Journal ArticleDOI
Proteome survey reveals modularity of the yeast cell machinery
Anne-Claude Gavin,Patrick Aloy,Paola Grandi,Roland Krause,Markus Boesche,Martina Marzioch,Christina Rau,Lars Juhl Jensen,Sonja Bastuck,Birgit Dümpelfeld,Angela Edelmann,Marie-Anne Heurtier,Verena Hoffman,Christian Hoefert,Karin Klein,Manuela Hudak,Anne-Marie Michon,Malgorzata Schelder,Markus Schirle,Marita Remor,Tatjana Rudi,Sean D. Hooper,Andreas Bauer,Tewis Bouwmeester,Georg Casari,Gerard Drewes,Gitte Neubauer,Jens Rick,Bernhard Kuster,Peer Bork,Robert B. Russell,Giulio Superti-Furga +31 more
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TLDR
This study reports the first genome-wide screen for complexes in an organism, budding yeast, using affinity purification and mass spectrometry and provides the largest collection of physically determined eukaryotic cellular machines so far and a platform for biological data integration and modelling.Abstract:
Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. Here we report the first genome-wide screen for complexes in an organism, budding yeast, using affinity purification and mass spectrometry. Through systematic tagging of open reading frames (ORFs), the majority of complexes were purified several times, suggesting screen saturation. The richness of the data set enabled a de novo characterization of the composition and organization of the cellular machinery. The ensemble of cellular proteins partitions into 491 complexes, of which 257 are novel, that differentially combine with additional attachment proteins or protein modules to enable a diversification of potential functions. Support for this modular organization of the proteome comes from integration with available data on expression, localization, function, evolutionary conservation, protein structure and binary interactions. This study provides the largest collection of physically determined eukaryotic cellular machines so far and a platform for biological data integration and modelling.read more
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Journal ArticleDOI
The genetic landscape of a cell.
Michael Costanzo,Anastasia Baryshnikova,Jeremy Bellay,Yungil Kim,Eric D. Spear,Carolyn S. Sevier,Huiming Ding,Judice L. Y. Koh,Kiana Toufighi,Sara Mostafavi,Jeany Prinz,Robert P. St.Onge,Benjamin VanderSluis,Taras Makhnevych,Franco J. Vizeacoumar,Solmaz Alizadeh,Sondra Bahr,Renee L. Brost,Yiqun Chen,Murat Cokol,Raamesh Deshpande,Zhijian Li,Zhen Yuan Lin,Wendy Liang,Michaela Marback,Jadine Paw,Bryan Joseph San Luis,Ermira Shuteriqi,Amy Hin Yan Tong,Nydia Van Dyk,Iain M. Wallace,Joseph Whitney,Matthew T. Weirauch,Guoqing Zhong,Hongwei Zhu,Walid A. Houry,Michael Brudno,Sasan Ragibizadeh,Balázs Papp,Csaba Pál,Frederick P. Roth,Guri Giaever,Corey Nislow,Olga G. Troyanskaya,Howard Bussey,Gary D. Bader,Anne-Claude Gingras,Quaid Morris,Philip M. Kim,Chris A. Kaiser,Chad L. Myers,Brenda J. Andrews,Charles Boone +52 more
TL;DR: A network based on genetic interaction profiles reveals a functional map of the cell in which genes of similar biological processes cluster together in coherent subsets, and highly correlated profiles delineate specific pathways to define gene function.
Journal ArticleDOI
Link communities reveal multiscale complexity in networks
TL;DR: In this article, the authors show that link communities are fundamental building blocks that reveal overlap and hierarchical organization in networks, and show that a large social network contains hierarchically organized community structures spanning inner-city to regional scales while maintaining pervasive overlap.
