Global Proteome Analyses of Lysine Acetylation and Succinylation Reveal the Widespread Involvement of both Modification in Metabolism in the Embryo of Germinating Rice Seed

Functions and mechanisms of non-histone protein acetylation in plants

Lysine acetylation, an evolutionarily conserved post-translational protein modification, is reversibly catalyzed by lysine acetyltransferases and lysine deacetylases. Lysine acetylation, which was first discovered on histones, mainly functions to configure the structure of chromatin and regulate gene transcriptional activity. Over the past decade, with advances in high-resolution mass spectrometry, a vast and growing number of non-histone proteins modified by acetylation in various plant species have been identified. Lysine acetylation of non-histone proteins is widely involved in regulating biological processes in plants such as photosynthesis, energy metabolism, hormone signal transduction and stress responses. Moreover, in plants, lysine acetylation plays crucial roles in regulating enzyme activity, protein stability, protein interaction and subcellular localization. This review summarizes recent progress in our understanding of the biological functions and mechanisms of non-histone protein acetylation in plants. Research prospects in this field are also noted.

Advances in understanding the roles of plant HAT and HDAC in non-histone protein acetylation and deacetylation

MAIN CONCLUSION

This review focuses on HATs and HDACs that modify non-histone proteins, summarizes functional mechanisms of non-histone acetylation as well as the roles of HATs and HDACs in rice and Arabidopsis. The growth and development of plants, as well as their responses to biotic and abiotic stresses, are governed by intricate gene and protein regulatory networks, in which epigenetic modifying enzymes play a crucial role. Histone lysine acetylation levels, modulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), are well-studied in the realm of transcriptional regulation. However, the advent of advanced proteomics has unveiled that non-histone proteins also undergo acetylation, with its underlying mechanisms now being clarified. Indeed, non-histone acetylation influences protein functionality through diverse pathways, such as modulating protein stability, adjusting enzymatic activity, steering subcellular localization, influencing interactions with other post-translational modifications, and managing protein-protein and protein-DNA interactions. This review delves into the recent insights into the functional mechanisms of non-histone acetylation in plants. We also provide a summary of the roles of HATs and HDACs in rice and Arabidopsis, and explore their potential involvement in the regulation of non-histone proteins.

Variation in a Poaceae-conserved fatty acid metabolic gene cluster controls rice yield by regulating male fertility

A wide variety of metabolic gene clusters exist in eukaryotic genomes, but fatty acid metabolic gene clusters have not been discovered. Here, combining with metabolic and phenotypic genome-wide association studies, we identify a major locus containing a six-gene fatty acid metabolic gene cluster on chromosome 3 (FGC3) that controls the cutin monomer hydroxymonoacylglycerols (HMGs) contents and rice yield, possibly through variation in the transcription of FGC3 members. We show that HMGs are sequentially synthesized in the endoplasmic reticulum by OsFAR2, OsKCS11, OsGPAT6, OsCYP704B2 and subsequently transported to the apoplast by OsABCG22 and OsLTPL82. Mutation of FGC3 members reduces HMGs, leading to defective male reproductive development and a significant decrease in yield. OsMADS6 and OsMADS17 directly regulate FGC3 and thus influence male reproduction and yield. FGC3 is conserved in Poaceae and likely formed prior to the divergence of Pharus latifolius. The eukaryotic fatty acid and plant primary metabolic gene cluster we identified show a significant impact on the origin and evolution of Poaceae and has potential for application in hybrid crop breeding.

Comprehensive Proteome and Acetylome Analysis of Needle Senescence in Larix gmelinii

Leaf senescence is essential for the growth and development of deciduous trees in the next season. Larix gmelinii, a deciduous coniferous tree, exhibits its most distinctive feature by turning yellow in the autumn and eventually shedding its leaves, resulting in significant changes in its appearance during the fall. Lysine acetylation plays an important role in diverse cellular processes; however, limited knowledge is available regarding acetylations in the needle senescence of L. gmelinii. In this study, the proteomics and acetylated modification omics of two phenotypic leaves, yellow and green (senescent and non-senescent) needles, were analyzed before autumn defoliation. In total, 5022 proteins and 4469 unique acetylation sites in 2414 lysine acylated proteins were identified, and this resulted in the discovery of 1335 differentially expressed proteins (DEPs) and 605 differentially expressed acetylated proteins (DAPs) in yellow versus green needles. There are significant differences between the proteome and acetylome; only 269 proteins were found to be DEP and DAP, of which 136 proteins were consistently expressed in both the DEP and DAP, 91 proteins were upregulated, and 45 proteins were down-regulated. The DEPs participate in the metabolism of starch and sucrose, while the DAPs are involved in glycolysis and the tricarboxylic acid cycle. Among them, DEPs underwent significant changes in glycolysis and citric acid cycling. Most of the enzymes involved in glycolysis and the citrate cycle were acetylated. DAPs were down-regulated in glycolysis and up-regulated in the citrate cycle. In all, the results of this study reveal the important role of lysine acetylation in the senescence of L. gmelinii needles and provide a new perspective for understanding the molecular mechanism of leaf senescence and tree seasonal growth.

Proteomic Analysis of Lysine Acetylation and Succinylation to Investigate the Pathogenicity of Virulent Pseudomonas syringae pv. tomato DC3000 and Avirulent Line Pseudomonas syringae pv. tomato DC3000 avrRpm1 on Arabidopsis thaliana

Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) is able to infect many economically important crops and thus causes substantial losses in the global agricultural economy. Pst DC3000 can be divided into virulent lines and avirulent lines. For instance, the pathogen effector avrRPM1 of avirulent line Pst-avrRpm1 (Pst DC3000 avrRpm1) can be recognized and detoxified by the plant. To further compare the pathogenicity mechanisms of virulent and avirulent Pst DC3000, a comprehensive analysis of the acetylome and succinylome in Arabidopsis thaliana was conducted following infection with virulent line Pst DC3000 and avirulent line Pst-avrRpm1. In this study, a total of 1625 acetylated proteins encompassing 3423 distinct acetylation sites were successfully identified. Additionally, 229 succinylated proteins with 527 unique succinylation sites were detected. A comparison of these modification profiles between plants infected with Pst DC3000 and Pst-avrRpm1 revealed significant differences. Specifically, modification sites demonstrated inconsistencies, with a variance of up to 10% compared to the control group. Moreover, lysine acetylation (Kac) and lysine succinylation (Ksu) displayed distinct preferences in their modification patterns. Lysine acetylation is observed to exhibit a tendency towards up-regulation in Arabidopsis infected with Pst-avrRpm1. Conversely, the disparity in the number of Ksu up-regulated and down-regulated sites was not as pronounced. Motif enrichment analysis disclosed that acetylation modification sequences are relatively conserved, and regions rich in polar acidic/basic and non-polar hydrophobic amino acids are hotspots for acetylation modifications. Functional enrichment analysis indicated that the differentially modified proteins are primarily enriched in the photosynthesis pathway, particularly in relation to light-capturing proteins. In conclusion, this study provides an insightful profile of the lysine acetylome and succinylome in A. thaliana infected with virulent and avirulent lines of Pst DC3000. Our findings revealed the potential impact of these post-translational modifications (PTMs) on the physiological functions of the host plant during pathogen infection. This study offers valuable insights into the complex interactions between plant pathogens and their hosts, laying the groundwork for future research on disease resistance and pathogenesis mechanisms.

Global Analysis of Lysine Lactylation of Germinated Seeds in Wheat

Protein lactylation is a newly discovered posttranslational modification (PTM) and is involved in multiple biological processes, both in mammalian cells and rice grains. However, the function of lysine lactylation remains unexplored in wheat. In this study, we performed the first comparative proteomes and lysine lactylomes during seed germination of wheat. In total, 8000 proteins and 927 lactylated sites in 394 proteins were identified at 0 and 12 h after imbibition (HAI). Functional enrichment analysis showed that glycolysis- and TCA-cycle-related proteins were significantly enriched, and more differentially lactylated proteins were enriched in up-regulated lactylated proteins at 12 HAI vs. 0 HAI through the KEGG pathway and protein domain enrichment analysis compared to down-regulated lactylated proteins. Meanwhile, ten particularly preferred amino acids near lactylation sites were found in the embryos of germinated seeds: AA*KlaT, A***KlaD********A, KlaA**T****K, K******A*Kla, K*Kla********K, KlaA******A, Kla*A, KD****Kla, K********Kla and KlaG. These results supplied a comprehensive profile of lysine lactylation of wheat and indicated that protein lysine lactylation played important functions in several biological processes.

