An enhanced network of energy metabolism,lysine acetylation,and growth-promoting protein accumulation is associated with heterosis in elite hybrid rice

Heterosis refers to the superior performance of a hybrid compared with its parental lines.Although several genetic and molecular models have been proposed to explain heterosis,it remains unclear how hybrid cells integrate complementary gene expression or activity to drive heterotic growth.In this work,we show that accumulation of growth-promoting and energy metabolism proteins,enhanced energy metabolism activities,and increased protein lysine acetylation were associated with superior growth of the panicle meristem in the elite hybrid rice Shanyou 63 relative to its parental varieties.Metabolism of nuclear/cytosolic acetylcoenzyme A was also enhanced in the hybrid,which paralleled increases in histone H3 acetylation to selectively target the expression of growth-promoting and metabolic genes.Lysine acetylation of cellular proteins,including TARGET OF RAPAMYCIN complex 1,ribosomal proteins,and energy metabolism enzymes,was also augmented and/or remodeled to modulate their activities.The data indicate that an enhanced network of energy-producing metabolic activity and growth-promoting histone acetylation/gene expression in the hybrid could contribute to its superior growth rate and may constitute a model to explain heterosis.

Lysine acetylation decreases enzyme activity and protein level of Escherichia coli lactate dehydrogenase

Lactate is an important bulk chemical with widespread applications and a major byproduct of other chemicals bioprocess in microbial fermentation.Lactate dehydrogenase A(LdhA)catalyzes the synthesis of lactate from pyruvate.Lysine acetylation is an evolutionarily conserved post-translational modification;however,the mech-anisms underlying the regulation of LdhA function by lysine acetylation in Escherichia coli remain poorly under-stood.Herein,we demonstrate acetylation of E.coli LdhA occurs via enzymatic and non-enzymatic mechanisms.Further,we show carbon source type and concentration affect the lysine acetylation status of LdhA via a non-enzymatic mechanism.Lysine acetylation significantly inhibits the enzymatic activity and protein level of LdhA.The results of the present study demonstrate lysine acetylation of E.coli LdhA is irreversible.Understanding of the effects of lysine acetylation on LdhA function may provide a new perspective for regulating lactate production in microbial synthesis.

Protein Lysine Acetylated/Deacetylated Enzymes and the Metabolism-Related Diseases

Lysine acetylation is a reversible posttranslational modifcation, an epigenetic phenomenon, referred to as transfer of an acetyl group from acetyl CoA to lysine ε- amino group of targeted protein, which is modulated by acetyltransferases (histone/ lysine (K) acetyltransferases, HATs/KATs) and deacetylases (histone/lysine (K) deacetylases, HDACs/KDACs). Lysine acetylation regulates various metabolic processes, such as fatty acid oxidation, Krebs cycle, oxidative phosphorylation, angiogenesis and so on. Thus disorders of lysine acetylation may be correlated with obesity, diabetes and cardiovascular disease, which are termed as the metabolic complication. With accumulating studies on proteomic acetylation, lysine acetylation also involves in cell immune status and degenerative diseases, for example, Alzheimer’s disease and Huntington’s disease. This review primarily summarizes the current studies of lysine acetylation in metabolism modulation and in metabolism-related diseases, such as cardiovascular disease and fat metabolism disorder.

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.

Acetylproteomics analyses reveal critical features of lysine-ε-acetylation in Arabidopsis and a role of 14-3-3 protein acetylation in alkaline response

