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Review

Progress of Acetylation Modification in Plants

by
Ruiqi Li
1,2,
Xuezhong Li
1,
Ying He
1,
Xiaoyuan Chen
2,
Jing Li
1 and
Chuxiong Zhuang
1,*
1
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
2
Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China
*
Author to whom correspondence should be addressed.
Agronomy 2025, 15(8), 1910; https://doi.org/10.3390/agronomy15081910
Submission received: 12 July 2025 / Revised: 4 August 2025 / Accepted: 7 August 2025 / Published: 8 August 2025
(This article belongs to the Section Plant-Crop Biology and Biochemistry)
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Abstract

Protein acetylation, a conserved post-translational modification, is collaboratively catalyzed by acetyltransferases and deacetylases and is widespread in plants. This study reviews recent research regarding two key types of acetylation: histone acetylation and non-histone acetylation. Histone acetylation, occurring primarily in the nucleus, regulates the structure of chromatin to control gene transcription on a large scale. This process is crucial for the precise regulation of the plant organ formation and development. Non-histone protein acetylation is widely distributed across various organelles and can finely regulate almost all key cellular processes and functions. Histone and non-histone acetylation work together to construct a complex and precise acetylation-modification regulatory network in plants. Finally, this study also analyzes current research challenges and prospects related to acetylation modifications. Elucidating the regulatory mechanisms of acetylation modifications in plants not only enables us to better understand the molecular mechanisms of plant growth and development but also provides a theoretical basis and potential targets for the genetic improvement and enhancement of stress resistance in crops, with significant scientific and practical value.

1. Introduction

Protein post-translational modifications (PTMs) refer to the chemical modifications that proteins undergo through enzymatic reactions after the polypeptide chain (primary translation product) is synthesized by the ribosome. As one of the core mechanisms implicated in the finely tuned regulation of cellular life activities, PTMs expand the functional diversity of proteins and precisely regulate their structure, activity, subcellular localization, stability, and interactions with other molecules, thus being widely present in both animal and plant cells. PTMs are evolutionarily conserved and exhibit functional diversity; their dynamic and reversible nature enables cells to flexibly respond to physiological and environmental signals, thereby maintaining the homeostasis of life activities. For plants, due to their unique biological characteristics, including photosynthesis, secondary metabolism, and responses to environmental cues in their sessile growth, PTMs have evolved distinct types and regulatory networks. By altering protein charge, hydrophobicity, conformation, or interaction capabilities, PTMs finely control protein functions and are crucial for cellular gene expression and the regulation of protein activity. The types of PTMs in plant proteins are diverse and include phosphorylation, ubiquitination, propionylation, and acetylation [1,2,3,4]. These modifications are crucial for the normal functioning of plant proteins and play important roles in various biological processes such as plant growth and development, stress adaptation, and metabolic regulation.
Lysine acetylation (LysAc) is one of the main mechanisms involved in the epigenetic regulation of plants. It involves the addition of the acetyl group (−COCH3) from the substrate acetyl-CoA to the ε-amino group (−NH2) of the lysine side chain under the action of histone acetyltransferases (HATs), forming ε-N-acetyllysine through covalent bonding. This modification is extensively present in various eukaryotic and prokaryotic organisms [5,6]. The acetylated ε-amino group can neutralize the positive charge of the lysine residue (−NH3+), altering the charge state of the protein molecule and thereby disrupting the electrostatic interactions between the modified site and other macromolecules [7]. The dynamic reversibility of LysAc is crucial for its regulatory functions: HATs catalyze the addition of the acetyl group, while histone deacetylases (HDACs) mediate its removal [8,9]. Through the coordinated action of HATs and HDACs, the balance between protein acetylation and deacetylation is dynamically maintained, thereby precisely regulating the transcription and expression of plant genes [10,11,12].
Depending on where LysAc occurs and its function, it is classified as histone or non-histone acetylation. Histone acetylation is crucial in the regulation of plant genes, directly influencing gene expression by altering the structure of chromatin. In contrast, non-histone acetylation is involved in controlling plant metabolic pathways and maintaining physiological functions. This paper comprehensively reviews the progress in plant LysAc research, focusing on two types of LysAc. For histone acetylation, it emphasizes its precise regulation of plant growth and development, particularly root development. Regarding non-histone acetylation, it examines the identification of acetylation sites in various plants and their control of physiological processes. By analyzing the role of LysAc in plant growth, gene expression, and environmental responses, this review aims to reveal its complex regulatory network in plant cells and guide future research. These findings enhance our understanding of LysAc regulation and provide a theoretical basis for exploring the molecular mechanisms of plant growth, evaluating stress response targets, and the breeding of stress-resistant varieties.