Weighted gene co-expression network analysis of nitrogen (N)-responsive genes and the putative role of G-quadruplexes in N use efficiency (NUE) in rice

Rice is an important target to improve crop nitrogen (N) use efficiency (NUE), and the identification and shortlisting of the candidate genes are still in progress. We analyzed data from 16 published N-responsive transcriptomes/microarrays to identify, eight datasets that contained the maximum number of 3020 common genes, referred to as N-responsive genes. These include different classes of transcription factors, transporters, miRNA targets, kinases and events of post-translational modifications. A Weighted gene co-expression network analysis (WGCNA) with all the 3020 N-responsive genes revealed 15 co-expression modules and their annotated biological roles. Protein-protein interaction network analysis of the main module revealed the hub genes and their functional annotation revealed their involvement in the ubiquitin process. Further, the occurrences of G-quadruplex sequences were examined, which are known to play important roles in epigenetic regulation but are hitherto unknown in N-response/NUE. Out of the 3020 N-responsive genes studied, 2298 contained G-quadruplex sequences. We compared these N-responsive genes containing G-quadruplex sequences with the 3601 genes we previously identified as NUE-related (for being both N-responsive and yield-associated). This analysis revealed 389 (17%) NUE-related genes containing G-quadruplex sequences. These genes may be involved in the epigenetic regulation of NUE, while the rest of the 83% (1811) genes may regulate NUE through genetic mechanisms and/or other epigenetic means besides G-quadruplexes. A few potentially important genes/processes identified as associated with NUE were experimentally validated in a pair of rice genotypes contrasting for NUE. The results from the WGCNA and G4 sequence analysis of N-responsive genes helped identify and shortlist six genes as candidates to improve NUE. Further, the hitherto unavailable segregation of genetic and epigenetic gene targets could aid in informed interventions through genetic and epigenetic means of crop improvement.

Lysine Succinylation of VBS Contributes to Sclerotia Development and Aflatoxin Biosynthesis in Aspergillus flavus

Aspergillus flavus is a common saprophytic and pathogenic fungus, and its secondary metabolic pathways are one of the most highly characterized owing to its aflatoxin (AF) metabolite affecting global economic crops and human health. Different natural environments can cause significant variations in AF synthesis. Succinylation was recently identified as one of the most critical regulatory post-translational modifications affecting metabolic pathways. It is primarily reported in human cells and bacteria with few studies on fungi. Proteomic quantification of lysine succinylation (Ksuc) exploring its potential involvement in secondary metabolism regulation (including AF production) has not been performed under natural conditions in A. flavus. In this study, a quantification method was performed based on tandem mass tag labeling and antibody-based affinity enrichment of succinylated peptides via high accuracy nano-liquid chromatography with tandem mass spectrometry to explore the succinylation mechanism affecting the pathogenicity of naturally isolated A. flavus strains with varying toxin production. Altogether, 1240 Ksuc sites in 768 proteins were identified with 1103 sites in 685 proteins quantified. Comparing succinylated protein levels between high and low AF-producing A. flavus strains, bioinformatics analysis indicated that most succinylated proteins located in the AF biosynthetic pathway were downregulated, which directly affected AF synthesis. Versicolorin B synthase is a key catalytic enzyme for heterochrome B synthesis during AF synthesis. Site-directed mutagenesis and biochemical studies revealed that versicolorin B synthase succinylation is an important regulatory mechanism affecting sclerotia development and AF biosynthesis in A. flavus. In summary, our quantitative study of the lysine succinylome in high/low AF-producing strains revealed the role of Ksuc in regulating AF biosynthesis. We revealed novel insights into the metabolism of AF biosynthesis using naturally isolated A. flavus strains and identified a rich source of metabolism-related enzymes regulated by succinylation.

Proteome-wide analysis of lysine β-hydroxybutyrylation in the myocardium of diabetic rat model with cardiomyopathy

Lysine ß-hydroxybutyrylation (kbhb), a novel modification of lysine residues with the ß-hydroxybuty group, is associated with ketone metabolism in numerous species. However, its potential role in diabetes, especially in diabetic cardiomyopathy (DCM), remains largely unexplored. In this study, using affinity enrichment and liquid chromatography-mass spectrometry (LC-MS/MS) method, we quantitatively analyze the kbhb residues on heart tissues of a DCM model rat. A total of 3,520 kbhb sites in 1,089 proteins were identified in this study. Further analysis showed that 336 kbhb sites in 143 proteins were differentially expressed between the heart tissues of DCM and wild-type rats. Among them, 284 kbhb sites in 96 proteins were upregulated, while 52 kbhb sites in 47 proteins were downregulated. Bioinformatic analysis of the proteomic results revealed that these kbhb-modified proteins were widely distributed in various components and involved in a wide range of cellular functions and biological processes (BPs). Functional analysis showed that the kbhb-modified proteins were involved in the tricarboxylic acid cycle, oxidative phosphorylation, and propanoate metabolism. Our findings demonstrated how kbhb is related to many metabolic pathways and is mainly involved in energy metabolism. These results provide the first global investigation of the kbhb profile in DCM progression and can be an essential resource to explore DCM's pathogenesis further.

TMT-based quantitative proteomic and physiological analyses on lotus plumule of artificially aged seed in long-living sacred lotus Nelumbo nucifera

Seed longevity is important for the maintenance of seed nutritional quality, vigor, and germination potential during storage. Sacred lotus is known as one of the longest living seeds in the world and their ability to maintain longevity has been widely investigated. In this study, a suitable controlled deterioration treatment (CDT) method was first established to evaluate the vigor loss of lotus plumule (LP), and then the Tandem Mass Tags (TMT)-based proteomic analysis was performed on LP from the CDT-treated seed to quantitatively and qualitatively analyze the protein profile dynamic. In total, 4002 proteins were successfully quantified, of them, 558 differently accumulated proteins (DAPs) were identified. Protein processing and RNA-related proteins were found more easily to be affected by CDT, which may directly result in seed vigor loss. Meanwhile, CDT resulted in remarkable up-regulation of numerous proteins related to antioxidation, photosynthesis, RNA and DNA stability, starch and sucrose mobilization, and cell membrane and wall stability, which potentially played key roles in maintaining the lotus seed vigor under CDT. Histological and physiological analyses were also performed to verify some proteome results. This study provided both fundamental data and new insights to further uncover the secret of lotus seed longevity. SIGNIFICANCE: Seed aging affects the seed quality and can result in direct economic losses. The exceptional longevity of sacred lotus seed has attracted extensive attention. In this study, an optimized CDT method was used to mimic the natural aging process of sacred lotus seed, and based on TMT-based quantitative proteomic analysis on the LP profile of CDT-treated seeds, a series of differentially accumulation of specific proteins (DEPs) were revealed related to CDT resistance. Correspondingly, the physiological state and histological structure of the LP along with the CDT were detected to verify the proteome data. This study provided comprehensive information for the molecular basis of lotus seed aging analysis and facilitate to screen seed longevity related proteins for other plant species.

Identification of Lysine Succinylome and Acetylome in the Vancomycin-Intermediate Staphylococcus aureus XN108

Protein posttranslational modifications (PTMs) play important roles in regulating numerous biological functions of prokaryotic and eukaryotic organisms. Lysine succinylation (Ksucc) and acetylation (Kac) are two important PTMs that have been identified in various bacterial species. However, the biological functions of Ksucc and Kac in vancomycin-intermediate S. aureus (VISA) remain unclear. In this study, we systematically identified 3,260 Ksucc sites in 799 proteins and 7,935 Kac sites across 1,710 proteins in the VISA strain XN108. Functional analyses revealed that both Ksucc and Kac sites were highly enriched in several critical metabolic pathways, including ribosomal metabolism, tricarboxylic acid cycle, and glycolysis. Furthermore, a remarkable cross talk between Ksucc and Kac modifications was observed that almost 75% of the succinylated sites were also frequently acetylated. In addition, we identified SaCobB, a Sirtuin 2-like lysine deacetylase, as a bifunctional enzyme with both deacetylation and desuccinylation activities in S. aureus. We demonstrated the first lysine succinylome and acetylome in a VISA and identified SaCobB, a functional enzyme taking part in the regulation of Ksucc and Kac in S. aureus. Our findings provide valuable information for further study on the regulatory mechanisms of PTMs in S. aureus. IMPORTANCE Lysine succinylation (Ksucc) and acetylation (Kac) are two important protein posttranslational modifications (PTMs) that regulate numerous biological functions in prokaryotes and eukaryotes. However, the functions of Ksucc and Kac in Staphylococcus aureus are seldom described. Understanding of Ksucc and Kac modifications in S. aureus will facilitate the development of new strategies to control infections. Herein, we quantified both Ksucc and Kac in a vancomycin-intermediate S. aureus (VISA) strain XN108, analyzed the interaction between these two PTMs, and identified SaCobB as a bifunctional enzyme with both deacetylation and desuccinylation activities. This study is the first description of dual PTMs, Ksucc and Kac profiles, in the VISA. The findings could provide valuable information for the following researches on the regulatory roles of PTMs in S. aureus.

