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Database Mining of Plant Peptide Homologues

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Database Mining of Plant Peptide Homologues Plant Biotechnology 38, 137–143 (2021) DOI: 10.5511/plantbiotechnology.20.0720a Short Communication Database mining of plant peptide homologues Na Yuan1,2, Chihiro Furumizu2, Baolong Zhang1, Shinichiro Sawa2,* 1 Institute of Crop Germplasm and Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; 2 Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto 860- 8555, Japan * E-mail: [email protected] Tel & Fax: +81-96-342-3439 Received June 10, 2020; accepted July 20, 2020 (Edited by S. Naramoto) Abstract In plant-pathogen interactions, pathogens employ secreted molecules, known as effectors to overcome physical barriers, modulate plant immunity, and facilitate colonization. Among these diverse effectors, some are found to mimic the plant peptides, to target host’s peptide receptors, and intervene in the peptide-regulated defense pathways and/or plant development. To better understand how pathogens have co-evolved with their plant hosts in order to improve disease management, we explored the presence of plant peptide mimics in microbes by bioinformatic analysis. In total, 36 novel peptide mimics belong to five plant peptide families were detected in bacterial and fungal kingdoms. Among them, phytosulfokine homologues were widely distributed in 22 phytopathogens and one bacterium, thereby constituted the largest proportion of the identified mimics. The putative functional peptide region is well conserved between plant and microbes, while the existence of a putative signal peptide varies between species. Our findings will increase understanding of plant- pathogen interactions, and provide new ideas for future studies of pathogenic mechanisms and disease management. Key words: homologues, mimics, pathogen effectors, plant peptides. In the co-evolutionary arms race between plants peptides. Plant peptide hormones are made of several to and pathogens, the plant possesses a large arsenal of hundreds of amino acids and play crucial roles in cell- immune receptors to sense and defend against microbial to-cell communication for regulating many aspects of challenges. Pathogens, in turn, have evolved diverse plant physiology (Hirakawa and Sawa 2019; Tavormina secreted effectors to suppress the plant’s immune et al. 2015). By mimicking plant peptides, pathogens responses, facilitate pathogen entry, and alter host can escape immune recognition and manipulate the physiology for pathogen colonization (Toruño et al. host’s gene expression to facilitate colonization. For 2016). For example, the bacterial effector Hrp outer example, effectors that mimic CLAVATA3/EMBRYO protein X1, secreted by the pathogen Pseudomonas SURROUNDING REGION-RELATED (CLE), syringae, can induce stomatal re-opening and enhance C-TERMINALLY ENCODED PEPTIDE (CEP), and pathogen entry by degrading multiple JASMONATE INFLORESCENCE DEFICIENT IN ABSCISSION ZIM DOMAIN transcriptional repressors, thereby, (IDA) peptides have been reported in sedentary plant- modulating jasmonic acid signaling (Gimenez-Ibanez parasitic nematodes (Bobay et al. 2013; Eves-Van Den et al. 2014). The fungal apoplastic effector Avirulence Akker et al. 2016; Guo et al. 2015; Kim et al. 2018; protein 2, a small cysteine-rich protein from the Lu et al. 2009; Wang et al. 2010, 2011). Elsewhere, tomato pathogen Cladosporium fulvum, contributes to the effector XA21-mediated immunity X has been pathogenic virulence by inhibiting several Cys proteases identified to mimic PLANT PEPTIDE CONTAINING that are required for basal host defense (van Esse et SULFATED TYROSINE (PSY) peptide to facilitate al. 2008). The identification of pathogen effectors and Xanthomonas oryzae pv. oryzae infection (Pruitt et their host targets is crucial, not only to enhance our al. 2017), and RAPID ALKALINIZATION FACTOR understanding of pathogenicity strategies but also (RALF) homologues have been found across a number to provide significant benefit to crop protection and of phytopathogenic fungi (Thynne et al. 2017). Many breeding. pathogen effectors still remain undiscovered, and these Growing evidence has been found for the existence of peptide mimics might be acting as important virulence pathogen effectors that mimic plant hormones, especially effectors in pathogenic strategies. Abbreviations: CLE, clavata3/embryo surrounding region-related; CEP, c-terminally encoded peptide; IDA, inflorescence deficient in abscission; IDL, IDA-like; PSK, phytosulfokine; PEP, plant elicitor peptide; PSY, plant peptide containing sulfated tyrosine. This article can be found at http://www.jspcmb.jp/ Published online January 30, 2021 Copyright © 2021 Japanese Society for Plant Biotechnology 138 Database mining of plant peptide