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PCoM-DB Update: A Protein Co-Migration Database for Photosynthetic Organisms

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Please use this identifier to cite or link to this item:http://hdl.handle.net/2115/68044

Title: PCoM-DB Update: A Protein Co-Migration Database for Photosynthetic Organisms
Authors: Takabayashi, Atsushi Browse this author
Takabayashi, Saeka Browse this author
Takahashi, Kaori Browse this author
Watanabe, Mai Browse this author
Uchida, Hiroko Browse this author
Murakami, Akio Browse this author
Fujita, Tomomichi Browse this author
Ikeuchi, Masahiko Browse this author
Tanaka, Ayumi Browse this author
Keywords: Blue-native PAGE
Photosynthetic organisms
Protein complex database
Protein-protein interaction
Issue Date: 6-Jan-2017
Publisher: Oxford University Press
Journal Title: Plant and Cell Physiology
Volume: 58
Issue: 1
Start Page: e10
Publisher DOI: 10.1093/pcp/pcw219
PMID: 28011869
Abstract: The identification of protein complexes is important for the understanding of protein structure and function and the regulation of cellular processes. We used blue-native PAGE and tandemmass spectrometry to identify protein complexes systematically, and built a web database, the protein co-migration database (PCoM-DB, http://pcomdb.lowtem.hokudai.ac.jp/proteins/top), to provide prediction tools for protein complexes. PCoM-DB provides migration profiles for any given protein of interest, and allows users to compare them with migration profiles of other proteins, showing the oligomeric states of proteins and thus identifying potential interaction partners. The initial version of PCoM-DB (launched in January 2013) included protein complex data for Synechocystis whole cells and Arabidopsis thaliana thylakoid membranes. Here we report PCoM-DB version 2.0, which includes new data sets and analytical tools. Additional data are included from whole cells of the pelagic marine picocya-nobacterium Prochlorococcus marinus, the thermophilic cyanobacterium Thermosynechococcus elongatus, the unicellular green alga Chlamydomonas reinhardtii and the bryophyte Physcomitrella patens. The Arabidopsis protein data now include data for intact mitochondria, intact chloroplasts, chloroplast stroma and chloroplast envelopes. The new tools comprise a multiple-protein search form and a heat map viewer for protein migration profiles. Users can compare migration profiles of a protein of interest among different organelles or compare migration profiles among different proteins within the same sample. For Arabidopsis proteins, users can compare migration profiles of a protein of interest with putative homologous proteins from non-Arabidopsis organisms. The updated PCoM-DB will help researchers find novel protein complexes and estimate their evolutionary changes in the green lineage.
Rights: This is a pre-copyedited, author-produced PDF of an article accepted for publication in Plant and cell physiology following peer review. The version of record PCoM-DB Update : A Protein Co-Migration Database for Photosynthetic Organisms, Atsushi Takabayashi,Saeka Takabayashi, Kaori Takahashi, Mai Watanabe, Hiroko Uchida, Akio Murakami, Tomomichi Fujita, Masahiko Ikeuchi, Ayumi Tanaka, Plant Cell Physiol (2017) 58 (1): e10 is available online at: https://doi.org/10.1093/pcp/pcw219
Type: article (author version)
URI: http://hdl.handle.net/2115/68044
Appears in Collections:低温科学研究所 (Institute of Low Temperature Science) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

Submitter: 高林 厚史

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