Peptides in plant–microbe interactions: Functional diversity and pharmacological applications

Abstract

As dynamic interfaces governing molecular recognition and signal transduction, interactions between plants and microbes fundamentally shape ecosystem dynamics and evolutionary trajectories. This review summarizes peptides involved in plant–microbe interactions, emphasizing their diversity, biological functions mediated at the cell surface, pharmacological applications, and recent methodological advances in their discovery. Plant-derived peptides, including cysteine-rich peptides (NCRs, RALFs, DEFs, nsLTPs) and post-translationally modified peptides (CLEs, CEPs, GLV/RGF, PSKs), regulate symbiotic relationships and plant defenses. Endophyte-derived peptides, notably Bacillus lipopeptides (surfactins, fengycins, iturins), exhibit pathogen inhibition and plant growth promotion. Additionally, plant polypeptides such as lipid transfer proteins, hevein-like peptides, thionins, defensins, and snakins significantly enhance plant immunity through direct antimicrobial action and systemic resistance. Technological advancements in isolation techniques, multi-omics approaches, bioinformatics, and artificial intelligence have accelerated peptide discovery. However, challenges remain regarding functional characterization, peptide stability, production costs, and ecological impacts. Addressing these through interdisciplinary research and collaboration will promote practical applications of peptides in agriculture and medicine.

1. Introduction

Interactions between plants and symbiotic or pathogenic microorganisms represent one of the core driving forces in maintaining ecosystem functions and facilitating evolutionary processes. In these dynamic interactions, secondary metabolites extensively participate in physiological processes such as plant defense responses, symbiotic relationship establishment, and environmental adaptation (Erb and Kliebenstein, 2020). Current research predominantly focuses on the functional roles of small molecule metabolites in plant-microbe interactions (Yu et al., 2022). Peptides serve as critical mediators of dynamic cell surface regulation and active molecules against pathogenic microorganisms, playing a central role in these processes. These interactions rely on molecular dialogues at the plant-microbe interface, where peptides coordinate multiple biological processes. Specifically, they exert direct antimicrobial effects by targeting pathogen cell membranes, mediate microbial colonization in the rhizosphere, facilitate long-distance signaling through extracellular vesicles, regulate immune responses, and integrate hormonal signaling systems (Segonzac and Monaghan, 2019). The functional diversity of peptide molecules in plant-microbe interactions still requires comprehensive exploration. Peptides demonstrate significant application potential in sustainable agricultural development and pharmaceutical innovation due to their unique structural configurations and functional plasticity. Systematically revealing the roles of peptides in plant-microbe interactions holds crucial importance for deciphering ecological interaction networks and developing novel biological agents.

This review aims to comprehensively synthesize current knowledge regarding the diversity, functions, applications, and discovery methodologies of peptides in plant-microbe interactions (Fig. 1). The key contents encompass: (1) description of functional peptides involved in different interaction types (plant-microbe mutualism vs. pathogenic invasion) (See Table 1, Table 2.); (2) summary of plant-derived peptides with pharmaceutical development potential and their biological activities (See Table 3.); (3) discussion of technological advancements in traditional isolation techniques, multi-omics integration strategies, as well as bioinformatics and artificial intelligence applications in peptide research; (4) analysis of current research challenges, accompanied by proposed solutions.

Fig. 1.

Schematic overview of the key concepts discussed in this review.

Table 1.

Peptides Regulating Symbiosis in Plant-Microbe Systems.

Type	Name	Origin	Plant-Microbe Systems	Function of peptides	References
NCRs	NCR peptides	plant	Legumes-soil bacteria	nitrogen-fixing symbiosis	(Guerra-Garcia and Sankari, 2025)
RALF family	MtRALFL1	plant	Medicago truncatula–rhizobia	nodulation	(Combier et al., 2008)
DEFs	MtDef4.2	plant	wheat-Puccinia triticina	mycorrhizal symbiosis; Anti-Puccinia triticina	(Kaur et al., 2017)
nsLTPs	AsE246	plant	Astragalus sinicus–rhizobia	transport plant-synthesized lipids	(Chen et al., 2023)
nsLTPs	AgLTP24	plant	Alnus glutinosa–Frankia alni	root nodule nitrogen fixation	(Gasser et al., 2023)
CLEs	MtCLE53	plant	Medicago truncatula– arbuscular mycorrhizal fungi (AMF)	regulate plant development and microbial interactions	(Karlo et al., 2020)
CLEs	SlCLE10/11	plant	tomato–AMF	suppress AM colonization of roots	(Wulf et al., 2024)
CEPs	SlCEP2	plant	tomato–AMF	enhances tomato lateral root formation	(Wulf et al., 2024)
GLV/RGFs	MtRGF3	plant	Medicago truncatula–rhizobium	suppress nodulation	(Li et al., 2020)
GLV/RGFs	GOLVEN10	plant	Medicago truncatula–rhizobium	modulate root morphology, nodule ontogeny	(Roy et al., 2024)
PSKs	MtPSK-ε	plant	Medicago truncatula–rhizobium	stimulate root elongation, lateral root formation, and nodulation	(Di et al., 2022)
CAMPs	CAMPs	plant	rice, pepper, tomato–SUTN9–2	plant defense and nitrogen fixation	(Greetatorn et al., 2025)
lipopeptide	iturin A/surfactin	endophytes	puba—B. amyloliquefaciens	anti-Listeria monocytogenes or B. cereus; biosurfactants	(Perez et al., 2017)
lipopeptide	WH1-fungin	endophytes	rice roots–B. amyloliquefaciens	anti-Rhizoctonia solani, Fusarium oxysporium, and other phytopathogens	(Qi et al., 2010)
lipopeptide	–	endophytes	maize–Bacillus	systemic acquired resistance	(Gond et al., 2015)
lipopeptide	iturins 41B-1	endophytes	cotton–B. amyloliquefaciens	plant defense responses and immunity	(Han et al., 2015)
peptaibols	Trichokonins VI (TK VI)	endophytes	rice–Trichoderma pseudokoningii	anti-Fusarium oxysporum	(Shi et al., 2012)
peptaibols	Trichokonins A (TKA)	endophytes	rice–Trichoderma longibrachiatum	anti-Xanthomonas oryzae pv.	(Zhang et al., 2022a)
peptaibols	18mer peptaibols	endophytes	cucumber–Trichoderma	plant defense responses	(Viterbo et al., 2007)
–	piperazic acid-containing homologs of JBIR-39 and JBIR-40	endophytes	Atropa belladonna-Streptomyces sp.	anti-B. subtilis	(Bekiesch et al., 2021)
cyclopentapeptide	xylapeptides A and B	endophytes	Sophora tonkinensis–Xylaria sp.	anti-B. subtilis and B. cereus	(Xu et al., 2017)
–	CgR2150, CgR3101	endophytes	potato–endophytes	inhibit multiple bacterial pathogens and phytopathogenic fungi	(Zhang et al., 2022b)
–	AtR905	endophytes	plant–Aspergillus terreus	anti-Ralstonia solanacearum and Clavibacter michiganensis	(Zhao et al., 2025)

Table 2.

