A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis

Mike Boxem; 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

doi:10.1016/j.cell.2008.07.009

A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis

Mike Boxem, 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 FanMike 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

Research output: Contribution to journal › Article › peer-review

168 Scopus citations

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.

Original language	English (US)
Pages (from-to)	534-545
Number of pages	12
Journal	Cell
Volume	134
Issue number	3
DOIs	https://doi.org/10.1016/j.cell.2008.07.009
State	Published - Aug 8 2008
Externally published	Yes

Keywords

PROTEINS

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology

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10.1016/j.cell.2008.07.009

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Boxem, M., Maliga, Z., Klitgord, N., Li, N., Lemmens, I., Mana, M., de Lichtervelde, L., Mul, J. D., van de Peut, D., Devos, M., Simonis, N., Yildirim, M. A., Cokol, M., Kao, H. L., de Smet, A. S., Wang, H., Schlaitz, A. L., Hao, T., Milstein, S., ... Vidal, M. (2008). A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis. Cell, 134(3), 534-545. https://doi.org/10.1016/j.cell.2008.07.009

Boxem, M, Maliga, Z, Klitgord, N, Li, N, Lemmens, I, Mana, M, de Lichtervelde, L, Mul, JD, van de Peut, D, Devos, M, Simonis, N, Yildirim, MA, Cokol, M, Kao, HL, de Smet, AS, Wang, H, Schlaitz, AL, Hao, T, Milstein, S, Fan, C, Tipsword, M, Drew, K, Galli, M, Rhrissorrakrai, K, Drechsel, D, Koller, D, Roth, FP, Iakoucheva, LM, Dunker, AK, Bonneau, R, Gunsalus, KC, Hill, DE, Piano, F, Tavernier, J, van den Heuvel, S, Hyman, AA & Vidal, M 2008, 'A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis', Cell, vol. 134, no. 3, pp. 534-545. https://doi.org/10.1016/j.cell.2008.07.009

@article{305c0790d1d44df09763bf4d1a8b92ef,

title = "A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis",

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.",

keywords = "PROTEINS",

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

note = "Funding Information: We are grateful to X. Xin and C. Boone for sharing of the cDNA library and yeast strains, to Joe Hargitai for unparalleled parallel computing support, to IBM's World Community Grid ( http://www.wcgrid.org ), and to M. Cusick for critical reading of the manuscript. Support was provided by the Leukemia Research Foundation to M.B., the W.M. Keck foundation to M.V., the FWO-V to I.L., National Institutes of Health grants R21RR023114 (M.B. P.I.), R01HG001715 (M.V. P.I.), R33CA105405 (M.V. P.I.), R33CA81658 (M.V. P.I.), R21CA113711 (L.M.I. P.I.), U54 CA011295 (J. Nevins, PI; M.V. subcontract), and CA95281 (S.v.d.H.), United States Army Medical Research Acquisition Activity grant W23RYX-3275-N605 (K.C.G.), New York State Foundation of Science, Technology, and Academic Research grant C040066 (K.C.G.), National Science Foundation grants MCB 0444818 to L.M.I. and BDI-0345474 to D.K. and grants IUAP-P6:28, UG-GOA12051401, and FWO-G.0031.06 to J.T. M.V. is a “Chercheur Qualifi{\'e} Honoraire” from the Fonds de la Recherche Scientifique (FRS-FNRS, French Community of Belgium). ",

year = "2008",

month = aug,

day = "8",

doi = "10.1016/j.cell.2008.07.009",

language = "English (US)",

volume = "134",

pages = "534--545",

journal = "Cell",

issn = "0092-8674",

publisher = "Cell Press",

number = "3",

}

TY - JOUR

T1 - A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis

AU - Boxem, Mike

AU - Maliga, Zoltan

AU - Klitgord, Niels

AU - Li, Na

AU - Lemmens, Irma

AU - Mana, Miyeko

AU - de Lichtervelde, Lorenzo

AU - Mul, Joram D.

AU - van de Peut, Diederik

AU - Devos, Maxime

AU - Simonis, Nicolas

AU - Yildirim, Muhammed A.

AU - Cokol, Murat

AU - Kao, Huey Ling

AU - de Smet, Anne Sophie

AU - Wang, Haidong

AU - Schlaitz, Anne Lore

AU - Hao, Tong

AU - Milstein, Stuart

AU - Fan, Changyu

AU - Tipsword, Mike

AU - Drew, Kevin

AU - Galli, Matilde

AU - Rhrissorrakrai, Kahn

AU - Drechsel, David

AU - Koller, Daphne

AU - Roth, Frederick P.

AU - Iakoucheva, Lilia M.

AU - Dunker, A. Keith

AU - Bonneau, Richard

AU - Gunsalus, Kristin C.

AU - Hill, David E.

AU - Piano, Fabio

AU - Tavernier, Jan

AU - van den Heuvel, Sander

AU - Hyman, Anthony A.

AU - Vidal, Marc

N1 - Funding Information: We are grateful to X. Xin and C. Boone for sharing of the cDNA library and yeast strains, to Joe Hargitai for unparalleled parallel computing support, to IBM's World Community Grid ( http://www.wcgrid.org ), and to M. Cusick for critical reading of the manuscript. Support was provided by the Leukemia Research Foundation to M.B., the W.M. Keck foundation to M.V., the FWO-V to I.L., National Institutes of Health grants R21RR023114 (M.B. P.I.), R01HG001715 (M.V. P.I.), R33CA105405 (M.V. P.I.), R33CA81658 (M.V. P.I.), R21CA113711 (L.M.I. P.I.), U54 CA011295 (J. Nevins, PI; M.V. subcontract), and CA95281 (S.v.d.H.), United States Army Medical Research Acquisition Activity grant W23RYX-3275-N605 (K.C.G.), New York State Foundation of Science, Technology, and Academic Research grant C040066 (K.C.G.), National Science Foundation grants MCB 0444818 to L.M.I. and BDI-0345474 to D.K. and grants IUAP-P6:28, UG-GOA12051401, and FWO-G.0031.06 to J.T. M.V. is a “Chercheur Qualifié Honoraire” from the Fonds de la Recherche Scientifique (FRS-FNRS, French Community of Belgium).

PY - 2008/8/8

Y1 - 2008/8/8

N2 - 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.

AB - 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.

KW - PROTEINS

UR - http://www.scopus.com/inward/record.url?scp=48649096489&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=48649096489&partnerID=8YFLogxK

U2 - 10.1016/j.cell.2008.07.009

DO - 10.1016/j.cell.2008.07.009

M3 - Article

C2 - 18692475

AN - SCOPUS:48649096489

SN - 0092-8674

VL - 134

SP - 534

EP - 545

JO - Cell

JF - Cell

IS - 3

ER -

A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis

Abstract

Keywords

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