2. Histone Acetylation Modifications Regulate Chromatin Structure and Gene Transcription

Acetylation was first found in histones. In research on the regulation of gene expression, scientists first hypothesized that histone acetylation might work by controlling RNA synthesis [13]. Numerous studies have shown that HATs and HDACs dynamically regulate the levels of histone acetylation. This plays a key role in crucial life processes such as cell differentiation, proliferation, and apoptosis. They are also involved in all stages of plant growth and development, such as vegetative growth, flower and fruit development, senescence, and responses to abiotic stress [14].
Chromatin, composed of DNA and histones, forms nucleosomes when DNA wraps around an octamer of the histones H2A, H2B, H3, and H4. During acetylation, HATs add acetyl groups to the lysine residues in histone tails, neutralizing their positive charge and reducing their electrostatic attraction to negatively charged DNA. This loosens chromatin, facilitating transcription factor binding and gene transcription [15]. Conversely, HDACs remove acetyl groups, restoring the positive charge and tightening chromatin, which is linked to transcriptional repression and gene silencing [16]. Recent advances, such as the development of ChIP-seq, have enabled the detailed genome-wide mapping of acetylated histones, offering new insights into histone acetylation regulation networks.

3. Histone Acetylation Modifications Regulate Plant Growth and Development

As a key mechanism regulating plant growth and development, histone acetylation regulates growth and development throughout the entire life cycle. Research on the functions of HATs and HDACs in plant growth and development has made significant progress. In Arabidopsis thaliana (A. thaliana), acetyltransferase general control nonderepressible5 (GCN5, also known as HAG1) participates in growth regulation by controlling the expression of multiple developmental genes. Its T-DNA insertion mutants show pleiotropic phenotypes, including dwarfism, a loss of apical dominance, and floral defects (affecting fertility) [17]. Additionally, in A. thaliana, the transcription factor ELONGATED HYPOCOTYL5 (HY5) mediates a decrease in histone H4 acetylation levels by directly interacting with deacetylase HDA15, suppressing the expression of cell wall-related and auxin signaling genes. This is involved in the negative regulation of hypocotyl cell elongation [18]. In wheat, GCN5 enhances histone acetylation levels by forming a complex with transcription factor MYB, promoting cuticular wax biosynthesis [19]. In rice, histone deacetylase histone deacetylase701 (HDT701) negatively regulates the expression of pathogen-resistance-related genes by controlling histone H4 acetylation levels [20]. Under salt stress, GCN5 rapidly regulates cell wall-related gene expression by altering the acetylation levels of histones H3K9 and H4K5, thus mitigating salt stress damage in A. thaliana and corn [21,22,23]. Further research shows that in rice, GCN5-mediated LysAc modification can expose the alteration/deficiency in activation 2 (ADA2) protein to specific E3 ubiquitin ligases, reducing its stability. This allows ADA2 to sense intracellular changes in the levels of acetyl-CoA, dynamically regulating HAT activity and histone acetylation levels. This mechanism is crucial in the adaptation of plants to environmental changes [24]. Moreover, the rice transcription factor OsGRAS30 enhances rice blast resistance by directly interacting with deacetylase HDAC1 and inhibiting its activity, increasing histone H3K27ac levels [25]. In summary, acetyltransferases and deacetylases dynamically regulate histone acetylation levels, participating in various stages of plant growth and reproductive development. They also play a key role in stress responses and disease resistance.