Lysine-ε-acetylation(Kac)is a post-translational modification(PTM)that is critical for metabolic regulation and cell signaling in mammals.However,its prevalence and importance in plants remain to be determined.Employing high-resolution tandem mass spectrometry,we analyzed protein lysine acetylation in five representative Arabidopsis organs with 2~3 biological replicates per organ.A total of 2887 Kac proteins and 5929 Kac sites were identified.This comprehensive catalog allows us to analyze proteome-wide features of lysine acetylation.We found that Kac proteins tend to be more uniformly expressed in different organs,and the acetylation status exhibits little correlation with the gene expression level,indicating that acetylation is unlikely caused by stochastic processes.Kac preferentially targets evolutionarily conserved proteins and lysine residues,but only a small percentage of Kac proteins are orthologous between rat and Arabidopsis.A large portion of Kac proteins overlap with proteins modified by other PTMs including ubiquitination,SUMOylation and phosphorylation.Although acetylation,ubiquitination and SUMOylation all modify lysine residues,our analyses show that they rarely target the same sites.In addition,we found that“reader”proteins for acetylation and phosphorylation,i.e.,bromodomain-containing proteins and GRF(General Regulatory Factor)/14-3-3 proteins,are intensively modified by the two PTMs,suggesting that they are main crosstalk nodes between acetylation and phosphorylation signaling.Analyses of GRF6/14-3-3λreveal that the Kac level of GRF6 is decreased under alkaline stress,suggesting that acetylation represses plant alkaline response.Indeed,K56ac of GRF6 inhibits its binding to and subsequent activation of the plasma membrane H+-ATPase AHA2,leading to hypersensitivity to alkaline stress.These results provide valuable resources for protein acetylation studies in plants and reveal that protein acetylation suppresses phosphorylation output by acetylating GRF/14-3-3 proteins.

Bromodomain and extra-terminal inhibitors emerge as potential therapeutic avenues for gastrointestinal cancers

Gastrointestinal(GI)cancers,including colorectal cancer,pancreatic cancer,liver cancer and gastric cancer,are severe social burdens due to high incidence and mortality rates.Bromodomain and extra-terminal(BET)proteins are epigenetic readers consisting of four conserved members(BRD2,BRD3,BRD4 and BRDT).BET family perform pivotal roles in tumorigenesis through transcriptional regulation,thereby emerging as potential therapeutic targets.BET inhibitors,disrupting the interaction between BET proteins and acetylated lysines,have been reported to suppress tumor initiation and progression in most of GI cancers.In this review,we will demonstrate how BET proteins participate in the GI cancers progression and highlight the therapeutic potential of targeting BET proteins for GI cancers treatment.

;）ownregulation of Rubisco Activity by Nonenzymatic Acetylation of RbcL

Atmospheric carbon dioxide （CO2） is assimilated by the most abundant but sluggish enzyme, ribulose- 1,5-bisphosphate carboxylase/oxygenase （Rubisco）. Here we show that acetylation of lysine residues of the Rubisco large subunit （RbcL）, including Lys201 and Lys334 in the active sites, may be an important mechanism in the regulation of Rubisco activities. It is well known that Lys201 reacts with CO2 for carba- mylation, a prerequisite for both carboxylase and oxygenase activities of Rubisco, and Lys334 contacts with ribulose-1,5-bisphosphate （RuBP）. The acetylation level of RbcL in plants is lower during the day and higher at night, inversely correlating with the Rubisco carboxylation activity. A search of the chloroplast proteome database did not reveal a canonical acetyltransferase; instead, we found that a plant-derived metabolite, 7-acetoxy-4-methylcoumarin （AMC）, can non-enzymatically acetylate both native Rubisco and synthesized RbcL peptides spanning Lys334 or Lys201. Furthermore, lysine residues were modified by synthesized 4-methylumbelliferone esters with different electro- and stereo-substitutes, resulting in varied Rubisco activities. 1-Chloroethyl 4-methylcoumarin-7-yl carbonate （CIMC） could transfer the chloroethyl carbamate group to lysine residues of RbcL and completely inactivate Rubisco, whereas bis（4-methylcoumarin-7-yl） carbonate （BMC） improved Rubisco activity through increasing the level of Lys201 carbamylation. Our findings indicate that RbcL acetylation negatively regulates Rubisco activity, and metabolic derivatives can be designed to dissect and improve CO2 fixation efficiency of plants through lysine modification.

