Plants produce numerous amino acid derivatives. Some are utilized by humans as medicines and nutrients, while many act as phytochemical signals regulating plant growth and stress tolerance. Fluctuating ecological conditions challenge plant development and agricultural productivity, making amino acid derivatives promising for agricultural applications to enhance plant resilience against biotic and environmental stresses. This review summarizes recent advances in understanding amino acid derivatives’ roles in plant growth and stress responses, outlines strategies for discovering novel amino acid derivatives and their regulatory networks in crops, and aims to provide a foundation for developing amino acid derivatives-based strategies to improve crop performance under changing environments.
1. Introduction
Plants, being sessile, require metabolic adaptability to cope with fluctuating environments, leading to the evolution of pathways producing diverse small molecules critical for growth and defense. These molecules are categorized as primary and secondary metabolites. Intermediates of glycolysis and the tricarboxylic acid cycle (TCA) serve as precursors for amino acid biosynthesis, which are further metabolized into amino acid derivatives such as indole phytoalexins, choline, betaine, and 5-aminolevulinic acid (ALA). Key amino acid derivatives like ethylene, auxin, gamma-aminobutyric acid (GABA), N-hydroxy pipecolic acid (NHP), melatonin, and nitric oxide (NO) act as signaling molecules modulating growth and stress tolerance. Amino acid derivatives also facilitate carbon shuttling; for example, coenzyme A helps plants withstand stresses like hypoxia and drought.
Agriculture faces challenges including climate change, land degradation, and pest infestations. Amino acid derivatives’ diverse biological activities make them attractive targets for improving crop productivity. While research on amino acid derivatives in Arabidopsis is advanced, studies on crop responses to environmental stress are nascent. Optimizing amino acid derivatives accumulation could enhance crop stress tolerance in variable agricultural environments.
Fig. 1. Plant amino acid derivatives involved in growth and stress tolerance. (Abbreviations: ALA, 5-aminolevulinic acid; Arg, arginine; GABA, gamma-aminobutyric acid; Glu, glutamate; Gly, glycine; Lys, lysine; IAA, indole-3-acetic acid; IAOx, Indole-3-acetaldoxime; α-KG, α-ketoglutarate; Met, methionine; NHP, N-hydroxy pipecolic acid; NO, Nitric oxide; OAA, oxaloacetate; PEP, phosphoenolpyruvate; 3PGA, 3-phosphoglyceric acid; SAM, S-adenosyl methionine; Ser, Serine; TCA, tricarboxylic acid cycle; Trp, tryptophan. Symbols represent plant growth and stress responses, not directly mapped to specific amino acid derivatives.)
2. Tryptophan-derivatized metabolites and their role in plant growth and defense
Tryptophan (Trp), an aromatic amino acid from the shikimate pathway, is a precursor for auxin, melatonin, and Trp-derived indole phytoalexins. Auxin regulates plant growth and differentiation, while melatonin acts as a master regulator in seed vigour, growth, and stress defense. In Brassica species, Trp-derived indolesulfur phytoalexins are crucial for pathogen resistance.
2.1. Melatonin
Melatonin biosynthesis in plants involves four genes (TDC, T5H, SNAT, ASMT/COMT) and responds to environmental signals like red light and heat stress. Endogenous melatonin is vital for plant growth; rice with disrupted biosynthesis shows growth retardation, while overexpression of key genes increases grain yield. Melatonin enhances tolerance to alkaline, salinity, and other stresses by activating ROS scavenging systems and regulating ion homeostasis.
Epigenetic regulation influences melatonin accumulation: histone deacetylase 9 inhibits it by reducing histone acetylation, while exogenous application elevates methylation of biosynthetic genes. Melatonin is oxidized to cyclic 3-hydroxymelatonin and 2-hydroxymelatonin, which regulate growth, flowering, seed germination, and senescence independently of melatonin signaling.
2.2. Trp-derived indole-sulfur metabolites
These metabolites, including camalexin and glucosinolates, accumulate in Brassicaceae. Biosynthesis starts with Trp conversion to indole-3-acetaldoxime by CYP79B2/3, followed by diversification via P450 enzymes. Side-chain modifications affect antimicrobial activity; for example, 4-methoxyindole-3-ylmethyl glucosinolate accumulation increases pathogen infection.
