Substrate and functional diversity of lysine acetylation revealed by a proteomics survey

MOZ and MORF, two large MYSTic HATs in normal and cancer stem cells

Genes of the human monocytic leukemia zinc-finger protein MOZ (HUGO symbol, MYST3) and its paralog MORF (MYST4) are rearranged in chromosome translocations associated with acute myeloid leukemia and/or benign uterine leiomyomata. Both proteins have intrinsic histone acetyltransferase activity and are components of quartet complexes with noncatalytic subunits containing the bromodomain, plant homeodomain-linked (PHD) finger and proline-tryptophan-tryptophan-proline (PWWP)-containing domain, three types of structural modules characteristic of chromatin regulators. Although leukemia-derived fusion proteins such as MOZ-TIF2 promote self-renewal of leukemic stem cells, recent studies indicate that murine MOZ and MORF are important for proper development of hematopoietic and neurogenic progenitors, respectively, thereby highlighting the importance of epigenetic integrity in safeguarding stem cell identity.

HDAC6, at the crossroads between cytoskeleton and cell signaling by acetylation and ubiquitination

Histone deacetylase 6 (HDAC6) is a unique enzyme with specific structural and functional features. It is actively or stably maintained in the cytoplasm and is the only member, within the histone deacetylase family, that harbors a full duplication of its deacetylase homology region followed by a specific ubiquitin-binding domain at the C-terminus end. Accordingly, this deacetylase functions at the heart of a cellular regulatory mechanism capable of coordinating various cellular functions largely relying on the microtubule network. Moreover, HDAC6 action as a regulator of the HSP90 chaperone activity adds to the multifunctionality of the protein, and allows us to propose a critical role for HDAC6 in mediating and coordinating various cellular events in response to different stressful stimuli.

N-lysine propionylation controls the activity of propionyl-CoA synthetase

Reversible protein acetylation is a ubiquitous means for the rapid control of diverse cellular processes. Acetyltransferase enzymes transfer the acetyl group from acetyl-CoA to lysine residues, while deacetylase enzymes catalyze removal of the acetyl group by hydrolysis or by an NAD(+)-dependent reaction. Propionyl-coenzyme A (CoA), like acetyl-CoA, is a high energy product of fatty acid metabolism and is produced through a similar chemical reaction. Because acetyl-CoA is the donor molecule for protein acetylation, we investigated whether proteins can be propionylated in vivo, using propionyl-CoA as the donor molecule. We report that the Salmonella enterica propionyl-CoA synthetase enzyme PrpE is propionylated in vivo at lysine 592; propionylation inactivates PrpE. The propionyl-lysine modification is introduced by bacterial Gcn-5-related N-acetyltransferase enzymes and can be removed by bacterial and human Sir2 enzymes (sirtuins). Like the sirtuin deacetylation reaction, sirtuin-catalyzed depropionylation is NAD(+)-dependent and produces a byproduct, O-propionyl ADP-ribose, analogous to the O-acetyl ADP-ribose sirtuin product of deacetylation. Only a subset of the human sirtuins with deacetylase activity could also depropionylate substrate. The regulation of cellular propionyl-CoA by propionylation of PrpE parallels regulation of acetyl-CoA by acetylation of acetyl-CoA synthetase and raises the possibility that propionylation may serve as a regulatory modification in higher organisms.

Regulation of protein turnover by acetyltransferases and deacetylases

Lysine acetylation was first discovered as a post-translational modification of histones and has long been considered as a direct regulator of chromatin structure and function. Histone acetyltransferases (HATs) and histone deacetylases (HDACs) are the enzymes involved in this modification and they were thought to act as critical gene silencers or activators. Further investigations indicated that lysine acetylation can also occur in non-histone proteins and pointed to HATs and HDACs as multifunctional factors, acting not only on transcription but also on a variety of other cellular processes. One of these processes is the regulation of protein stability. Indeed, at least four independent HATs, namely CBP, p300, PCAF and TAF1, and one HDAC, HDAC6, possess intrinsic ubiquitin-linked functions in addition to their regular HAT/HDAC activities. Furthermore HATs and HDACs can be found in multi-subunit complexes with enzymes of the ubiquitination machinery. Moreover, lysine acetylation itself was found to directly or indirectly affect protein stability. These observations reveal therefore a tight link between protein lysine acetylation and ubiquitination and designate the acetylation machinery as a determinant element in the control of cellular proteolytic activities.