Plant-Derived Peptides in Defense Against Pathogens.

Type	Name	Origin	Transgenic plants	Target Organisms	References
LTPs	–	tomato	–	anti-Fusarium oxysporum	(Slezina et al., 2021)
LTPs	Ace-AMP1	Allium cepa	rice	anti-Magnaporthe grisea, Rhizoctonia solani, and Xanthomonas oryzae pv,Blumeria graminis f. sp. tritici	(Patkar and Chattoo, 2006) (Roy-Barman et al., 2006)
LTPs	AtLTP4.4	Arabidopsis	wheat	anti-Fusarium graminearum	(Slezina et al., 2021)
hevein-like peptides	–	Triticum kiharae	–	anti-Fusarium oxysporum and Fusarium solani	(Odintsova et al., 2009)
hevein-like peptides	ginkgotides	gymnosperms	–	anti- Aspergillus niger and Fusarium oxysporum	(Wong et al., 2016)
thionins	β-Purothionin	wheat	Arabidopsis	anti-Pseudomonas syringae and Fusarium oxysporum	(Oard and Enright, 2006)
thionins	–	rice	–	anti-Meloidogyne graminicola and Pythium graminicola	(Ji et al., 2015)
–	AtPep1	Arabidopsis thaliana	–	activate innate immune responses	(Huffaker et al., 2006)
defensins	PsD1	Pisum sativum	–	antifungal activity	(Almeida et al., 2000)
defensins	So-D2, So-D7	Spinacia oleracea	–	anti-Clavibacter sepedonicus and Ralstonia solanacearum	(Segura et al., 1998)
snakins	SN-1	Solanum tuberosum cv. Desireé	–	amplify defense responses	(van Loon et al., 2006)
snakins	SN-2	Solanum tuberosum cv. Desireé	Solanum lycopersicum	anti-Clavibacter michiganensis subsp. michiganensis	(Balaji and Smart, 2012)

Table 3.

Plant-Derived Peptides in Pharmaceutical Fields.

Name	Origin	Bioactivities	Target Organisms	Other bioactivities	References
DmAMP1, HsAFP1, and RsAFP2	plant	anti human pathogenic microorganisms	Aspergillus flavus, Candida albicans, Candida krusei, and Fusarium proliferatum	–	(Thevissen et al., 2007)
OsAFP1	rice Oryza sativa	anti human pathogenic microorganisms	Candida albicans	–	(Ochiai et al., 2018)
cyclotides	sweet violet Viola odorata	anti human pathogenic microorganisms	Salmonella enterica serovar Typhimurium LT2, Escherichia coli, and Staphylococcus aureus	–	(Pranting et al., 2010; Strömstedt et al., 2017)
bleogens	cactaceae Pereskia bleo	anti human pathogenic microorganisms	Candida albicans and Candida tropicalis	–	(Loo et al., 2017)
hispidalin	Benincasa hispida	anti human pathogenic microorganisms	Escherichia coli, Pseudomonas aeruginosa, Bacillus cereus, Staphylococcus aureus, Salmonella enterica, Aspergillus flavus, Penicillium chrysogenum, Fusarium Solani, Colletotrichum gloeosporioides, and Curvularia geniculata	–	(Sharma et al., 2014)
cyclotides	Oldenlandia affinis	anti human pathogenic microorganisms	anti-plasmodial	anti-inflammatory	(Nworu et al., 2017)
iturins and fengycins	plant-derived Bacillus subtilis	anti human pathogenic microorganisms	Alcaligenes faecalis, Achromobacter xylosoxidans, Pseudomonas alcaligenes, and Pseudomonas putida,Klebsiella aerogenes, Escherichia coli, and Pseudomonas aeruginosa	inhibit planktonic and sessile growth	(de Souza Freitas et al., 2020)
Peoriaerin II	Millettia pachycarpa-derived Paenibacillus peoriae	anti human pathogenic microorganisms	Staphylococcus aureus, Escherichia coli, and Candida species	–	(Ngashangva et al., 2021a)
RsAFP2	Raphanus sativus	anti human pathogenic microorganisms	Candida albicans	synergize with the antifungal drug caspofungin	(Vriens et al., 2016)
CaThi	Capsicum annuum	anti human pathogenic microorganisms	Saccharomyces cerevisiae, Candida albicans, Candida tropicalis, Escherichia coli and Pseudomonas aeruginosa	synergize with the antifungal drug fluconazole	(Taveira et al., 2014) (Taveira et al., 2017)
CyO2	Viola odorata L. Violaceae	anti human pathogenic microorganisms	HIV-1-infected Cells and Infectious Viral Particles	–	(Gerlach et al., 2013)
alstotides	Alstonia scholaris	anti human pathogenic microorganisms	infectious bronchitis virus (IBV) and dengue virus	–	(Nguyen et al., 2015)
Luffin P1	sponge gourd Luffa cylindrica	anti human pathogenic microorganisms	HIV-1	–	(Ng et al., 2011)
Pep-RTYM	Acacia catechu	anti human pathogenic microorganisms	dengue virus (DENV)	–	(Panya et al., 2020)
leucinostatin A	Taxus baccata-derived Acremonium sp.	anticancer	prostate stromal cells (prostate cancer)	–	(Kawada et al., 2010)
beauvericin	plant-derived Fusarium sp.	anticancer	MDA-MB-231 (breast cancer), PC-3 M (prostate cancer), A549 (human non-small cell lung cancer), CCRF-CEM (human leukemia), HepG2 (human hepatocellular carcinoma), SH-SY5Y (human neuroblastoma), KBv200 (human oral squamous carcinoma cell), A375SM (human melanoma), etc.	immunomodulatory	(Liu et al., 2024)
new peptide-type 1 and 2	Dendrobium officinale-derived Streptomyces	anticancer	Hep3B2.1–7 (liver cancer) and H1299 (Lung Cancer)	–	(Zhao et al., 2020)
viscotoxins	mistletoe	anticancer	rat osteosarcoma and human lymphocytes	–	(Büssing et al., 1999a; Büssing et al., 1999b; Kong et al., 2004)
Pyrularia thionin	American mistletoe Pyrularia pubera	anticancer	HeLa (cervical cancer), B16 (murine melanoma)	–	(Evans et al., 1989)
PaDef	Persea americana var. drymifolia	anticancer	breast cancer and chronic myeloid leukemia		(Guzmán-Rodríguez et al., 2016) (Jiménez-Alcántar et al., 2022)
NaD1	Tobacco	anticancer	monocytic lymphoma U937	–	(Poon et al., 2014)
CyO2	Viola odorata L. Violaceae	anticancer	breast cancer	–	(Gerlach et al., 2010)
colletotrichamides A-E	halophyte-derived Colletotrichum gloeosporioides JS419	Alzheimer intervention	HT22 cells	–	(Bang et al., 2019)
BZR-cotoxin I and BZR-cotoxin IV	Rhazya stricta-derived Bipolaris sorokiniana LK12	Alzheimer intervention	acetylcholinesterase, lipid peroxidation, urease	–	(Ali et al., 2016)
cyclic peptide	cucumber roots-derived Paecilomyces formosus LHL10	diabetes intervention	urease and α-glucosidase	–	(Bilal et al., 2018)
–	Acacia nilotica-derived Aspergillus awamori	diabetes intervention	α-amylase and α-glucosidase	–	(Singh et al., 2016) (Singh and Kaur, 2016)

