1、Precise control of protein function is essential for the organization and function of biological systems.Among different regulatory processes,reversible post-translational modifications(PTMs)provide an elegant mechanism to govern protein function.A key advantage of PTMs is that they can be dynamical
2、ly regulated at a much faster rate and with a lower energy cost than protein turnover.Eukaryotic proteomes contain hundreds of different types of PTM;however,only a few of them,such as phosphorylation,glycosylation,methylation,acetylation,ubiquitylation and sumoylation,have been studied extensively.
3、Although the physiological importance of PTMs has been known for more than half a century,the wide-spread occurrence of PTMs only started to become clear in the first years of the 21st century,when advances in high-resolution mass spectrometry enabled detection of thousands of low-abundance PTM site
4、s1.It is also increasingly appreciated that combinations of PTMs can generate distinct protein isoforms with varying functions,which vastly expand the functional diversity of mammalian proteomes2.Lysine acetylation is an evolutionarily conserved PTM occurring in both prokaryotes and eukaryotes.Acety
5、lation was first discovered on histones by Vincent Allfrey and colleagues in 1964(ref.3).Subsequently,acetylation was found on high-mobility group(HMG)proteins4,which are chromatin-binding non-histone proteins,and on tubulin5.In the mid-1990s to late 1990s,acetylation of the transcription factor p53
6、 was discovered,the first mam-malian histone acetyltransferases(HATs)and histone deacetylases(HDACs)were identified,the bromodomain was identified as an acetyl-lysine reader domain,and potent deacetylase inhibitors were discovered(reviewed elsewhere6).These groundbreaking discoveries set the stage f
7、or the field of non-histone protein acetylation.We wish to clarify that the term acetylation can encompass other types of protein acetylation,such as amino-terminal protein acetylation and O-linked acetylation of serine and threonine.Unless otherwise specified,in this Review,acetylation refers only
8、to N-lysine acetylation.Over the past decade,advances in mass spectrometry-based proteomics have vastly expanded the catalogue of endogenously acetylated proteins,provided an unbiased view of the acetylome and revealed new insights into the scope and regulation of non-histone protein acetylation.In
9、appreciation of the extent of non-histone acetylation,HATs and HDACs were renamed to lysine acetyltrans-ferases(KATs)and lysine deacetylases(KDACs),respec-tively.The identification of thousands of acetylation sites has spurred great interest in a wide range of biomed-ical research communities,and no
10、n-histone protein acetyl ation has been implicated in all major biological processes(see below).In this Review,we provide an overview of the expand-ing landscape of non-histone protein acetylation.We dis-cuss the subcellular,compartment-specific generation of the acetyl group donor acetyl-CoA,enzyma
11、tic regulation of acetylation and the emerging non-enzymatic mecha-nisms of acetylation.The major focus is on acetylation;however,related lysine acylations are also briefly discussed.Although it is challenging to comprehensively review this rapidly growing field,we discuss a plethora of functionally
12、 characterized acetylation sites on non-histone proteins BromodomainA protein domain of 110 amino acids that binds to acetylated lysine and is found in many proteins involved in transcription regulation.Lysine acylationsPost-translational modifications of lysine with different types of acyl-CoA,such
13、 as acetyl-CoA,butyryl-CoA,propionyl-CoA,succinyl-CoA,glutaryl-CoA and crotonyl-CoA.Functions and mechanisms of non-histone protein acetylationTakeoNarita ,BrianT.Weinert and ChunaramChoudhary *Abstract|N-lysine acetylation was discovered more than half a century ago as a post-translational modifica