Lysine propionylation and butyrylation are novel post-translational modifications in histones

The positively charged lysine residue plays an important role in protein folding and functions. Neutralization of the charge often has a profound impact on the substrate proteins. Accordingly all the known post-translational modifications at lysine have pivotal roles in cell physiology and pathology. Here we report the discovery of two novel, in vivo lysine modifications in histones, lysine propionylation and butyrylation. We confirmed, by in vitro labeling and peptide mapping by mass spectrometry, that two previously known acetyltransferases, p300 and CREB-binding protein, could catalyze lysine propionylation and lysine butyrylation in histones. Finally p300 and CREB-binding protein could carry out autopropionylation and autobutyrylation in vitro. Taken together, our results conclusively establish that lysine propionylation and lysine butyrylation are novel post-translational modifications. Given the unique roles of propionyl-CoA and butyryl-CoA in energy metabolism and the significant structural changes induced by the modifications, the two modifications are likely to have important but distinct functions in the regulation of biological processes.

A newly discovered post-translational modification--the acetylation of serine and threonine residues

Recent studies on a bacterial virulence factor, YopJ of Yersinia, have led to the realization that the acetylation of serine and threonine residues could be an important form of post-translational modification in eukaryotes. Although the identification of the machinery used for the addition and removal of acetyl groups on serine or threonine residues is in its infancy, the enzymes thus-far studied provide early insight into the mechanism of this newly discovered post-translational modification, and hint at its potential importance. For example, acetylation can compete with phosphorylation targeted to the same residues and could, therefore, alter the course of signaling pathways. What are the implications for signal transduction in eukaryotes and how widespread could acetylation of serine and threonine prove to be?

Mitochondrial phosphoproteome revealed by an improved IMAC method and MS/MS/MS

IMAC in combination with mass spectrometry is a promising approach for global analysis of protein phosphorylation. Nevertheless this approach suffers from two shortcomings: inadequate efficiency of IMAC and poor fragmentation of phosphopeptides in the mass spectrometer. Here we report optimization of the IMAC procedure using (32)P-labeled tryptic peptides and development of MS/MS/MS (MS3) for identifying phosphopeptide sequences and phosphorylation sites. The improved IMAC method allowed recovery of phosphorylated tryptic peptides up to approximately 77% with only minor retention of unphosphorylated peptides. MS3 led to efficient fragmentation of the peptide backbone in phosphopeptides for sequence assignment. Proteomics of mitochondrial phosphoproteins using the resulting IMAC protocol and MS3 revealed 84 phosphorylation sites in 62 proteins, most of which have not been reported before. These results revealed diverse phosphorylation pathways involved in the regulation of mitochondrial functions. Integration of the optimized batchwise IMAC protocol with MS3 offers a relatively simple and more efficient approach for proteomics of protein phosphorylation.

Identification of histone H3 lysine 36 acetylation as a highly conserved histone modification

Histone lysine acetylation is a major mechanism by which cells regulate the structure and function of chromatin, and new sites of acetylation continue to be discovered. Here we identify and characterize histone H3K36 acetylation (H3K36ac). By mass spectrometric analyses of H3 purified from Tetrahymena thermophila and Saccharomyces cerevisiae (yeast), we find that H3K36 can be acetylated or methylated. Using an antibody specific to H3K36ac, we show that this modification is conserved in mammals. In yeast, genome-wide ChIP-chip experiments show that H3K36ac is localized predominantly to the promoters of RNA polymerase II-transcribed genes, a pattern inversely related to that of H3K36 methylation. The pattern of H3K36ac localization is similar to that of other sites of H3 acetylation, including H3K9ac and H3K14ac. Using histone acetyltransferase complexes purified from yeast, we show that the Gcn5-containing SAGA complex that regulates transcription specifically acetylates H3K36 in vitro. Deletion of GCN5 completely abolishes H3K36ac in vivo. These data expand our knowledge of the genomic targets of Gcn5, show H3K36ac is highly conserved, and raise the intriguing possibility that the transition between H3K36ac and H3K36me acts as an "acetyl/methyl switch" governing chromatin function along transcription units.

