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Palmer NA, Alvarez S, Naldrett MJ, Muhle A, Sarath G, Edmé SJ, Tatineni S, Mitchell RB, Yuen G. Dynamic Reconfiguration of Switchgrass Proteomes in Response to Rust ( Puccinia novopanici) Infection. Int J Mol Sci 2023; 24:14630. [PMID: 37834079 PMCID: PMC10572835 DOI: 10.3390/ijms241914630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Switchgrass (Panicum virgatum L.) can be infected by the rust pathogen (Puccinia novopanici) and results in lowering biomass yields and quality. Label-free quantitative proteomics was conducted on leaf extracts harvested from non-infected and infected plants from a susceptible cultivar (Summer) at 7, 11, and 18 days after inoculation (DAI) to follow the progression of disease and evaluate any plant compensatory mechanisms to infection. Some pustules were evident at 7 DAI, and their numbers increased with time. However, fungal DNA loads did not appreciably change over the course of this experiment in the infected plants. In total, 3830 proteins were identified at 1% false discovery rate, with 3632 mapped to the switchgrass proteome and 198 proteins mapped to different Puccinia proteomes. Across all comparisons, 1825 differentially accumulated switchgrass proteins were identified and subjected to a STRING analysis using Arabidopsis (A. thaliana L.) orthologs to deduce switchgrass cellular pathways impacted by rust infection. Proteins associated with plastid functions and primary metabolism were diminished in infected Summer plants at all harvest dates, whereas proteins associated with immunity, chaperone functions, and phenylpropanoid biosynthesis were significantly enriched. At 18 DAI, 1105 and 151 proteins were significantly enriched or diminished, respectively. Many of the enriched proteins were associated with mitigation of cellular stress and defense.
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Affiliation(s)
- Nathan A. Palmer
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Sophie Alvarez
- Proteomics and Metabolomics Core Facility, Center for Biotechnology, University of Nebraska at Lincoln, Lincoln, NE 68588-0664, USA; (S.A.); (M.J.N.)
| | - Michael J. Naldrett
- Proteomics and Metabolomics Core Facility, Center for Biotechnology, University of Nebraska at Lincoln, Lincoln, NE 68588-0664, USA; (S.A.); (M.J.N.)
| | - Anthony Muhle
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Gautam Sarath
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Serge J. Edmé
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Satyanarayana Tatineni
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
- Department of Plant Pathology, University of Nebraska at Lincoln, Lincoln, NE 68583-0722, USA;
| | - Robert B. Mitchell
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Gary Yuen
- Department of Plant Pathology, University of Nebraska at Lincoln, Lincoln, NE 68583-0722, USA;
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Greenbug (Schizaphis graminum) herbivory significantly impacts protein and phosphorylation abundance in switchgrass (Panicum virgatum). Sci Rep 2020; 10:14842. [PMID: 32908168 PMCID: PMC7481182 DOI: 10.1038/s41598-020-71828-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023] Open
Abstract
Switchgrass (Panicum virgatum L.) is an important crop for biofuel production but it also serves as host for greenbugs (Schizaphis graminum Rondani; GB). Although transcriptomic studies have been done to infer the molecular mechanisms of plant defense against GB, little is known about the effect of GB infestation on the switchgrass protein expression and phosphorylation regulation. The global response of the switchgrass cultivar Summer proteome and phosphoproteome was monitored by label-free proteomics shotgun in GB-infested and uninfested control plants at 10 days post infestation. Peptides matching a total of 3,594 proteins were identified and 429 were differentially expressed proteins in GB-infested plants relative to uninfested control plants. Among these, 291 and 138 were up and downregulated by GB infestation, respectively. Phosphoproteome analysis identified 310 differentially phosphorylated proteins (DP) from 350 phosphopeptides with a total of 399 phosphorylated sites. These phosphopeptides had more serine phosphorylated residues (79%), compared to threonine phosphorylated sites (21%). Overall, KEGG pathway analysis revealed that GB feeding led to the enriched accumulation of proteins important for biosynthesis of plant defense secondary metabolites and repressed the accumulation of proteins involved in photosynthesis. Interestingly, defense modulators such as terpene synthase, papain-like cysteine protease, serine carboxypeptidase, and lipoxygenase2 were upregulated at the proteome level, corroborating previously published transcriptomic data.
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