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

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.

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Fig: Classification of small secreted proteins (SSPs) in plants: Plant SSPs can be derived from protein precursors, which can be either nonfunctional or functional, or translated from small open reading frames (sORFs). SSPs derived from functional protein precursors often contain an N-terminal signal sequence (NSS), which is removed during maturation. SSPs synthesized from nonfunctional precursors can be further divided into three categories: post-translationally modified (PTM) SSPs, Cys-rich SSPs, and non-Cys-rich/non-PTM SSPs. In addition, SSPs can be encoded by sORFs that locate at upstream of main ORFs (uORFs), in transcripts of long non-coding RNAs (lncRNAs), or primary transcripts of miRNAs (pri-miRNAs).

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.

Hu, XL., Lu, H., Hassan, M.M. et al. Advances and perspectives in discovery and functional analysis of small secreted proteins in plants.Hortic Res 8, 130 (2021). https://doi.org/10.1038/s41438-021-00570-7

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