4. The Impact of Histone Acetyltransferases on Plant Root Development

Root development is vital for plant growth, nutrient uptake, and environmental adaptation [26,27]. Elucidating acetylation’s role in the regulation of root development can enhance crop productivity and help plants cope with environmental changes. Histone acetylation significantly impacts cell differentiation and proliferation—processes that are highly active during root development. In A. thaliana, histone acetylation maintains homeostasis in the stem cell zone, regulates cell division and differentiation, and thus contributes to root development. Mutations in histone deacetylase 6 (HDA6) alter the acetylation states of histones at the promoters of ENHANCER OF TRIPTYCHON AND CAPRICE1 (ETC1) and GLABRA2 (GL2), leading to a looser chromatin structure and upregulating their expression. As key regulators of root epidermal cell development, the abnormal expression of these genes disrupts epidermal cell alignment, resulting in an abnormal root morphology, such as an altered growth direction and root hair defects [28].
Additionally, the acetylation dynamics of histone H3.1 are closely related to cell population state transitions. Changes in its acetylation level regulate the transition of roots from cell proliferation to differentiation, ensuring a normal root morphology and structure [29]. Further studies have revealed that histone acetylation affects gene expression by influencing the mobility of chromatin. For instance, regarding fluorescence recovery after photobleaching (FRAP) and two-photon photoactivation in A. thaliana, it was found that altering the acetylation level of the core histone H2B during root cell differentiation affects its binding to chromatin. This, in turn, significantly changes the mobility of histone and the expression of development/differentiation-related genes, thereby maintaining the normal morphology and function of root development and differentiation [30]. In rice, histone acetylation regulates root architecture by controlling root meristem activity. The transcription factor WUSCHEL-RELATED HOMEOBOX 11 (WOX11) recruits the ADA2-GCN5 complex to specifically regulate the expression of root development genes, guiding cell differentiation and forming complete root structures [31]. Moreover, inhibiting the acetylation of histones H3 and H4 alters the expression of root epidermal cell pattern genes such as CPC (CAPRICE), GL2, and WER (WEREWOLF) in A. thaliana, causing abnormal cell differentiation and affecting the overall epidermal cell pattern [32,33]. In summary, by dynamically regulating the structure of chromatin and gene expression, histone acetylation precisely influences the differentiation, proliferation, and pattern formation of root cells, making it one of the core regulatory mechanisms of plant root development.

5. Non-Histone Protein Acetylation Plays a Broader Role in Regulating Plant Growth and Development

For a long time, acetylation research mainly focused on histones. However, recent studies have shown that HATs and HDACs also acetylate non-histone proteins in cells. In 1997, the first non-histone protein found to undergo acetylation was p53 [34]. This discovery indicated that LysAc could regulate both histone and non-histone protein functions. With the rise of high-throughput acetylation proteomics, many non-histone acetylation modifications in plants have been systematically identified. These modifications are common post-translational protein modifications in plants and are widely involved in key physiological processes such as photosynthesis, metabolic regulation, and signal transduction [4,35,36]. This greatly expands the regulatory scope of acetylation in plant life activities.

6. Non-Histone Acetylation Modifications Are Present in Various Plant Cell Organelles

Many studies have indicated that non-histone LysAc is widespread in plants, including rice, legumes, maize, and A. thaliana. Cell-localization analyses of these modifications have revealed that LysAc is common in cytoplasm, nuclei, mitochondria, and chloroplasts (Table 1) [4,37,38,39,40]. In 1988, spinach chloroplast-encoded Rubisco large subunits (RbcLs) were first found in vitro with non-histone LysAc [41]. Later, nucleus-encoded, chloroplast-targeted non-histone LysAc was also reported [37,42]. With advancements in proteomics, research on the distribution and function of non-histone LysAc has made breakthroughs in multiple species. In A. thaliana, Finkemeier et al. identified 91 LysAc sites on 74 proteins [4]. In strawberry, 1392 acetylation sites on 684 proteins were found, greatly enhancing our understanding of plant acetylation and confirming its role in diverse cellular metabolism and processes [35]. In rice, Xiong et al. reported in 2016 that among 716 acetylated proteins with 1337 acetylation sites, approximately 42% were in chloroplasts, higher than in other organelles; this indicated that LysAc enrichment occurs in chloroplasts [38]. Subsequent studies found 4868 acetylated lysine residues on 1952 proteins across rice tissues such as seeds, anthers, and embryos, confirming its presence at different developmental stages [43,44,45,46]. In soybean (Glycine max), immunoenrichment combined with mass spectrometry identified over 400 LysAc sites on 245 proteins distributed across major organelles, with functions in signaling, protein folding, and metabolism [39]. In pea seedling mitochondria, 664 LysAc sites on 358 proteins were identified, linking mitochondrial protein acetylation to various physiological processes [47]. In maize, the analysis of 2791 sites in 912 acetylated proteins from de-etiolated seedlings treated with the pathogen toxin HC-toxin (HCT) revealed that LysAc modifications exist in multiple classes of functional proteins, including metabolic enzymes, transcription factors, cytoskeletal proteins, signal transduction proteins, cell cycle regulatory proteins, stress-responsive proteins, and ribosomal proteins [40]. Additionally, the first analysis of the maize de-etiolated seedling identified 814 LysAc sites on 462 proteins, including seven conserved acetylated lysine residues in RbcL compared to A. thaliana, suggesting the evolutionary conservation of this modification [48].
In summary, non-histone LysAc, a common post-translational modification in plants, is widely distributed across multiple species, tissues, and organelles, and is deeply involved in key physiological processes such as metabolic regulation, signal transduction, and protein folding. The extensive distribution of acetylated lysine residues in different cellular compartments indicates that plants can rapidly sense environmental changes and dynamically adjust metabolic functions through this modification mechanism. This dynamic regulatory property not only helps plants maintain growth and developmental homeostasis in complex environments but also provides an important molecular basis for their adaptation to adverse conditions such as drought, high temperature, and pathogen infection.

