Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.
Subscribe

Logo for

Science 333 (6042): 601-607

Copyright © 2011 by the American Association for the Advancement of Science

Evidence for Network Evolution in an Arabidopsis Interactome Map

Arabidopsis Interactome Mapping Consortium*,{dagger}

Abstract: Plants have unique features that evolved in response to their environments and ecosystems. A full account of the complex cellular networks that underlie plant-specific functions is still missing. We describe a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing about 6200 highly reliable interactions between about 2700 proteins. A global organization of plant biological processes emerges from community analyses of the resulting network, together with large numbers of novel hypothetical functional links between proteins and pathways. We observe a dynamic rewiring of interactions following gene duplication events, providing evidence for a model of evolution acting upon interactome networks. This and future plant interactome maps should facilitate systems approaches to better understand plant biology and improve crops.

* All authors with their affiliations and contributions are listed at the end of the paper.

{dagger} To whom correspondence should be addressed. E-mail: marc_vidal{at}dfci.harvard.edu; ecker{at}salk.edu; pascal_braun{at}dfci.harvard.edu; david_hill{at}dfci.harvard.edu

THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
MCScanX-transposed: detecting transposed gene duplications based on multiple colinearity scans.
Y. Wang, J. Li, and A. H. Paterson (2013)
Bioinformatics 29, 1458-1460
   Abstract »    Full Text »    PDF »
Cross-Species Protein Interactome Mapping Reveals Species-Specific Wiring of Stress Response Pathways.
J. Das, T. V. Vo, X. Wei, J. C. Mellor, V. Tong, A. G. Degatano, X. Wang, L. Wang, N. A. Cordero, N. Kruer-Zerhusen, et al. (2013)
Science Signaling 6, ra38
   Abstract »    Full Text »    PDF »
AtWRKY40 and AtWRKY63 Modulate the Expression of Stress-Responsive Nuclear Genes Encoding Mitochondrial and Chloroplast Proteins.
O. Van Aken, B. Zhang, S. Law, R. Narsai, and J. Whelan (2013)
Plant Physiology 162, 254-271
   Abstract »    Full Text »    PDF »
Protein-Protein Interactions in the Regulation of WRKY Transcription Factors.
Y. Chi, Y. Yang, Y. Zhou, J. Zhou, B. Fan, J.-Q. Yu, and Z. Chen (2013)
Mol Plant
   Abstract »    Full Text »    PDF »
The Potential of Text Mining in Data Integration and Network Biology for Plant Research: A Case Study on Arabidopsis.
S. Van Landeghem, S. De Bodt, Z. J. Drebert, D. Inze, and Y. Van de Peer (2013)
PLANT CELL 25, 794-807
   Abstract »    Full Text »    PDF »
Graphlet-based measures are suitable for biological network comparison.
W. Hayes, K. Sun, and N. Przulj (2013)
Bioinformatics 29, 483-491
   Abstract »    Full Text »    PDF »
Biostatistical approaches for the reconstruction of gene co-expression networks based on transcriptomic data.
L. Lopez-Kleine, L. Leal, and C. Lopez (2013)
Briefings in Functional Genomics
   Abstract »    Full Text »    PDF »
Linking the signaling cascades and dynamic regulatory networks controlling stress responses.
A. Gitter, M. Carmi, N. Barkai, and Z. Bar-Joseph (2013)
Genome Res. 23, 365-376
   Abstract »    Full Text »    PDF »
Arabidopsis Calmodulin-binding Protein IQ67-Domain 1 Localizes to Microtubules and Interacts with Kinesin Light Chain-related Protein-1.