2. Functional peptides regulating symbiosis in plant-microbe systems

Plant-microbe symbiotic relationships constitute a crucial interaction pattern shaped through long-term co-evolution in natural ecosystems. Microorganisms mainly include bacteria and fungi and establish stable endosymbiotic relationships with plant hosts (Faeth, 2002). Recent studies reveal that such symbiotic systems mediate bidirectional regulation through metabolite exchange. Peptides play multifaceted roles in maintaining host symbiosis, from conventional antimicrobial defenses to synergistic networks encompassing biocontrol, stress adaptation, and growth regulation (Ali et al., 2024).

2.1. Plant-derived peptides

Plant peptides play critical roles in symbiotic processes between plants and microorganisms, including symbiosis establishment and nutrient coordination. Two major peptides categories are involved: Cys-Rich Peptide Families and post-translationally modified (PTM) Peptide Families.

The Cys-Rich Peptide Families primarily consist of nodule-specific cysteine-rich (NCR) peptides, Defensin (DEF), Non-specific Lipid Transfer Protein (nsLTP) and Rapid Alkalinization Factor (RALF) families. Legumes produce NCR peptides during nitrogen-fixing symbiosis with soil bacteria, which critically regulate plant-rhizobia interactions through signaling pathways (Guerra-Garcia and Sankari, 2025). Functioning as symbiotic plant effectors, these peptides penetrate bacterial membranes to orchestrate bacterial differentiation (Van de Velde et al., 2010). DEFs, serving as immune-active peptides, participate in mycorrhizal symbiosis regulation. Overexpression of wheat MtDef4.2 confers resistance against Puccinia triticina without compromising mycorrhizal symbiosis (Kaur et al., 2017). The nsLTPs, ubiquitously present in plants, contribute to symbiotic membrane dynamics. Astragalus sinicus-derived AsE246 facilitates lipid transport to symbiosome membranes (Chen et al., 2023), and AgLTP24 induces Frankia actinobacteria gene expression, underscoring their conserved functions in membrane remodeling and microbial communication (Gasser et al., 2023). RALF (Rapid Alkalinization Factor), functioning as a ligand for CrRLK1L receptor kinases such as FERONIA, modulates plant development and immunity through its regulatory effects on cell wall integrity (CWI), extracellular pH changes, and ROS bursts (Zhang et al., 2020a). The RALF-FER complex induces extracellular alkalinization by regulating proton pump activity. This mechanism exerts dual physiological effects: it suppresses cell elongation (e.g., root growth) while promoting tip growth in root hairs (Haruta et al., 2014). Overexpression MtRALFL1 in Medicago truncatula leads to observable changes in nodulation patterns. This suggests that MtRALFL1 plays a role in the early signaling or structural processes required for successful nodulation (Combier et al., 2008).

The PTM Peptide Families mainly comprise CLavata3/Embryo-surrounding region-related peptides (CLEs), C-terminally encoded peptides (CEPs), Golven/Root Meristem Growth Factors (GLV/RGF) and Phytosulfokines (PSKs). CLE peptides regulate both plant development and microbial interactions. Medicago truncatula MtCLE53 shows reduced expression under phosphate deficiency but is induced by phosphate availability and arbuscular mycorrhizal fungi (AMF) colonization (Karlo et al., 2020). In non-leguminous plants, tomato SlCLE11 inhibits mycorrhizal development (Wulf et al., 2024). CEPs, vital mineral nutrient modulators in seed plants, also mediate plant-fungal symbiosis: SlCEP2 downregulates proteins involved in auxin synthesis and signaling, thereby enhances tomato lateral root formation (Hsieh et al., 2022). The GLV/RGF peptide family, widespread in land plants, governs root hair development and meristem maintenance. Medicago truncatula MtRGF3 suppresses nodulation-related gene expression (Li et al., 2020), whereas the GOLVEN10 peptide influences root morphology, nodule development, and plant-environment interactions by regulating key transcriptional pathways (Roy et al., 2024). PSKs, Tyr-sulfated PTM pentapeptides, regulate cell proliferation and differentiation, root growth, abiotic stress response, and innate immunity. For example, rhizobacteria-induced MtPSK-ε stimulates root elongation, lateral root formation, and nodulation when applied exogenously (Di et al., 2022).

