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JXB Advance Access originally published online on May 8, 2009
Journal of Experimental Botany 2009 60(11):3067-3073; doi:10.1093/jxb/erp134
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© 2009 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. This paper is available online free of all access charges (see http://jxb.oxfordjournals.org/open_access.html for further details)

RESEARCH PAPER

Isolation and identification of ubiquitin-related proteins from Arabidopsis seedlings

Tomoko Igawa1 *, Masayuki Fujiwara1, Hirotaka Takahashi2, Tatsuya Sawasaki2, Yaeta Endo2, Motoaki Seki3, Kazuo Shinozaki3, Yoichiro Fukao1 and Yuki Yanagawa1 *,{dagger}

1The Plant Science Education Unit, The Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0101, Japan
2Cell-Free Science and Technology Research Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
3RIKEN Bioresource Center, 3-1-1 Takayama-cho, Tsukuba, Ibaraki 305-0074, Japan

{dagger} To whom correspondence should be addressed: E-mail: yyana{at}bs.naist.jp

The majority of proteins in eukaryotic cells are modified according to highly regulated mechanisms to fulfill specific functions and to achieve localization, stability, and transport. Protein ubiquitination is one of the major post-translational modifications occurring in eukaryotic cells. To obtain the proteomic dataset related to the ubiquitin (Ub)-dependent regulatory system in Arabidopsis, affinity purification with an anti-Ub antibody under native condition was performed. Using MS/MS analysis, 196 distinct proteins represented by 251 distinct genes were identified. The identified proteins were involved in metabolism (23.0%), stress response (21.4%), translation (16.8%), transport (6.7%), cell morphology (3.6%), and signal transduction (1.5%), in addition to proteolysis (16.8%) to which proteasome subunits (14.3%) is included. On the basis of potential ubiquitination-targeting signal motifs, in-gel mobilities, and previous reports, 78 of the identified proteins were classified as ubiquitinated proteins and the rest were speculated to be associated proteins of ubiquitinated proteins. The degradation of three proteins predicted to be ubiquitinated proteins was inhibited by a proteasome inhibitor, suggesting that the proteins were regulated by Ub/proteasome-dependent proteolysis.

Key words: Arabidopsis seedling, MS, ubiquitin-related protein

* These authors contributed equally to this work.

Received 15 December 2008; Revised 9 March 2009 Accepted 6 April 2009


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