The analysis of lysine succinylation modification reveals the mechanism of oxybenzone damaging of pakchoi (Brassica rapa L. ssp. chinensis)

Oxybenzone (OBZ), one of a broad spectrum of ultraviolet (UV) absorbents, has been proven to be harmful to both plants and animals, while omics analysis of big data at the molecular level is still lacking. Lysine succinylation (Ksuc) is an important posttranslational modification of proteins that plays a crucial role in regulating the metabolic network in organisms under stress. Here, we report the changes in intracellular Ksuc modification in plants under OBZ stress. A total of 1276 succinylated sites on 507 proteins were identified. Among these sites, 181 modified proteins were hypersulfinylated/succinylated in OBZ-stressed pakchoi leaves. Differentially succinylated proteins (DSPs) are distributed mainly in the chloroplast, cytoplasm, and mitochondria and are distributed mainly in primary metabolic pathways, such as reactive oxygen species (ROS) scavenging, stress resistance, energy generation and transfer, photosynthetic carbon fixation, glycolysis, and the tricarboxylic acid (TCA) cycle. Comprehensive analysis shows that Ksuc mainly changes the carbon flow distribution, enhances the activity of the antioxidant system, affects the biosynthesis of amino acids, and increases the modification of histones. The results of this study first showed the profiling of the Kusc map under OBZ treatment and proposed the adaptive mechanism of pakchoi in response to pollutants and other abiotic stresses at the posttranslational level, which revealed the importance of Ksuc in the regulation of various life activities and provides a reference dataset for future research on molecular function.

Oncometabolites drive tumorigenesis by enhancing protein acylation: from chromosomal remodelling to nonhistone modification

Metabolites are intermediate products of cellular metabolism catalysed by various enzymes. Metabolic remodelling, as a biochemical fingerprint of cancer cells, causes abnormal metabolite accumulation. These metabolites mainly generate energy or serve as signal transduction mediators via noncovalent interactions. After the development of highly sensitive mass spectrometry technology, various metabolites were shown to covalently modify proteins via forms of lysine acylation, including lysine acetylation, crotonylation, lactylation, succinylation, propionylation, butyrylation, malonylation, glutarylation, 2-hydroxyisobutyrylation and β-hydroxybutyrylation. These modifications can regulate gene expression and intracellular signalling pathways, highlighting the extensive roles of metabolites. Lysine acetylation is not discussed in detail in this review since it has been broadly investigated. We focus on the nine aforementioned novel lysine acylations beyond acetylation, which can be classified into two categories: histone acylations and nonhistone acylations. We summarize the characteristics and common functions of these acylation types and, most importantly, provide a glimpse into their fine-tuned control of tumorigenesis and potential value in tumour diagnosis, monitoring and therapy.

Quantitative Acetylome Analysis of Soft Wheat Seeds during Artificial Ageing

Lysine acetylation (Kac) is a protein post-translational modification (PTM) widely found in plants that plays vital roles in metabolic pathways. Although seed germination and development are regulated by Kac, its potential function in seed ageing remains to be investigated. Our preliminary study demonstrated that Kac levels were altered during wheat seed artificial ageing. However, its specific role in this process still needs to be elucidated. Here, we performed quantitative acetylation proteomics analysis of soft wheat seeds with different germination rates during artificial ageing. A total of 175 acetylation proteins and 255 acetylation modification sites were remarkably changed. The differentially acetylated proteins were enriched in metabolism; response to harsh intracellular environment, such as ROS; protein storage and processing. Notably, expression, point mutation to mimic Kac by K to Q mutation at K80 and K138, protein purification and enzyme activity detection revealed that the Kac of ROS-scavenging glutathione transferase attenuated its activity, indicating that the defense ability of wheat seeds to stress gradually diminished, and the ageing process was inevitable. Collectively, our data provide a basis for further understanding the roles of Kac in seed ageing and might aid in the development of new techniques to prolong seed viability and food quality.

Protein succinylation associated with the progress of hepatocellular carcinoma

Although post‐translational modification is critical to tumorigenesis, how succinylation modification of lysine sites influences hepatocellular carcinoma (HCC) remains obscure. 90 tumours and paired adjacent normal tissue of liver cancer were enrolled for succinylation staining. 423 HCC samples with 20 genes related to succinylation modification from TCGA were downloaded for model construction. Statistical methods were employed to analyse the data, including the Non‐Negative Matrix Factorization (NMF) algorithm, t‐Distributed Stochastic Neighbour Embedding (t‐SNE) algorithm, and Cox regression analysis. The staining pan‐succinyllysine antibody staining indicated that tumour tissues had a higher succinyllysine level than adjacent tissues (p < 0.001), which could be associated with a worse prognosis (p = 0.02). The survival was associated with pathological stage, tumour recurrence status and succinyllysine intensity in the univariate or multivariable cox survival analysis model. The risk model from 20 succinyllysine‐related genes had the best prognosis prediction. The high expression of succinylation modification in HCC contributed to the worse patient survival prognosis. Model construction of 20 genes related to succinylation modification (MEAF6, OXCT1, SIRT2, CREBBP, KAT5, SIRT4, SIRT6, SIRT7, CPT1A, GLYATL1, SDHA, SDHB, SDHC, SDHD, SIRT1, SIRT3, SIRT5, SUCLA2, SUCLG1 and SUCLG2) could be reliable in predicting prognosis in HCC.

Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

BACKGROUND

Bermudagrass (Cynodon dactylon L.) is an important warm-season turfgrass species with well-developed stolons, which lay the foundation for the fast propagation of bermudagrass plants through asexual clonal growth. However, the growth and development of bermudagrass stolons are still poorly understood at the molecular level.

RESULTS

In this study, we comprehensively analyzed the acetylation and succinylation modifications of proteins in fast-growing stolons of the bermudagrass cultivar Yangjiang. A total of 4657 lysine acetylation sites on 1914 proteins and 226 lysine succinylation sites on 128 proteins were successfully identified using liquid chromatography coupled to tandem mass spectrometry, respectively. Furthermore, 78 proteins and 81 lysine sites were found to be both acetylated and succinylated. Functional enrichment analysis revealed that acetylated proteins regulate diverse reactions of carbohydrate metabolism and protein turnover, whereas succinylated proteins mainly regulate the citrate cycle. These results partly explained the different growth disturbances of bermudagrass stolons under treatment with sodium butyrate and sodium malonate, which interfere with protein acetylation and succinylation, respectively. Moreover, 140 acetylated proteins and 42 succinylated proteins were further characterized having similarly modified orthologs in other grass species. Site-specific mutations combined with enzymatic activity assays indicated that the conserved acetylation of catalase and succinylation of malate dehydrogenase both inhibited their activities, further implying important regulatory roles of the two modifications.

CONCLUSION

In summary, our study implied that lysine acetylation and succinylation of proteins possibly play important regulatory roles in the fast growth of bermudagrass stolons. The results not only provide new insights into clonal growth of bermudagrass but also offer a rich resource for functional analyses of protein lysine acetylation and succinylation in plants.

Crotonylation versus acetylation in petunia corollas with reduced acetyl-CoA due to PaACL silencing

Protein acetylation and crotonylation are important posttranslational modifications of lysine. In animal cells, the correlation of acetylation and crotonylation has been well characterized and the lysines of some proteins are acetylated or crotonylated depending on the relative concentrations of acetyl-CoA and crotonyl-CoA. However, in plants, the correlation of acetylation and crotonylation and the effects of the relative intracellular concentrations of crotonyl-CoA and acetyl-CoA on protein crotonylation and acetylation are not well known. In our previous study, PaACL silencing changed the content of acetyl-CoA in petunia (Petunia hybrida) corollas, and the effect of PaACL silencing on the global acetylation proteome in petunia was analyzed. In the present study, we found that PaACL silencing did not significantly alter the content of crotonyl-CoA. We performed a global crotonylation proteome analysis of the corollas of PaACL-silenced and control petunia plants; we found that protein crotonylation was closely related to protein acetylation and that proteins with more crotonylation sites often had more acetylation sites. Crotonylated proteins and acetylated proteins were enriched in many common Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. However, PaACL silencing resulted in different KEGG pathway enrichments of proteins with different levels of crotonylation sites and acetylation sites. PaACLB1-B2 silencing did not led to changes in the opposite direction in crotonylation and acetylation levels at the same lysine site in cytoplasmic proteins, which indicated that cytoplasmic lysine acetylation and crotonylation might not depend on the relative concentrations of acetyl-CoA and crotonyl-CoA. Moreover, the global crotonylome and acetylome were weakly positively correlated in the corollas of PaACL-silenced and control plants.

