Literature DB >> 18692475

A protein domain-based interactome network for C. elegans early embryogenesis.

Mike Boxem1, Zoltan Maliga, Niels Klitgord, Na Li, Irma Lemmens, Miyeko Mana, Lorenzo de Lichtervelde, Joram D Mul, Diederik van de Peut, Maxime Devos, Nicolas Simonis, Muhammed A Yildirim, Murat Cokol, Huey-Ling Kao, Anne-Sophie de Smet, Haidong Wang, Anne-Lore Schlaitz, Tong Hao, Stuart Milstein, Changyu Fan, Mike Tipsword, Kevin Drew, Matilde Galli, Kahn Rhrissorrakrai, David Drechsel, Daphne Koller, Frederick P Roth, Lilia M Iakoucheva, A Keith Dunker, Richard Bonneau, Kristin C Gunsalus, David E Hill, Fabio Piano, Jan Tavernier, Sander van den Heuvel, Anthony A Hyman, Marc Vidal.   

Abstract

Many protein-protein interactions are mediated through independently folding modular domains. Proteome-wide efforts to model protein-protein interaction or "interactome" networks have largely ignored this modular organization of proteins. We developed an experimental strategy to efficiently identify interaction domains and generated a domain-based interactome network for proteins involved in C. elegans early-embryonic cell divisions. Minimal interacting regions were identified for over 200 proteins, providing important information on their domain organization. Furthermore, our approach increased the sensitivity of the two-hybrid system, resulting in a more complete interactome network. This interactome modeling strategy revealed insights into C. elegans centrosome function and is applicable to other biological processes in this and other organisms.

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Year:  2008        PMID: 18692475      PMCID: PMC2596478          DOI: 10.1016/j.cell.2008.07.009

Source DB:  PubMed          Journal:  Cell        ISSN: 0092-8674            Impact factor:   41.582


  59 in total

1.  High-throughput yeast two-hybrid assays for large-scale protein interaction mapping.

Authors:  A J Walhout; M Vidal
Journal:  Methods       Date:  2001-07       Impact factor: 3.608

Review 2.  Assembly of cell regulatory systems through protein interaction domains.

Authors:  Tony Pawson; Piers Nash
Journal:  Science       Date:  2003-04-18       Impact factor: 47.728

3.  Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans.

Authors:  Fabio Piano; Aaron J Schetter; Diane G Morton; Kristin C Gunsalus; Valerie Reinke; Stuart K Kim; Kenneth J Kemphues
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4.  Functional organization of the yeast proteome by systematic analysis of protein complexes.

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Journal:  Nature       Date:  2002-01-10       Impact factor: 49.962

5.  Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans.

Authors:  B Sönnichsen; L B Koski; A Walsh; P Marschall; B Neumann; M Brehm; A-M Alleaume; J Artelt; P Bettencourt; E Cassin; M Hewitson; C Holz; M Khan; S Lazik; C Martin; B Nitzsche; M Ruer; J Stamford; M Winzi; R Heinkel; M Röder; J Finell; H Häntsch; S J M Jones; M Jones; F Piano; K C Gunsalus; K Oegema; P Gönczy; A Coulson; A A Hyman; C J Echeverri
Journal:  Nature       Date:  2005-03-24       Impact factor: 49.962

6.  Roles for 147 embryonic lethal genes on C.elegans chromosome I identified by RNA interference and video microscopy.

Authors:  P Zipperlen; A G Fraser; R S Kamath; M Martinez-Campos; J Ahringer
Journal:  EMBO J       Date:  2001-08-01       Impact factor: 11.598

7.  A comprehensive two-hybrid analysis to explore the yeast protein interactome.

Authors:  T Ito; T Chiba; R Ozawa; M Yoshida; M Hattori; Y Sakaki
Journal:  Proc Natl Acad Sci U S A       Date:  2001-03-13       Impact factor: 11.205

