Proteomics profiling of ethylene-induced tomato flower pedicel abscission

The control of abscission is an important agricultural concern because of its substantial effect on crop yield and quality. Changes in gene expression are correlated with the ethylene-mediated execution of abscission. However, only few large-scale proteomic studies focused on tomato pedicel abscissi...

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Published inJournal of proteomics Vol. 121; pp. 67 - 87
Main Authors Zhang, Xiao-lin, Qi, Ming-fang, Xu, Tao, Lu, Xiu-jun, Li, Tian-lai
Format Journal Article
LanguageEnglish
Published Netherlands Elsevier B.V 21.05.2015
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Abstract The control of abscission is an important agricultural concern because of its substantial effect on crop yield and quality. Changes in gene expression are correlated with the ethylene-mediated execution of abscission. However, only few large-scale proteomic studies focused on tomato pedicel abscission. Isobaric tag for relative and absolute quantification labeling was used to examine the protein and phosphoprotein changes in the tomato pedicel AZ (AZ) treated with ethylene or 1-methylcyclopropene. Among the 1429 quantified proteins, 383 unique peptides corresponding to 166 proteins showed higher than 1.5-fold change in abundance. A total of 450 phosphopeptides were detected, among which 85 phosphopeptides corresponding to 73 phosphoproteins were significantly regulated (>1.5-fold abundance change) in response to ethylene. Protein and phosphoprotein sets showed 26 similar proteins. Six phosphorylation motifs were extracted from the 138 phosphorylation sites. By analyzing translational and modification levels, we found that the modification level was not due to the translational changes. Comparison between the protein and phosphoprotein functions revealed that the proteins acted mainly in the metabolic process and showed catalytic activity, whereas most of the phosphoproteins showed signaling and transporting activities. Data revealed the unique features of the AZ phosphoproteomics, thereby suggesting the involvement of a complex network of kinase–substrate and phosphatase–substrate interactions in response to ethylene. Some phosphorylation sites from calcium-dependent protein kinase (CDPK5S523), CDPK5S527, and SRL3S329 were also found to perform protective functions for AZ and to be helpful in ethylene signal transduction. Organ abscission has both positive and negative roles. Abscission is conducive for the fall of ripe fruits and the release and dispersion of seeds, but abscission has been a major limiting factor for crop productivity. Hence, more details about the process may aid in the regulation of organ abscission. However, at present, the detailed mechanism of abscission is still unclear. In tomato, several transcriptome analyses were performed using pedicels as materials. Yet, no large-scale proteomics and phosphoproteomic studies of abscission zone have been reported so far. Hence, in this present study, we determined the ethylene-induced changes in the proteomics and phosphoproteomics of tomato flower AZ tissue using the isobaric tag for relative and absolute quantification (iTRAQ). Proteomics data from both data sets revealed the differentially expressed proteins that are associated with the translational and modification levels relevant to abscission mechanism. Two key proteins (CDPK (CDPK5S523 and CDPK5S527) and SRL3S329) among ethylene signal transduction and defense-related proteins were obtained from the phosphoproteins. The set of tomato phosphorylation sites presented in this work is useful in at least two ways. First, as a database resource, the data would facilitate research on the identified phosphoproteins. Second, the identified sites of the related proteins could provide enough knowledge for further experiments. Hence, our results contribute to the understanding of the mechanism of abscission in plants. [Display omitted] •We examine the protein and phosphoprotein changes in the tomato pedicel AZ.•We examine the correlation of protein fold changes with transcripts.•GO annotation and KEGG analysis•Phosphorylation motif analysis for the phosphorylation level significantly changed the phosphopeptides.•Key protein's Western blot analysis
AbstractList The control of abscission is an important agricultural concern because of its substantial effect on crop yield and quality. Changes in gene expression are correlated with the ethylene-mediated execution of abscission. However, only few large-scale proteomic studies focused on tomato pedicel abscission. Isobaric tag for relative and absolute quantification labeling was used to examine the protein and phosphoprotein changes in the tomato pedicel AZ (AZ) treated with ethylene or 1-methylcyclopropene. Among the 1429 quantified proteins, 383 unique peptides corresponding to 166 proteins showed higher than 1.5-fold change in abundance. A total of 450 phosphopeptides were detected, among which 85 phosphopeptides corresponding to 73 phosphoproteins were significantly regulated (>1.5-fold abundance change) in response to ethylene. Protein and phosphoprotein sets showed 26 similar proteins. Six phosphorylation motifs were extracted from the 138 phosphorylation sites. By analyzing translational and modification levels, we found that the modification level was not due to the translational changes. Comparison between the protein and phosphoprotein functions revealed that the proteins acted mainly in the metabolic process and showed catalytic activity, whereas most of the phosphoproteins showed signaling and transporting activities. Data revealed the unique features of the AZ phosphoproteomics, thereby suggesting the involvement of a complex network of kinase-substrate and phosphatase-substrate interactions in response to ethylene. Some phosphorylation sites from calcium-dependent protein kinase (CDPK5(S523)), CDPK5(S527), and SRL3(S329) were also found to perform protective functions for AZ and to be helpful in ethylene signal transduction. Organ abscission has both positive and negative roles. Abscission is conducive for the fall of ripe fruits and the release and dispersion of seeds, but abscission has been a major limiting factor for crop productivity. Hence, more details about the process may aid in the regulation of organ abscission. However, at present, the detailed mechanism of abscission is still unclear. In tomato, several transcriptome analyses were performed using pedicels as materials. Yet, no large-scale proteomics and phosphoproteomic studies of abscission zone have been reported so far. Hence, in this present study, we determined the ethylene-induced changes in the proteomics and phosphoproteomics of tomato flower AZ tissue using the isobaric tag for relative and absolute quantification (iTRAQ). Proteomics data from both data sets revealed the differentially expressed proteins that are associated with the translational and modification levels relevant to abscission mechanism. Two key proteins (CDPK (CDPK5(S523) and CDPK5(S527)) and SRL3(S329)) among ethylene signal transduction and defense-related proteins were obtained from the phosphoproteins. The set of tomato phosphorylation sites presented in this work is useful in at least two ways. First, as a database resource, the data would facilitate research on the identified phosphoproteins. Second, the identified sites of the related proteins could provide enough knowledge for further experiments. Hence, our results contribute to the understanding of the mechanism of abscission in plants.