In addition, recent studies have increasingly revealed the crucial roles of other peptides in plant-microbial symbiotic systems, identified that mediate plant defense and nitrogen fixation processes. For instance, cationic antimicrobial peptides (CAMPs) isolated from rice, pepper, and tomato have been shown to significantly upregulate specific gene expression in Bradyrhizobium sp. SUTN9–2. The adaptive mechanisms of SUTN9–2 enable its survival under CAMP stress, with such survival competence directly influencing its symbiotic establishment efficiency across different plant species, particularly affecting survival rates, cellular differentiation patterns, and nitrogen-fixing activity during host interactions (Greetatorn et al., 2025). Jing et al. (2025) demonstrated synergistic regulation of root peptides in Angelica sinensis Diels through soil nutrients and fungal communities, optimizing plant defense efficacy.

2.2. Endophytic microorganism-derived peptides

As specialized microbial communities colonizing healthy plant tissues, endophytes must adapt to host microenvironments while overcoming defensive compounds generated by plant immune systems (Kumar and Nautiyal, 2023). Their ecological adaptation strategy centers on synthesizing biologically active secondary metabolites that simultaneously promote host growth and enhance stress resistance through mechanisms such as pathogen antagonism or induced systemic resistance. Among these metabolites, peptide-based compounds hold significant importance.

Lipopeptides produced by endophytic Bacillus species have been extensively studied. The lipopeptide antibiotics surfactins, fengycins, and iturins are renowned for their antifungal activities (Cazorla et al., 2007). Subsequent research revealed that concentrated lipopeptide extracts disrupt bacterial cell surface ultrastructure through membrane permeability alteration (Etchegaray et al., 2008). Fira et al. (2018) demonstrated the potent antimicrobial activity of Bacillus-derived lipopeptides and validated their biocontrol potential in plant pathogen suppression. Bacteriocin subtilosin A and lipopeptides iturin A/surfactin isolated from Bacillus amyloliquefaciens in puba, a regional fermentation product from cassava, show dual functionality against pathogens like Listeria monocytogenes or B. cereus and potential as biosurfactants (Perez et al., 2017). Furthermore, B. amyloliquefaciens WH1 isolated from rice roots produces WH1-fungin, a broad-spectrum antifungal lipopeptide effective against Rhizoctonia solani, Fusarium oxysporium, and other phytopathogens. Its mechanism involves inhibiting fungal cell wall glucan synthesis and binding mitochondrial ATPase to activate apoptosis via mitochondrial-dependent pathways (Qi et al., 2010). These peptides in endophytes not only act directly on pathogenic microorganisms, but also on the host, inducing host resistance and promoting host growth. For instance, maize-associated Bacillus lipopeptides induce systemic acquired resistance by upregulating defense-related genes (Gond et al., 2015). Similarly, iturins from cotton endophyte B. amyloliquefaciens 41B-1 activate plant defense responses and mediate pathogen-associated molecular pattern-triggered immunity (Han et al., 2015).

Peptaibols are a class of linear antimicrobial peptides with unique biological activities, inhibiting the growth of fungal pathogens, promoting plant growth, and inducing plant resistance. Most peptaibols originate from Trichoderma, a genus of filamentous fungi widely distributed in soil and plant rhizospheres (Daniel & Rodrigues Filho, 2007; Pereira-Dias et al., 2023). Trichokonins VI (TK VI), a type of peptaibol from Trichoderma pseudokoningii, exhibited antibiotic activities against plant fungal pathogens such as Fusarium oxysporum by inducing programmed cell death (Shi et al., 2012). Trichokonins A (TKA) from Trichoderma longibrachiatum exhibits antimicrobial activity against the Gram-negative bacterium Xanthomonas oryzae pv., positioning it as a promising agent for controlling bacterial leaf blight on rice (Zhang et al., 2022a). Additionally, 18mer peptaibols from Trichoderma virens play a crucial role in chemical communication between Trichoderma and plants, effectively triggering plant defense responses (Viterbo et al., 2007).

Moreover, researchers continue to identify antimicrobial peptides from diverse endophytic sources. Bekiesch et al. (2021) isolated six new piperazic acid (PA) -containing congeners of known peptides JBIR-39 and JBIR-40 from the culture broth of endophytic Streptomyces sp. AB100 residing in Atropa belladonna buds, demonstrating antibacterial activity against B. subtilis. Xu et al. (2017) characterized two novel cyclopentapeptides (xylapeptides A and B) from Xylaria sp., an endophytic fungus of Sophora tonkinensis, with xylapeptide B exhibiting potent antimicrobial effects against B. subtilis and B. cereus. Zhang et al. (2022b) identified two antimicrobial peptides (CgR2150 and CgR3101) through indicator strain-embedded library screening technology by analyzing 20 potential endophytes from potato tubers. These peptides significantly inhibited multiple bacterial pathogens (Xanthomonas oryzae pv. oryzae, Xanthomonas oryzae pv. oryzicola, Clavibacter michiganensis, and Clavibacter fangii) and phytopathogenic fungi (Fusarium graminearum, Rhizoctonia solani, and Botrytis cinerea). Zhao et al. Greetatorn et al. (2025) discovered AtR905, a novel antimicrobial peptide from endophytic Aspergillus terreus, that showed inhibitory activity against Ralstonia solanacearum and Clavibacter michiganensis. However, further studies are required to evaluate its field applicability and ecological impacts.

