AUTHOR=Lin Fan , Williams Brad J. , Thangella Padmavathi A. V. , Ladak Adam , Schepmoes Athena A. , Olivos Hernando J. , Zhao Kangmei , Callister Stephen J. , Bartley Laura E. 

TITLE=Proteomics Coupled with Metabolite and Cell Wall Profiling Reveal Metabolic Processes of a Developing Rice Stem Internode

JOURNAL=Frontiers in Plant Science

VOLUME=Volume 8 - 2017

YEAR=2017

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2017.01134

DOI=10.3389/fpls.2017.01134

ISSN=1664-462X

ABSTRACT=Internodes of grass stems function in mechanical support, transport, and, in some species, are a major sink organ for carbon in the form of cell wall polymers. This study reports cell wall composition, proteomic, and metabolite analyses of the second internode below the panicle (internode II) for rice (Oryza sativa L.). Cellulose, lignin, and xylose increase as a percentage of cell wall material through the elongation and maturation zones of rice internode II at booting stage, indicating active cell wall synthesis. Liquid-chromatography tandem mass spectrometry (LC-MS/MS) of trypsin-digested proteins from internode II at booting revealed 2547 proteins with at least two unique peptides in two biological replicates. The dataset includes many glycosyltransferases, acyltransferases, glycosyl hydrolases, cell wall-localized proteins, and protein kinases that have or may have functions in cell wall biosynthesis or remodeling. Phospho-enrichment of internode II peptides identified 21 unique phosphopeptides belonging to 20 phosphoproteins including a leucine rich repeat-III family receptor like kinase. GO over-representation and KEGG pathway analyses highlight the abundance of proteins involved in biosynthetic processes, especially synthesis of secondary metabolites such as phenylpropanoids and flavonoids. LC-MS/MS of hot methanol-extracted secondary metabolites from internode II at four stages (booting/elongation, early mature, mature, and post mature) indicated that internode secondary metabolites are distinct from those of roots and leaves, and differ across stem maturation. This work fills a void of in-depth proteomics and metabolomics data for grass stems, specifically for rice, and provides baseline knowledge for more detailed studies of cell wall synthesis and other biological processes characteristic of internode development, toward improving grass agronomic properties.