title: PCoM-DB Update: A Protein Co-Migration Database for Photosynthetic Organisms.
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 tandem mass 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 picocyanobacterium 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.
authors.affiliation: Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo, Japan.|CREST, JST, Kita-ku, Sapporo, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Takabayashi
authors.affiliation: Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo, Japan.|Department of Public Health, Graduate School of Medicine Hokkaido University, Kita-ku, Sapporo, Japan.
authors.forename: Saeka
authors.initials: S
authors.lastname: Takabayashi
authors.affiliation: Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo, Japan.
authors.forename: Kaori
authors.initials: K
authors.lastname: Takahashi
authors.affiliation: Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan.
authors.forename: Mai
authors.initials: M
authors.lastname: Watanabe
authors.affiliation: Kobe University Research Center for Inland Seas, Awaji, Japan.
authors.forename: Hiroko
authors.initials: H
authors.lastname: Uchida
authors.affiliation: Kobe University Research Center for Inland Seas, Awaji, Japan.
authors.forename: Akio
authors.initials: A
authors.lastname: Murakami
authors.affiliation: Faculty of Science, Hokkaido University, N10 W8 Kita-ku, Sapporo 060-0810, Japan Tokyo, Tokyo, Japan.
authors.forename: Tomomichi
authors.initials: T
authors.lastname: Fujita
authors.affiliation: Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan.
authors.forename: Masahiko
authors.initials: M
authors.lastname: Ikeuchi
authors.affiliation: Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo, Japan.|CREST, JST, Kita-ku, Sapporo, Japan.
authors.forename: Ayumi
authors.initials: A
authors.lastname: Tanaka
mesh_terms: D020418:Algal Proteins / Q000378:metabolism; D017360:Arabidopsis / Q000378:metabolism*; D001426:Bacterial Proteins / Q000378:metabolism; D044002:Bryophyta / Q000378:metabolism*; D016825:Chlamydomonas reinhardtii / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods; D000458:Cyanobacteria / Q000145:classification / Q000378:metabolism; D030562:Databases, Protein; D004586:Electrophoresis / Q000379:methods; D020407:Internet; D010788:Photosynthesis; D010940:Plant Proteins / Q000378:metabolism; D053719:Tandem Mass Spectrometry / Q000379:methods; D014584:User-Computer Interface
chemical_list: D020418:Algal Proteins; D001426:Bacterial Proteins; D010940:Plant Proteins
keywords: Blue-native PAGE; Photosynthetic organisms; Protein complex database; Protein–protein interaction