7. Non-Histone Protein Acetylation Is Involved in Diverse Physiological and Biochemical Processes

In plants, non-histone LysAc participates in various physiological and biochemical processes such as photosynthesis, energy metabolism, plant hormone signal transduction, and stress responses by regulating gene expression, metabolic pathways, and the activity of enzymes/transcription factors. It plays a key role in carbon utilization and the metabolic flux regulation of central metabolic enzymes [53,54].
Numerous studies have indicated that non-histone LysAc, as one of the core mechanisms regulating photosynthesis, is widespread in protein subunits of the photosynthetic electron transport chain and nearly all Calvin cycle enzymes [35,38,49,52,55,56,57,58]. The efficient regulation of photosynthesis is achieved through the dynamic modulation of acetylation levels (Figure 1).
In strawberry, about 50% of LysAc proteins are in chloroplasts, directly regulating the function of photosystem proteins, ATP synthase, and Calvin cycle enzymes, thereby significantly impacting light capture, electron transport, and carbon fixation [35]. In A. thaliana, key Rubisco sites undergo LysAc modification, which alters its conformation or assembly, thereby regulating its catalytic efficiency [4]. Rice LysAc proteins related to photosynthesis cover PSII, LHCb, Rubisco subunits, and chloroplastic ATP synthase β-subunits, optimizing metabolism by regulating protein activity, stability, and assembly [51,52]. In maize etiolated seedlings, significant changes in the LysAc levels of PSII/PSI subunits, chlorophyll synthesis proteins, and dark-reaction enzymes indicate LysAc’s involvement in both light-reaction energy capture, transfer protection, and dark reaction material transformation [48].
As the site of the light reactions, thylakoid architecture is intimately linked to LysAc. The chloroplast acetyltransferase GCN5-related N-acetyltransferases 2 (GNAT2) helps build thylakoids: its loss prevents LHCII from properly docking with PSI and causes pronounced photosynthetic defects. Likewise, the chloroplast-localized acetyltransferase NUCLEAR SHUTTLE INTERACTING (NSI) is essential for light-dependent reorganization of thylakoid complexes; mutants lacking NSI show altered acetylation states of numerous chloroplast proteins and impaired thylakoid assembly [59]. The chloroplastic NSI acetyltransferase mutant, unable to recombine thylakoid complexes in a light-dependent manner, alters the acetylation of various chloroplastic proteins [60]. LysAc also directly participates in photosynthetic metabolism by regulating key enzyme activities. In A. thaliana, elevated acetylation at Lys201 and Lys334 of the RbcL significantly suppresses its catalytic activity, indicating that LysAc acts as a direct negative regulator of Rubisco [61]. The acetylation of PORA, a NADPH (nicotinamide adenine dinucleotide phosphate)-dependent protochlorophyllide oxidoreductase A involved in chlorophyll biosynthesis and regulated by histone deacetylases, affects chlorophyll adaptation and photo-morphogenesis under different light conditions [62]. Under low light, histone deacetylase HDA14 controls the activation of Rubisco by regulating the LysAc level of RuBisCO activase (RCA) [50]. The LysAc level of thioredoxin AtFNR1/2, linked to light response, is also involved in the integration of light signals [63].
Notably, in A. thaliana, LysAc and phosphorylation are jointly regulated by the circadian clock in different organs (rosette leaves, roots, flowers, leaf sheaths) and seedlings, affecting proteins involved in light capture, translation, metabolism, and cellular transport [49]. While the research varies across plant species such as strawberry, Arabidopsis, rice, and maize, LysAc’s regulatory mechanism of photosynthesis is highly conserved. From electron transfer in light reactions to carbon fixation in dark reactions, and from thylakoid structure maintenance to key enzyme activity regulation, LysAc dynamically adjusts protein functions. This enables plants to adapt to varying light environments and maintain photosynthetic efficiency, making LysAc a universal and critical regulatory mechanism.
Plant mitochondria are the core site of oxidative phosphorylation and photorespiratory energy metabolism [64], and their proteins are rich in acetylation modifications [65]. Among these, lysine acetylation plays a key role in energy metabolism—by regulating metabolic strategies to help cells store energy [66]. In A. thaliana, 120 acetylated mitochondrial non-histone proteins contain 243 acetylation sites, covering nearly all key enzymes in the tricarboxylic acid cycle and glycolysis (Figure 2) [67]. The acetylation of metabolic enzymes, including those in glycolysis and the TCA cycle, directly impacts their activity, thereby affecting energy production and storage. The ADA2 protein’s acetylation level is dynamically regulated via its interaction with specific E3 ubiquitin ligases, which is crucial for sensing changes in the level of cellular acetyl-CoA and regulating HAT activity. This regulatory mechanism underscores the significance of acetylation in energy metabolism [24].
In rice, many of the 1024 acetylated proteins are mitochondrial and involved in oxidative carbon and sugar metabolism [52]. Changes in their acetylation levels can affect protein functions, influencing mitochondrial energy metabolism and transport. The overexpression of OsSNAT1 in rice increases leaf melatonin, while the expression of OsSNAT2 is melatonin-inhibited [68,69]. In pea seedling mitochondria, acetylated proteins are identified in key pathways such as glycolysis and amino acid metabolism [39,47]. Acetyl-CoA, a reflection of cellular nutrition and energy status, is regulated by acetyltransferases such as GCN5 in A. thaliana, which adjusts cellular acetyl-CoA levels by modifying ADA2 acetylation [24]. Notably, in vitro deacetylation of key lysine residues in glyceraldehyde-3-phosphate dehydrogenase cytosolic 2 (GAPC2) significantly enhances its activity, directly impacting glycolysis [4]. The acetylation of all key enzymes in the TCA cycle (tricarboxylic acid cycle) and respiratory chain further confirms acetylation’s central role in the regulation of plant energy metabolism.
Non-histone protein acetylation occurs not only in key organelles for metabolic regulation but also at various stages of plant growth, development, and reproductive development. During the regulation of flowering, it plays a crucial role through specific mechanisms. For instance, the Harbinger transposon-derived SANT-domain-containing protein interacts directly with HDA6 to form a complex that is essential in histone deacetylation and the control of flowering time in plants [70]. In rice, the deacetylase OsHDAC1 interacts with OsGSK2 and deacetylates it, inhibiting OsGSK2 activity. This leads to the accumulation of OsBZR1, a positive regulator of lateral root formation in rice, thus regulating lateral root development [71].
A high-resolution proteomic and acetylation proteomic analysis of Camellia sinensis cv. “Anji Bai Cha” (an albino tea cultivar) during its periodic bleaching process identified 3161 LysAc sites, of which 468 changed significantly during leaf color transition [72]. This suggests that LysAc may regulate the periodic bleaching of “Anji Bai Cha.” Cytoplasmic male sterility (CMS) is a maternally inherited trait in plants that prevents them from producing functional pollen, leading to the loss of male reproductive capacity [73]. In kenaf (Hibiscus cannabinus L.) CMS lines, the protein and LysAc levels of protein disulfide isomerase (PDIL) are significantly reduced. PDIL, which is crucial in embryo maturation and the development of the pollen tube, plays an important role in pollen development [74]. The significant reduction in PDIL’s LysAc level in CMS lines indicates that changes in cytoplasmic LysAc levels can affect pollen development and lead to CMS [75].

