In Planta Transcriptome and Proteome Profiles of Spongospora subterranea in Resistant and Susceptible Host Environments Illuminates Regulatory Principles Underlying Host–Pathogen Interaction

Abstract

Spongospora subterranea is an obligate biotrophic pathogen, causing substantial economic loss to potato industries globally. Currently, there are no fully effective management strategies for the control of potato diseases caused by S. subterranea. To further our understanding of S. subterranea biology during infection, we characterized the transcriptome and proteome of the pathogen during the invasion of roots of a susceptible and a resistant potato cultivar. A total of 7650 transcripts from S. subterranea were identified in the transcriptome analysis in which 1377 transcripts were differentially expressed between two cultivars. In proteome analysis, we identified 117 proteins with 42 proteins significantly changed in comparisons between resistant and susceptible cultivars. The functional annotation of transcriptome data indicated that the gene ontology terms related to the transportation and actin processes were induced in the resistant cultivar. The downregulation of enzyme activity and nucleic acid metabolism in the resistant cultivar suggests a probable influence of these processes in the virulence of S. subterranea. The protein analysis results indicated that the majority of differentially expressed proteins were related to the metabolic processes and transporter activity. The present study provides a comprehensive molecular insight into the multiple layers of gene regulation that contribute to S. subterranea infection and development in planta and illuminates the role of host immunity in affecting pathogen responses.

Multi-omics reveals mechanisms of resistance to potato root infection by Spongospora subterranea

“…RAW files were processed using Spectronaut software (v 14.7) whereby the DIA-MS spectra were used to generate a spectral library using the Pulsar search engine and the FASTA file of 53,106 entries comprising the UniProt proteome for Solanum tuberosum . Further details of Xcalibur and Spectronaut software parameter setting are described in Balotf et al 51 . Proteins identified on the basis of a single matching peptide were excluded.…”

Large-Scale Protein and Phosphoprotein Profiling to Explore Potato Resistance Mechanisms to Spongospora subterranea Infection

“…To ensure ongoing disease pressure, an additional 20 ml of fresh inoculum suspension of S. subterranea was added to each pot, 2 weeks after planting. Plant growth condition and inoculation has been described in Balotf et al (2021) . After 6 weeks in the greenhouse, the leaves of the infected and control plants were collected, frozen in liquid nitrogen, and stored at −80°C for protein extraction ( n = 4).…”

“…For phosphopeptide analysis, the dried samples were reconstituted in 10 μl of HPLC loading buffer, of which 4 μl was injected then separated under the same conditions, using a shorter (1 h) segmented gradient. The data-independent acquisition mass spectrometry (DIA-MS) method used for both total peptide and phosphopeptide analysis has been previously described in Balotf et al (2021) . Raw MS files were processed using Spectronaut software (v15) using the directDIA approach.…”

Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant–Pathogen Interactions

“…Several recent studies have employed DIA approaches for the analysis of the interaction between pathogens and their host plants. A DIA-MS workflow was used to profile the proteome of S. subterranea in resistant and susceptible potato cultivars [ 96 ]. The finding of this study illuminated the regulatory principles underlying Spongospora –potato interaction.…”