New lysine-acetylated proteins screened by immunoaffinity and liquid chromatography-mass spectrometry

The lack of selective extraction specific for lysine-acetylated proteins has been a major problem in the field of acetylation biology,though acetylation plays a key role in many biological processes.In this paper,we report for the first time the proteomic screening of lysine-acetylated proteins from a mouse liver tissue,by a new approach of immunoaffinity purification of lysine-acetylated peptides combined with nano-HPLC/MS/MS analysis.We have found 20 lysine-acetylated proteins with 21 lysine-acetylated sites,among which 12 lysine-acetylated proteins and 16 lysine-acetylated sites have never been reported before.Notably,three acetyltransferases harboring in mitochondrion are newly discovered acetyltransferases responsible for the acetylation of nonhistone proteins.We have explored the significant patterns of residue preference by the hierarchical clustering analysis of amino acid residues surrounding acetylation sites,which could be helpful to the prediction of new sites of lysine acetylation.Our findings provide more candidates for studying the important roles played by acetylation in diverse cellular pathways and related human diseases.

PLMD：An updated data resource of protein lysine modifications

Post-translational modifications（PTMs） occurring at protein lysine residues,or protein lysine modifications（PLMs）,play critical roles in regulating biological processes.Due to the explosive expansion of the amount of PLM substrates and the discovery of novel PLM types,here we greatly updated our previous studies,and presented a much more integrative resource of protein lysine modification database（PLMD）.In PLMD,we totally collected and integrated 284,780 modification events in 53,501 proteins across 176 eukaryotes and prokaryotes for up to 20 types of PLMs,including ubiquitination, acetylation, sumoylation, methylation ,succinylation,malonylation,glutarylation,giycation,formylation,hydroxylation,butyrylation,propionylation,crotonylation,pupylation,neddylation,2-hydroxyisobutyrylation,phosphoglycerylation,carboxylation,lipoylation and biotinylation.Using the data set,a motif-based analysis was performed for each PLM type,and the results demonstrated that different PLM types preferentially recognize distinct sequence motifs for the modifications.Moreover,various PLMs synergistically orchestrate specific cellular biological processes by mutual crosstalks with each other,and we totally found 65,297 PLM events involved in 90 types of PLM co-occurrences on the same lysine residues.Finally,various options were provided for accessing the data,while original references and other annotations were also present for each PLM substrate.Taken together,we anticipated the PLMD database can serve as a useful resource for further researches of PLMs.PLMD 3.0 was implemented in PHP ＋ MySQL and freely available at http：//plmd.biocuckoo.org.

Histone Deacetylase AtSRT1 Links Metabolic Flux and Stress Response in Arabidopsis

How plant metabolic flux alters gene expression to optimize plant growth and response to stress remains largely unclear. Here, we report that Arabidopsis thaliana NAD＊-dependent histone deacetylase AtSRT1 negatively regulates plant tolerance to stress and glycolysis but stimulates mitochondrial respiration. We found that AtSRT1 interacts with Arabidopsis cMyc-Binding Protein 1 （AtMBP-1）, a transcriptional repressor produced by alternative translation of the cytosolic glycolytic enolase gene LOS2/EN02. We demonstrated that AtSRT1 could associate with the chromatin of AtMBP-I targets LOS2/EN02 and STZ/ZATIO, both of which encode key stress regulators, and reduce the H3K9ac levels at these genes to repress their transcription. Overexpression of both AtSRT1 and AtMBP-1 had synergistic effects on the expression of glycolytic genes, glycolytic enzymatic activities, and mitochondrial respiration. Furthermore, we found that AtMBP-1 is lysine-acetylated and vulnerable to proteasomal protein degradation, while AtSRT1 could remove its lysine acetylation and significantly enhance its stability in vivo. Taken together, these results indicate that AtSRT1 regulates primary metabolism and stress response by both epigenetic regulation and modulation of AtMBP-1 transcriptional activity in Arabidopsis.

