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

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.

Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP‐TF and determination of its transcriptional effect

“…The heterogeneous expression of the functional PtrEPSP‐TF or its loss‐of‐function alleles in rice did not trigger apparent morphological change in leaf and height during the vegetable growth. To visualize secondary cell walls, transverse cross sections of the S8 segment of rice internode II (Lin et al, ) were stained with phloroglucinol‐HCl, which turns lignin into a red‐purple color. Under a low‐magnification dissecting microscope, each sclerenchyma cell of the empty‐vector control was clearly observed, and their cell walls were stained red (Figure a).…”

Identification and functional analysis of proteins in response to light intensity, temperature and water potential in Brassica rapa hypocotyl

“…For example, Irshad et al () used 2‐dimensional analysis to identify 137 proteins in cell wall protein dynamics in elongating cells. Since then, the application of high‐throughput LC/MS–MS improved the protein numbers in proteomics research (Duruflé et al , Lin et al ). The proteomic research on hypocotyl elongation resulted in the detection of 1209 proteins in A. thaliana (Novak et al ).…”

Cell Wall Proteins Play Critical Roles in Plant Adaptation to Phosphorus Deficiency

“…Compared to CWP extraction, the approaches for separation, identification, and quantification of CWPs are better developed [40,41,42]. With the aid of various proteomics techniques, CWPs have been widely identified in different organs of many plant species, including Medicago ( Medicago truncatula ) [17,18,30,36,43,44,45,46], maize ( Zea mays ) [47], chickpea ( Cicer arietinum ) [48], rice ( Oryza sativa ) [34,49,50,51,52], potato [53], flax [54], and sugarcane ( Saccharum officinarum ) cell suspension cultures [55]. These identified CWPs can be functionally classified as proteases, structural proteins, proteins functioning in carbohydrate metabolism, proteins acting as oxidoreductases, proteins associated with lipid metabolism, proteins related to signaling transduction, proteins with predicted interaction domains, miscellaneous proteins, and unknown function proteins [18].…”