8. The Role of Non-Histone Protein Acetylation in Plant Responses to Biotic and Abiotic Stresses

Protein post-translational modifications (PTMs) act as dynamic molecular switches that modulate protein functions to coordinate cellular responses, serving as an immediate regulatory mechanism for plants to combat biotic and abiotic stresses [76]. As sessile organisms, plants rely on adaptive internal mechanisms to cope with persistent unfavorable conditions. Quantitative acetylome studies have shown that environmental changes can significantly affect the acetylation status of photosynthesis-related proteins (Figure 3) [77].
In biotic stress defense, jasmonic acid (JA) in A. thaliana is a central regulator, and its signaling relies on the reversible acetylation of TOPLESS (TPL) by GCN5 and HDA6 [78]. In rice, the acetylation of OsLOX14, a key JA biosynthesis enzyme, is regulated by HDA706; reduced acetylation enhances the stability of OsLOX14 and the antiviral capacity [79]. Lower acetylation of the K304 residue of Serine/arginine protein kinases (Srpks) activates antioxidant enzyme transcription, bolstering tomato antifungal defense [80]. Additionally, in tomato, FOLSir2 regulates FOLGska2 activation by deacetylating FolGsk3’s K271, impacting antifungal immunity [81].
In abiotic stress, Exogenous HCT treatment in maize reveals that non-histone protein acetylation is dynamically regulated by endogenous histone deacetylases during immune responses [40]. In rice cold tolerance, OsHDA716 reduces OsbZIP46 acetylation, promoting its degradation and lowering cold tolerance [82]. Under salt stress, the acetylation of GAPC2 and chloroplast photosynthesis-related proteins increases [58]. The changes in photosynthetic protein acetylation under oxidative stress confirm acetylation’s role in oxidative stress responses [52]. In drought stress, TaHDA8 in wheat regulates root development by deacetylating TaAREB3, revealing the mechanism via which lysine deacetylation enhances drought adaptation [83]. Overall, acetylation modifications play a central role in plant stress responses by regulating protein functions through multiple mechanisms.

