexes show higher levels of proteome organization, including assembly into larger, multiprotein complex entities, suggesting sequential steps in biological processes, and extensive sharing of components, implying protein multifunctionality. Incorporation of structural models for 484 proteins, single-particle electron microscopy, and cellular electron tomograms provided supporting structural details for this proteome organization. The data set provides a blueprint of the minimal cellular machinery required for life.
引用
收藏
页码:1235 / 1240
页数:6
相关论文
共 49 条
[1]   The molecular architecture of cadherins in native epidermal desmosomes [J].
Al-Amoudi, Ashraf ;
Diez, Daniel Castano ;
Betts, Matthew J. ;
Frangakis, Achilleas S. .
NATURE, 2007, 450 (7171) :832-U8
[2]   Large-scale identification of protein-protein interaction of Escherichia coli K-12 [J].
Arifuzzaman, M ;
Maeda, M ;
Itoh, A ;
Nishikata, K ;
Takita, C ;
Saito, R ;
Ara, T ;
Nakahigashi, K ;
Huang, HC ;
Hirai, A ;
Tsuzuki, K ;
Nakamura, S ;
Altaf-Ul-Amin, M ;
Oshima, T ;
Baba, T ;
Yamamoto, N ;
Kawamura, T ;
Ioka-Nakamichi, T ;
Kitagawa, M ;
Tomita, M ;
Kanaya, S ;
Wada, C ;
Mori, H .
GENOME RESEARCH, 2006, 16 (05) :686-691
[3]   Announcing the worldwide Protein Data Bank [J].
Berman, H ;
Henrick, K ;
Nakamura, H .
NATURE STRUCTURAL BIOLOGY, 2003, 10 (12) :980-980
[4]   Towards cellular systems in 4D [J].
Bork, P ;
Serrano, L .
CELL, 2005, 121 (04) :507-509
[5]   Interaction network containing conserved and essential protein complexes in Escherichia coli [J].
Butland, G ;
Peregrín-Alvarez, JM ;
Li, J ;
Yang, WH ;
Yang, XC ;
Canadien, V ;
Starostine, A ;
Richards, D ;
Beattie, B ;
Krogan, N ;
Davey, M ;
Parkinson, J ;
Greenblatt, J ;
Emili, A .
NATURE, 2005, 433 (7025) :531-537
[6]   Re-annotating the Mycoplasma pneumoniae genome sequence:: adding value, function and reading frames [J].
Dandekar, T ;
Huynen, M ;
Regula, JT ;
Ueberle, B ;
Zimmermann, CU ;
Andrade, MA ;
Doerks, T ;
Sánchez-Pulido, L ;
Snel, B ;
Suyama, M ;
Yuan, YP ;
Herrmann, R ;
Bork, P .
NUCLEIC ACIDS RESEARCH, 2000, 28 (17) :3278-3288
[7]   Dynamic complex formation during the yeast cell cycle [J].
de Lichtenberg, U ;
Jensen, LJ ;
Brunak, S ;
Bork, P .
SCIENCE, 2005, 307 (5710) :724-727
[8]  
Desiere F, 2006, NUCLEIC ACIDS RES, V34, pD655, DOI [10.1093/nar/gkj040, 10.1007/978-1-60761-444-9_19]
[9]  
Gasteiger E., 2005, The Proteomics Protocols Handbook, P571, DOI [DOI 10.1385/1-59259-890-0:571, 10.1385/159259-890-0:571, DOI 10.1385/159259-890-0:571]
[10]   Proteome survey reveals modularity of the yeast cell machinery [J].
Gavin, AC ;
Aloy, P ;
Grandi, P ;
Krause, R ;
Boesche, M ;
Marzioch, M ;
Rau, C ;
Jensen, LJ ;
Bastuck, S ;
Dümpelfeld, B ;
Edelmann, A ;
Heurtier, MA ;
Hoffman, V ;
Hoefert, C ;
Klein, K ;
Hudak, M ;
Michon, AM ;
Schelder, M ;
Schirle, M ;
Remor, M ;
Rudi, T ;
Hooper, S ;
Bauer, A ;
Bouwmeester, T ;
Casari, G ;
Drewes, G ;
Neubauer, G ;
Rick, JM ;
Kuster, B ;
Bork, P ;
Russell, RB ;
Superti-Furga, G .
NATURE, 2006, 440 (7084) :631-636