Proteomics (SWATH-MS) informed by transcriptomics approach of tropical herbPersicaria minorleaves upon methyl jasmonate elicitation

Abstract

BackgroundJasmonic acid (JA) and its derivative, methyl JA (MeJA) are hormonal cues released by plants that signal defense response to curb damages from biotic and abiotic stresses. To study such response, a tropical herbal plant, Persicaria minor, which possesses pungent smell and various bioactivities including antimicrobial and anticancer, was treated with MeJA. Such elicitation has been performed in hairy root cultures and plants such as Arabidopsis and rice, yet how MeJA influenced the proteome of an herbal species like P. minor is unknown.MethodIn this study, P. minor plants were exogenously elicited with MeJA and leaf samples were subjected to SWATH-MS proteomics analysis. A previously published translated transcriptome database was used as a reference proteome database for a comprehensive protein sequence catalogue and to compare their differential expression.ResultsFrom this proteomics informed by transcriptomics approach, we have successfully profiled 751 proteins of which 40 proteins were significantly different between control and MeJA-treated samples. Furthermore, a correlation analysis between both proteome and the transcriptome data sets suggests that significantly upregulated proteins were positively correlated with their cognate transcripts (Pearson’s r = 0.677) while a weak correlation was observed for downregulated proteins (r = 0.147).DiscussionMeJA treatment induced the upregulation of proteins involved in various biochemical pathways including stress response mechanism, lipid metabolism, secondary metabolite production, DNA degradation and cell wall degradation. Conversely, proteins involved in energy expensive reactions such as photosynthesis, protein synthesis and structure were significantly downregulated upon MeJA elicitation. Overall protein-transcript correlation was also weak (r = 0.341) suggesting the existence of post-transcriptional regulation during such stress. In conclusion, proteomics analysis using SWATH-MS analysis supplemented by the transcriptome database allows comprehensive protein profiling of this non-model herbal species upon MeJA treatment.

Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology

“…This may suggest the concerted molecular upregulation of defense-related proteins to overcome stress signals and infection. Meanwhile, proteins related to growth such as photosynthetic and structural proteins were significantly suppressed in these studies, perhaps as a response toward the stress signal to conserve energy and recycling molecular resources ( Ye et al., 2017 ; Aizat et al., 2018b ). Interestingly, such downregulation was mainly observed at the protein level, but not the transcript level ( Aizat et al., 2018b ), perhaps as a mechanism to quickly resume protein synthesis, when the stress is relieved.…”

“…On the other hand, an interesting emerging pattern arises when transcript-protein is compared between specific protein groups. For example, significantly upregulated proteins were positively correlated with their cognate transcripts in the stress response of various plants (Ye et al, 2017;Aizat et al, 2018b). Specifically, proteins related to defense such as proteases and peroxidases in MeJA-treated P. minor (Aizat et al, 2018b) and secondary metabolite biosynthesis such as flavonoid in phytoplasma-infected Ziziphus jujuba Mill.…”

“…Another example includes methyl jasmonate (MeJA) stress hormone treatment on Persicaria minor Huds. herbal plants, with poor overall proteome-transcriptome correlation (r=0.341) (Aizat et al, 2018b). Similarly, transcripts and proteins related to ethylene pathway (ethylene receptors [ETRs] and downstream signaling proteins, constitutive triple response-like proteins [CTRs], and ethylene insensitive 2 [EIN2]) were not well correlated during the ripening process of tomato (Solanum lycopersicum) (Mata et al, 2018).…”

“…This suggests the existence of post-transcriptional and post-translational regulation (such as proteasomal degradation) for the majority components of stress and ripening pathways. Despite transcriptome can be weakly correlated to proteome, it serves as an excellent database for protein identification in proteomics informed by transcriptomics approach for non-model plants (Aizat et al, 2018b;Wan Zakaria et al, 2019) as well as studying allele-specific expression (van Wesemael et al, 2018).…”

“…For example, significantly upregulated proteins were positively correlated with their cognate transcripts in the stress response of various plants ( Ye et al., 2017 ; Aizat et al., 2018b ). Specifically, proteins related to defense such as proteases and peroxidases in MeJA-treated P. minor ( Aizat et al., 2018b ) and secondary metabolite biosynthesis such as flavonoid in phytoplasma-infected Ziziphus jujuba Mill. leaf ( Ye et al., 2017 ) were upregulated coherently with their transcripts.…”