The WD-repeat protein superfamily in Arabidopsis: conservation and divergence in structure and function

Van Nocker, Steven; Ludwig, Philip
January 2003
BMC Genomics;2003, Vol. 4, p50
Academic Journal
Background: The WD motif (also known as the Trp-Asp or WD40 motif) is found in a multitude of eukaryotic proteins involved in a variety of cellular processes. Where studied, repeated WD motifs act as a site for protein-protein interaction, and proteins containing WD repeats (WDRs) are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. In the model plant Arabidopsis thaliana, members of this superfamily are increasingly being recognized as key regulators of plant-specific developmental events. Results: We analyzed the predicted complement of WDR proteins from Arabidopsis, and compared this to those from budding yeast, fruit fly and human to illustrate both conservation and divergence in structure and function. This analysis identified 237 potential Arabidopsis proteins containing four or more recognizable copies of the motif. These were classified into 143 distinct families, 49 of which contained more than one Arabidopsis member. Approximately 113 of these families or individual proteins showed clear homology with WDR proteins from the other eukaryotes analyzed. Where conservation was found, it often extended across all of these organisms, suggesting that many of these proteins are linked to basic cellular mechanisms. The functional characterization of conserved WDR proteins in Arabidopsis reveals that these proteins help adapt basic mechanisms for plant-specific processes. Conclusions: Our results show that most Arabidopsis WDR proteins are strongly conserved across eukaryotes, including those that have been found to play key roles in plant-specific processes, with diversity in function conferred at least in part by divergence in upstream signaling pathways, downstream regulatory targets and/or structure outside of the WDR regions.


Related Articles

  • Integration of interactive, multi-scale network navigation approach with Cytoscape for functional genomics in the big data era. Praneenararat, Thanet; Takagi, Toshihisa; Iwasaki, Wataru // BMC Genomics;2012, Vol. 13 Issue Suppl 7, p1 

    Background: The overwhelming amount of network data in functional genomics is making its visualization cluttered with jumbling nodes and edges. Such cluttered network visualization, which is known as "hair-balls", is significantly hindering data interpretation and analysis of researchers....

  • Transcriptomics and Functional Genomics of ROS-Induced Cell Death Regulation by RADICAL-INDUCED CELL DEATH1. Brosché, Mikael; Blomster, Tiina; Salojärvi, Jarkko; Cui, Fuqiang; Sipari, Nina; Leppälä, Johanna; Lamminmäki, Airi; Tomai, Gloria; Narayanasamy, Shaman; Reddy, Ramesha A.; Keinänen, Markku; Overmyer, Kirk; Kangasjärvi, Jaakko // PLoS Genetics;Feb2014, Vol. 10 Issue 2, p1 

    Plant responses to changes in environmental conditions are mediated by a network of signaling events leading to downstream responses, including changes in gene expression and activation of cell death programs. Arabidopsis thaliana RADICAL-INDUCED CELL DEATH1 (RCD1) has been proposed to regulate...

  • Systems biology: Plant networks. Muers, Mary // Nature Reviews Genetics;Sep2011, Vol. 12 Issue 9, p586 

    The article discusses research being done on 6,000 binary protein-protein interactions in Arabidopsis thaliana, in which it references the studies including "Arabidopsis Interactome Mapping Consortium. Evidence for network evolution in an Arabidopsis interactome map" in the 2011 issue of "Science."

  • Systems biology: A plant membrane-linked interactome.  // Nature Methods;Jul2014, Vol. 11 Issue 7, p714 

    The article reports on the move of A. M. Jones and colleagues in using the established year split-ubiquitin assay to assess the interactions of more than 3,000 membrane proteins from Arabidopsis, a small flowering plant.

  • Isolation of Heat Shock Factor HsfA1a-binding Sites in vivo Revealed Variations of Heat Shock Elements in Arabidopsis Thaliana. Lihong Guo; Shanna Chen; Kaihui Liu; Yanfang Liu; Lianghua Ni; Keqin Zhang; Lemin Zhang // Plant & Cell Physiology;Sep2008, Vol. 49 Issue 9, p1306 

    The information about DNA-binding sites of regulatory protein is important to understanding the regulatory network of DNA–protein interactions in the genome. In this report we integrated chromatin immunoprecipitation with DNA cloning to isolate genomic sites bound in vivo by heat shock...

  • The Arabidopsis ESCRT protein-protein interaction network. Shahriari, Mojgan; Richter, Klaus; Keshavaiah, Channa; Sabovljevic, Aneta; Huelskamp, Martin; Schellmann, Swen // Plant Molecular Biology;May2011, Vol. 76 Issue 1/2, p85 

    In yeast, endosomal sorting of monoubiquitylated transmembrane proteins is performed by a subset of the 19 'class E vacuolar protein sorting' proteins. The core machinery consists of 11 proteins that are organised in three complexes termed ESCRT I-III (endosomal sorting complex required for...

  • Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets. Hsiang Ho; Milenkovic, Tijana; Memiševic, Vesna; Aruri, Jayavani; Przulj, Nataša; Ganesan, Anand K. // BMC Systems Biology;2010, Vol. 4, p84 

    Background: RNA-mediated interference (RNAi)-based functional genomics is a systems-level approach to identify novel genes that control biological phenotypes. Existing computational approaches can identify individual genes from RNAi datasets that regulate a given biological process. However,...

  • Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis. Lysenko, Artem; Defoin-Platel, Michael; Hassani-Pak, Keywan; Taubert, Jan; Hodgman, Charlie; Rawlings, Christopher J.; Saqi, Mansoor // BMC Bioinformatics;2011, Vol. 12 Issue 1, p203 

    Background: Combining multiple evidence-types from different information sources has the potential to reveal new relationships in biological systems. The integrated information can be represented as a relationship network, and clustering the network can suggest possible functional modules. The...

  • Construction of a chloroplast protein interaction network and functional mining of photosynthetic proteins in Arabidopsis thaliana. Qing-Bo Yu; Guang Li; Guan Wang; Jing-Chun Sun; Peng-Cheng Wang; Chen Wang; Hua-Ling Mi; Wei-Min Ma; Jian Cui; Yong-Lan Cui; Kang Chong; Yi-Xue Li; Yu-Hua Li; Zhongming Zhao; Tie-Liu Shi; Zhong-Nan Yang // Cell Research;Oct2008, Vol. 18 Issue 10, p1007 

    Chloroplast is a typical plant cell organelle where photosynthesis takes place. In this study, a total of 1 808 chloroplast core proteins in Arabidopsis thaliana were reliably identified by combining the results of previously published studies and our own predictions. We then constructed a...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics