Dynamic reconfiguration of switchgrass proteomes in response to rust (Puccinia Novopanici) infection

Authors: Palmer, Nathan - Nate; ALVAREZ, SOPHIE - University Of Nebraska; NALDRETT, MICHAEL - University Of Nebraska; Muhle, Anthony; Sarath, Gautam; Mitchell, Robert - Rob; Edme, Serge; Tatineni, Satyanarayana - Ts; YUEN, GARY - University Of Nebraska

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/26/2023
Publication Date: 9/28/2023
Citation: Palmer, N.A., Alvarez, S., Naldrett, M.J., Muhle, A.A., Sarath, G., Mitchell, R., Edme, S.J., Tatineni, S., Yuen, G. 2023. Dynamic reconfiguration of switchgrass proteomes in response to rust (Puccinia Novopanici) infection. International Journal of Molecular Sciences. 24(19). Article 14630. https://doi.org/10.3390/ijms241914630.
DOI: https://doi.org/10.3390/ijms241914630

Interpretive Summary: Switchgrass can be grown for forage and bioenergy uses, but the fungal rust pathogen (Puccinia novopanici) can infect plants reducing yields and biomass quality. However, the mechanisms within switchgrass cell that allow them to prevent the spread of the rust pathogen are largely unknown. Here, two switchgrass cultivars with divergent levels of rust resistance were used to evaluate changes in switchgrass proteins over time during rust infection. The proteins present in switchgrass cells were isolated and analyzed using mass spectrometry (proteomics). In the susceptible cultivar Summer, rust infection caused the accumulation of proteins needed for cell defense and to mitigate many aspects of cellular stress, while the levels of proteins needed for growth and normal development were decreased. In the resistant cultivar Kanlow, some proteins involved in cellular stress were also observed, but the plants did not suffer significant reduction to growth-related proteins. Overall, these data indicate that the changes in key metabolic pathways contribute to the susceptible versus the resistant response. The genes encoding these proteins represent important indicators that could be used to develop more rust-resistant switchgrass cultivars.

Technical Abstract: Switchgrass (Panicum virgatum) can be infected by the rust pathogen (Puccinia novopanici) resulting in lowering biomass yields and quality. Here, two cultivars with divergent rust resistance were used to evaluate the dynamic changes in proteomes following rust inoculation. Label-free shotgun proteomics was conducted on leaf extracts harvested from a susceptible cultivar Summer at 7, 11, and 18 DAI, and leaves collected at 18 DAI from controls and infected plants of the more resistant cultivar Kanlow. A total of 3,908 proteins were identified with high confidence of which 3,710 were mapped to the switchgrass proteome and 198 proteins were mapped to different Puccinia proteomes. Across all comparisons, 1,835 DAPs were identified. EDAPs and DDAPs were subjected to a STRING analysis using Arabidopsis orthologs to deduce switchgrass cellular pathways impacted by rust infection. Proteins associated with plastid functions and primary metabolism were part of the DDAP modules in Summer plants at all harvest dates. In Kanlow at 18 DAI, DDAPs were also associated with plastid pigment biosynthesis, but evidence of linages to primary metabolism was less obvious. In Summer plants ribosomal, immunity signaling, and defense-related proteins were part of the EDAPs at 7 DAI, and by 11 DAI proteins with immunity, chaperone functions, and phenylpropanoid biosynthesis were significantly enriched. Among EDAPs at 18 DAI, 587 and 296 proteins were found to have Arabidopsis orthologs in Summer and Kanlow plants respectively. Of these proteins, 212 were found in common between the two cultivars. Many of 212 EDAPs were part of STRING modules linked to mitigation of cellular stress and defense. However, the large difference in the number of EDAPs in Summer plants relative to Kanlow plants at 18 DAI, indicated a divergence in the defense responses that could underpin susceptibility and resistance to rust in these switchgrass germplasm.