3. Bioactive plant-derived peptides in defense against pathogens

Plants exhibit non-host resistance, a broad-spectrum defense mechanism that generally provides protection against most pathogens. The initial defense strategy involves preformed physical barriers (including the cuticle and cell walls) combined with antimicrobial compounds collectively known as phytoanticipins (Osbourn, 1996). Pathogens capable of overcoming these primary defenses must subsequently confront a sophisticated two-layered immune system that plants have developed through prolonged evolutionary adaptation. This system encompasses two core defense layers: The primary mechanism operates through pattern recognition receptors (PRRs) that detect pathogen-associated molecular patterns (PAMPs), thereby activating pattern-triggered immunity (PTI). When pathogens breach this initial defense by secreting effector proteins, plants employ intracellular nucleotide-binding leucine-rich repeat (NLR) proteins to recognize these invasive effectors, subsequently initiating the secondary defense tier known as effector-triggered immunity (ETI) usually accompanied by hypersensitive response (HR) causing programmed cell death at infection sites, and systemic acquired resistance (SAR) that establishes whole-plant pathogen protection (Bigeard et al., 2015). This spatiotemporally coordinated defense network systematically induces expression of multiple antimicrobial components, including: antimicrobial peptides (AMPs), pathogenesis-related (PR) proteins, ribosome-inactivating proteins (RIPs), and defensive secondary metabolites (Souza Cândido et al., 2011). Among these, AMPs function as central effector molecules through direct antimicrobial activity and host resistance enhancement. Major AMPs include lipid transfer proteins (LTPs), hevein-like peptides, thionins, defensins, snakins and RALFs, each contributing distinct mechanisms to plant immunity.

LTPs can be induced by environmental stresses (such as drought, cold, and saline conditions) as well as bacterial and fungal pathogens. LTPs play a role in trichome development, forming physical barriers against pathogens and arthropods (Missaoui et al., 2022). LTPs are involved in the transport of cutin monomers and wax. This structural modification significantly enhances the mechanical strength of the cell wall, making it difficult for pathogens to invade through physical penetration or enzymatic degradation (Gao et al., 2022). Transcriptome analysis proved that both LTPs and snakins of tomato Solanum lycopersicu L. contributed to the response to Fusarium oxysporum infection and inducing factors, and participate in the stress response of plants (Slezina et al., 2021). Multiple studies have revealed the broad-spectrum antimicrobial potential of LTPs. Transgenic rice expressing the Allium cepa homologous gene (Ace-AMP1) that encodes nonspecific-lipid transfer proteins (nsLTP) exhibited antimicrobial activity against Magnaporthe grisea, Rhizoctonia solani, and Xanthomonas oryzae pv (Patkar and Chattoo, 2006). Furthermore, transgenic wheat expressing Ace-AMP1 demonstrated antifungal activity against Blumeria graminis f. sp. tritici (Roy-Barman et al., 2006). Additionally, transgenic wheat expressing AtLTP4.4 showed antimicrobial activity against Fusarium graminearum (McLaughlin et al., 2021).

Hevein-like peptides contain chitin-binding domains in pathogen cell walls and generally exhibit significant antifungal activity (Slavokhotova et al., 2017). A novel hevein-like peptide WAMP-1a purified from seeds of Triticum kiharae inhibits Fusarium oxysporum and Fusarium solani through chitinase activity suppression (Odintsova et al., 2009). Ginkgotides, hevein-like peptides identified in ginkgo, are widely distributed across gymnosperms and demonstrate inhibitory effects against phytopathogens Aspergillus niger and Fusarium oxysporum. Given their remarkable resistance to thermal, acidic, exopeptidase, and endopeptidase degradation, these peptides also show potential as scaffolds for peptide engineering (Wong et al., 2016).

Thionins exert antimicrobial effects by inserting their amphipathic α-helical structures into bacterial or fungal membrane phospholipid bilayers, leading to membrane potential collapse and cytoplasmic content leakage (Pelegrini and Franco, 2005). β-purothionin derived from wheat endosperm demonstrates broad-spectrum antimicrobial activity, and the introduction of its encoding gene into Arabidopsis significantly inhibits the growth of Pseudomonas syringae and Fusarium oxysporum (Oard and Enright, 2006). Furthermore, thionins in rice function as defense-related antimicrobial peptides that enhance resistance against root-knot nematode Meloidogyne graminicola and oomycete Pythium graminicola by suppressing pathogen colonization through membrane disruption and hormone-regulated defense pathways (Ji et al., 2015).

Defensins, like thionins utilize conserved γ-core domains to specifically bind ergosterol in fungal cell membranes, disrupting membrane integrity and inducing reactive oxygen species (ROS) bursts (Sathoff et al., 2019). Across diverse plant species and crops, defensins have been demonstrated to play crucial roles against fungal pathogens. PsD1, a defensin from pea (Pisum sativum), inhibits growth across multiple species by interacting with sphingolipids on fungal envelopes and inducing membrane permeabilization, ultimately leading to growth arrest (Almeida et al., 2000). Additionally, So-D2 and So-D7 defensins isolated from spinach (Spinacia oleracea) leaves demonstrate distinct antimicrobial activities against the phytopathogens Clavibacter sepedonicus and Ralstonia solanacearum, respectively (Segura et al., 1998). Furthermore, during infection, pathogen-associated molecules containing endogenous peptides activate innate immune responses. A notable example is AtPep1 in Arabidopsis thaliana, derived from its precursor PROPEP1, which triggers transcriptional activation of the defensive gene defensin (PDF1.2) (Huffaker et al., 2006).

The snakin family not only directly eliminate pathogens but also activate plant systemic acquired resistance (SAR). For instance, potato Snakin-1 induces the accumulation of pathogenesis-related protein PR1 and amplifies defense responses via salicylic acid (SA) signaling cascades (van Loon et al., 2006). Furthermore, transgenic tomato (Solanum lycopersicum) expressing snakin-2 demonstrates enhanced resistance against Clavibacter michiganensis subsp. michiganensis (Cmm), with pathogen invasiveness being significantly restricted through this genetic modification (Balaji and Smart, 2012).

RALF, an endogenous plant peptide hormone, binds to the heterocomplex of receptor kinase FERONIA (FER). The RALF-FER complex suppresses pattern-triggered immune responses, such as reactive oxygen species (ROS) bursts, by disrupting the FLS2-BAK1 receptor complex (Stegmann et al., 2017). Fungal pathogens secrete F-RALF peptides that mimic plant RALFs. These pathogen-derived peptides activate FER signaling, thereby inhibiting host immunity and facilitating infection (Masachis et al., 2016). Functioning as a cell wall integrity sensor, FER dynamically regulates the nano-environment of plasma membrane receptor kinases through perception of cell wall status. Notably, cell wall perturbations—such as inhibition of cellulose synthesis—alter the diffusion behavior of plasma membrane proteins. RALF signaling coordinates the spatiotemporal specificity of immune and growth signals by modulating membrane nanodomain organization (Gronnier et al., 2022).

