Proteomics (SWATH-MS) informed by transcriptomics approach of tropical herb Persicaria minor leaves upon methyl jasmonate elicitation

Wan Mohd Aizat Wan Kamaruddin, Sarah Ibrahim, Reyhaneh Rahnamaie-Tajadod, Kok Keong Loke, Hoe Han Goh, Normah Mohd. Noor

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Background. Jasmonic 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. Method. In 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. Results. From this proteomics informed by transcriptomics approach, we have suc- cessfully 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). Discussion. MeJA treatment induced the upregulation of proteins involved in various biochemical pathways including stress response mechanism, lipid metabolism, sec- ondary 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 com- prehensive protein profiling of this non-model herbal species upon MeJA treatment.

Original languageEnglish
Article numbere5525
JournalPeerJ
Volume2018
Issue number8
DOIs
Publication statusPublished - 1 Jan 2018

Fingerprint

methyl jasmonate
transcriptomics
Proteomics
proteomics
herbs
leaves
Proteins
proteins
proteome
transcriptome
Proteome
Databases
Transcriptome
Down-Regulation
degradation
Persicaria minor
protein structure
jasmonic acid
smell
biotic stress

Keywords

  • Label-free proteomics
  • LC-MS/MS
  • Methyl jasmonate
  • Polygonum minus
  • SWATH-MS analysis

ASJC Scopus subject areas

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Proteomics (SWATH-MS) informed by transcriptomics approach of tropical herb Persicaria minor leaves upon methyl jasmonate elicitation. / Wan Kamaruddin, Wan Mohd Aizat; Ibrahim, Sarah; Rahnamaie-Tajadod, Reyhaneh; Loke, Kok Keong; Goh, Hoe Han; Mohd. Noor, Normah.

In: PeerJ, Vol. 2018, No. 8, e5525, 01.01.2018.

Research output: Contribution to journalArticle

Wan Kamaruddin, Wan Mohd Aizat ; Ibrahim, Sarah ; Rahnamaie-Tajadod, Reyhaneh ; Loke, Kok Keong ; Goh, Hoe Han ; Mohd. Noor, Normah. / Proteomics (SWATH-MS) informed by transcriptomics approach of tropical herb Persicaria minor leaves upon methyl jasmonate elicitation. In: PeerJ. 2018 ; Vol. 2018, No. 8.
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AU - Rahnamaie-Tajadod, Reyhaneh

AU - Loke, Kok Keong

AU - Goh, Hoe Han

AU - Mohd. Noor, Normah

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N2 - Background. Jasmonic 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. Method. In 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. Results. From this proteomics informed by transcriptomics approach, we have suc- cessfully 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). Discussion. MeJA treatment induced the upregulation of proteins involved in various biochemical pathways including stress response mechanism, lipid metabolism, sec- ondary 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 com- prehensive protein profiling of this non-model herbal species upon MeJA treatment.

AB - Background. Jasmonic 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. Method. In 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. Results. From this proteomics informed by transcriptomics approach, we have suc- cessfully 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). Discussion. MeJA treatment induced the upregulation of proteins involved in various biochemical pathways including stress response mechanism, lipid metabolism, sec- ondary 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 com- prehensive protein profiling of this non-model herbal species upon MeJA treatment.

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KW - Polygonum minus

KW - SWATH-MS analysis

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