Turnover of these metabolites occurs via myrosinases or nitrilases, with intermediates modulating glucosinolate levels. They are secreted to the plant-pathogen interface by PDR transporters; defective transporters increase susceptibility to pathogens. These metabolites also prevent fungal dysbiosis in roots and shape the rhizosphere microbiome.
Fig. 2. Tryptophan derivatized metabolites and their role in plant growth and defense. (Abbreviations: ASMT, N-acetylserotonin methyltransferase; COMT, caffeic acid O-methyltransferase; IAA, indole-3-acetic acid; IPyA, indole-3-pyruvic acid; IAOx, Indole-3-acetaldoxime; I3C, indole-3-carbinol; I3G, indol-3-ylmethyl-glucosinolate; M2H, melatonin 2-hydroxylase; M3H, melatonin 3-hydroxylase; 1MI3G, 1-methoxyindole-3-ylmethyl glucosinolate; 4MI3G, 4-methoxyindole-3-ylmethyl glucosinolate; 4OH-ICN, 4-hydroxyindole-3-carbonylnitrile; SNAT, serotonin N-acetyltransferase; TAA1, tryptophan aminotransferase 1; TARs, TAA1-related proteins; T5H, tryptamine 5-hydroxylase; TDC, tryptophan decarboxylase; TPH, tryptophan hydroxylase; Trp, tryptophan; Trp-AT, tryptophan aminotransferase; VAS1, reversal of SAV3 phenotype 1; YUCs, YUCCAs. Green arrows indicate promotion, orange arrows inhibition.)
3. Glycine derivatives alleviate abiotic stress injury
Glycine is central to amino acid metabolism, photorespiration, and development. It is synthesized via three pathways, with serine conversion being the primary route. Key synthesis genes regulate amino acid pools, root development, and pathogen resistance.
Glycine derivatives choline and betaine are important for abiotic stress tolerance. Exogenous choline enhances salt tolerance via lipid reprogramming and reduces cadmium accumulation. Choline analogs promote photosynthesis by upregulating electron transfer genes. Choline is converted to glycine betaine, an osmolyte that modulates ROS homeostasis and improves photosynthesis. Glycine betaine alleviates salt and drought stress, regulates phosphate uptake, and synergizes with melatonin to enhance seed vigour.
4. NHP, a lysine derivative balances plant growth and systemic acquired resistance (SAR)
Lysine, a limiting amino acid in cereals, is synthesized via the diaminopimelate pathway. It is a precursor for cadaverine, α-aminoadipate, and NHP. Cadaverine regulates root growth, while α-aminoadipate may contribute to disease resistance. NHP, a mobile molecule, is synthesized by three enzymes, and its methylated form (MeNHP) enhances pathogen resistance.
Exogenous NHP induces SAR in Arabidopsis mutants lacking biosynthetic genes. NHP accumulates in non-inoculated leaves after pathogen attack, suggesting phloem translocation. Basal salicylic acid (SA) and NPR1 are essential for NHP-mediated SAR; NHP induces SA biosynthesis and JA signaling. WRKY70 regulates late NHP-responsive gene transcription independently of SA.
NHP homeostasis is mediated by glycosylation: AtUGT76B1 glycosylates NHP, balancing growth and stress tolerance. Overexpression of UGT76B1 reduces NHP pools and promotes growth but abolishes pathogen resistance, while mutants show dwarfism and constant defense responses.
Fig. 3. Lysine metabolism pathway in plants. (Abbreviations: AASA, aminoadipic semialdehyde; AASADH, aminoadipic semialdehyde dehydrogenase; ALD1, aberrant growth and death2-like defense response protein 1; FMO1, flavin monooxygenase 1; LKR, ketoglutarate reductase; L/ODCs, lysine/ornithine decarboxylases; NHP, N-hydroxy-pipecolic acid; P2C, piperideine-2-carboxylic acid; Pip, pipecolic acid; SARD4, systemic acquired resistance deficient 4; SDH, saccharopine dehydrogenase; UGT76B1, UDP-dependent glycosyl transferase 76 B1.)
5. GABA, the glutamate derivative, modulates plant tolerance and root growth
Glutamate, from plastid nitrogen assimilation, acts as a nitrogen donor and signaling molecule regulating seed germination and root architecture via Ca²⁺ interactions. It is catabolized to GABA in the cytosol by glutamate decarboxylase (GAD), which is activated by stress-induced cytosolic Ca²⁺. GABA biosynthesis mutants show early wilting under drought.