14、tion of histones and has been extensively studied in the context of transcription regulation.In the past decade,proteomic analyses have revealed that non-histone proteins are frequently acetylated and constitute a major portion of the acetylome in mammalian cells.Indeed,non-histone protein acetylati
15、on is involved in key cellular processes relevant to physiology and disease,such as gene transcription,DNA damage repair,cell division,signal transduction,protein folding,autophagy and metabolism.Acetylation affects protein functions through diverse mechanisms,including by regulating protein stabili
16、ty,enzymatic activity,subcellular localization and crosstalk with other post-translational modifications and by controlling proteinprotein and proteinDNA interactions.In this Review,we discuss recent progress in our understanding of the scope,functional diversity and mechanisms of non-histone protei
17、n acetylation.The Novo Nordisk Foundation Center for Protein Research,Faculty of Health Sciences,University of Copenhagen,Copenhagen,Denmark.*e-mail:chuna.choudharycpr.ku.dkhttps:/doi.org/10.1038/s41580-018-0081-3 Post-translational modificationsREVIEWSNature reviews|Molecular cell Biologyto illustr
18、ate the functional diversity and mechanistic principles of acetylation.We also briefly describe the disease and therapeutic relevance of acetylation and con-clude with a discussion of key open questions and future perspectives.Because histone acylation was extensively covered in a recent review7,it
19、will not be covered here.the scope of non-histone acetylationUntil the beginning of the 21st century,acetylation was mostly identified on individual proteins using conven-tional approaches,such as invitro acetyltransferase assays with radioisotope-labelled acetyl-CoA or using acetyl-lysine antibodie
20、s.In 2006,a combination of acetylated peptide immunoaffinity-enrichment and high-resolution mass spectrometry enabled the identification of hun-dreds of acetylation sites8.Subsequently,the identifica-tion of thousands of acetylation sites from human cell lines was reported9.These unbiased proteomic
21、analyses showed that acetylation was a surprisingly common modification of proteins in diverse cellular compart-ments.Many ensuing studies firmly established that,in addition to histones,acetylation occurs on tens of thou-sands of non-histone proteins in evolutionarily diverse organisms10.In recent
22、years,mass spectrometry-based studies have quantified the relative changes at thousands of acetylation sites in response to genetic,chemical and metabolic perturbations and provided insights into the dynamic regulation of lysine acetylation1115.regulation of acetylationAcetylation is generated by KA
23、T-catalysed transfer of an acetyl group from acetyl-CoA to the-amino side chain of lysine and is reversed by KDACs(fig.1a).Recent studies show that acetylation also occurs through non-enzymatic mechanisms and is affected by the availability of acetyl-CoA(Box1).Regulation of acetyl-CoA synthesisAcety
24、l-CoA is a key metabolite with essential cellular functions,such as energy generation in the mitochon-dria and biosynthesis of lipids in the cytoplasm.Because acetyl-CoA is membrane impermeable,mitochondrial and non-mitochondrial pools of acetyl-CoA are gener-ated independently(fig.1b).Depending on
25、the nutrient source,mitochondrial acetyl-CoA is generated by the pyruvate dehydrogenase complex(PDC),by-oxidation of fatty acids or through amino acid metabolism.The non-mitochondrial pool of acetyl-CoA is generated in the cytoplasm and the nucleus by ATP-citrate lyase(ACLY)and acyl-CoA synthetase s