K. Burstenbinder, T. Savchenko, J. Muller, A. W. Adamson, G. Stamm, R. Kwong, B. J. Zipp, D. C. Dinesh, and S. Abel (2013)
J. Biol. Chem. 288, 1871-1882
   Abstract »    Full Text »    PDF »
PrePPI: a structure-informed database of protein-protein interactions.
Q. C. Zhang, D. Petrey, J. I. Garzon, L. Deng, and B. Honig (2013)
Nucleic Acids Res. 41, D828-D833
   Abstract »    Full Text »    PDF »
SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis.
S. K. Tanz, I. Castleden, C. M. Hooper, M. Vacher, I. Small, and H. A. Millar (2013)
Nucleic Acids Res. 41, D1185-D1191
   Abstract »    Full Text »    PDF »
Evolutionary Rate and Duplicability in the Arabidopsis thaliana Protein-Protein Interaction Network.
D. Alvarez-Ponce and M. A. Fares (2012)
Genome Biol Evol 4, 1263-1274
   Abstract »    Full Text »    PDF »
A Triple Helix-Loop-Helix/Basic Helix-Loop-Helix Cascade Controls Cell Elongation Downstream of Multiple Hormonal and Environmental Signaling Pathways in Arabidopsis.
M.-Y. Bai, M. Fan, E. Oh, and Z.-Y. Wang (2012)
PLANT CELL 24, 4917-4929
   Abstract »    Full Text »    PDF »
The Intrinsically Disordered N-terminal Region of AtREM1.3 Remorin Protein Mediates Protein-Protein Interactions.
M. Marin, V. Thallmair, and T. Ott (2012)
J. Biol. Chem. 287, 39982-39991
   Abstract »    Full Text »    PDF »
The MORPH Algorithm: Ranking Candidate Genes for Membership in Arabidopsis and Tomato Pathways.
O. Tzfadia, D. Amar, L. M. T. Bradbury, E. T. Wurtzel, and R. Shamir (2012)
PLANT CELL 24, 4389-4406
   Abstract »    Full Text »    PDF »
Proteasome-Mediated Turnover of Arabidopsis MED25 Is Coupled to the Activation of FLOWERING LOCUS T Transcription.
S. Inigo, A. N. Giraldez, J. Chory, and P. D. Cerdan (2012)
Plant Physiology 160, 1662-1673
   Abstract »    Full Text »    PDF »
ALLENE OXIDE CYCLASE (AOC) gene family members of Arabidopsis thaliana: tissue- and organ-specific promoter activities and in vivo heteromerization*.
I. Stenzel, M. Otto, C. Delker, N. Kirmse, D. Schmidt, O. Miersch, B. Hause, and C. Wasternack (2012)
J. Exp. Bot.
   Abstract »    Full Text »    PDF »
Systems Analysis of Plant Functional, Transcriptional, Physical Interaction, and Metabolic Networks.
G. W. Bassel, A. Gaudinier, S. M. Brady, L. Hennig, S. Y. Rhee, and I. De Smet (2012)
PLANT CELL 24, 3859-3875
   Abstract »    Full Text »    PDF »
Ubiquitin-Mediated Control of Plant Hormone Signaling.
D. R. Kelley and M. Estelle (2012)
Plant Physiology 160, 47-55
   Full Text »    PDF »
Application of the Gini Correlation Coefficient to Infer Regulatory Relationships in Transcriptome Analysis.
C. Ma and X. Wang (2012)
Plant Physiology 160, 192-203
   Abstract »    Full Text »    PDF »
Rice Mitogen-Activated Protein Kinase Interactome Analysis Using the Yeast Two-Hybrid System.
R. Singh, M.-O. Lee, J.-E. Lee, J. Choi, J. H. Park, E. H. Kim, R. H. Yoo, J.-I. Cho, J.-S. Jeon, R. Rakwal, et al. (2012)
Plant Physiology 160, 477-487
   Abstract »    Full Text »    PDF »
BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference.
J. Garcia-Garcia, S. Schleker, J. Klein-Seetharaman, and B. Oliva (2012)
Nucleic Acids Res. 40, W147-W151
   Abstract »    Full Text »    PDF »
Systematic Identification of Functional Plant Modules through the Integration of Complementary Data Sources.
K. S. Heyndrickx and K. Vandepoele (2012)
Plant Physiology 159, 884-901
   Abstract »    Full Text »    PDF »
Functionalization of a protosynaptic gene expression network.