Histone Deacetylase HDA9 and WRKY53 Transcription Factor Are Mutual Antagonists in Regulation of Plant Stress Response

Epigenetic regulation of gene expression is important for plant adaptation to environm ental changes.Previous results showed that Arabidopsis RPD3-like histone deacetylase HDA9 is known to function in repressing plant response to stress in Arabidopsis.However,how HDA9 targets to specific chromatin loci and controls gene expression netw orks involved in plant response to stress remains largely unclear.Here,we show that HDA9 represses stress tolerance response by interacting with and regulating the DNA binding and transcriptional activity of WRKY53,which functions as a high-hierarchy positive regulator of stress response.We found that WRKY53 is post-translationally modified by lysine acetylation at multiple sites,some of which are removed by HDA9,resulting in inhibition of WRKY53 transcription activity.Conversely,WRKY53 negatively regulates HDA9 histone deacetylase activity.Collectively,our results indicate that HDA9 and WRK53 are reciprocal negative regulators of each other's activities,illustrating how the functional interplay between a chromatin regulator and a transcription factor regulates stress tolerance in plants.

Proteomic identification and functional characterization of MYH9, Hsc70, and DNAJA1 as novel substrates of HDAC6 deacetylase activity

Histone deacetylase 6 （HDAC6）, a predominantly cyto- plasmic protein deacetylase, participates in a wide range of cellular processes through its deacetylase activity. However, the diverse functions of HDAC6 can- not be fully elucidated with its known substrates. In an attempt to explore the substrate diversity of HDAC6, we performed quantitative proteomic analyses to monitor changes in the abundance of protein lysine acetylation in response to HDAC6 deficiency. We identified 107 proteins with elevated acetylation in the liver of HDAC6 knockout mice. Three cytoplasmic proteins, including myosin heavy chain 9 （MYH9）, heat shock cognate pro- tein 70 （HscT0）, and dnaJ homolog subfamily A member 1 （DNAJA1）, were verified to interact with HDAC6. The acetylation levels of these proteins were negatively regulated by HDAC6 both in the mouse liver and in cultured cells. Functional studies reveal that HDAC6- mediated deacetylation modulates the actin-binding ability of MYH9 and the interaction between Hsc70 and DNAJA1. These findings consolidate the notion that HDAC6 serves as a critical regulator of proteinacetylation with the capability of coordinating various cellular functions.

ERα promotes transcription of tumor suppressor gene ApoA-I by establishing H3K27ac-enriched chromatin microenvironment in breast cancer cells

Apolipoprotein A-I(Apo A-I),the main protein component of high-density lipoprotein(HDL),plays a pivotal role in reverse cholesterol transport(RCT).Previous studies indicated a reduction of serum Apo A-I levels in various types of cancer,suggesting Apo A-I as a potential cancer biomarker.Herein,ectopically overexpressed Apo A-I in MDA-MB-231 breast cancer cells was observed to have antitumor effects,inhibiting cell proliferation and migration.Subsequent studies on the mechanism of expression regulation revealed that estradiol(E2)/estrogen receptorα(ERα)signaling activates Apo A-I gene transcription in breast cancer cells.Mechanistically,our Ch IP-seq data showed that ERαdirectly binds to the estrogen response element(ERE)site within the Apo A-I gene and establishes an acetylation of histone 3 lysine 27(H3 K27 ac)-enriched chromatin microenvironment.Conversely,Fulvestrant(ICI 182780)treatment blocked ERαbinding to ERE within the Apo A-I gene and downregulated the H3 K27 ac level on the Apo A-I gene.Treatment with p300 inhibitor also significantly decreased the Apo A-I messenger RNA(m RNA)level in MCF7 cells.Furthermore,the analysis of data from The Cancer Genome Atlas(TCGA)revealed a positive correlation between ERαand Apo A-I expression in breast cancer tissues.Taken together,our study not only revealed the antitumor potential of Apo A-I at the cellular level,but also found that ERαpromotes the transcription of Apo A-I gene through direct genomic effects,and p300 may act as a co-activator of ERαin this process.