26、hort-chain fam-ily member 2(ACSS2),as well as by the nuclear PDC.Acetyl-CoA can freely diffuse between the cytoplasm and the nucleus through the nuclear pores.Acetylation is directly linked to acetyl-CoA levels,and cell compartment-specific generation of acetyl-CoA can locally drive acetylation.For
27、example,nuclear ACLY,ACSS2 and PDC are reported to regulate histone acetylation and gene transcription through localized production of acetyl-CoA16.In yeast,depletion of mitochondrial acetyl-CoA only ablates acetylation of mitochondrial proteins,without affecting acetyl ation of nuclear proteins17.I
28、n mice,deletion of both acetyl-CoA carboxylase 1(ACC1)and ACC2,which convert cyto-plasmic acetyl-CoA into malonyl-CoA(fig.1b),results in increased protein acetylation18,likely through an increase in the levels of acetyl-CoA.Fluctuations in acetyl-CoA levels by genetic and dietary manipulations corre
29、late with changes in acetylation levels,further indi-cating that acetyl-CoA is a rate-limiting factor for many acetylation events(reviewed elsewhere13).Lysine acetyltransferasesThe exact number of bona fide KATs in the human pro-teome is unclear.Among the reported KATs,13 are well-characterized(cano
30、nical)and most of them are classified into three families:GCN5,p300 and MYST19(fig.1c).The remaining KATs,-tubulin N-acetyltransferase 1(TAT1;also known as ATAT1),establishment of cohe-sion 1 homologue 1(ESCO1)and ESCO2,and histone acetyltransferase 1(HAT1;also known as KAT1),are relatively dissimil
31、ar to each other.With the exception of TAT1,all the canonical KATs are primarily localized in the nucleus and acetylate histones and non-histone proteins.Compared with protein kinases,much less is known about the substrate specificities of KATs.The substrate specificity of KATs is thought to be defi
32、ned by their specific subcellular localization,interacting proteins and the accessibility of lysine in substrate pro-teins.Many KATs have non-overlapping substrates,but some of the closely related KATs can acetylate the same sites and show functional redundancy;for example,CREB-binding protein(CBP;a
33、lso known as KAT3A)and p300(also known as KAT3B)acetylate histone H3 Lys18(H3K18)and H3K27(ref.20),GCN5(also known as KAT2A)and p300/CBP-associated factor(PCAF;also known as KAT2B)acetylate H3K9(ref.20),KAT6A and KAT6B acetylate H3K23(ref.21),and ESCO1 and ESCO2 acetylate structural maintenance of c
34、hromosomes protein 3(SMC3)Lys105 and Lys106(refs22,23).In addition to the canonical KATs,a growing num-ber of proteins have been reported to function as non-canonical KATs19.However,we do not discuss non-canonical KATs here because very little is known about their substrate specificity and enzymatic
35、 mechanisms.We think that a more rigorous demonstration of their KAT activities is necessary before they can be classi-fied as genuine KATs.For example,ARD1,which is the catalytic subunit of the N-terminal acetyltransferase A complex,is implicated in lysine acetylation of several non-histone protein
36、s(Supplementary Table 1),but its lysine acetyltransferase activity has been questioned24.The deletion of another reported KAT,ACAT1(ref.25),had no measurable impact on the acetylome of HCT116 cells(B.T.W.and C.C.,unpublished observations).Furthermore,acetylation of almost all sites on sev-eral repor
37、ted KATs nuclear receptor co-activator 1 (NCOA1),NCOA2 and NCOA3(ref.14)is reduced by inhibition of CBP and p300(ref.26),indicating that instead they are possibly targets of CBP and/or p300.Lysine deacetylasesThe human genome encodes 18 KDACs,which can be grouped into two major categories:Zn2+-depen
38、dent HDACs and NAD+-dependent sirtuin deacetylases-Amino side chainThe amino group located on the epsilon carbon of the lysine side CBP(KAT3A)p300(KAT3B)Classical deacetylases(Zn2+-dependent)Sirtuin deacetylases(NAD+-dependent)Deacetylase classMYST TIP60(KAT5)MOZ(KAT6A)MORF(KAT6B)HBO1(KAT7)MOF(KAT8)
