Why do essential proteins tend to be clustered in the yeast interactome network?

被引:15
作者
Lu, Chenqi [1 ]
Hu, Xiaohua [1 ]
Wang, Guiying [1 ,2 ]
Leach, L. J. [3 ]
Yang, Shengjie [1 ]
Kearsey, M. J. [3 ]
Luo, Z. W. [1 ,3 ]
机构
[1] Fudan Univ, Lab Populat & Quantitat Genet, Inst Biostat, SKLGE,Sch Life Sci, Shanghai 200433, Peoples R China
[2] Tongji Univ, Sch Life Sci & Technol, Shanghai 200092, Peoples R China
[3] Univ Birmingham, Sch Biosci, Birmingham B15 2TT, W Midlands, England
基金
英国生物技术与生命科学研究理事会;
关键词
SACCHAROMYCES-CEREVISIAE; COMPLEXES; MODULARITY; CENTRALITY; LETHALITY; MAP;
D O I
10.1039/b921069e
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Recently, the debate on the centrality-lethality rule is resolved by the "second-generation" high-throughput Y2H data from the yeast interactome network, which suggests no significant correlation between the degree of connectedness and essentiality of proteins. However, it is still not clear why essential proteins strongly tend to interact with each other. Previously, the concept of essential protein-protein interactions was proposed to explain the mechanism underlying the clustering of essential proteins. In this article we show that 67 to 75% of the excessive interactions between essential proteins (IBEPs) in the yeast interactome network can be attributed to interactions within protein complexes characterised by the same deletion phenotype for subunits within the complex. Furthermore, 20 to 78% of the excess in IBEPs are caused by the strongly modular structure of the network and by variation in protein essentiality among modules. Not only do proteins function as an interactive network in cellular processes, but furthermore, many proteins do not take part in the network alone, but integrate into protein complexes and many functionally related complexes integrate into modules. So, the local structure of protein complexes as both functional and structural modules are the main contributory factors in the clustering of essential proteins.
引用
收藏
页码:871 / 877
页数:7
相关论文
共 32 条
[1]   Analyzing yeast protein-protein interaction data obtained from different sources [J].
Bader, GD ;
Hogue, CWV .
NATURE BIOTECHNOLOGY, 2002, 20 (10) :991-997
[2]   Evolutionary and physiological importance of hub proteins [J].
Batada, Nizar N. ;
Hurst, Laurence D. ;
Tyers, Mike .
PLOS COMPUTATIONAL BIOLOGY, 2006, 2 (07) :748-756
[3]   Protein domain connectivity and essentiality [J].
Costa, L. da F. ;
Rodrigues, F. A. ;
Travieso, G. .
APPLIED PHYSICS LETTERS, 2006, 89 (17)
[4]   Comparing community structure identification -: art. no. P09008 [J].
Danon, L ;
Díaz-Guilera, A ;
Duch, J ;
Arenas, A .
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, 2005, :219-228
[5]   Bioinformatics analysis of experimentally determined protein complexes in the yeast Saccharomyces cerevisiae [J].
Dezso, Z ;
Oltvai, ZN ;
Barabási, AL .
GENOME RESEARCH, 2003, 13 (11) :2450-2454
[6]   Functional organization of the yeast proteome by systematic analysis of protein complexes [J].
Gavin, AC ;
Bösche, M ;
Krause, R ;
Grandi, P ;
Marzioch, M ;
Bauer, A ;
Schultz, J ;
Rick, JM ;
Michon, AM ;
Cruciat, CM ;
Remor, M ;
Höfert, C ;
Schelder, M ;
Brajenovic, M ;
Ruffner, H ;
Merino, A ;
Klein, K ;
Hudak, M ;
Dickson, D ;
Rudi, T ;
Gnau, V ;
Bauch, A ;
Bastuck, S ;
Huhse, B ;
Leutwein, C ;
Heurtier, MA ;
Copley, RR ;
Edelmann, A ;
Querfurth, E ;
Rybin, V ;
Drewes, G ;
Raida, M ;
Bouwmeester, T ;
Bork, P ;
Seraphin, B ;
Kuster, B ;
Neubauer, G ;
Superti-Furga, G .
NATURE, 2002, 415 (6868) :141-147
[7]   Functional profiling of the Saccharomyces cerevisiae genome [J].
Giaever, G ;
Chu, AM ;
Ni, L ;
Connelly, C ;
Riles, L ;
Véronneau, S ;
Dow, S ;
Lucau-Danila, A ;
Anderson, K ;
André, B ;
Arkin, AP ;
Astromoff, A ;
El Bakkoury, M ;
Bangham, R ;
Benito, R ;
Brachat, S ;
Campanaro, S ;
Curtiss, M ;
Davis, K ;
Deutschbauer, A ;
Entian, KD ;
Flaherty, P ;
Foury, F ;
Garfinkel, DJ ;
Gerstein, M ;
Gotte, D ;
Güldener, U ;
Hegemann, JH ;
Hempel, S ;
Herman, Z ;
Jaramillo, DF ;
Kelly, DE ;
Kelly, SL ;
Kötter, P ;
LaBonte, D ;
Lamb, DC ;
Lan, N ;
Liang, H ;
Liao, H ;
Liu, L ;
Luo, CY ;
Lussier, M ;
Mao, R ;
Menard, P ;
Ooi, SL ;
Revuelta, JL ;
Roberts, CJ ;
Rose, M ;
Ross-Macdonald, P ;
Scherens, B .
NATURE, 2002, 418 (6896) :387-391
[8]   Functional cartography of complex metabolic networks [J].
Guimerà, R ;
Amaral, LAN .
NATURE, 2005, 433 (7028) :895-900
[9]   Molecular evolution in large genetic networks: Does connectivity equal constraint? [J].
Hahn, MW ;
Conant, GC ;
Wagner, A .
JOURNAL OF MOLECULAR EVOLUTION, 2004, 58 (02) :203-211
[10]   Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks [J].
Hahn, MW ;
Kern, AD .
MOLECULAR BIOLOGY AND EVOLUTION, 2005, 22 (04) :803-806