ROS-stimulated Protein Lysine Acetylation Is Required for Crown Root Development in Rice

INTRODUCTION

As signal molecules in aerobic organisms, locally accumulated ROS have been reported to balance cell division and differentiation in the root meristem. Protein posttranslational modifications such as lysine acetylation play critical roles in controlling a variety of cellular processes. However, the mechanism by which ROS regulate root development is unknown. In addition, how protein lysine acetylation is regulated and whether cellular ROS levels affect protein lysine acetylation remain unclear.

OBJECTIVES

We aimed to elucidate the relationship between ROS and protein acetylation by exploring a rice mutant plant that displays a decreased level of ROS in postembryonic crown root (CR) cells and severe defects in CR development.

METHODS

First, proteomic analysis was used to find candidate proteins responsible for the decrease of ROS detected in the wox11 mutant. Then, biochemical, molecular, and genetic analyses were used to study WOX11-regulated genes involved in ROS homeostasis. Finally, acetylproteomic analysis of wild type and wox11 roots treated with or without potassium iodide (KI) and peroxide (H₂O₂) were used to study the effects of ROS on protein acetylation in rice CR cells.

RESULTS

We demonstrated that WOX11 was required to maintain ROS homeostasis by upregulating peroxidase genes in the crown root meristem. Acetylproteomic analysis revealed that WOX11-dependent peroxide (H₂O₂) levels in CR cells promoted lysine acetylation of many non-histone proteins enriched for nitrogen metabolism and peptide/protein synthesis pathways. Further analysis revealed that the redox state affected histone deacetylases (HDACs) activity, which was likely related to the high levels of protein lysine acetylation in CR cells.

CONCLUSION

WOX11-controlled ROS level in CR meristem cells is required for protein lysine acetylation which represents a mechanism of ROS-promoted CR development in rice.

Dynamics and Functional Interplay of Nonhistone Lysine Crotonylome and Ubiquitylome in Vascular Smooth Muscle Cell Phenotypic Remodeling

Background

The crotonylation of histones is discovered of late as one of the post-translational modifications (PTMs) that can regulate gene expression. However, the function of crotonylation on nonhistone proteins in vascular smooth muscle cells (VSMCs) is unclear. Here, we aim to find the cellular characteristics of crotonylated nonhistone proteins and the cross talk with ubiquitinated proteins in VSMC phenotypic remodeling using the modified omics and proteomic analysis.

Methods

We performed the modified omics and proteomic analysis of VSMCs before and after the stimulation with platelet-derived growth factor-BB (PDGF-BB). The crotonylated and ubiquitinated pan-antibody was used to enrich proteins and then subjected to a high-throughput mass spectrometry analysis. The enrichment analysis was performed within differentially modified proteins in regard to GO terms, KEGG, and protein domains.

Results

As a result, there were 2,138 crotonylation sites in 534 proteins and 1,359 ubiquitination sites corresponding to 657 proteins. These crotonylated proteins detected after PDGF-BB stimulation might be involved in various vital cellular pathways and carry out important functions in VSMCs. Some of them closely took part in significant physiological processes of VSMC phenotypic remodeling, including glycolysis/gluconeogenesis, vascular smooth muscle contraction, and the PI3K-Akt signaling pathway. Furthermore, the KEGG pathway enrichment analysis showed the involvement of ubiquitinated proteins in the physiological processes of VSMC phenotypic remodeling, including glycolysis/gluconeogenesis, vascular smooth muscle contraction, RAS signaling pathway, or the PI3K-Akt signaling pathway. A cross talk analysis showed that there were 199 sites within the 177 proteins modified by crotonylation and ubiquitination simultaneously. Protein–protein interaction (PPI) network analysis indicated that crotonylated and ubiquitinated proteins play an important role in cellular bioprocess commonly and possibly have a synergistic effect.

Conclusion

In summary, our bioinformatics analysis shows that the crotonylation and ubiquitination of nonhistone proteins play an essential role in VSMC phenotypic transformation induced by PDGF-BB stimulation. The cross talk between crotonylation and ubiquitination in glycolysis is possibly a novel mechanism during VSMC phenotypic remodeling.

Qualitative Proteome-Wide Analysis Reveals the Diverse Functions of Lysine Crotonylation in Dendrobium huoshanense

The lysine crotonylation of histone proteins is a newly identified posttranslational modification with diversified cellular functions. However, there are few reports on lysine crotonylation of non-histone proteins in medicinal plant cells. By using high-resolution liquid chromatography-mass spectrometry (LC-MS) coupled with highly sensitive-specific immune-affinity antibody analysis, a whole crotonylation proteome analysis of Dendrobium huoshanense was performed. In total, 1,591 proteins with 4,726 lysine crotonylation sites were identified; among them, 11 conserved motifs were identified. Bioinformatic analyses linked crotonylated proteins to the drought stress response and multiple metabolic pathways, including secondary metabolite biosynthesis, transport and catabolism, energy production and conversion, carbohydrate transport and metabolism, translation, and ribosomal structure and biogenesis. This study contributes toward understanding the regulatory mechanism of polysaccharide biosynthesis at the crotonylation level even under abiotic stress.

Comprehensive Profiling of Paper Mulberry (Broussonetia papyrifera) Crotonylome Reveals the Significance of Lysine Crotonylation in Young Leaves

Lysine crotonylation is a newly discovered and reversible posttranslational modification involved in various biological processes, especially metabolism regulation. A total of 5159 lysine crotonylation sites in 2272 protein groups were identified. Twenty-seven motifs were found to be the preferred amino acid sequences for crotonylation sites. Functional annotation analyses revealed that most crotonylated proteins play important roles in metabolic processes and photosynthesis. Bioinformatics analysis suggested that lysine crotonylation preferentially targets a variety of important biological processes, including ribosome, glyoxylate and dicarboxylate metabolism, carbon fixation in photosynthetic organisms, proteasome and the TCA cycle, indicating lysine crotonylation is involved in the common mechanism of metabolic regulation. A protein interaction network analysis revealed that diverse interactions are modulated by protein crotonylation. These results suggest that lysine crotonylation is involved in a variety of biological processes. HSP70 is a crucial protein involved in protecting plant cells and tissues from thermal or abiotic stress responses, and HSP70 protein was found to be crotonylated in paper mulberry. This systematic analysis provides the first comprehensive analysis of lysine crotonylation in paper mulberry and provides important resources for further study on the regulatory mechanism and function of the lysine crotonylated proteome.

First analyses of lysine succinylation proteome and overlap between succinylation and acetylation in Solenopsis invicta Buren (Hymenoptera: Formicidae)

BACKGROUND

Lysine succinylation (Ksu) exists in both eukaryotes and prokaryotes, and influences a variety of metabolism processes. However, little attention has been paid to Ksu in insects, especially the notorious invasive pest Solenopsis invicta.

RESULTS

In this study, the first analyses of Ksu proteome and overlap between Ksu and lysine acetylation (Kac) in S. invicta were presented. 3753 succinylated sites in 893 succinylated proteins were tested. The dihydrolipoyl dehydrogenase, V-type proton ATPase subunit G, and tubulin alpha chain all had evolutionary conservatism among diverse ant or bee species. Immunoblotting validation showed that there were many Ksu protein bands with a wide range of molecular mass. In addition, 1230 sites in 439 proteins were highly overlapped between Ksu and Kac. 54.05% of Ksu proteins in cytoplasm were acetylated. The results demonstrated that Ksu may play a vital part in the allergization, redox metabolism, sugar, fat, and protein metabolism, energy production, immune response, and biosynthesis of various secondary metabolites.

CONCLUSIONS

Ksu and Kac were two ubiquitous protein post-translational modifications participated in a variety of biological processes. Our results may supply rich resources and a starting point for the molecular basic research of regulation on metabolic pathways and other biological processes by succinylation and acetylation.

Advances in proteome-wide analysis of plant lysine acetylation

Lysine acetylation (LysAc) is a conserved and important post-translational modification (PTM) that plays a key role in plant physiological and metabolic processes. Based on advances in Lys-acetylated protein immunoenrichment and mass-spectrometric technology, LysAc proteomics studies have been performed in many species. Such studies have made substantial contributions to our understanding of plant LysAc, revealing that Lys-acetylated histones and nonhistones are involved in a broad spectrum of plant cellular processes. Here, we present an extensive overview of recent research on plant Lys-acetylproteomes. We provide in-depth insights into the characteristics of plant LysAc modifications and the mechanisms by which LysAc participates in cellular processes and regulates metabolism and physiology during plant growth and development. First, we summarize the characteristics of LysAc, including the properties of Lys-acetylated sites, the motifs that flank Lys-acetylated lysines, and the dynamic alterations in LysAc among different tissues and developmental stages. We also outline a map of Lys-acetylated proteins in the Calvin-Benson cycle and central carbon metabolism-related pathways. We then introduce some examples of the regulation of plant growth, development, and biotic and abiotic stress responses by LysAc. We discuss the interaction between LysAc and Nα-terminal acetylation and the crosstalk between LysAc and other PTMs, including phosphorylation and succinylation. Finally, we propose recommendations for future studies in the field. We conclude that LysAc of proteins plays an important role in the regulation of the plant life cycle.