8.  A map of the interactome network of the metazoan C. elegans.

Authors:  Siming Li; Christopher M Armstrong; Nicolas Bertin; Hui Ge; Stuart Milstein; Mike Boxem; Pierre-Olivier Vidalain; Jing-Dong J Han; Alban Chesneau; Tong Hao; Debra S Goldberg; Ning Li; Monica Martinez; Jean-François Rual; Philippe Lamesch; Lai Xu; Muneesh Tewari; Sharyl L Wong; Lan V Zhang; Gabriel F Berriz; Laurent Jacotot; Philippe Vaglio; Jérôme Reboul; Tomoko Hirozane-Kishikawa; Qianru Li; Harrison W Gabel; Ahmed Elewa; Bridget Baumgartner; Debra J Rose; Haiyuan Yu; Stephanie Bosak; Reynaldo Sequerra; Andrew Fraser; Susan E Mango; William M Saxton; Susan Strome; Sander Van Den Heuvel; Fabio Piano; Jean Vandenhaute; Claude Sardet; Mark Gerstein; Lynn Doucette-Stamm; Kristin C Gunsalus; J Wade Harper; Michael E Cusick; Frederick P Roth; David E Hill; Marc Vidal
Journal:  Science       Date:  2004-01-02       Impact factor: 47.728

9.  SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent.

Authors:  Norman E Davey; Denis C Shields; Richard J Edwards
Journal:  Nucleic Acids Res       Date:  2006-07-19       Impact factor: 16.971

10.  InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.

Authors:  Haidong Wang; Eran Segal; Asa Ben-Hur; Qian-Ru Li; Marc Vidal; Daphne Koller
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583

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  106 in total

1.  Solving a meiotic LEGO puzzle: transverse filaments and the assembly of the synaptonemal complex in Caenorhabditis elegans.

Authors:  R Scott Hawley
Journal:  Genetics       Date:  2011-10       Impact factor: 4.562

2.  Physical interaction between coat morphogenetic proteins SpoVID and CotE is necessary for spore encasement in Bacillus subtilis.

Authors:  Melissa de Francesco; Jake Z Jacobs; Filipa Nunes; Mónica Serrano; Peter T McKenney; Ming-Hsiu Chua; Adriano O Henriques; Patrick Eichenberger
Journal:  J Bacteriol       Date:  2012-07-06       Impact factor: 3.490

3.  The two faces of TOE-2.

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Journal:  Worm       Date:  2015-02-03

Review 4.  Bacterial protein networks: properties and functions.

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Journal:  Nat Rev Microbiol       Date:  2015-08-10       Impact factor: 60.633

5.  ModLink+: improving fold recognition by using protein-protein interactions.

Authors:  Oriol Fornes; Ramon Aragues; Jordi Espadaler; Marc A Marti-Renom; Andrej Sali; Baldo Oliva
Journal:  Bioinformatics       Date:  2009-04-08       Impact factor: 6.937

6.  In Vivo Interaction Proteomics in Caenorhabditis elegans Embryos Provides New Insights into P Granule Dynamics.

Authors:  Jia-Xuan Chen; Patricia G Cipriani; Desirea Mecenas; Jolanta Polanowska; Fabio Piano; Kristin C Gunsalus; Matthias Selbach
Journal:  Mol Cell Proteomics       Date:  2016-02-24       Impact factor: 5.911

7.  Hypothesis: Bifunctional mitochondrial proteins have centrosomal functions.

Authors:  Akilah Moore; Andy Golden
Journal:  Environ Mol Mutagen       Date:  2009-10       Impact factor: 3.216

8.  A yeast two-hybrid approach for probing protein-protein interactions at the centrosome.

Authors:  Brian J Galletta; Nasser M Rusan
Journal:  Methods Cell Biol       Date:  2015-05-27       Impact factor: 1.441

Review 9.  Edgotype: a fundamental link between genotype and phenotype.

Authors:  Nidhi Sahni; Song Yi; Quan Zhong; Noor Jailkhani; Benoit Charloteaux; Michael E Cusick; Marc Vidal
Journal:  Curr Opin Genet Dev       Date:  2013-11-26       Impact factor: 5.578

Review 10.  Protein-protein interaction networks: how can a hub protein bind so many different partners?

Authors:  Chung-Jung Tsai; Buyong Ma; Ruth Nussinov
Journal:  Trends Biochem Sci       Date:  2009-12       Impact factor: 13.807

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