39、Subcellular localization Nucleus CytoplasmbacdGlucoseAcetyl-CoAGlycolysisFatty acidsCitratePyruvateACLYAcetyl-CoAACLYAcetyl-CoAFatty acid synthesisCitratePyruvatePDCACSS2Malonyl-CoAACC1 andACC2AcetateACSS2MitochondrionNucleus TAT1 ESCO1 ESCO2 HAT1(KAT1)OtherSubcellular localization Nucleus Nucleolus
40、 Cytoplasm MitochondriaKATNon-enzymaticLysine Acetyl-CoACH2NH3CH+SCCH3OCoASHCoA+0CCH3OHDACsH2ONAD+Sirtuins2 or 3-O-acetyl-ADP-riboseNHCOCH2CH2CH2Lysine CH2NH3CH+NHCOCH2CH2CH2CH2CHNHCOCH2CH2CH2Acetyl-lysineCCH3OCH2CHNHCOCH2CH2CH2Acetyl-lysineAcetyltransferase familyPDCGCN5 GCN5(KAT2A)PCAF(KAT2B)IIIa
41、HDAC4 HDAC5 HDAC7 HDAC9 HDAC1 HDAC2 HDAC3 HDAC8III SIRT1 SIRT2 SIRT3 SIRT4 SIRT5 SIRT6 SIRT7Other TCF1 LEF1IIb HDAC6 HDAC10IV HDAC11AcetateFatty acid-oxidation TCAcycleFig.1|regulation of reversible lysine acetylation.a|Lysine acetylation occurs through lysine acetyltransferase(KAT)-catalysed transf
42、er of an acetyl group from acetyl-CoA to the-amino side chain of lysine.Alternatively,acetyl-CoA can acetylate lysine non-enzymatically.Acetylation is reversed by Zn2+-dependent histone deacetylases(HDACs),or by the NAD+-dependent sirtuin family of deacetylases.HDAC-catalysed deacetylation generates
43、 deacetylated lysine and acetate,whereas sirtuin-catalysed deacetylation produces deacetylated lysine,nicotinamide and 2 or 3-O-acetyl-ADP-ribose.b|In mitochondria,acetyl-CoA is generated from pyruvate by the pyruvate dehydrogenase complex(PDC),or by the-oxidation of fatty acids.Mitochondrial acetyl
44、-CoA feeds into the tricarboxylic acid(TCA)cycle.The TCA cycle intermediate citrate can be exported from mitochondria to the cytoplasm,where it freely diffuses into and out of the nucleus.Cytoplasmic and nuclear acetyl-CoA pools are generated by ATP-citrate lyase(ACLY),acyl-CoA synthetase short-chai
45、n family member 2(ACSS2)and the PDC.Cytoplasmic acetyl-CoA can be converted into malonyl-CoA by acetyl-CoA carboxylase 1(ACC1)and ACC2 and used for the synthesis of fatty acids.c|Most of the canonical mammalian KATs are classified into three major families:GCN5,p300 and MYST.The remaining(other)KATs
46、 are relatively dissimilar to each other.The subcellular localization of KATs is indicated.d|Lysine deacetylases(KDACs)are divided into two categories:the classical Zn2+-dependent HDACs and NAD+-dependent sirtuin deacetylases.KDACs can be further grouped into class I,class IIa,class IIb,class III an
47、d class IV.The transcription factors Tcell-specific transcription factor 1(TCF1)and lymphoid enhancer-binding factor 1(LEF1)are recently reported KDACs that are unrelated to other KDACs.The subcellular localization of KDACs is indicated.In part d,the enzymes indicated with a yellow background either
48、 lack deacetylase activity or are involved in removing lysine acylations other than acetylation.CBP,CREB-binding protein;ESCO,establishment of cohesion 1 homologue;GCN5,general control of amino acid synthesis protein 5;HAT1,histone acetyltransferase 1;HBO1,histone acetyltransferase binding to ORC1;M
49、OF,males-absent on the first protein;MORF,MOZ-related factor;MOZ,monocytic leukaemia zinc finger protein;PCAF,p300/CBP-associated factor;SIRT,sirtuin;TAT1,-tubulin N-acetyltransferase 1;TIP60,60 kDa Tat-interactive protein.Nature reviews|Molecular cell BiologyReviews(fig.1d).The Zn2+-dependent HDACs
50、 share a highly conserved deacetylase domain and are often referred to as classical HDACs or classical KDACs.On the basis of their phylogenetic conservation and sequence sim-ilarities,the classical KDACs are further divided into four classes:class I,class IIa,class IIb and class IV27,28(fig.1d).Clas