Acetylation of conserved lysines fine-tunes mitochondrial malate dehydrogenase activity in land plants

Plants need to rapidly and flexibly adjust their metabolism to changes of their immediate environment. Since this necessity results from the sessile lifestyle of land plants, key mechanisms for orchestrating central metabolic acclimation are likely to have evolved early. Here, we explore the role of lysine acetylation as a post-translational modification to directly modulate metabolic function. We generated a lysine acetylome of the moss Physcomitrium patens and identified 638 lysine acetylation sites, mostly found in mitochondrial and plastidial proteins. A comparison with available angiosperm data pinpointed lysine acetylation as a conserved regulatory strategy in land plants. Focusing on mitochondrial central metabolism, we functionally analyzed acetylation of mitochondrial malate dehydrogenase (mMDH), which acts as a hub of plant metabolic flexibility. In P. patens mMDH1, we detected a single acetylated lysine located next to one of the four acetylation sites detected in Arabidopsis thaliana mMDH1. We assessed the kinetic behavior of recombinant A. thaliana and P. patens mMDH1 with site-specifically incorporated acetyl-lysines. Acetylation of A. thaliana mMDH1 at K169, K170, and K334 decreases its oxaloacetate reduction activity, while acetylation of P. patens mMDH1 at K172 increases this activity. We found modulation of the malate oxidation activity only in A. thaliana mMDH1, where acetylation of K334 strongly activated it. Comparative homology modeling of MDH proteins revealed that evolutionarily conserved lysines serve as hotspots of acetylation. Our combined analyses indicate lysine acetylation as a common strategy to fine-tune the activity of central metabolic enzymes with likely impact on plant acclimation capacity.

Plant proteomic research for improvement of food crops under stresses: a review

Crop improvement approaches have been changed due to technological advancements in traditional plant-breeding methods. Abiotic and biotic stresses limit plant growth and development, which ultimately lead to reduced crop yield. Proteins encoded by genomes have a considerable role in the endurance and adaptation of plants to different environmental conditions. Biotechnological applications in plant breeding depend upon the information generated from proteomic studies. Proteomics has a specific advantage to contemplate post-translational modifications, which indicate the functional effects of protein modifications on crop production. Subcellular proteomics helps in exploring the precise cellular responses and investigating the networking among subcellular compartments during plant development and biotic/abiotic stress responses. Large-scale mass spectrometry-based plant proteomic studies with a more comprehensive overview are now possible due to dramatic improvements in mass spectrometry, sample preparation procedures, analytical software, and strengthened availability of genomes for numerous plant species. Development of stress-tolerant or resilient crops is essential to improve crop productivity and growth. Use of high throughput techniques with advanced instrumentation giving efficient results made this possible. In this review, the role of proteomic studies in identifying the stress-response processes in different crops is summarized. Advanced techniques and their possible utilization on plants are discussed in detail. Proteomic studies accelerate marker-assisted genetic augmentation studies on crops for developing high yielding stress-tolerant lines or varieties under stresses.

The rice RNase P protein subunit Rpp30 confers broad-spectrum resistance to fungal and bacterial pathogens

RNase P functions either as a catalytic ribonucleoprotein (RNP) or as an RNA-free polypeptide to catalyse RNA processing, primarily tRNA 5' maturation. To the growing evidence of non-canonical roles for RNase P RNP subunits including regulation of chromatin structure and function, we add here a role for the rice RNase P Rpp30 in innate immunity. This protein (encoded by LOC_Os11g01074) was uncovered as the top hit in yeast two-hybrid assays performed with the rice histone deacetylase HDT701 as bait. We showed that HDT701 and OsRpp30 are localized to the rice nucleus, OsRpp30 expression increased post-infection by Pyricularia oryzae (syn. Magnaporthe oryzae), and OsRpp30 deacetylation coincided with HDT701 overexpression in vivo. Overexpression of OsRpp30 in transgenic rice increased expression of defence genes and generation of reactive oxygen species after pathogen-associated molecular pattern elicitor treatment, outcomes that culminated in resistance to a fungal (P. oryzae) and a bacterial (Xanthomonas oryzae pv. oryzae) pathogen. Knockout of OsRpp30 yielded the opposite phenotypes. Moreover, HA-tagged OsRpp30 co-purified with RNase P pre-tRNA cleavage activity. Interestingly, OsRpp30 is conserved in grass crops, including a near-identical C-terminal tail that is essential for HDT701 binding and defence regulation. Overall, our results suggest that OsRpp30 plays an important role in rice immune response to pathogens and provides a new approach to generate broad-spectrum disease-resistant rice cultivars.

Global analysis of lysine acetylation in soybean leaves

Protein lysine acetylation (Kac) is an important post-translational modification in both animal and plant cells. Global Kac identification has been performed at the proteomic level in various species. However, the study of Kac in oil and resource plant species is relatively limited. Soybean is a globally important oil crop and resouce plant. In the present study, lysine acetylome analysis was performed in soybean leaves with proteomics techniques. Various bioinformatics analyses were performed to illustrate the structure and function of these Kac sites and proteins. Totally, 3148 acetylation sites in 1538 proteins were detected. Motif analysis of these Kac modified peptides extracted 17 conserved motifs. These Kac modified protein showed a wide subcellular location and functional distribution. Chloroplast is the primary subcellular location and cellular component where Kac proteins were localized. Function and pathways analyses indicated a plenty of biological processes and metabolism pathways potentially be influenced by Kac modification. Ribosome activity and protein biosynthesis, carbohydrate and energy metabolism, photosynthesis and fatty acid metabolism may be regulated by Kac modification in soybean leaves. Our study suggests Kac plays an important role in soybean physiology and biology, which is an available resource and reference of Kac function and structure characterization in oil crop and resource plant, as well as in plant kingdom.

Histone deacetylases control lysine acetylation of ribosomal proteins in rice

Lysine acetylation (Kac) is well known to occur in histones for chromatin function and epigenetic regulation. In addition to histones, Kac is also detected in a large number of proteins with diverse biological functions. However, Kac function and regulatory mechanism for most proteins are unclear. In this work, we studied mutation effects of rice genes encoding cytoplasm-localized histone deacetylases (HDAC) on protein acetylome and found that the HDAC protein HDA714 was a major deacetylase of the rice non-histone proteins including many ribosomal proteins (r-proteins) and translation factors that were extensively acetylated. HDA714 loss-of-function mutations increased Kac levels but reduced abundance of r-proteins. In vitro and in vivo experiments showed that HDA714 interacted with r-proteins and reduced their Kac. Substitutions of lysine by arginine (depleting Kac) in several r-proteins enhance, while mutations of lysine to glutamine (mimicking Kac) decrease their stability in transient expression system. Ribo-seq analysis revealed that the hda714 mutations resulted in increased ribosome stalling frequency. Collectively, the results uncover Kac as a functional posttranslational modification of r-proteins which is controlled by histone deacetylases, extending the role of Kac in gene expression to protein translational regulation.

Comprehensive Proteomic Analysis of Lysine Acetylation in Nicotiana benthamiana After Sensing CWMV Infection

Protein lysine acetylation (Kac) is an important post-translational modification mechanism in eukaryotes that is involved in cellular regulation. To investigate the role of Kac in virus-infected plants, we characterized the lysine acetylome of Nicotiana benthamiana plants with or without a Chinese wheat mosaic virus (CWMV) infection. We identified 4,803 acetylated lysine sites on 1,964 proteins. A comparison of the acetylation levels of the CWMV-infected group with those of the uninfected group revealed that 747 sites were upregulated on 422 proteins, including chloroplast localization proteins and histone H3, and 150 sites were downregulated on 102 proteins. Nineteen conserved motifs were extracted and 51 percent of the acetylated proteins located on chloroplast. Nineteen Kac sites were located on histone proteins, including 10 Kac sites on histone 3. Bioinformatics analysis results indicated that lysine acetylation occurs on a large number of proteins involved in biological processes, especially photosynthesis. Furthermore, we found that the acetylation level of chloroplast proteins, histone 3 and some metabolic pathway-related proteins were significantly higher in CWMV-infected plants than in uninfected plants. In summary, our results reveal the regulatory roles of Kac in response to CWMV infection.