9. Acetylation Modifications Interact with Other PTMs to Influence Gene Expression

At present, evidence shows that protein acetylation and other post-translational modifications (e.g., phosphorylation and ubiquitination) jointly coordinate regulatory networks to influence gene expression [11]. In A. thaliana, mutations in the five HDAC-active sites and two phosphorylation sites of deacetylase HDA15 eliminate its activity, highlighting phosphorylation’s key role in modulating HDA15’s structure and function [84]. Histone deacetylase HDA6 interacts with the histone methyltransferases SUVH4, SUVH5, and SUVH6 [85]. Through histone H3K9 methylation and H3 deacetylation, they cooperatively regulate transposons. Moreover, changes in HDA6’s phosphorylation levels affect its enzymatic activity [86]. By deacetylating BIN2’s K189, HDA6 influences BIN2’s activity. BIN2 is also regulated by the phosphatase BSU1; its dephosphorylation inactivates BIN2 [87]. This indicates that BIN2’s activity is regulated by both phosphorylation and acetylation. Histone deacetylase OsHDA706 acts as a broad-spectrum antiviral regulator. In transgenic rice overexpressing OsHDA706, the JA pathway genes are markedly up regulated. Studies show that OsHDA706 directly deacetylates OsLOX14, a rate-limiting enzyme in JA biosynthesis. Removal of acetyl groups from K310 and K317 of OsLOX14 suppresses its ubiquitination and enhances protein stability, leading to OsLOX14 accumulation. Thus, OsHDA706 boosts JA levels by deacetylating and stabilizing the non-histone substrate OsLOX14 [79]. OsHDA716 inhibits rice cold tolerance by binding to and deacetylating OsbZIP46 (basic leucine zipper protein 46), thereby reducing its transcriptional activity and protein stability and promoting its ubiquitin-mediated degradation [82]. These studies demonstrate that protein acetylation modifications can alter protein stability via ubiquitination, thus regulating biological functions. This highlights the cooperative role of acetylation with other post-translational modifications in gene expression and cellular regulation.

10. Conclusions and Perspectives

To date, research on protein acetylation has primarily focused on histone acetylation and its transcriptional roles. The specific mechanisms that govern the numerous non-histone lysine acetylation sites within cellular organelles, which are implicated in a variety of biological processes, remain largely unexplored. Owing to the significant progress in proteomics, researchers can now identify a broad array of acetylated proteins and acetylation sites. Nevertheless, the precise mechanisms by which these sites influence the physiological and biochemical processes of plants through subtle changes in acetylation remain elusive. Although LysAc can modulate protein conformation, stability, enzyme activity, protein–protein interactions, and stress resistance, details of the mechanisms require further investigation.
LysAc sites can function as molecular switches and are designed to modulate cellular signaling, gene expression, or enzyme activity within plant proteins. By systematically comparing conserved acetylation sites across different species (e.g., A. thaliana, Oryza sativa, Zea mays), we will distill a universal “cross-species acetylation module.” This will enable rapid translation of laboratory findings to elite crops, facilitating plug-and-play improvements from model plants to the field. By introducing point mutations at key non-histone lysine acetylation sites to generate acetylated or non-acetylated analogs, their physiological functions can be unveiled. With the emergence of methods for the computational prediction of protein structure, such as AlphaFold, the three-dimensional structures of the vast majority of protein sequences have been predicted [88,89], enabling researchers to simulate and predict changes in protein structures following acetylation; this can then be experimentally validated, offering novel methodological insights for subsequent studies. LysAc research will not only enhance our understanding of the complex regulatory networks of gene expression, metabolic processes, and signal transduction but also provide new perspectives on plant stress adaptation mechanisms (such as under multiple stresses of drought, salinity, and pathogen infection). This lays a theoretical foundation for developing stress-resistant crop varieties and identifies potential targets for further research. Furthermore, the crosstalk between LysAc and other PTMs will foster integrative multi-omics approaches, offering systems-level insights into plant regulation. These advancements enrich our theoretical knowledge of the physiological regulation of plants and enable new breakthroughs and opportunities regarding basic and applied plant biology research.

Author Contributions

Research design, C.Z. and J.L.; material sampling and data analysis, R.L., X.L., X.C., and Y.H.; manuscript—writing and revision, C.Z., J.L., and R.L. All authors have read and agreed to the published version of the manuscript.

