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Resurrected protein interaction networks reveal the innovation potential of ancient whole genome duplication

(2018) PLANT CELL. 30(11). p.2741-2760
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Abstract
The evolution of plants is characterized by whole-genome duplications, sometimes closely associated with the origin of large groups of species. The gamma (gamma) genome triplication occurred at the origin of the core eudicots, which comprise similar to 75% of flowering plants. To better understand the impact of whole-genome duplication, we studied the protein interaction network of MADS domain transcription factors, which are key regulators of reproductive development. We reconstructed, synthesized, and tested the interactions of ancestral proteins immediately before and closely after the triplication and directly compared these ancestral networks to the extant networks of Arabidopsis thaliana and tomato (Solanum lycopersicum). We found that gamma expanded the MADS domain interaction network more strongly than subsequent genomic events. This event strongly rewired MADS domain interactions and allowed for the evolution of new functions and installed robustness through new redundancy. Despite extensive rewiring, the organization of the network was maintained through gamma. New interactions and protein retention compensated for its potentially destructive impact on network organization. Post gamma, the network evolved from an organization around the single hub SEP3 to a network organized around multiple hubs and well-connected proteins lost, rather than gained, interactions. The data provide a resource for comparative developmental biology in flowering plants.
Keywords
MADS-BOX GENES, PHYLOGENETIC ANALYSIS, INTERACTION MAP, TRANSCRIPTION FACTORS, REGULATORY NETWORK, FLOWERING SIGNALS, DOMAIN PROTEINS, CORE EUDICOTS, EVOLUTION, ARABIDOPSIS

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Chicago
Zhang, Zhicheng, Heleen Coenen, Philip Ruelens, Rashmi Hazarika, Tareq Al Hindi, Georgianna Oguis, Vera Van Noort, and Koen Geuten. 2018. “Resurrected Protein Interaction Networks Reveal the Innovation Potential of Ancient Whole Genome Duplication.” Plant Cell 30 (11): 2741–2760.
APA
Zhang, Z., Coenen, H., Ruelens, P., Hazarika, R., Al Hindi, T., Oguis, G., Van Noort, V., et al. (2018). Resurrected protein interaction networks reveal the innovation potential of ancient whole genome duplication. PLANT CELL, 30(11), 2741–2760.
Vancouver
1.
Zhang Z, Coenen H, Ruelens P, Hazarika R, Al Hindi T, Oguis G, et al. Resurrected protein interaction networks reveal the innovation potential of ancient whole genome duplication. PLANT CELL. 2018;30(11):2741–60.
MLA
Zhang, Zhicheng et al. “Resurrected Protein Interaction Networks Reveal the Innovation Potential of Ancient Whole Genome Duplication.” PLANT CELL 30.11 (2018): 2741–2760. Print.
@article{8544967,
  abstract     = {The evolution of plants is characterized by whole-genome duplications, sometimes closely associated with the origin of large groups of species. The gamma (gamma) genome triplication occurred at the origin of the core eudicots, which comprise similar to 75\% of flowering plants. To better understand the impact of whole-genome duplication, we studied the protein interaction network of MADS domain transcription factors, which are key regulators of reproductive development. We reconstructed, synthesized, and tested the interactions of ancestral proteins immediately before and closely after the triplication and directly compared these ancestral networks to the extant networks of Arabidopsis thaliana and tomato (Solanum lycopersicum). We found that gamma expanded the MADS domain interaction network more strongly than subsequent genomic events. This event strongly rewired MADS domain interactions and allowed for the evolution of new functions and installed robustness through new redundancy. Despite extensive rewiring, the organization of the network was maintained through gamma. New interactions and protein retention compensated for its potentially destructive impact on network organization. Post gamma, the network evolved from an organization around the single hub SEP3 to a network organized around multiple hubs and well-connected proteins lost, rather than gained, interactions. The data provide a resource for comparative developmental biology in flowering plants.},
  author       = {Zhang, Zhicheng and Coenen, Heleen and Ruelens, Philip and Hazarika, Rashmi and Al Hindi, Tareq and Oguis, Georgianna and Van Noort, Vera and Geuten, Koen},
  issn         = {1040-4651},
  journal      = {PLANT CELL},
  language     = {eng},
  number       = {11},
  pages        = {2741--2760},
  title        = {Resurrected protein interaction networks reveal the innovation potential of ancient whole genome duplication},
  url          = {http://dx.doi.org/10.1105/tpc.18.00409},
  volume       = {30},
  year         = {2018},
}

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