Proteomics and Post-Translational Modifications of Starch Biosynthesis-Related Proteins in Developing Seeds of Rice

Rice (Oryza sativa L.) is a foremost staple food for approximately half the world's population. The components of rice starch, amylose, and amylopectin are synthesized by a series of enzymes, which are responsible for rice starch properties and functionality, and then affect rice cooking and eating quality. Recently, proteomics technology has been applied to the establishment of the differentially expressed starch biosynthesis-related proteins and the identification of posttranslational modifications (PTMs) target starch biosynthesis proteins as well. It is necessary to summarize the recent studies in proteomics and PTMs in rice endosperm to deepen our understanding of starch biosynthesis protein expression and regulation, which will provide useful information to rice breeding programs and industrial starch applications. The review provides a comprehensive summary of proteins and PTMs involved in starch biosynthesis based on proteomic studies of rice developing seeds. Starch biosynthesis proteins in rice seeds were differentially expressed in the developing seeds at different developmental stages. All the proteins involving in starch biosynthesis were identified using proteomics methods. Most starch biosynthesis-related proteins are basically increased at 6-20 days after flowering (DAF) and decreased upon the high-temperature conditions. A total of 10, 14, 2, 17, and 7 starch biosynthesis related proteins were identified to be targeted by phosphorylation, lysine acetylation, succinylation, lysine 2-hydroxyisobutyrylation, and malonylation, respectively. The phosphoglucomutase is commonly targeted by five PTMs types. Research on the function of phosphorylation in multiple enzyme complex formation in endosperm starch biosynthesis is underway, while the functions of other PTMs in starch biosynthesis are necessary to be conducted in the near future.

First Succinylome Profiling of Vibrio alginolyticus Reveals Key Role of Lysine Succinylation in Cellular Metabolism and Virulence

Recent studies have shown that a key strategy of many pathogens is to use post-translational modification (PTMs) to modulate host factors critical for infection. Lysine succinylation (Ksuc) is a major PTM widespread in prokaryotic and eukaryotic cells, and is associated with the regulation of numerous important cellular processes. Vibrio alginolyticus is a common pathogen that causes serious disease problems in aquaculture. Here we used the affinity enrichment method with LC-MS/MS to report the first identification of 2082 lysine succinylation sites on 671 proteins in V. alginolyticus, and compared this with the lysine acetylation of V. alginolyticus in our previous work. The Ksuc modification of SodB and PEPCK proteins were further validated by Co-immunoprecipitation combined with Western blotting. Bioinformatics analysis showed that the identified lysine succinylated proteins are involved in various biological processes and central metabolism pathways. Moreover, a total of 1,005 (25.4%) succinyl sites on 502 (37.3%) proteins were also found to be acetylated, which indicated that an extensive crosstalk between acetylation and succinylation in V. alginolyticus occurs, especially in three central metabolic pathways: glycolysis/gluconeogenesis, TCA cycle, and pyruvate metabolism. Furthermore, we found at least 50 (7.45%) succinylated virulence factors, including LuxS, Tdh, SodB, PEPCK, ClpP, and the Sec system to play an important role in bacterial virulence. Taken together, this systematic analysis provides a basis for further study on the pathophysiological role of lysine succinylation in V. alginolyticus and provides targets for the development of attenuated vaccines.

Advances on Post-translational Modifications Involved in Seed Germination

Seed germination and subsequent seedling establishment are important developmental processes that undergo extremely complex changes of physiological status and are precisely regulated at transcriptional and translational levels. Phytohormones including abscisic acid (ABA) and gibberellin (GA) are the critical signaling molecules that modulate the alteration from relative quiescent to a highly active state in seeds. Transcription factors such as ABA insensitive5 (ABI5) and DELLA domain-containing proteins play the central roles in response to ABA and GA, respectively, which antagonize each other during seed germination. Recent investigations have demonstrated that the regulations at translational and post-translational levels, especially post-translational modifications (PTMs), play a decisive role in seed germination. Specifically, phosphorylation and ubiquitination were shown to be involved in regulating the function of ABI5. In this review, we summarized the latest advancement on the function of PTMs involved in the regulation of seed germination, in which the PTMs for ABI5- and DELLA-containing proteins play the key roles. Meanwhile, the studies on PTM-based proteomics during seed germination and the crosstalk of different PTMs are also discussed. Hopefully, it will facilitate in obtaining a comprehensive understanding of the physiological functions of different PTMs in seed germination.

Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives

For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.

Ubiquitinome Profiling Reveals the Landscape of Ubiquitination Regulation in Rice Young Panicles

Ubiquitination, an essential post-transcriptional modification (PTM), plays a vital role in nearly every biological process, including development and growth. Despite its functions in plant reproductive development, its targets in rice panicles remain unclear. In this study, we used proteome-wide profiling of lysine ubiquitination in rice (O. sativa ssp. indica) young panicles. We created the largest ubiquitinome dataset in rice to date, identifying 1638 lysine ubiquitination sites on 916 unique proteins. We detected three conserved ubiquitination motifs, noting that acidic glutamic acid (E) and aspartic acid (D) were most frequently present around ubiquitinated lysine. Enrichment analysis of Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of these ubiquitinated proteins revealed that ubiquitination plays an important role in fundamental cellular processes in rice young panicles. Interestingly, enrichment analysis of protein domains indicated that ubiquitination was enriched on a variety of receptor-like kinases and cytoplasmic tyrosine and serine-threonine kinases. Furthermore, we analyzed the crosstalk between ubiquitination, acetylation, and succinylation, and constructed a potential protein interaction network within our rice ubiquitinome. Moreover, we identified ubiquitinated proteins related to pollen and grain development, indicating that ubiquitination may play a critical role in the physiological functions in young panicles. Taken together, we reported the most comprehensive lysine ubiquitinome in rice so far, and used it to reveal the functional role of lysine ubiquitination in rice young panicles.

Advances on Plant Ubiquitylome-From Mechanism to Application

Post-translational modifications (PTMs) of proteins enable modulation of their structure, function, localization and turnover. To date, over 660 PTMs have been reported, among which, reversible PTMs are regarded as the key players in cellular signaling. Signaling mediated by PTMs is faster than re-initiation of gene expression, which may result in a faster response that is particularly crucial for plants due to their sessile nature. Ubiquitylation has been widely reported to be involved in many aspects of plant growth and development and it is largely determined by its target protein. It is therefore of high interest to explore new ubiquitylated proteins/sites to obtain new insights into its mechanism and functions. In the last decades, extensive protein profiling of ubiquitylation has been achieved in different plants due to the advancement in ubiquitylated proteins (or peptides) affinity and mass spectrometry techniques. This obtained information on a large number of ubiquitylated proteins/sites helps crack the mechanism of ubiquitylation in plants. In this review, we have summarized the latest advances in protein ubiquitylation to gain comprehensive and updated knowledge in this field. Besides, the current and future challenges and barriers are also reviewed and discussed.

Proteome and lysine acetylome analysis reveals insights into the molecular mechanism of seed germination in wheat

Seed germination is the first stage in wheat growth and development, directly affecting grain yield and quality. As an important post-translation modification, lysine acetylation participates in diverse biological functions. However, little is known regarding the quantitative acetylproteome characterization during wheat seed germination. In this study, we generated the first comparative proteomes and lysine acetylomes during wheat seed germination. In total, 5,639 proteins and 1,301 acetylated sites on 722 proteins were identified at 0, 12 and 24 h after imbibitions. Several particularly preferred amino acids were found near acetylation sites, including K^acS, K^acT, K^acK, K^acR, K^acH, K^acF, K^acN, K^ac*E, FK^ac and K^ac*D, in the embryos during seed germination. Among them, K^acH, K^acF, FK^ac and K^acK were conserved in wheat. Biosynthetic process, transcriptional regulation, ribosome and proteasome pathway related proteins were significantly enriched in both differentially expressed proteins and differentially acetylated proteins through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. We also revealed that histone acetylation was differentially involved in epigenetic regulation during seed germination. Meanwhile, abscisic acid and stress related proteins were found with acetylation changes. In addition, we focused on 8 enzymes involved in carbohydrate metabolism, and found they were differentially acetylated during seed germination. Finally, a putative metabolic pathway was proposed to dissect the roles of protein acetylation during wheat seed germination. These results not only demonstrate that lysine acetylation may play key roles in seed germination of wheat but also reveal insights into the molecular mechanism of seed germination in this crop.

