Abstract
Signal peptide is an essential part during protein translocation for extracellular expression in the plants. A secretomics approach was performed to identify secretory proteins from oil palm and predict the presence of the signal peptide in each protein. The transcriptome and secretome profiles were generated from oil palm ramets. A combination of bioinformatics tools including SignalP, TargetP, TMHMM, and SecretomeP was used to predict both classical and leaderless secretory proteins. The secretome analysis from transcriptome data revealed 2259 genes that encoded secretory proteins. The proteome analysis identified a total of 37 proteins from which 10 classical secretory proteins can be distinguished. It was important to note that oil palm ramet’s secretome was dominated by stress or defence related proteins which may act as protection during certain plant developmental stages. We also found that some proteins can be both intracellular and extracellular protein. Among 10 identified classical secretory proteins, the signal peptides of oil palm beta-1,3-glucanase and putative class III chitinase were interesting for further study due to their high cleavage site scores. Overall, this study provided broader view of oil palm secretomes and specific signal peptides for extracellular expression.
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Abbreviations
- SP:
-
Signal peptide
- CSP:
-
Classical secretory protein
- LSP:
-
Leaderless secretory protein
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The authors would like to express their great appreciation to the director of Plant Production and Biotechnology Division for permission to publish this article.
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This project was fully funded by PT SMART Tbk.
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CD: conceptualization, methodology, writing—original draft and visualization. RAR: conceptualization, methodology and data curation. ZAT: methodology, software, data curation and vizualization. WA: resources. CU: writing—review, editing and supervision. TL: writing—review, editing, supervision and funding acquisition.
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Darmawan, C., Rohman, R.A., Tanjung, Z.A. et al. The prediction of specific oil palm extracellular signal peptides using plant secretomics approach. J Proteins Proteom 13, 29–38 (2022). https://doi.org/10.1007/s42485-021-00081-y
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DOI: https://doi.org/10.1007/s42485-021-00081-y