Advances and perspectives in discovery and functional analysis of small secreted proteins in plants

Xiao Li Hu; Haiwei Lu; Md Mahmudul Hassan; Jin Zhang; Guoliang Yuan; Paul E. Abraham; Him K. Shrestha; Manuel I. Villalobos Solis; Jin Gui Chen; Timothy J. Tschaplinski; Mitchel J. Doktycz; Gerald A. Tuskan; Zong Ming (Max) Cheng; Xiaohan Yang

doi:10.1038/s41438-021-00570-7

Advances and perspectives in discovery and functional analysis of small secreted proteins in plants

Xiao Li Hu, Haiwei Lu, Md Mahmudul Hassan, Jin Zhang, Guoliang Yuan, Paul E. Abraham, Him K. Shrestha, Manuel I. Villalobos Solis, Jin Gui Chen, Timothy J. Tschaplinski, Mitchel J. Doktycz, Gerald A. Tuskan, Zong Ming (Max) Cheng, Xiaohan Yang

Research output: Contribution to journal › Review article › peer-review

24 Scopus citations

Abstract

Small secreted proteins (SSPs) are less than 250 amino acids in length and are actively transported out of cells through conventional protein secretion pathways or unconventional protein secretion pathways. In plants, SSPs have been found to play important roles in various processes, including plant growth and development, plant response to abiotic and biotic stresses, and beneficial plant–microbe interactions. Over the past 10 years, substantial progress has been made in the identification and functional characterization of SSPs in several plant species relevant to agriculture, bioenergy, and horticulture. Yet, there are potentially a lot of SSPs that have not been discovered in plant genomes, which is largely due to limitations of existing computational algorithms. Recent advances in genomics, transcriptomics, and proteomics research, as well as the development of new computational algorithms based on machine learning, provide unprecedented capabilities for genome-wide discovery of novel SSPs in plants. In this review, we summarize known SSPs and their functions in various plant species. Then we provide an update on the computational and experimental approaches that can be used to discover new SSPs. Finally, we discuss strategies for elucidating the biological functions of SSPs in plants.

Original language	English
Article number	130
Journal	Horticulture Research
Volume	8
Issue number	1
DOIs	https://doi.org/10.1038/s41438-021-00570-7
State	Published - Dec 2021

Funding

The writing of this manuscript was supported by the Laboratory Directed Research and Development program of Oak Ridge National Laboratory, and the U.S. DOE BER Genomic Science Program, as part of the Secure Ecosystem Engineering and Design and the Plant-Microbe Interfaces Scientific Focus Areas. X.-L.H. received financial support from the China Scholarship Council. This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). The authors declare no competing interests.

Funders	Funder number
U.S. Department of Energy
Oak Ridge National Laboratory
China Scholarship Council

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Hu, X. L., Lu, H., Hassan, M. M., Zhang, J., Yuan, G., Abraham, P. E., Shrestha, H. K., Villalobos Solis, M. I., Chen, J. G., Tschaplinski, T. J., Doktycz, M. J., Tuskan, G. A., Cheng, Z. M., & Yang, X. (2021). Advances and perspectives in discovery and functional analysis of small secreted proteins in plants. Horticulture Research, 8(1), Article 130. https://doi.org/10.1038/s41438-021-00570-7

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abstract = "Small secreted proteins (SSPs) are less than 250 amino acids in length and are actively transported out of cells through conventional protein secretion pathways or unconventional protein secretion pathways. In plants, SSPs have been found to play important roles in various processes, including plant growth and development, plant response to abiotic and biotic stresses, and beneficial plant–microbe interactions. Over the past 10 years, substantial progress has been made in the identification and functional characterization of SSPs in several plant species relevant to agriculture, bioenergy, and horticulture. Yet, there are potentially a lot of SSPs that have not been discovered in plant genomes, which is largely due to limitations of existing computational algorithms. Recent advances in genomics, transcriptomics, and proteomics research, as well as the development of new computational algorithms based on machine learning, provide unprecedented capabilities for genome-wide discovery of novel SSPs in plants. In this review, we summarize known SSPs and their functions in various plant species. Then we provide an update on the computational and experimental approaches that can be used to discover new SSPs. Finally, we discuss strategies for elucidating the biological functions of SSPs in plants.",

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AU - Cheng, Zong Ming (Max)

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Advances and perspectives in discovery and functional analysis of small secreted proteins in plants

Abstract

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UN SDGs

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