A new opening for the tricky untargeted investigation of natural and modified short peptides

Short peptides are of extreme interest in clinical and food research fields, nevertheless they still represent a crucial analytical issue. The main aim of this paper was the development of an analytical platform for a considerable advancement in short peptides identification. For the first time, short sequences presenting both natural and post-translationally modified amino acids were comprehensively studied thanks to the generation of specific databases. Short peptide databases had a dual purpose. First, they were employed as inclusion lists for a suspect screening mass-spectrometric analysis, overcoming the limits of data dependent acquisition mode and allowing the fragmentation of such low-abundance substances. Moreover, the databases were implemented in Compound Discoverer 3.0, a software dedicated to the analysis of short molecules, for the creation of a data processing workflow specifically dedicated to short peptide tentative identification. For this purpose, a detailed study of short peptide fragmentation pathways was carried out for the first time. The proposed method was applied to the study of short peptide sequences in enriched urine samples and led to the tentative identification more than 200 short natural and modified short peptides, the highest number ever reported.

Proteome-Wide Analyses Reveal the Diverse Functions of Lysine 2-Hydroxyisobutyrylation in Oryza sativa

BACKGROUND

Lysine 2-hydroxyisobutyrylation (Khib), a newly identified post-translational modification, is known to regulate transcriptional activity in animals. However, extensive studies of the lysine 2-hydroxyisobutyrylome in plants and animals have yet to be performed.

RESULTS

In this study, using LC-MS/MS qualitative proteomics strategies, we identified 4163 Khib sites on 1596 modified proteins in rice (Oryza sativa) seedlings. Motif analysis revealed 10 conserved motifs flanking the Khib sites, and subcellular localization analysis revealed that 44% of the Khib proteins are localized in the chloroplast. Gene ontology function, KEGG pathway, and protein domain enrichment analyses revealed that Khib occurs on proteins involved in diverse biological processes and is especially enriched in carbon metabolism and photosynthesis. Among the modified proteins, 20 Khib sites were identified in histone H2A and H2B, while only one site was identified in histone H4. Protein-protein interaction (PPI) network analysis further demonstrated that Khib participates in diverse biological processes including ribosomal activity, biosynthesis of secondary metabolites, and metabolic pathways. In addition, a comparison of lysine 2-hydroxyisobutyrylation, acetylation, and crotonylation in the rice proteome showed that 45 proteins with only 26 common lysine sites are commonly modified by three PTMs. The crosstalk of modified sites and PPI among these PTMs may form a complex network with both similar and different regulatory mechanisms.

CONCLUSIONS

In summary, our study comprehensively profiles the lysine 2-hydroxyisobutyrylome in rice and provides a better understanding of its biological functions in plants.

Systematic identification and comparative analysis of lysine succinylation between the green and white parts of chimeric leaves of Ananas comosus var. bracteatus

Background

Lysine succinylation, an important protein posttranslational modification (PTM), is widespread and conservative. The regulatory functions of succinylation in leaf color has been reported. The chimeric leaves of Ananas comosus var. bracteatus are composed of normal green parts and albino white parts. However, the extent and function of lysine succinylation in chimeric leaves of Ananas comosus var. bracteatus has yet to be investigated.

Results

Compared to the green (Gr) parts, the global succinylation level was increased in the white (Wh) parts of chimeric leaves according to the Western blot and immunohistochemistry analysis. Furthermore, we quantitated the change in the succinylation profiles between the Wh and Gr parts of chimeric leaves using label-free LFQ intensity. In total, 855 succinylated sites in 335 proteins were identified, and 593 succinylated sites in 237 proteins were quantified. Compared to the Gr parts, 232 (61.1%) sites in 128 proteins were quantified as upregulated targets, and 148 (38.9%) sites in 70 proteins were quantified as downregulated targets in the Wh parts of chimeric leaves using a 1.5-fold threshold (P < 0.05). These proteins with altered succinylation level were mainly involved in crassulacean acid metabolism (CAM) photosynthesis, photorespiration, glycolysis, the citric acid cycle (CAC) and pyruvate metabolism.

Conclusions

Our results suggested that the changed succinylation level in proteins might function in the main energy metabolism pathways—photosynthesis and respiration. Succinylation might provide a significant effect in the growth of chimeric leaves and the relationship between the Wh and Gr parts of chimeric leaves. This study not only provided a basis for further characterization on the function of succinylated proteins in chimeric leaves of Ananas comosus var. bracteatus but also provided a new insight into molecular breeding for leaf color chimera.

Comparative acetylome analysis of wild-type and fuzzless-lintless mutant ovules of upland cotton (Gossypium hirsutum Cv. Xu142) unveils differential protein acetylation may regulate fiber development

Protein acetylation (KAC) is a significant post-translational modification, which plays an essential role in the regulation of growth and development. Unfortunately, related studies are inadequately available in angiosperms, and to date, there is no report providing insight on the role of protein acetylation in cotton fiber development. Therefore, we first compared the lysine-acetylation proteome (acetylome) of upland cotton ovules in the early fiber development stages by using wild-type as well as its fuzzless-lintless mutant to identify the role of KAC in the fiber development. A total of 1696 proteins with 2754 acetylation sites identified with the different levels of acetylation belonging to separate subcellular compartments suggesting a large number of proteins differentially acetylated in two cotton cultivars. About 80% of the sites were predicted to localize in the cytoplasm, chloroplast, and mitochondria. Seventeen significantly enriched acetylation motifs were identified. Serine and threonine and cysteine located downstream and upstream to KAC sites. KEGG pathway enrichment analysis indicated oxidative phosphorylation, fatty acid, ribosome and protein, and folate biosynthesis pathways enriched significantly. To our knowledge, this is the first report of comparative acetylome analysis to compare the wild-type as well as its fuzzless-lintless mutant acetylome data to identify the differentially acetylated proteins, which may play a significant role in cotton fiber development.

Quantitative ubiquitylomics approach for characterizing the dynamic change and extensive modulation of ubiquitylation in rice seed germination

During seed germination, cells embark on extensive post-transcriptional and post-translational modifications (PTM), providing a perfect platform to study these events in embryo rebooting from relative quiescenct to highly active state. PR-619, a deubiquitylase inhibitor, delayed the rice seed germination and resulted in the accumulation of ubiquitylated proteins, which indicated the protein ubiquitylation is involved in this process. Using the K-Ɛ-GG antibody enrichment method integrated with high-resolution mass spectrometry, a list of 2576 lysine ubiquitylated (Kub) sites in 1171 proteins was compiled for rice embryos at 0, 12 and 24 h after imbibition (HAI). Of these, the abundance of 1419 Kub sites in 777 proteins changed significantly. Most of them substantially increased within the first 12 HAI, which is similar to the dynamic state previously observed for protein phosphorylation, implying that the first 12 HAI are essential for subsequent switch during rice seed germination. We also quantitatively analyzed the embryo proteome in these samples. Generally, a specific protein's abundance in the ubiquitylome was uncorrelated to that in the proteome. The differentially ubiquitinated proteins were greatly enriched in the categories of protein processing, DNA and RNA processing/regulation related, signaling, and transport. The DiGly footprint of the Kub sites was significantly reduced on K48, a linkage typically associated with proteasome-mediated degradation. These observations suggest ubiquitylation may modulate the protein function more than providing 26S degradation signals in the early stage of rice seed germination. Revealing this comprehensive ubiquitylome greatly increases our understanding of this critical PTM during seed germination.

High-Resolution Lysine Acetylome Profiling by Offline Fractionation and Immunoprecipitation

Acetylation of lysine side chains at their ε-amino group is a reversible posttranslational modification (PTM), which can affect diverse protein functions. Lysine acetylation was first described on histones, and nowadays gains more and more attention due to its more general occurrence in proteomes, and its possible crosstalk with other protein modifications. Here we describe a workflow to investigate the acetylation of lysine-containing peptides on a large scale. For this high-resolution lysine acetylome analysis, dimethyl-labeled peptide samples are pooled and offline-fractionated using hydrophilic interaction liquid chromatography (HILIC). The offline fractionation is followed by an immunoprecipitation and liquid chromatography-tandem mass spectrometry (LC-MS/MS) for data acquisition and subsequent data analysis.

Comprehensive Analysis of the Lysine Succinylome and Protein Co-modifications in Developing Rice Seeds

Lysine succinylation has been recognized as a post-translational modification (PTM) in recent years. It is plausible that succinylation may have a vaster functional impact than acetylation because of bulkier structural changes and more significant charge differences on the modified lysine residue. Currently, however, the quantity and identity of succinylated proteins and their corresponding functions in cereal plants remain largely unknown. In this study, we estimated the native succinylation occupancy on lysine was between 2% to 10% in developing rice seeds. Eight hundred fifty-four lysine succinylation sites on 347 proteins have been identified by a thorough investigation in developing rice seeds. Six motifs were revealed as preferred amino acid sequence arrangements for succinylation sites, and a noteworthy motif preference was identified in proteins associated with different biological processes, molecular functions, pathways, and domains. Remarkably, heavy succinylation was detected on major seed storage proteins, in conjunction with critical enzymes involved in central carbon metabolism and starch biosynthetic pathways for rice seed development. Meanwhile, our results showed that the modification pattern of in vitro nonenzymatically succinylated proteins was different from those of the proteins isolated from cells in Western blots, suggesting that succinylation is not generated via nonenzymatic reaction in the cells, at least not completely. Using the acylation data obtained from the same rice tissue, we mapped many sites harboring lysine succinylation, acetylation, malonylation, crotonylation, and 2-hydroxisobutyrylation in rice seed proteins. A striking number of proteins with multiple modifications were shown to be involved in critical metabolic events. Given that these modification moieties are intermediate products of multiple cellular metabolic pathways, these targeted lysine residues may mediate the crosstalk between different metabolic pathways via modifications by different moieties. Our study exhibits a platform for extensive investigation of molecular networks administrating cereal seed development and metabolism via PTMs.

