Science. 2011 Jul 29;333(6042):601-7. doi: 10.1126/science.1203877.
Evidence for network evolution in an Arabidopsis interactome map.
Braun P, Carvunis AR, Charloteaux B, Dreze M, Ecker JR, Hill DE, Roth FP, Vidal M, Galli M, Balumuri P, Bautista V, Chesnut JD, Kim RC, de los Reyes C, Gilles P, Kim CJ, Matrubutham U, Mirchandani J, Olivares E, Patnaik S, Quan R, Ramaswamy G, Shinn P, Swamilingiah GM, Wu S, Ecker JR, Dreze M, Byrdsong D, Dricot A, Duarte M, Gebreab F, Gutierrez BJ, MacWilliams A, Monachello D, Mukhtar MS, Poulin MM, Reichert P, Romero V, Tam S, Waaijers S, Weiner EM, Vidal M, Hill DE, Braun P, Galli M, Carvunis AR, Cusick ME, Dreze M, Romero V, Roth FP, Tasan M, Yazaki J, Braun P, Ecker JR, Carvunis AR, Ahn YY, Barabási AL, Charloteaux B, Chen H, Cusick ME, Dangl JL, Dreze M, Ecker JR, Fan C, Gai L, Galli M, Ghoshal G, Hao T, Hill DE, Lurin C, Milenkovic T, Moore J, Mukhtar MS, Pevzner SJ, Przulj N, Rabello S, Rietman EA, Rolland T, Roth FP, Santhanam B, Schmitz RJ, Spooner W, Stein J, Tasan M, Vandenhaute J, Ware D, Braun P, Vidal M.
Source
Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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.
- PMID:
- 21798944
- [PubMed - indexed for MEDLINE]
- PMCID:
- PMC3170756
Free PMC ArticleFig. 1
Quality of AI-1MAIN. (A) Fraction of PRS, RRS or AI-1MAIN sample pairs positive in Y2H or in wNAPPA at a scoring threshold of 1.5. Error bars: standard error of the proportion. P-values: one-sided two-sample t-tests (3). PRS pairs are more often detected than RRS pairs in wNAPPA (P = 2 × 10−8, one-sided two-sample t-test) and Y2H (P < 2.2 × 10−16, one-sided Fisher’s exact test). (B) The number of literature-curated interactions recovered reflects AI-1MAIN framework parameters (6). Top: network representations of LCIBINARY and AI-1MAIN. Bottom left: data sets are represented by squared Venn diagrams; size is proportional to the number of interactions (3). Bottom right: observed and expected overlap given sensitivity and completeness of AI-1MAIN (see main text and (3)). PRS pairs were removed from LCIBINARY multiple evidence for this analysis. Error bars: two standard deviations from the expected counts.
Science. 2011 July 29;333(6042):601-607.
Fig. 2
Plant signaling networks in AI-1. (A) Putative ubiquitination subnetwork extracted from LCIBINARY and AI-1. Bar plot: number of protein-protein interactions between proteins in the ubiquitination cascade in LCIBINARY and AI-1 (outside and within space 1). (B) Protein-protein interactions in AI-1 suggest a modular assembly of transcriptional hormone-response regulators and support a global regulatory role for TPL.
Science. 2011 July 29;333(6042):601-607.
Fig. 3
Communities in AI-1MAIN (bottom) and in a typical randomized network (top left; fig. S9). Only largest connected component of networks are shown. Colored regions indicate communities enriched in GO annotations summarized by the indicated terms (table S10). Upper right: distribution of randomized networks as a function of the total and GO annotation enriched number of communities they contain; white arrow: position of the shown randomized network, red dot and arrow: position of AI-1MAIN. GA: gibberellic acid, JA: jasmonic acid, TCA: tricarboxylic acid.
Science. 2011 July 29;333(6042):601-607.
Fig. 4
Evidence for network evolution in AI-1MAIN. (A) Interaction rewiring over time according to the duplication-divergence model (24). (B) Average fraction of interactors shared between pairs of paralogous proteins with no (n=4), low (n=10), and high (n=3) functional divergence (28). Error bars: standard error of the mean. P-value: one-sided Kendall ranking correlation test (τ= association) (3). (C) Average fraction of shared interactors, corrected for low experimental coverage (3), and average protein sequence identity between pairs of paralogous proteins as a function of the estimated Δ time-since-duplication. Error bars: standard error of the mean (3). Dashed black line: corrected average fraction of shared interactors of non-paralogous pairs. myrs: million years. (D) Corrected average fraction of shared interactors (3), for pairs of paralogous proteins originating from polyploidy events (n=109) as compared to other paralogous protein pairs of similar age (n=147). Error bars: standard error of the mean (3). P-values: Mann-Whitney U-test. (E) Corrected average fraction of shared interactors (3), for pairs of paralogous proteins encoded by gene pairs with high or low co-expression correlation (top and bottom tertile, respectively) as a function of phylogeny-based age group. Error bars: standard error of the mean (3). P < 0.05 (*), < 0.01 (**), < 0.001 (***).
Science. 2011 July 29;333(6042):601-607.
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