GABA concentration is balanced by ALMT transporters: TaALMT1 facilitates GABA efflux and influx under different conditions. GABA interacts with ALMT9 to reduce guard cell anion accumulation, limiting stomatal opening during drought. It also modulates aluminum and alkaline tolerance by inhibiting ALMT-mediated anion transport.
Cytosolic GABA is transported to mitochondria, entering the TCA cycle to sustain energy supply during stress. GABA inhibits root growth: catabolism mutants show reduced primary root length, and exogenous application suppresses adventitious root formation by inhibiting auxin transport.
Fig. 4. GABA metabolism and its roles in plant abiotic stress tolerance and root development. (Abbreviations: ALMT, aluminum-activated malate transporter; GABA permease; GABA-T, GABA transaminase; GABP, Glu, glutamate; glutamate dehydrogenase (GDH); GAD, glutamate decarboxylase; α-KG, α-ketoglutarate; SSA, succinic semialdehyde; SSADH, succinic semialdehyde dehydrogenase; Succ, succinate; TCA, tricarboxylic acid.)
6. ALA, the glutamate derivative, modulates plant abiotic stress tolerance via photosynthesis
ALA is widely used to enhance abiotic stress tolerance in agriculture, improving salinity, drought, and low-temperature resistance, as well as fruit yield and quality. It is the first substrate for the tetrapyrrole pathway, synthesized in plastids via three enzymes, with GluTR as the rate-limiting step. GluTR stability is regulated by binding proteins and protease-mediated turnover.
Exogenous ALA increases photosynthetic efficiency by providing substrates for chlorophyll and heme biosynthesis and upregulating photosynthesis-related genes. It also improves root water absorption via ABA signaling under osmotic stress and promotes fruit maturation through ethylene biosynthesis.
7. Methionine derivatives in plant development and stress tolerance
Methionine, which enhances salt tolerance, is generated from homocysteine. In the Yang cycle, it is converted to S-adenosyl methionine (SAM), a key methyl donor and precursor for ethylene, polyamines, and nicotianamine. SAM supports plant defense via methyltransferase-mediated synthesis of defense compounds and maintains cell wall properties through polysaccharide methylation.
SAMS, the enzyme synthesizing SAM, regulates responses to drought, salinity, and other stresses. Overexpression of SlSAMS1 in tomato increases stress tolerance via enhanced polyamine synthesis and ethylene emission. SAM homeostasis is linked to ethylene and polyamine biosynthesis; disruption of MTA metabolism (a byproduct) impairs seedling growth.
Ethylene, a gaseous hormone derived from SAM, enhances flooding tolerance by modulating root architecture and aerenchyma formation. It activates stress-responsive genes and regulates translation under submergence. Nicotianamine forms complexes with metal cations, facilitating their uptake. In grasses, it is a precursor for phytosiderophores that chelate iron, with synthetic analogs showing potential as iron fertilizers.
8. Arginine derivatives in plant growth and stress tolerance
Arginine is a precursor for polyamines (putrescine, spermidine, spermine) and NO. Putrescine is synthesized from arginine and ornithine; spermidine and spermine require SAM-derived aminopropyl groups. Spermidine synthase mutants are embryo-lethal, while thermospermine regulates stem elongation and xylem specification. Exogenous polyamines enhance stress tolerance by scavenging ROS and inhibiting ABA-induced stomatal closure.
Polyamines are oxidized by CuAO and PAO, generating H₂O₂ which mediates stress tolerance, protoxylem differentiation, and pollen tube growth. CuAO1 and CuAO8 induce NO production, linking polyamines to NO signaling.
Fig. 5. Methionine and arginine-derived metabolites in plant growth and stress tolerance. (Abbreviations: ACC, 1-aminocyclopropane-1-carboxylic acid; ACL5, thermospermine synthase; ACO, ACC oxidase; ACS, ACC synthase; ADC, arginine decarboxylase; ASL, argininosuccinate lyase; ASSY, argininosuccinate synthase; CuAO8, copper amine oxidase; dsSAM, decarboxylated SAM; Hcy, homocysteine; JA, jasmonic acid; MTA, 5′-methylthioadenosine; NO, nitric oxide; ODC, ornithine decarboxylase; OTC, ornithine transcarbamylase; PAO, polyamine oxidases; SAH, S-adenosyl homocysteine; SAM, S-adenosyl methionine; SPDS, spermidine synthase; SPMS, spermine synthase.)