Journal ArticleDOI
High-Quality Binary Protein Interaction Map of the Yeast Interactome Network
Haiyuan Yu,Pascal Braun,Muhammed A. Yildirim,Irma Lemmens,Kavitha Venkatesan,Julie M. Sahalie,Tomoko Hirozane-Kishikawa,Fana Gebreab,Nan Li,Nicolas Simonis,Tong Hao,Jean François Rual,Amélie Dricot,Alexei Vazquez,Ryan R. Murray,Christophe Simon,Leah Tardivo,Stanley Tam,Nenad Svrzikapa,Changyu Fan,Anne-Sophie De Smet,Adriana Motyl,Michael E. Hudson,Juyong Park,Juyong Park,Xiaofeng Xin,Michael E. Cusick,Troy Moore,Charles Boone,Michael Snyder,Frederick P. Roth,Albert-László Barabási,Albert-László Barabási,Jan Tavernier,David E. Hill,Marc Vidal +35 more
TL;DR: A comparative quality assessment of current yeast interactome data sets is carried out, demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information.
Journal ArticleDOI
Interactome Networks and Human Disease
Marc Vidal,Michael E. Cusick,Albert-László Barabási,Albert-László Barabási,Albert-László Barabási +4 more
TL;DR: In this paper, the authors discuss different types of interactome networks and the insights that can come from analyzing them, including how they can be mapped and integrated with each other, what global properties are starting to emerge from interactome network models, and how these properties may relate to human disease.
Journal ArticleDOI
Widespread translational inhibition by plant miRNAs and siRNAs.
Peter Brodersen,Lali Sakvarelidze-Achard,Marianne Bruun-Rasmussen,Patrice Dunoyer,Yoshiharu Y. Yamamoto,Leslie E. Sieburth,Olivier Voinnet +6 more
TL;DR: Analysis provides evidence that plant miRNA–guided silencing has a widespread translational inhibitory component that is genetically separable from endonucleolytic cleavage, and shows that the same is true of silencing mediated by small interfering RNA (siRNA) populations.
References
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Lethality and centrality in protein networks
TL;DR: It is demonstrated that the phenotypic consequence of a single gene deletion in the yeast Saccharomyces cerevisiae is affected to a large extent by the topological position of its protein product in the complex hierarchical web of molecular interactions.
Journal ArticleDOI
Functional organization of the yeast proteome by systematic analysis of protein complexes
Anne-Claude Gavin,Markus Bösche,Roland Krause,Paola Grandi,Martina Marzioch,Andreas Bauer,Jörg Schultz,Jens Rick,Anne-Marie Michon,Cristina-Maria Cruciat,Marita Remor,Christian Höfert,Malgorzata Schelder,Miro Brajenovic,Heinz Ruffner,Alejandro Merino,Karin Klein,Manuela Hudak,David Dickson,Tatjana Rudi,Volker Gnau,Angela Bauch,Sonja Bastuck,Bettina Huhse,Christina Leutwein,Marie-Anne Heurtier,Richard R. Copley,Angela Edelmann,Erich Querfurth,Vladimir Rybin,Gerard Drewes,Manfred Raida,Tewis Bouwmeester,Peer Bork,Bertrand Séraphin,Bernhard Kuster,Gitte Neubauer,Giulio Superti-Furga +37 more
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Journal ArticleDOI
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
Peter Uetz,Loic Giot,Gerard Cagney,Traci A. Mansfield,Richard S. Judson,James R. Knight,Daniel Lockshon,Vaibhav A. Narayan,Maithreyan Srinivasan,Pascale Pochart,Alia Qureshi-Emili,Ying Li,Brian C. Godwin,Diana Conover,Theodore S. Kalbfleisch,Govindan Vijayadamodar,Meijia Yang,Mark Johnston,Stanley Fields,Jonathan M. Rothberg +19 more
TL;DR: Examination of large-scale yeast two-hybrid screens reveals interactions that place functionally unclassified proteins in a biological context, interactions between proteins involved in the same biological function, and interactions that link biological functions together into larger cellular processes.
Journal ArticleDOI
Large-scale analysis of the yeast proteome by multidimensional protein identification technology.
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Journal ArticleDOI
An automated method for finding molecular complexes in large protein interaction networks.
TL;DR: A novel graph theoretic clustering algorithm, "Molecular Complex Detection" (MCODE), that detects densely connected regions in large protein-protein interaction networks that may represent molecular complexes is described.
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