The control of abscission is an important agricultural concern because of its substantial effect on crop yield and quality. Changes in gene expression are correlated with the ethylene-mediated execution of abscission. However, only few large-scale proteomic studies focused on tomato pedicel abscission. Isobaric tag for relative and absolute quantification labeling was used to examine the protein and phosphoprotein changes in the tomato pedicel AZ (AZ) treated with ethylene or 1-methylcyclopropene. Among the 1429 quantified proteins, 383 unique peptides corresponding to 166 proteins showed higher than 1.5-fold change in abundance. A total of 450 phosphopeptides were detected, among which 85 phosphopeptides corresponding to 73 phosphoproteins were significantly regulated (>1.5-fold abundance change) in response to ethylene. Protein and phosphoprotein sets showed 26 similar proteins. Six phosphorylation motifs were extracted from the 138 phosphorylation sites. By analyzing translational and modification levels, we found that the modification level was not due to the translational changes. Comparison between the protein and phosphoprotein functions revealed that the proteins acted mainly in the metabolic process and showed catalytic activity, whereas most of the phosphoproteins showed signaling and transporting activities. Data revealed the unique features of the AZ phosphoproteomics, thereby suggesting the involvement of a complex network of kinase–substrate and phosphatase–substrate interactions in response to ethylene. Some phosphorylation sites from calcium-dependent protein kinase (CDPK5S523), CDPK5S527, and SRL3S329 were also found to perform protective functions for AZ and to be helpful in ethylene signal transduction. Organ abscission has both positive and negative roles. Abscission is conducive for the fall of ripe fruits and the release and dispersion of seeds, but abscission has been a major limiting factor for crop productivity. Hence, more details about the process may aid in the regulation of organ abscission. However, at present, the detailed mechanism of abscission is still unclear. In tomato, several transcriptome analyses were performed using pedicels as materials. Yet, no large-scale proteomics and phosphoproteomic studies of abscission zone have been reported so far. Hence, in this present study, we determined the ethylene-induced changes in the proteomics and phosphoproteomics of tomato flower AZ tissue using the isobaric tag for relative and absolute quantification (iTRAQ). Proteomics data from both data sets revealed the differentially expressed proteins that are associated with the translational and modification levels relevant to abscission mechanism. Two key proteins (CDPK (CDPK5S523 and CDPK5S527) and SRL3S329) among ethylene signal transduction and defense-related proteins were obtained from the phosphoproteins. The set of tomato phosphorylation sites presented in this work is useful in at least two ways. First, as a database resource, the data would facilitate research on the identified phosphoproteins. Second, the identified sites of the related proteins could provide enough knowledge for further experiments. Hence, our results contribute to the understanding of the mechanism of abscission in plants. [Display omitted] •We examine the protein and phosphoprotein changes in the tomato pedicel AZ.•We examine the correlation of protein fold changes with transcripts.•GO annotation and KEGG analysis•Phosphorylation motif analysis for the phosphorylation level significantly changed the phosphopeptides.•Key protein's Western blot analysis
Author Li, Tian-lai
Qi, Ming-fang
Lu, Xiu-jun
Zhang, Xiao-lin
Xu, Tao
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  orcidid: 0000-0002-0855-1953
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  givenname: Tao
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  organization: Department of Horticulture, Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, China
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  organization: Department of Horticulture, Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, China
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Keywords iTRAQ
Phosphoprotein
Protein
Ethylene
Abscission
Language English
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Snippet The control of abscission is an important agricultural concern because of its substantial effect on crop yield and quality. Changes in gene expression are...
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pubmed
elsevier
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Publisher
StartPage 67
SubjectTerms Abscission
Amino Acid Motifs
Catalysis
Cyclopropanes - chemistry
Ethylene
Ethylenes - chemistry
Flowers - drug effects
Flowers - metabolism
Gene Expression Regulation, Plant - drug effects
iTRAQ
Lycopersicon esculentum - drug effects
Lycopersicon esculentum - metabolism
Phosphopeptides - chemistry
Phosphoprotein
Phosphorylation
Plant Proteins - metabolism
Protein
Protein Folding
Proteome - metabolism
Proteomics
RNA, Messenger - metabolism
Signal Transduction
Title Proteomics profiling of ethylene-induced tomato flower pedicel abscission
URI https://dx.doi.org/10.1016/j.jprot.2015.03.023
https://www.ncbi.nlm.nih.gov/pubmed/25829262
Volume 121
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