Funding

This research was supported by the Sci-Tech Innovation 2030 Agenda grants 2023ZD0407103-05 and 2023ZD040710309 (CZ) and by the Guangdong Basic and Applied Basic Research Foundation 2019B030302006 (JL).

Data Availability Statement

Not applicable.

Conflicts of Interest

The authors declare that they have no competing interests.

Abbreviations

The following abbreviations are used in this manuscript:
ADA2alteration/deficiency in activation 2
ATPadenosine triphosphate
BPGAglycerate 1,3-bisphosphate
CBBCalvin–Benson–Bassham
CMScytoplasmic male sterility
CPCCAPRICE
Cytb 6fcytochrome b6f
DHAPdihydroxyacetone phosphate
ETC1ENHANCER OF TRIPTYCHON AND CAPRICE1
FBPasefructose 1,6-bisphosphatase
FRAPfluorescence recovery after photobleaching
F6-Pfructose 6-phosphate
GAPDHglyceraldehyde 3-phosphate dehydrogenase
GAPC2glyceraldehyde-3-phosphate dehydrogenase cytosolic 2
GCN5general control nonderepressible 5
GL2GLABRA2
GPIglucose phosphate isomerase
HATshistone acetyltransferases
HCTHC-toxin
HDACshistone deacetylases
HDT701histone deacetylase701
JAjasmonic acid
G3Pglyceraldehyde 3-phosphate
LysAclysine acetylation
NADPHnicotinamide adenine dinucleotide phosphate
NSInuclear shuttle interacting
PDILprotein disulfide isomerase
PGKphosphoglycerate kinase
PGAphosphoglycerate
PORAprotochlorophyllide oxidoreductase A
PSIphotosystem I
PSI-LHCIphotosystem I light-harvesting complex I
PSIIphotosystem II
PSII-LHCIIphotosystem II light-harvesting complex II
PTMsprotein post-translational modifications
RbcLRubisco large subunit
RCARuBisCO activase
RPEribulose phosphate epimerase;
RuBPribulose 1,5-bisphosphonate
Rubiscoribulose 1,5-bisphosphate carboxylase/oxygenase
Ru5Pribulose 5-phosphate
RPIribose-5-phosphate isomerase
R5Pribose-5-phosphate
SBPsedoheptulose-1,7-bisphosphate
SBPasesedoheptulose-1,7-bisphosphatase
S7Psedoheptulose-7-phosphate
TCA cycletricarboxylic acid cycle
TPLTOPLESS
TPItriose phosphate isomerase
WERWEREWOLF
WOX11WUSCHEL-RELATED HOMEOBOX 11
Xu5Pxylulose-5-phosphate
2PG2-phosphoglycerate
3-PGA3-phosphoglycerate