Global Proteomic Analysis Reveals Widespread Lysine Succinylation in Rice Seedlings

Lysine succinylation (Ksu) is a dynamic and reversible post-translational modification that plays an important role in many biological processes. Although recent research has analyzed Ksu plant proteomes, little is known about the scope and cellular distribution of Ksu in rice seedlings. Here, we report high-quality proteome-scale Ksu data for rice seedlings. A total of 710 Ksu sites in 346 proteins with diverse biological functions and subcellular localizations were identified in rice samples. About 54% of the sites were predicted to be localized in the chloroplast. Six putative succinylation motifs were detected. Comparative analysis with succinylation data revealed that arginine (R), located downstream of Ksu sites, is the most conserved amino acid surrounding the succinylated lysine. KEGG pathway category enrichment analysis indicated that carbon metabolism, tricarboxylic acid cycle (TCA) cycle, oxidative phosphorylation, photosynthesis, and glyoxylate and dicarboxylate metabolism pathways were significantly enriched. Additionally, we compared published Ksu data from rice embryos with our data from rice seedlings and found conserved Ksu sites between the two rice tissues. Our in-depth survey of Ksu in rice seedlings provides the foundation for further understanding the biological function of lysine-succinylated proteins in rice growth and development.

Quantitative succinyl-proteome profiling of Chinese hickory (Carya cathayensis) during the grafting process

BACKGROUND

Chinese hickory (Carya cathayensis) is a popular nut plant having high economic value. Grafting is applied to accelerate the transition from vegetative phase to reproductive phase. Lysine succinylation occurs frequently in the proteins associated with metabolic pathways, which may participate in the regulation of the grafting process. However, the exact regulatory mechanism underlying grafting process in Chinese hickory has not been studied at post-translational modification level.

RESULTS

A comprehensive proteome-wide lysine succinylation profiling of Chinese hickory was explored by a newly developed method combining affinity enrichment and high-resolution LC-MS/MS. In total, 259 succinylation sites in 202 proteins were identified, representing the first comprehensive lysine succinylome in Chinese hickory. The succinylation was biased to occur in the cytosolic proteins of Chinese hickory. Moreover, four conserved succinylation motifs were identified in the succinylated peptides. Comparison of two grafting stages of Chinese hickory revealed that the differential expressed succinylated proteins were mainly involved in sugar metabolism, carbon fixation, amino acid metabolism and plant-pathogen interaction. Besides, seven heat shock proteins (HSPs) with 11 succinylation sites were also identified, all of which were observed to be up-regulated during the grafting process.

CONCLUSIONS

Succinylation of the proteins involved in amino acid biosynthesis might be required for a successful grafting. Succinylated HSPs might play a role in stress tolerance of the grafted Chinese hickory plants. Our results can be a good resource for functional validation of the succinylated proteins and a starting point for the investigation of molecular mechanisms during lysine succinylation occurring at grafting site.

Shotgun Proteomic Analysis Highlights the Roles of Long-Lived mRNAs and De Novo Transcribed mRNAs in Rice Seeds upon Imbibition

During seed germination, proteins are translated not only from mRNAs newly transcribed upon imbibition but also from long-lived mRNAs that are synthesized during seed maturation and stored in the mature dry seeds. To clarify the distinct roles of proteins translated from long-lived mRNAs and de novo transcribed mRNAs in germinating rice embryos, proteome analysis based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) combining the use of a transcriptional inhibitor was performed. We observed that α-amanitin significantly represses transcription in germinating embryos; nevertheless, the embryos could germinate, albeit slowly. The proteomic analysis revealed that a total of 109 proteins were translated from long-lived mRNAs associated with germination as well as 222 proteins whose expression were dependent on de novo transcription upon imbibition. Transcriptomic datasets available in public databases demonstrated that mRNAs of the 222 proteins notably increased during germination while those of the 109 proteins highly accumulated in dry embryos and constitutively expressed upon imbibition. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that many of the 109 proteins from long-lived mRNAs are implicated in energy production such as glycolysis or annotated as nucleotide binding proteins, while the 222 proteins are involved in pathways such as pyruvate metabolism and TCA cycle following glycolysis, and momilactones biosynthesis. We propose that long-lived mRNAs support initial energy production and activation of translational machinery upon imbibition whereas de novo transcription accelerates the energy production after glycolysis, which enables rice seeds to germinate vigorously.

Label-Free Quantitative Acetylome Analysis Reveals Toxoplasma gondii Genotype-Specific Acetylomic Signatures

Distinct genotypic and pathogenic differences exist between Toxoplasma gondii genotypes. For example, genotype I is highly virulent, whereas genotype II and genotype III are less virulent. Moreover, Chinese 1 genotype (ToxoDB#9) is also virulent. Here, we compare the acetylomes of genotype 1 (RH strain) and Chinese 1 genotype (ToxoDB#9, PYS strain) of T. gondii. Using mass spectrometry enriched for acetylated peptides, we found a relationship between the levels of protein acetylation and parasite genotype-specific virulence. Notably, lysine acetylation was the largest (458 acetylated proteins) in RH strain, followed by PYS strain (188 acetylated proteins), whereas only 115 acetylated proteins were detected in PRU strain. Our analysis revealed four, three, and four motifs in RH strain, PRU strain and PYS strain, respectively. Three conserved sequences around acetylation sites, namely, xxxxxK^AcHxxxx, xxxxxK^AcFxxxx, and xxxxGK^AcSxxxx, were detected in the acetylome of the three strains. However, xxxxxK^AcNxxxx (asparagine) was found in RH and PYS strains but was absent in PRU strain. Our analysis also identified 15, 3, and 26 differentially expressed acetylated proteins in RH strain vs. PRU strain, PRU strain vs. PYS strain and PYS strain vs. RH strain, respectively. KEGG pathway analysis showed that a large proportion of the acetylated proteins are involved in metabolic processes. Pathways for the biosynthesis of secondary metabolites, biosynthesis of antibiotics and microbial metabolism in diverse environments were featured in the top five enriched pathways in all three strains. However, acetylated proteins from the virulent strains (RH and PYS) were more enriched in the pyruvate metabolism pathway compared to acetylated proteins from PRU strain. Increased levels of histone-acetyl-transferase and glycyl-tRNA synthase were detected in RH strain compared to PRU strain and PYS strain. Both enzymes play roles in stress tolerance and proliferation, key features in the parasite virulence. These findings reveal novel insight into the acetylomic profiles of major T. gondii genotypes and provide a new important resource for further investigations of the roles of the acetylated parasite proteins in the modulation of the host cell response to the infection of T. gondii.

Fabrication of Furan-Functionalized Quinazoline Hybrids: Their Antibacterial Evaluation, Quantitative Proteomics, and Induced Phytopathogen Morphological Variation Studies

The limited number of agrochemicals targeting plant bacterial diseases has driven us to develop highly efficient, low-cost, and versatile antibacterial alternatives. Herein, a novel type of simple furan-functionalized quinazolin-4-amines was systematically fabricated and screened for their antibacterial activity. Bioassay results revealed that compounds C₁ and E₄ could substantially block the growth of two frequently mentioned pathogens Xanthomonas oryzae pv oryzae and X. axonopodis pv citri in vitro, displaying appreciable EC₅₀ values of 7.13 and 10.3 mg/L, respectively. This effect was prominently improved by comparing those of mainly used agrochemicals. An in vivo experiment against bacterial blight further illustrated their viable applications as antimicrobial ingredients. Quantitative proteomics demonstrated that C₁ possessed a remarkable ability to manipulate the upregulation and downregulation of expressed proteins, which probably involved d-glucose and biotin metabolic pathways. This finding was substantially verified by parallel reaction monitoring analysis. Scanning electron microscopy images and fluorescence spectra also indicated that the designed compounds had versatile capacities for destroying the integrity of bacteria. Given these remarkable characteristics, furan-functionalized quinazoline hybrids can serve as a viable platform for developing innovative antibiotic alternatives against bacterial infections.