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

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dc.contributor.authorLin, Fan
dc.contributor.authorWilliams, Brad J.
dc.contributor.authorThangella, Padmavathi A. V.
dc.contributor.authorLadak, Adam
dc.contributor.authorSchepmoes, Athena A.
dc.contributor.authorOlivos, Hernando J.
dc.contributor.authorZhao, Kangmei
dc.contributor.authorCallister, Stephen J.
dc.contributor.authorBartley, Laura E.
dc.date.accessioned2019-04-01T19:03:34Z
dc.date.available2019-04-01T19:03:34Z
dc.date.issued2017-07-13
dc.description.abstractInternodes 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.en_US
dc.description.peerreviewYesen_US
dc.description.sponsorshipThis work was supported by the U.S. National Science Foundation (grant numbers EPS-0814361, 0923247, and CHE-1626372), the U.S. Department of Energy (DOE), Office of Science (DE-SC0006904), and the U.S. Department of Agriculture National Institute of Food and Agriculture, (2010-38502-21836). A portion of this research was performed in the Environmental Molecular Sciences Laboratory at the Pacific Northwest National Laboratory (PNNL). The Environmental Molecular Sciences Laboratory is a DOE Office of Biological and Environmental Research scientific user facility on the PNNL campus. PNNL is a multiprogram national laboratory operated by Battelle for the DOE under contract DE-AC05-76RL01830. Collaboration with EMSL was supported through Projects 49477 and 49510. Any opinions, findings, conclusions, or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the funding agencies. Open access fees fees for this article provided whole or in part by OU Libraries Open Access Fund.en_US
dc.identifier.citationLin F, Williams BJ, Thangella PAV, Ladak A, Schepmoes AA, Olivos HJ, Zhao K, Callister SJ and Bartley LE (2017) Proteomics Coupled with Metabolite and Cell Wall Profiling Reveal Metabolic Processes of a Developing Rice Stem Internode. Front. Plant Sci. 8:1134. doi: 10.3389/fpls.2017.01134en_US
dc.identifier.doi10.3389/fpls.2017.01134en_US
dc.identifier.urihttps://hdl.handle.net/11244/317826
dc.languageen_USen_US
dc.rightsAttribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.subjectcell wallen_US
dc.subjectproteomeen_US
dc.subjectmetaboliteen_US
dc.subjectphosphoproteinen_US
dc.subjectOryza sativa L.en_US
dc.subjectculmen_US
dc.titleProteomics Coupled with Metabolite and Cell Wall Profiling Reveal Metabolic Processes of a Developing Rice Stem Internodeen_US
dc.typeArticleen_US
ou.groupCollege of Arts and Sciences::Department of Microbiology and Plant Biologyen_US

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