Evidence for Network Evolution in an Arabidopsis Interactome Map

By Rosa Quan, G. Ramaswamy, P. Shinn, Geetha M. Swamilingiah, Stacy Wu, R. Joseph, Ecker, Melissa Duarte, Fana Gebreab, B. J. Gutierrez and 35 more. 2011

894 citations recorded by the source corpus.

An analysis of protein-protein interactions in Arabidopsis identifies the plant interactome. 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.

Subfields: Biochemistry, Molecular Biology

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Citations in the corpus

Differential network biology (2012, neutral): “For instance, the systematic identiﬁcation of pairwise protein interactions (Stelzl et al , 2005; Tarassov et al , 2008; Yu et al , 2008; Consortium, 2011) or protein complexes (Butland et al , 2005; Gavin et al , 2006; Krogan et al , 2006; Sowa et al , 2009) has been a widely used strategy for…”
Graphlet-based measures are suitable for biological network comparison (2013, background): “00159 Arabidopsis Interactome Mapping Consortium (2011) WB 2817 4527 0.00114 BioGRID (ver. 3.1.74) YB 5607 57 143 0.00364 BioGRID (ver. 3.1.74) FB 7372 24 063 0.00089 BioGRID (ver. 3.1.74) HB 8920 35 386 0.00089 BioGRID (ver. 3.1.74) HR 9141 41 456 0.00099 Radivojac et al. (2008) HH 9465 37 039 0.”
Mapping genome-wide transcription-factor binding sites using DAP-seq (2017, methodology): “For high-throughput processing of samples, we use the Gateway-compatible pIX-HALO in vitro expression vector, 26,27 which has both T7 and SP6 promoters.”