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Figure 1. Lysine acetylation modifications in the light reaction and dark reaction (Calvin cycle) of photosynthesis. The identified acetylated protein subunits exist in the electron transport chain as shown in the table (indicated by the arrow below the complex). The Lys-acetylated enzymes relevant to the Calvin–Benson cycle noted with orange boxes. PSI-LHCI, photosystem I light-harvesting complex I; PSII-LHCII, photosystem II light-harvesting complex II; Cyt b6f, cytochrome b6f. Rubisco, ribulose 1,5-bisphosphate carboxylase/oxygenase; 3-PGA, 3-phosphoglycerate; PGK, phosphoglycerate kinase; BPGA, glycerate 1,3-bisphosphate; GAPDH, glyceraldehyde 3-phosphate dehydrogenase; G3P, glyceraldehyde 3-phosphate; TPI, triose phosphate isomerase; DHAP, dihydroxyacetone phosphate; FBPase, fructose 1,6-bisphosphatase; F6-P, fructose 6-phosphate; GPI, glucose phosphate isomerase; Ru5P, ribulose 5-P; 2PG, 2-phosphoglycerate; PGA, phosphoglycerate; SBPase, sedoheptulose-1,7-bisphosphatase; RPE, ribulose phosphate epimerase; RPI, ribose-5-phosphate isomerase; R5P, ribose-5-phosphate; SBP, sedoheptulose-1,7-bisphosphate; S7P, sedoheptulose-7-phosphate; Xu5P, xylulose-5-phosphate. The acetylated proteins identified are listed below.
Figure 1. Lysine acetylation modifications in the light reaction and dark reaction (Calvin cycle) of photosynthesis. The identified acetylated protein subunits exist in the electron transport chain as shown in the table (indicated by the arrow below the complex). The Lys-acetylated enzymes relevant to the Calvin–Benson cycle noted with orange boxes. PSI-LHCI, photosystem I light-harvesting complex I; PSII-LHCII, photosystem II light-harvesting complex II; Cyt b6f, cytochrome b6f. Rubisco, ribulose 1,5-bisphosphate carboxylase/oxygenase; 3-PGA, 3-phosphoglycerate; PGK, phosphoglycerate kinase; BPGA, glycerate 1,3-bisphosphate; GAPDH, glyceraldehyde 3-phosphate dehydrogenase; G3P, glyceraldehyde 3-phosphate; TPI, triose phosphate isomerase; DHAP, dihydroxyacetone phosphate; FBPase, fructose 1,6-bisphosphatase; F6-P, fructose 6-phosphate; GPI, glucose phosphate isomerase; Ru5P, ribulose 5-P; 2PG, 2-phosphoglycerate; PGA, phosphoglycerate; SBPase, sedoheptulose-1,7-bisphosphatase; RPE, ribulose phosphate epimerase; RPI, ribose-5-phosphate isomerase; R5P, ribose-5-phosphate; SBP, sedoheptulose-1,7-bisphosphate; S7P, sedoheptulose-7-phosphate; Xu5P, xylulose-5-phosphate. The acetylated proteins identified are listed below.
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Figure 2. Lysine acetylation modifications in the TCA cycle and glycolysis. The Lys-acetylated enzymes relevant to the TCA cycle noted with orange boxes; the Lys-acetylated enzymes relevant to the glycolysis cycle noted with blue boxes. TCA cycle: tricarboxylic acid cycle.
Figure 2. Lysine acetylation modifications in the TCA cycle and glycolysis. The Lys-acetylated enzymes relevant to the TCA cycle noted with orange boxes; the Lys-acetylated enzymes relevant to the glycolysis cycle noted with blue boxes. TCA cycle: tricarboxylic acid cycle.
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Figure 3. The regulation of acetylation modification during the growth and development of plants (taking rice as an example).
Figure 3. The regulation of acetylation modification during the growth and development of plants (taking rice as an example).
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Table 1. Lysine acetylomes identified in plant species.
Table 1. Lysine acetylomes identified in plant species.
SpeciesNumber of Kac SitesNumber of Kac ProteinsTissues/OrgansMain LocationReferences
Arabidopsis thaliana9174LeavesChloroplast[4]
Arabidopsis thaliana348204MitochondriaMitochondria[49]
Arabidopsis thaliana21521022LeavesChloroplast, mitochondria, cytoplasm, nucleus[50]
Arabidopsis thaliana6457LeavesChloroplast, mitochondria, cytoplasm, nucleus[51]
Fragaria ananassa1392684LeavesChloroplast, mitochondria, cytoplasm, nucleus[35]
Oryza sativa1337716Leaves, stems, rootsChloroplast, mitochondria, cytoplasm, nucleus[36]
Oryza sativa1003692SeedsVacuole, mitochondria, cytoplasm, nucleus[44]
Oryza sativa1536890Callus, root, leaves, panicleChloroplast, mitochondria, cytoplasm, nucleus[45]
Oryza sativa16691024LeavesRibosome, chloroplast, mitochondria, nucleus[52]
Oryza sativa48681952SeedsRibosome[46]
Glycine max245400+SeedsMitochondria, cytoplasm, nucleus[39]
Pisum sativum358664MitochondriaMitochondria[47]
Zea mays9122791LeavesChloroplast, mitochondria, cytoplasm, nucleus[40]
Zea mays462814LeavesChloroplast, mitochondria, cytoplasm, nucleus[48]
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Li, R.; Li, X.; He, Y.; Chen, X.; Li, J.; Zhuang, C. Progress of Acetylation Modification in Plants. Agronomy 2025, 15, 1910. https://doi.org/10.3390/agronomy15081910

AMA Style

Li R, Li X, He Y, Chen X, Li J, Zhuang C. Progress of Acetylation Modification in Plants. Agronomy. 2025; 15(8):1910. https://doi.org/10.3390/agronomy15081910

Chicago/Turabian Style

Li, Ruiqi, Xuezhong Li, Ying He, Xiaoyuan Chen, Jing Li, and Chuxiong Zhuang. 2025. "Progress of Acetylation Modification in Plants" Agronomy 15, no. 8: 1910. https://doi.org/10.3390/agronomy15081910

APA Style

Li, R., Li, X., He, Y., Chen, X., Li, J., & Zhuang, C. (2025). Progress of Acetylation Modification in Plants. Agronomy, 15(8), 1910. https://doi.org/10.3390/agronomy15081910

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