Current research on plant immunity primarily focuses on plasma membrane- and cytoplasm-localized proteins. However, the apoplast—a critical compartment for secretion and accumulation of both non-self and self-molecules under stress conditions—plays an equally vital role in plant immune responses (Farvardin et al., 2020). In rice, the pathogen-induced peptide OsRALF26 is secreted into the extracellular space. This peptide induces disease resistance through recognition by FLR1 and exhibits long-distance transport capacity across plant tissues (Lim and Lee, 2024). Although OsRALF26 belongs to the RALF-related peptide family and shares functional similarities with canonical RALFs (e.g., AtRALF23) in receptor interaction and immune activation, its structural divergence significantly expands our understanding of functional diversity within the RALF family (Kwon et al., 2024).

Furthermore, ETI establishes advanced defense mechanisms through metabolic reprogramming and programmed cell death (PCD). Plants restrict pathogen nutrient acquisition through precise regulation of primary metabolic pathways. Hairpin-like peptides (alpha-hairpinins) exhibit trypsin-inhibitory and ribosome-inhibitory activities to suppress microbial protein synthesis (Slavokhotova and Rogozhin, 2020). During effector-triggered immunity (ETI), plants initiate programmed cell death (PCD) via localized hypersensitive response (HR), effectively confining pathogens to infection sites and enhancing disease resistance (Kushalappa et al., 2022). Certain peptides also participate in long-distance signaling of systemic acquired resistance (SAR). For instance, systemin, an 18-amino acid peptide hormone, coordinates local and systemic immune responses by being transported through phloem vessels to activate defense gene expression in distal tissues (Zhang et al., 2020b). Moreover, the PTI and ETI immune systems maintain dynamic equilibrium through coordinated signaling, ensuring efficient allocation of defense resources (Yu et al., 2024). For example, flg22, a bacterial flagellin-derived peptide serving as a PTI trigger, induces expression of prePIPs (precursors of pathogen-associated molecular pattern-induced secreted peptides) to establish positive feedback loops that amplify PTI signaling. PIP further activates the same pathway through RLK7 receptors, enhancing PTI effects while suppressing excessive ETI-mediated immune responses (Wang et al., 2023).

In summary, plants establish a multidimensional defense system through the integration of physical barrier construction, chemical secretion, metabolic regulation, and cell death mechanisms. As core effector molecules within this system, bioactive peptides not only exhibit direct antimicrobial functions but also orchestrate signal transduction pathways and systemic resistance establishment, achieving precise and efficient plant immune responses.

4. Development of bioactive peptides applications in pharmaceutical fields

During plant-microbe interactions, peptides play pivotal roles not only in maintaining symbiotic homeostasis but also in pathogen defense. Furthermore, peptides have emerged as hotspots in natural product research and biotechnological development due to their unique advantages, including structural plasticity, target specificity, and biocompatibility. Growing evidence demonstrates that bioactive peptides hold distinctive value within plant-microbe interaction networks while exhibiting significant therapeutic potential in pharmaceutical applications, particularly in antimicrobial and antitumor applications.

In vitro studies of plant peptides demonstrate that numerous peptides exhibit broad-spectrum antimicrobial activity against human pathogens. These peptides typically have the characteristics of broad-spectrum antibacterial and low resistance induction, showing substantial therapeutic potential. Defensins targeting sphingolipids have emerged as promising molecules for next-generation antifungal agents (Rollin-Pinheiro et al., 2016). Compared to conventional azole-derived antifungals, plant defensins such as DmAMP1, HsAFP1, and RsAFP2 demonstrate enhanced efficacy against clinical pathogens including Aspergillus flavus, Candida albicans, Candida krusei, and Fusarium proliferatum (Thevissen et al., 2007). The rice (Oryza sativa) defensin OsAFP1 shows antimicrobial effects through inducting apoptosis and targeting cell wall component, positioning it as a promising candidate for combating human pathogenic fungi (Ochiai et al., 2018). Diverse cyclotides from sweet violet (Viola odorata) demonstrate broad-spectrum activity against multiple human pathogens including Salmonella enterica serovar Typhimurium LT2, Escherichia coli, and Staphylococcus aureus (Pranting et al., 2010; Strömstedt et al., 2017). Bleogens from Pereskia bleo, classified as hevein-like peptides, display potent antifungal activity against C. albicans and Candida tropicalis while maintaining non-cytotoxicity toward mammalian cells, demonstrating safety profiles conducive to pharmaceutical development (Loo et al., 2017). The cationic peptide hispidalin, derived from Benincasa hispida seeds, inhibits multiple pathogenic fungi and bacteria (Sharma et al., 2014), with additional advantages including protease stability and low hemolytic toxicity (Meng et al., 2019). For other antimicrobial aspects, cyclotide-enriched extracts from the West African medicinal plant Oldenlandia affinis exhibit notable antimalarial activity (Nworu et al., 2017).

Endophytic microbes residing as symbionts within plant tissues have been recognized as valuable sources of potential AMPs. The iturins and fengycins isolated from Bacillus subtilis TR47II exhibit antimicrobial activity against multiple Gram-negative bacteria while maintaining non-toxicity to mammalian cells. Their inhibitory effects on both planktonic and sessile growth further highlight the potential of these peptides as biocontrol agent (de Souza Freitas et al., 2020). Through integrated genomic and metabolomic molecular network analysis of Paenibacillus peoriae IIBSD35, a Gram-positive endophyte isolated from the medicinal plant Millettia pachycarpa Benth., researchers identified a novel antimicrobial peptide named Peoriaerin II. This peptide demonstrates broad-spectrum antimicrobial activity against S. aureus, E. coli, and Candida species, indicating substantial developmental potential (Ngashangva et al., 2021).

Moreover, studies exploring peptide-drug combinations have expanded their clinical applicability. For instance, the radish Raphanus sativus defensin RsAFP2 exhibits fungal inhibitory effects that synergize with the antifungal drug caspofungin, effectively preventing Candida albicans biofilm formation (Vriens et al., 2016). The thionin-like peptide CaThi, isolated from chili pepper Capsicum annuum fruits, demonstrates broad-spectrum antimicrobial activity (Taveira et al., 2014), also shows synergistic effects when combined with the clinical azole antifungal fluconazole (Taveira et al., 2017).