homologues in microbes With the growing availability of microbial whole- location of the CLE domain, displaying an untypical genome sequences and tools for bioinformatic analysis, CLE structure. The CLE homologues of Actinobacteria, we are increasingly able to compare genes from disparate Acidimicrobiaceae, and Thiotrichales bacteria, which organisms to identify potential peptide mimics that have been reported as endophytes, lack an apparent might be involved in phytopathogen emergence (Thynne signal peptide domain (Supplementary Figure S1). For et al. 2015). In this study, we examined the distribution Gemmatimonadetes bacterium, the CLE homologues of plant peptide homologues in microbes using Protein Basic Local Alignment Search Tool (BLAST) in National Table 1. Bacteria species identified as containing CLE peptide Center for Biotechnology Information (NCBI) analysis. homologues. Length Presence of The protein sequences of reported Arabidopsis peptide Species name Protein ID families, including CLE, CEP, IDA/IDL (IDA-like), PSY, (aa) signal peptide RALF, PHYTOSULFOKINE (PSK), PLANT ELICITOR Bacteira PEPTIDE (PEP), ROOT GROWTH FACTOR (RGF), Actinobacteria HYDROXYPROLINE-RICH GLYCOPEPTIDE Actinobacteria sp. HBW17759.1 348 No OLB81324.1 248 No SYSTEMINS (HYPSYS), SYSTEMINS (SYS), PLANT Acidimicrobiia DEFENSINs (PDFs), S-LOCUS CYSTEINE-RICH Acidimicrobiales PROTEIN (SCR), were downloaded from The Acidimicrobiaceae sp. MBD52750.1 63 No Arabidopsis Information Resource (http://arabidopsis. Proteobacteria org) and used as queries to search for microbial peptide Gammaproteobacteria homologues in NCBI non-redundant protein database. Thiotrichales Thiotrichales sp. MAX27851.1 75 No By excluding the organism of Viridiplantae (taxid: Gemmatimonadetes 33090), we conducted the BLASTP search for the whole Gemmatimonadetes sp. OLB11964.1 301 Yes sequences and peptide motif sequences of each peptide PYO41156.1 310 Yes family. All searches used the default BLOSUM62 scoring matrix, and an expect threshold of 10. After excluding the peptide homologues that have been annotated or reported, we used the filtered candidates as queries to search for additional genes to ensure the identification of as many homologues as possible. The signal peptide and cleavage site were examined by the SignalP 4.0 Server (http://www.cbs.dtu.dk/services/SignalP-4.0/; Petersen et al. 2011). Peptide homologues were aligned with Multiple Sequence Alignment Program v.7 (https://mafft. cbrc.jp/alignment/software/; Katoh and Standley 2013). Phylogenetic trees were constructed using the neighbor- joining algorithm with 1,000 bootstrap replications in Molecular Evolutionary Genetics Analysis software 7 (Kumar et al. 2016). Two CLE sequences from Lotus japonicus (LjCLE-RS1 and -RS2) and five from the Globodera rostochiensis (GrCLEs) and Heterodera glycines (HgCLEs) were download from Universal Protein Resource (http://www.uniprot.org) and added in the phylogenetic analysis of CLE family. The CLE family is one of the most extensively studied plant peptides. It is critical for cell-to-cell communication and is involved in multiple physiological processes (Hirakawa and Sawa 2019; Leasure and He 2012; Miyawaki et al. 2013; Yamada and Sawa 2013). Figure 1. Alignment and phylogenetic analysis of the CLE domain in microbes and plants. Aligned CLE peptide domain sequences from In this study, we identified six novel CLE-like genes Actinobacteria bacterium, Acidimicrobiaceae bacterium, Thiotrichales in the bacteria kingdom from the Actinobacteria, bacterium, Gemmatimonadetes bacterium, Globodera rostochiensis, Proteobacteria, and Gemmatimonadetes phyla (Table 1) Heterodera glycines, Lotus japonicus and Arabidopsis thaliana are with protein size that ranges from 63 to 348 amino acids. presented. Identical residues are marked with asterisks. CLE41, 42, 44 While each gene contains a highly variable middle region and 46 consist of B-type CLE. CLV3 and the rest CLE peptides belong to A-type CLE. The phylogenetic tree was constructed using the and a conserved CLE domain, there are some variations neighbor-joining method in MEGA7. The branch support values refer in the existence of a signal peptide domain and in the to the percentage posterior probability of each clade. Copyright © 2021 Japanese Society for Plant Biotechnology N. Yuan et al. 139 possess a predicted hydrophobic signal peptide domain while those of Gemmatimonadetes and Actinobacteria at the N-terminal, and a conserved CLE domain in the (HBW17759.1) bacteria were closer to AtCLE1, AtCLE3, middle of the sequence (Supplementary Figure S2). The AtCLE4, LjCLE-RS1 and LjCLE-RS2, GrCLE4, and arginine located after the putative CLE domain in these HgCLEs (Figure 1). CLE3 orthologues have been homologues (Supplementary Figure S2) may support detected
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