9. Strategies to mine novel amino acid derivatives and elucidate their regulatory network
Plant amino acid derivatives exhibit structure diversity to promote growth and adapt to variable environmental conditions. The functional versatility of plant amino acid derivatives can be roughly categorized into two groups. First, many plant amino acid derivatives are synthesized in a wide range of plant species. These plant amino acid derivatives engage in multiple biological processes in stress responses, or act as signaling molecules. The latter also contribute to growth and development, with melatonin as an example. Second, plants in the same lineage may produce similar chemical signatures in response to specific stresses. Glucosinolates accumulate in the Brassicaceae species for pathogen resistance. This structural diversity of plant amino acid derivatives contributes to their diverse biological effects to resist environmental changes. Genetic and multi-omics strategies will be instrumental in identifying these novel amino acid derivatives and their biosynthetic pathways. Furthermore, metabolite–protein interactions strategies can be employed to elucidate the molecular mechanisms of plant amino acid derivatives in plant growth and tolerance.
Fig. 6. Overview of strategies discussed in this review that are used to mine plant amino acid derivatives and their regulatory network. (Abbreviations: mGWAS, metabolic genome-wide association study; mQTL, metabolic quantitative trait loci.)
9.1. Genetic and multi-omics strategies to characterize bioactive amino acid derivatives and the candidate genes
Forward genetic strategies remain a reliable way to identify candidate genes with specific traits, despite being time-consuming and labor-intensive. Well-annotated genomes and segregating populations or natural accessions allow genome-wide association study (GWAS) and quantitative trait loci (QTL) analysis feasible. These approaches have been widely used to identify metabolic and genetic variants contributing to agronomic traits and abiotic stress resistance in plants. Metabolic GWAS and metabolic QTL assays integrate genotypes and metabotypes, enabling the dissection of small molecules and genetic variants associated with traits.
Integration of metabolome, transcriptome, proteome, phenome and genome has opened new avenues for gene and novel amino acid derivatives discovery. Since genes in the same metabolic pathway usually express in similar manners and are conserved in the same species, co-expression network analysis, homology-based cloning and genome-wide gene family analysis are also used to elucidate new candidate genes in a specific metabolic pathway.
Biosynthetic genes in metabolic pathway generally respond to growth and development stages or stress conditions, causing plant amino acid derivatives to be biosynthesized in a spatial–temporal specific manner. Some small molecules are usually at microgram or even nanogram levels per gram in plants. Despite their low abundance, the spatiotemporal specificity allows for high accumulation in particular plant tissues or cells. Thus, spatiotemporal and single-cell omics are highly valuable for elucidating the metabolic and regulatory network in the biosynthetic cells responsible for these cell-specific chemical signatures. Arabidopsis root cells, plant protoplasts and nuclei have been isolated for single-cell omics analysis, and other plant cell types are accessible by cell-wall-degrading enzymes. Live single-cell mass spectrometry (Live-MS) is a prominent platform for single-cell metabolite profiling, utilizing nano-electrospray ionization tips to extract cellular content under video-microscopy. Live-MS could also monitor physiological changes in plant amino acid derivatives levels during stress responses at specific time points and cellular levels, showing that this method could elucidate the mechanisms underlying trace plant amino acid derivatives-mediated physiological processes.
Following the identification of candidate genes and novel amino acid derivatives, overexpression, CRISPR/Cas9 and RNA interference can be used to validate these genes. Metabolomics analysis (GC–MS, LC-MS and NMR) in these transgenic plants can validate novel plant amino acid derivatives associated with environmental adaptation. To minimize background interference from abundant, non-biologically active metabolites, it is necessary to investigate the role of plant amino acid derivatives in plant defense through the knockout mutants that are unable to accumulate the metabolites. The biological roles of plant amino acid derivatives are typically verified in vivo through chemical complementation via exogenous feeding.