Furthermore, multiple peptides exhibit antiviral activities. The cyclotide cycloviolacin O₂ (CyO2) disrupts viral integrity and enhances the efficacy of antiretroviral drugs (Gerlach et al., 2013). Cystine knot α-amylase inhibitors-type knottins (alstotides) derived from Alstonia scholaris have been shown to function as cell-penetrating inhibitors against infectious bronchitis virus (IBV) and dengue virus (Nguyen et al., 2015). Alpha-hairpinins, a class of peptides with diverse biological activities including trypsin-inhibitory and ribosome-inactivating, demonstrate particular advantages in antiviral applications. For instance, Luffin P1 from sponge gourd (Luffa cylindrica) effectively inhibits HIV replication and transport (Ng et al., 2011). A novel bioactive peptide Pep-RTYM, identified in the Asian medicinal plant Acacia catechu, potently inhibits dengue virus (DENV) by preventing viral interaction with cellular receptors, highlighting its therapeutic potential (Panya et al., 2020).

Beyond their remarkable performance in antimicrobial and antiviral applications, peptides demonstrate unique potential in anticancer therapy, characterized by high bioactivity and notable target specificity (Sonowal et al., 2024). Peptides isolated from endophytes have been extensively studied. The peptide leucinostatin A, discovered in the endophytic fungus Acremonium sp. of European yew (Taxus baccata), exhibits both anticancer and antifungal properties (Strobel and Hess, 1997). Subsequent research by Manabu Kawada reveals that leucinostatin A suppresses prostate cancer growth through downregulation of insulin-like growth factor-I (IGF—I) expression in prostate stromal cells (Kawada et al., 2010). The cyclic hexapeptide beauvericin (BEA), derived from plant-endophytic Fusarium species, exhibits broad biological activities including significant anticancer properties. Mechanistic studies indicate that BEA primarily induces cancer cell apoptosis via reactive oxygen species (ROS)-dependent pathways (Liu et al., 2024). Two novel peptides isolated from endophytic Streptomyces strains of the medicinal orchid Dendrobium officinale demonstrate potent cytotoxicity against cancer cells, highlighting their therapeutic promise (Zhao et al., 2020).

Some plant peptides have anti-cancer activities of various cancer cells, and also have the potential to develop anti-cancer treatments. Multiple studies confirm the cytotoxicity of viscotoxins against rat osteosarcoma and human lymphocytes (Büssing et al., 1999a; Büssing et al., 1999b; Kong et al., 2004). Pyrularia thionin from American mistletoe (Pyrularia pubera) displays anticancer activity against cervical cancer cells (HeLa) and murine melanoma cells (B16) (Evans et al., 1989). The plant defensin PaDef demonstrates biotechnological potential against chronic myeloid leukemia (Jiménez-Alcántar et al., 2022) and breast cancer MCF-7 cell lines (Guzmán-Rodríguez et al., 2016). Poon et al. (2014) revealed that the defensin NaD1 exerts anticancer activity against monocytic lymphoma U937 cells through direct binding to plasma membrane phospholipid phosphatidylinositol 4,5-bisphosphate (PIP2). CyO2 from sweet violet (Viola odorata) exhibits selective toxicity toward cancer cell lines without harming normal cells, positioning it as a viable anticancer agent (Gerlach et al., 2010). These findings collectively demonstrate the potential of plant-derived peptides as promising candidates for cancer therapeutic interventions.

With expanding research perspectives, the biological activities of peptides in metabolic disorders and neurodegenerative diseases are being progressively elucidated. For Alzheimer's disease, five unique cyclic lipopeptides with neuroprotective activities, designated colletotrichamides A-E, are isolated from the halophyte-associated fungus Colletotrichum gloeosporioides JS419. Among these, cyclic peptide C exhibits robust neuroprotective activity in HT22 cells (Bang et al., 2019). Additionally, two known cyclic peptides (BZR-cotoxin I and BZR-cotoxin IV) from the endophytic fungus Bipolaris sorokiniana LK12, isolated from Rhazya stricta leaves, show moderate acetylcholinesterase inhibition, anti-lipid peroxidation, and urease inhibitory activities (Ali et al., 2016). In diabetes intervention, Bilal et al. (2018) conducted enzymatic assays and purification of the endophytic fungus Paecilomyces formosus LHL10 from cucumber roots, identifying a cyclic peptide with significant inhibitory effects on urease and α-glucosidase. Singh et al. (2016) revealed that metabolites from Acacia nilotica-derived Aspergillus awamori inhibited α-amylase and α-glucosidase. Subsequent purification confirmed peptide-based inhibitors with high stability, demonstrating commercial development potential (Singh and Kaur, 2016).

5. Methods for peptide discovery

As important bioactive substances in plants, peptides have demonstrated broad application prospects in pharmaceuticals, food science, and agriculture in recent years. Researchers have developed diverse methodologies for the discovery, identification and isolation of these peptides. Early studies employed plant tissue isolation and purification combined with bioactivity-guided screening to identify peptide compounds. The procedure initiates with the acquisition of crude extracts from plant tissues or symbiotic microbial cultures. Bioactivity profiling is then conducted through antimicrobial activity assays and other bioassays to identify bioactive fractions. Subsequently, chromatographic techniques (e.g., MPLC, HPLC and TLC) are employed to purify the active components. Final structural elucidation is achieved via mass spectrometry (MS) for molecular weight determination and amino acid analysis to determine the peptide sequence and structural configuration (Piovesana et al., 2018). Traditional approaches have been refined through innovations such as the One Strain Many Compounds (OSMAC) strategy, which enhances peptide diversity by modifying culture conditions or implementing microbial co-cultivation systems to induce novel peptide production, followed by isolation and characterization (Zhang et al., 2024). Technological advancements have driven the evolution of this methodology through novel induction protocols, including the integration of epigenetic modulators or microbial quorum-sensing molecules, significantly improving cyclic peptide synthesis efficiency in fungal systems (Pinedo-Rivilla et al., 2022). Although these bioactivity-driven isolation strategies have proven useful in discovering novel peptides, but traditional methods remain time- and labor-intensive, with significant challenges in detecting and characterizing low-abundance peptides.

