Look Closely, the Beautiful May Be Small: Precursor-Derived Peptides in Plants

Olsson, Vilde; Joos, Lisa; Zhu, Shanshuo; Gevaert, Kris; Butenko, Melinka A.; Smet, Ive De

doi:10.1146/annurev-arplant-042817-040413

Cited by 144 publications

(124 citation statements)

References 221 publications

(330 reference statements)

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“…Choosing the peptide sequence to be synthesized can be a difficult task, especially for novel SSP genes that do not belong to established and previously investigated families. In vivo peptide maturation (i.e., peptidase processing and addition of side chain modifications) in the ER (i.e., the secretory pathway) is generally poorly understood (Olsson et al, 2018;Stührwohldt & Schaller, 2019;Stührwohldt, Schardon, Stintzi, & Schaller, 2017). For a novel SSP gene, it is therefore advisable to initially select and synthesize several staggered peptides based on gene alignments and/or HMMs (Fig.…”

Section: Of 35mentioning

confidence: 99%

“…RNA-seq provides the strongest argument for the existence and expression of unannotated small genes and sORFs with low expression, such as those encoding SSPs. Determining which of the expressed sORFs encode potential SSP-coding genes or simply are novel members of established SSP gene families is another challenge that requires additional filtering steps or approaches as outlined here (Basic Protocols 1 and 2) and elsewhere (e.g., de Bang et al, 2017;Ghorbani et al, 2015;Hastwell, de Bang, Gresshoff, & Ferguson, 2017;Murphy et al, 2012;Olsson et al, 2018).…”

Section: Of 35mentioning

confidence: 99%

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Identification and Functional Investigation of Genome‐Encoded, Small, Secreted Peptides in Plants

et al. 2019

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Hundreds to thousands of small secreted peptides (SSPs) are encoded in plant genomes but have been overlooked, and most remain unannotated and unstudied. Despite their low profile, they have been found to confer dramatic effects on growth and development of plants. With the growing appreciation of their significance, the development of appropriate methods to identify and functionally assess the myriad SSPs encoded in plant genomes has become critical. Here, we provide protocols for the computational and physiological analysis of SSPs in plant genomes. We first describe our methodology successfully used for genome‐wide identification and annotation of SSP‐coding genes in the model legume Medicago truncatula, which can be readily adapted for other plant species. We then provide protocols for the functional analysis of SSPs using various synthetic peptide screens. Considerations for the design and handling of peptides are included. © 2019 by John Wiley & Sons, Inc.

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Section: Of 35mentioning

confidence: 99%

Section: Of 35mentioning

confidence: 99%

Identification and Functional Investigation of Genome‐Encoded, Small, Secreted Peptides in Plants

et al. 2019

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“…In plants, several small secreted peptides (SSPs) function as hormonal signalling molecules that respond to internal and external stimuli [1]. SSPs are known to be involved in different processes, ranging from organ growth to biotic and abiotic responses [2,3].…”

Section: Introductionmentioning

confidence: 99%

Genomic structure and transcript analysis of the Rapid Alkalinization Factor (RALF) gene family during host-pathogen crosstalk in Fragaria vesca and Fragaria x ananassa strawberry

et al. 2020

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Rapid Alkalinization Factors (RALFs) are cysteine-rich peptides ubiquitous within plant kingdom. They play multiple roles as hormonal signals in diverse processes, including root elongation, cell growth, pollen tube development, and fertilization. Their involvement in hostpathogen crosstalk as negative regulators of immunity in Arabidopsis has also been recognized. In addition, peptides homologous to RALF are secreted by different fungal pathogens as effectors during early stages of infection. Previous studies have identified nine RALF genes in the diploid strawberry (Fragaria vesca) genome. This work describes the genomic organization of the RALF gene families in commercial octoploid strawberry (Fragaria × ananassa) and the re-annotated genome of F. vesca, and then compares findings with orthologs in Arabidopsis thaliana. We reveal the presence of 15 RALF genes in F. vesca genotype Hawaii 4 and 50 in Fragaria x ananassa cv. Camarosa, showing a non-homogenous localization of genes among the different Fragaria x ananassa subgenomes. Expression analysis of Fragaria x ananassa RALF genes upon infection with Colletotrichum acutatum or Botrytis cinerea showed that FanRALF3-1 was the only fruit RALF gene upregulated after fungal infection. In silico analysis was used to identify distinct pathogen inducible elements upstream of the FanRALF3-1 gene. Agroinfiltration of strawberry fruit with deletion constructs of the FanRALF3-1 promoter identified a 5' region required for Fan-RALF3-1 expression in fruit, but failed to identify a region responsible for fungal induced expression.

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“…Various methods have been used to investigate the interactions between CLE peptides and LRR-RLK/RLPs, such as genetic and physiological approaches, directly quantifying physical interactions and phosphor-proteomics. However, only a small number of possible ligand-receptor pairs have been identi ed [19,20]. CLE peptides regulate the growth and development of various tissues in Arabidopsis, such as the apical and vascular meristems.…”

Section: Introductionmentioning

confidence: 99%

Predicting and Clustering Plant CLE Genes with a New Method Developed Specifically for Short Amino Acid Sequences

Zhang

Liu

Kücükoglu

et al. 2020

Preprint

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Background: The CLV3/ESR-RELATED (CLE) gene family encodes small secreted peptides (SSPs) and plays vital roles in plant growth and development by promoting cell-to-cell communication. The prediction and classification of CLE genes is challenging because of their low sequence similarity. Results: We developed a machine learning-aided method for predicting CLE genes by using a CLE motif-specific residual score matrix and a novel clustering method based on the Euclidean distance of 12 amino acid residues from the CLE motif in a site-weight dependent manner. In total, 2156 CLE candidates—including 627 novel candidates—were predicted from 69 plant species. The results from our CLE motif-based clustering are consistent with previous reports using the entire pre-propeptide. Characterization of CLE candidates provided systematic statistics on protein lengths, signal peptides, relative motif positions, amino acid compositions of different parts of the CLE precursor proteins, and decisive factors of CLE prediction. The approach taken here provides information on the evolution of the CLE gene family and provides evidence that the CLE and IDA/IDL genes share a common ancestor. Conclusions: Our new approach is applicable to SSPs or other proteins with short conserved domains and hence, provides a useful tool for gene prediction, classification and evolutionary analysis.

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Look Closely, the Beautiful May Be Small: Precursor-Derived Peptides in Plants

Cited by 144 publications

References 221 publications

Identification and Functional Investigation of Genome‐Encoded, Small, Secreted Peptides in Plants

Identification and Functional Investigation of Genome‐Encoded, Small, Secreted Peptides in Plants

Genomic structure and transcript analysis of the Rapid Alkalinization Factor (RALF) gene family during host-pathogen crosstalk in Fragaria vesca and Fragaria x ananassa strawberry

Predicting and Clustering Plant CLE Genes with a New Method Developed Specifically for Short Amino Acid Sequences

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