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

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

doi:10.3389/fpls.2017.01134

Fan Lin, Athena A Schepmoes + Show 7 more

Open Access

https://doi.org/10.3389/fpls.2017.01134

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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 rice elongating internode. Cellulose, lignin, and xylose increase as a percentage of cell wall material along eight segments of the second rice internode (internode II) at booting stage, from the younger to the older internode segments, indicating active cell wall synthesis. Liquid-chromatography tandem mass spectrometry (LC-MS/MS) of trypsin-digested proteins from this internode at booting reveals 2,547 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 abundances of proteins involved in biosynthetic processes, especially the 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) indicates 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.

Highlights

The grass family, Poaceae, includes the cereal crops and represents one of the most wide-spread plant taxonomic groups in terrestrial ecosystems (Kellogg, 2001)
Peptides were separated and eluted from the analytical column with a step gradient of solvent A (0.1% formic acid in water) and solvent B (99.9% acetonitrile, 0.1% formic acid) at 400 nL/min at room temperature
The LC gradient consisted of solvent A (0.1% formic acid in water) and solvent B (99.9% acetonitrile, 0.1% formic acid) starting at 5% B and ramping to 35% B over 90 min, ramping to 50% B at 95 min, ramping to 85% B at 97 min, back to 5% at 107 min and re-equilibrated until 120 min

Summary

Introduction

The grass family, Poaceae, includes the cereal crops and represents one of the most wide-spread plant taxonomic groups in terrestrial ecosystems (Kellogg, 2001). Known as culms, mechanically support reproductive structures, transport nutrients, and act as structural and non-structural carbohydrate storage organs (Moldenhauer et al, 2013). Many important biological processes including cell division, cell wall synthesis, and cell wall remodeling occur during stem development (Bosch et al, 2011; Cui et al, 2012). Among these processes, the change in cell walls is especially important for stem mechanical properties (Gritsch and Murphy, 2005; Wang et al, 2012). The developmental stage of stems influences susceptibility to pests and pathogens (Viajante and Heinrichs, 1987; Bandong and Litsinger, 2005)

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