9.2. Metabolite–protein interactions strategies to unravel molecular mechanism of plant amino acid derivatives
The interplay between plant amino acid derivatives and signaling pathways in stress response is currently not well-addressed. Investigation of the molecular recognition between metabolites and their interacting proteins could elucidate the functional roles of plant amino acid derivatives and their associated signaling pathways in plant stress tolerance and communication. However, identifying these interactions is challenging due to the vast diversity and abundance of plant amino acid derivatives and proteins in plant cells.
Large-scale screening strategies are employed to explore metabolite-protein interactions, including protein-centric, metabolite-centric and interactome-wide techniques. Protein-centric methods dissect metabolites that interact with a protein of interest by untargeted metabolomics techniques. Abscisic acid was co-purified with PYL5 receptor by LC-MS, confirming that protein-centric strategies could be used to identify the regulatory plant amino acid derivatives in future. High-resolution NMR relaxometry can directly decipher weak metabolite−macromolecule interactions in biological fluids. This technique requires no invasive procedure or separation steps, providing a suitable tool for studying endogenous metabolite-protein interactions in native plant cells. Metabolite-centric strategies identify all protein partners for known signaling molecules by proteomics techniques. Cyclophilin 20-3 was identified using JA as a ligand, revealing its role in linking JA to ROS signaling under stress. Unlike protein-centric methods, metabolite-centric strategies can characterize amino acid derivatives binding sites by bottom-up proteomic analysis, providing the putative clues for their binding interfaces within plant amino acid derivatives-protein complexes.
Interactome-wide techniques capture the global profile of protein-metabolite interaction in an untargeted, proteome- and metabolome-wide manner. A prominent method is PROtein–Metabolite Interactions using Size separation (PROMIS). PROMIS utilizes native cell lysates to detect endogenous protein-metabolite interactions, and untargeted metabolite-protein complexes have been successfully obtained from Arabidopsis cell cultures. As the only available untargeted method, it proves invaluable for uncovering novel small-molecule interactions which influence developmental, environmental, and genetic outcomes.
10. Plant amino acid derivatives in agriculture: challenges, opportunities and perspectives
Climate change is increasing the magnitude and frequency of extreme temperatures, and altering global rainfall patterns, leading to high temperature stress, salinity stress, nutrient deficiencies, water scarcity, pest and disease pressure for crop productivity. Over-exploitation of agricultural resources further accelerates agricultural ecosystem degradation, resulting in land degradation and reduction in soil fertility. All these factors impair crop growth and productivity. Climate change reduced the growth rate of agricultural total factor productivity by approximately 21% between 1961 and 2020. Plant amino acid derivatives are positive regulators in improving plant stress tolerance, which makes them an attractive target for agriculture to improve plant productivity and health. Some naturally occurring plant amino acid derivatives show herbicidal, fungicidal or insecticidal activity, and could be used in modern crop protection chemistry, such as drugs and agrochemicals. Exogenous agricultural application of plant amino acid derivatives can be achieved by synthetic biology and synthetic chemical approaches with low cost and high efficiency.
Genetic manipulation of plant amino acid derivatives might contribute to improving crop adaptation and sustainable agriculture as well. Typically, transcription factors that regulate the levels of biosynthetic genes could increase the accumulation of plant amino acid derivatives. Epigenetic regulation of biosynthesis genes enables rapid plant amino acid derivatives responses to stress signals. Histone modifications occur with camalexin biosynthesis genes to regulate camalexin accumulation and pathogen response. Tuning plant amino acid derivatives levels can balance plant growth and stress tolerance, two vital complementary components by which plants respond to adverse environments, such as the glycosylation of the NHP pool.
Despite the identified plant amino acid derivatives involved in plant growth and stress resilience, their structural diversity suggests that further research will likely uncover additional, currently unknown, plant amino acid derivatives with similar or novel functions. Classical molecular genetic analysis, high-throughput omics sequencing of population materials, and improved network analysis will permit the characterization of metabolites and increase our understanding of their roles in crop interactions with the surrounding environment. High-coverage metabolome analyses, such as data-independent targeted quantitative metabolomics and nitrogen-based NMR, will aid in detecting the complexity and structural diversity of plant amino acid derivatives in various ecological contexts. PROMIS would serve as a valuable tool to identify novel regulatory plant amino acid derivatives and their interacting proteins in plant cells. This knowledge could be valuable for increasing crop productivity in challenging environments through the application of plant amino acid derivatives strategies.