C. Conaco, D. S. Bassett, H. Zhou, M. L. Arcila, S. M. Degnan, B. M. Degnan, and K. S. Kosik (2012)
PNAS 109, 10612-10618
   Abstract »    Full Text »    PDF »
Diversity in Genetic In Vivo Methods for Protein-Protein Interaction Studies: from the Yeast Two-Hybrid System to the Mammalian Split-Luciferase System.
B. Stynen, H. Tournu, J. Tavernier, and P. Van Dijck (2012)
Microbiol. Mol. Biol. Rev. 76, 331-382
   Abstract »    Full Text »    PDF »
Tackling Drought Stress: RECEPTOR-LIKE KINASES Present New Approaches.
A. Marshall, R. B. Aalen, D. Audenaert, T. Beeckman, M. R. Broadley, M. A. Butenko, A. I. Cano-Delgado, S. de Vries, T. Dresselhaus, G. Felix, et al. (2012)
PLANT CELL 24, 2262-2278
   Abstract »    Full Text »    PDF »
Structural and Functional Analysis of VQ Motif-Containing Proteins in Arabidopsis as Interacting Proteins of WRKY Transcription Factors.
Y. Cheng, Y. Zhou, Y. Yang, Y.-J. Chi, J. Zhou, J.-Y. Chen, F. Wang, B. Fan, K. Shi, Y.-H. Zhou, et al. (2012)
Plant Physiology 159, 810-825
   Abstract »    Full Text »    PDF »
The 14-3-3 proteins of Arabidopsis regulate root growth and chloroplast development as components of the photosensory system.
J. D. Mayfield, A.-L. Paul, and R. J. Ferl (2012)
J. Exp. Bot. 63, 3061-3070
   Abstract »    Full Text »    PDF »
Protein-Protein Interactions in Plants.
Y. Fukao (2012)
Plant Cell Physiol. 53, 617-625
   Abstract »    Full Text »    PDF »
ANAP: An Integrated Knowledge Base for Arabidopsis Protein Interaction Network Analysis.
C. Wang, A. Marshall, D. Zhang, and Z. A. Wilson (2012)
Plant Physiology 158, 1523-1533
   Abstract »    Full Text »    PDF »
A Comprehensive Dataset of Genes with a Loss-of-Function Mutant Phenotype in Arabidopsis.
J. Lloyd and D. Meinke (2012)
Plant Physiology 158, 1115-1129
   Abstract »    Full Text »    PDF »
New Technologies for 21st Century Plant Science.
D. W. Ehrhardt and W. B. Frommer (2012)
PLANT CELL 24, 374-394
   Abstract »    Full Text »    PDF »
JAZ8 Lacks a Canonical Degron and Has an EAR Motif That Mediates Transcriptional Repression of Jasmonate Responses in Arabidopsis.
C. Shyu, P. Figueroa, C. L. DePew, T. F. Cooke, L. B. Sheard, J. E. Moreno, L. Katsir, N. Zheng, J. Browse, and G. A. Howe (2012)
PLANT CELL 24, 536-550
   Abstract »    Full Text »    PDF »
The TOPLESS Interactome: A Framework for Gene Repression in Arabidopsis.
B. Causier, M. Ashworth, W. Guo, and B. Davies (2012)
Plant Physiology 158, 423-438
   Abstract »    Full Text »    PDF »
Advances in Omics and Bioinformatics Tools for Systems Analyses of Plant Functions.
K. Mochida and K. Shinozaki (2011)
Plant Cell Physiol. 52, 2017-2038
   Abstract »    Full Text »    PDF »
Plant Oxygen Sensing Is Mediated by the N-End Rule Pathway: A Milestone in Plant Anaerobiosis.
R. Sasidharan and A. Mustroph (2011)
PLANT CELL 23, 4173-4183
   Abstract »    Full Text »    PDF »
The JAZ Proteins: A Crucial Interface in the Jasmonate Signaling Cascade.
L. Pauwels and A. Goossens (2011)
PLANT CELL 23, 3089-3100
   Abstract »    Full Text »    PDF »
A Cellular Roadmap for the Plant Kingdom.
C. R. Landry (2011)
Science 333, 532-533
   Abstract »    Full Text »    PDF »
Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network.
M. S. Mukhtar, A.-R. Carvunis, M. Dreze, P. Epple, J. Steinbrenner, J. Moore, M. Tasan, M. Galli, T. Hao, M. T. Nishimura, et al. (2011)
Science 333, 596-601
   Abstract »    Full Text »    PDF »

To Advertise     Find Products

Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882