Physiologia Plantarum 135: 331–341. 2009 Copyright ª Physiologia Plantarum 2009, ISSN 0031-9317 Proteomic analysis of the secretome of rice calli Won Kyong Cho a,† , Xiong Yan Chen a,† , Hyosub Chu a , Yeonggil Rim a , Suwha Kim b , Sun Tae Kim a , Seon-Won Kim a , Zee-Yong Park b and Jae-Yean Kim a, * a Division of Applied Life Science (BK21 Program), Graduate School, Environmental Biotechnology National Core Research Center, PMBBRC, Gyeongsang National University, Jinju 660-701, Korea b Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-711, Korea Correspondence *Corresponding author, e-mail: kimjy@gnu.ac.kr Received 10 October 2008; revised 27 November 2008 doi: 10.1111/j.1399-3054.2008.01198.x The cell wall and extracellular matrix in higher plants include secreted proteins that play critical roles in a wide range of cellular processes, such as structural integrity and biogenesis. Compared with the intensive cell wall proteomic studies in Arabidopsis, the list of cell wall proteins identified in monocot species is lacking. Therefore, we conducted a large-scale proteomic analysis of secreted proteins from rice. Highly purified secreted rice proteins were obtained from the medium of a suspension of callus culture and were analyzed with multidimensional protein identification technology (MudPIT). As a result, we could detect a total of 555 rice proteins by MudPIT analysis. Based on bioinformatic analyses, 27.7% (154 proteins) of the identified proteins are considered to be secreted proteins because they possess a signal peptide for the secretory pathway. Among the 154 identified proteins, 27% were functionally categorized as stress response proteins, followed by metabolic proteins (26%) and factors involved in protein modification (24%). Comparative analysis of cell wall proteins from Arabidopsis and rice revealed that one third of the secreted rice proteins overlapped with those of Arabidopsis. Furthermore, 25 novel rice-specific secreted proteins were found. This work presents the large scale of the rice secretory proteome from culture medium, which contributes to a deeper understanding of the rice secretome. Introduction Plant cells are surrounded by a rigid cell wall that consists of a complex and dynamic structure. Cell walls provide structural support, protect the cell from external attack from pathogens and maintain the cellular shape in response to osmotic and mechanical stresses. They also play pivotal roles in cell expansion and division as well as in recognition of signals between various organisms (Brownlee 2002, Carpita and Gibeaut 1993, Jamet et al. 2008, Pennell 1998, Roberts 1994). Primary cell walls consist of three major high-molecular-weight polysacchar- ides, cellulose microfibrils, hemicelluloses and pectins, as well as highly glycosylated proteins. The cellulose micro- fibrils are composed of hydrogen-bonded chains of beta- 1,4-glucose and are synthesized from cellulose synthase complexes in the plasma membrane, whereas hemicellu- loses and pectins are synthesized in the Golgi apparatus (Cosgrove 2005, Somerville et al. 2004, Taylor 2008). Abbreviations – GH, glycosyl hydrolase; GPDL, glycerophosphoryl diester phosphodiesterase; GPI, glycosylphosphatidylinositol; HIPL1, Hedgehog-interacting protein-like 1; Hsp70, heat-shock protein 70; LC-ESI-MS/MS, liquid chromatography–electrospray ionization–tandem MS; LLR, leucine-rich repeats; MudPIT, multidimensional protein identification technology; NB, Nitsch’s basal; PI, protease inhibitor; pI, isoelectric point; RLK, receptor-like kinase. † These authors contributed equally to this work. Physiol. Plant. 135, 2009 331 Physiologia Plantarum An International Journal for Plant Biology