The advancement of omics technologies has established novel ways for comprehensively elucidating functional peptides. Genomic and transcriptomic approaches enable the mining of peptide-encoding genes: through sequencing plant or symbiotic microbial genomes, bioinformatic strategies can identify signal peptide sequences, small-molecular-weight precursor proteins, or NRPS/RiPP synthase gene clusters to predict potential bioactive peptides (Bachmann et al., 2014). For instance, genome mining of endophytic Streptomyces species reveals abundant NRPS and RiPP gene clusters, indicating their capacity to synthesize diverse novel peptides (Ikeda et al., 2014). Höng et al. (2021) analyzed transcriptomic data from 1000 plant species, identifying 133 novel thionin sequences with structural divergences from canonical thionins, suggesting a new class of peptides with unexplored 3D configurations. Proteomics, particularly secretome analysis, is increasingly applied to peptide research, enabling the detection of small proteins/peptides secreted by plants into growth media or intercellular spaces under specific stimuli (Subramanian and Smith, 2015). Metabolomics leverages mass spectrometry-based techniques to uncover novel peptide metabolic pathways in model organisms like Arabidopsis thaliana (Fernie and Tohge, 2017). Integrated multi-omics approaches further decode peptide mechanisms. For example, combining transcriptomic, metabolomic, and proteomic data elucidates the systemic activation of plant defense pathways upon exogenous peptide treatment. The bioactive peptide Peoriaerin II was identified through the integration of genomic data with LC-MS profiling and metabolome-guided molecular networking of P. peoriae IBSD35 (Ngashangva et al., 2021b). Collectively, the synergy of genomics-transcriptomics-proteomics-metabolomics has significantly expanded the discovery landscape of functional peptides and accelerated systematic screening strategies.

The exponential growth of sequence data and candidate peptides has established bioinformatics and artificial intelligence (AI) as indispensable tools in functional peptide discovery. The development of large-scale antimicrobial peptide (AMP) databases provides critical resources for research, including DAMPD (Seshadri Sundararajan et al., 2012), CAMP (Waghu et al., 2016), LAMP (Zhao et al., 2013), DRAMP (Fan et al., 2016) and KNOTTIN (Postic et al., 2018). These repositories collectively catalog thousands of known AMPs with structural and activity annotations. Based on these datasets, researchers have developed diverse machine learning (ML) models to predict antimicrobial activity of novel sequences (Mwangi et al., 2023). These models utilize sequence-derived features—including amino acid composition, physicochemical properties, and secondary structure propensity—to classify the antimicrobial potential of candidate peptides. Deep learning architectures, such as convolutional neural networks (CNNs) and recurrent neural networks (RNNs), have recently demonstrated superior accuracy over traditional scoring methods by autonomously extracting high-order sequence patterns (Junet and Daura, 2021; Müller et al., 2018). Beyond predictive analytics, AI enables de novo peptide design through evolutionary algorithms and generative models (e.g., GANs, VAEs), which explore chemical space to optimize antimicrobial efficacy and reduce toxicity (Li et al., 2024). For instance, our group implemented a diffusion model-based framework (VE-Net) to generate structurally diverse AMPs, establishing a “generation-screening-validation” pipeline that significantly accelerates bioactive peptide discovery (Wang et al., 2025). In plant-microbe interaction studies, bioinformatics facilitates multi-omics integration by correlating peptide gene expression dynamics with microbial community shifts to infer biological functions. Collectively, bioinformatics and AI have revolutionized the functional peptide pipeline—from discovery and prediction to rational design—enabling rapid identification of novel peptides with translational potential.

6. Challenges and perspectives

Despite the promising potential of functional peptides, current research still faces critical limitations. Initially, systematic mechanistic studies remain insufficient. Although thousands of candidate peptides have been identified, the biological functions and mechanism remain undefined. Furthermore, peptides functionality often exhibits pleiotropic effects, with mechanisms influenced by environmental factors, host organisms, and microbial communities through coordinated regulation. Current research still lacks comprehensive understanding of peptides interaction networks and dynamic regulatory mechanisms. Additionally, functional peptides encounter challenges in stability and practical production. Peptides are generally susceptible to protease degradation, exhibiting instability in both natural environments and human physiological systems. Consequently, future studies must prioritize enhancing peptide stability and reducing production costs to enable practical applications. Furthermore, the environmental impacts of peptides necessitate long-term evaluation. In agricultural applications, peptides may disrupt soil microbial communities and compromise ecological equilibrium. Collectively, both fundamental research and applied development in functional peptides remain at exploratory stages.

To address these challenges, researchers have developed innovative strategies. For instance, integrating multi-omics data encompassing genomics, transcriptomics, proteomics, and metabolomics facilitates comprehensive elucidation of peptides action mechanisms. Structural biology approaches and molecular simulations are increasingly employed to characterize peptide-target interactions, providing critical insights for rational peptide design. Moreover, synthetic biology platforms enable efficient and targeted biosynthesis of plant-derived peptides, accelerating their transition from basic research to industrial applications, thereby optimizing their functions and enabling large-scale production across pharmaceutical, agricultural, and environmental sectors. Furthermore, clinical translation is being accelerated through strategies to reduce peptide immunogenicity, enhance stability, and develop novel delivery systems, unlocking their therapeutic potential. Additionally, agricultural applications require breakthroughs in formulation technologies and delivery methods, such as developing sustained-release carriers to prolong field efficacy. Concurrently, regulatory agencies must progressively refine evaluation frameworks for biopesticides to facilitate the industrialization.

In conclusion, peptides—emerging mediators of plant-microbe interactions—are poised to play increasingly vital roles in agriculture and medicine. Through interdisciplinary innovation and industrial collaboration, maximizing their application potential will provide sustainable solutions for agricultural productivity and human health.

CRediT authorship contribution statement

Minghui Song: Writing – original draft, Investigation, Data curation. Yunbing Zhou: Writing – original draft, Formal analysis, Data curation. Gang Li: Writing – review & editing, Conceptualization. Anna S. Barashkova: Writing – review & editing. Eugene A. Rogozhin: Writing – review & editing, Conceptualization. Wenqiang Chang: Writing – review & editing, Funding acquisition, Conceptualization.

Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Data availability

No data was used for the research described in the article.