Regulation of SRC family coactivators by post-translational modifications

Initially identified as a group of auxiliary protein factors involved in transcriptional regulation by steroid hormone receptors as well as by other members of the nuclear receptor superfamily, the steroid receptor coactivators (SRCs) have since then been implicated in the transcriptional regulation of other transcription factors which are important components of very different signaling pathways. Members of the SRC family have been shown to interact with myogenin, MEF-2, transcriptional enhancer factor (TEF), NF-kappaB, AP-1, STAT, p53, and E2F1, suggesting that SRC coactivators participate in diverse cellular processes. Recent evidence indicates that various post-translational modifications play critical roles in determining the final transcriptional output and specificity of SRC coactivators. In this review, we summarized the current knowledge concerning post-translational modifications, dynamic interplay between different modifications, and patho-physiological relevance of the modifications of SRC proteins.

SIR2: a potential target for calorie restriction mimetics

Calorie restriction (CR) extends lifespan in a wide variety of species and mitigates diseases of aging in mammals. Here, we describe the evidence that the silent information regulator 2 (SIR2) gene, which encodes a nicotinamide adenine dinucleotide (NAD)-dependent deacetylase, regulates lifespan and mediates CR in lower species such as Saccharomyces cerevisiae and Caenorhabditis elegans. We discuss the emerging roles of mammalian SIR2 homologs in regulating physiological changes triggered by CR and their potential connections to diseases of aging. We conclude with the recent advances on small molecules that activate the enzymatic activity of SIR2 as potential CR mimetics. The SIR2 family represents an evolutionarily conserved lifespan regulator. Modulating the activity of SIR2 might provide effective CR mimetics to combat diseases of aging.

Regulation of alternative splicing by signal transduction pathways

Alternative splicing is now recognized as a ubiquitous mechanism for controlling gene expression in a tissue-specific manner. A growing body of work from the past few years as begun to also highlight the existence of networks of signal-responsive alternative splicing in a variety of cell types. While the mechanisms by which signal transduction pathways influence the splicing machinery are relatively poorly understood, a few themes have begun to emerge for how extracellular stimuli can be communicated to specific RNA-binding proteins that control splice site selection by the spliceosome. This chapter describes our current understanding of signal-induced alternative splicing with an emphasis on these emerging themes and the likely directions for future research.

Histone deacetylase 3 interacts with and deacetylates myocyte enhancer factor 2

The myocyte enhancer factor 2 (MEF2) family of transcription factors is not only important for controlling gene expression in normal cellular programs, like muscle differentiation, T-cell apoptosis, neuronal survival, and synaptic differentiation, but has also been linked to cardiac hypertrophy and other pathological conditions. Lysine acetylation has been shown to modulate MEF2 function, but it is not so clear which deacetylase(s) is involved. We report here that treatment of HEK293 cells with trichostatin A or nicotinamide upregulated MEF2D acetylation, suggesting that different deacetylases catalyze the deacetylation. Related to the trichostatin A sensitivity, histone deacetylase 4 (HDAC4) and HDAC5, two known partners of MEF2, exhibited little deacetylase activity towards MEF2D. In contrast, HDAC3 efficiently deacetylated MEF2D in vitro and in vivo. This was specific, since HDAC1, HDAC2, and HDAC8 failed to do so. While HDAC4, HDAC5, HDAC7, and HDAC9 are known to recognize primarily the MEF2-specific domain, we found that HDAC3 interacts directly with the MADS box. In addition, HDAC3 associated with the acetyltransferases p300 and p300/CBP-associated factor (PCAF) to reverse autoacetylation. Furthermore, the nuclear receptor corepressor SMRT (silencing mediator of retinoid acid and thyroid hormone receptor) stimulated the deacetylase activity of HDAC3 towards MEF2 and PCAF. Supporting the physical interaction and deacetylase activity, HDAC3 repressed MEF2-dependent transcription and inhibited myogenesis. These results reveal an unexpected role for HDAC3 and suggest a novel pathway through which MEF2 activity is controlled in vivo.

Kinetic and Mass Spectrometric Analysis of p300 Histone Acetyltransferase Domain Autoacetylation

Acetylation of proteins by p300 histone acetyltransferase plays a critical role in the regulation of gene expression. The prior discovery of an autoacetylated regulatory loop in the p300 histone acetyltransferase (HAT) domain prompted us to further explore the mechanisms of p300 autoacetylation. Here we have described a kinetic and mass spectrometric analysis of p300 HAT autoacetylation. The rate of p300 HAT autoacetylation was approximately fourth order with respect to p300 HAT domain concentration and thus appeared to be a highly cooperative process. By showing that a catalytically defective p300 HAT domain could be efficiently acetylated by active p300 HAT, we deduced that autoacetylation occurs primarily by an intermolecular mechanism. This was further confirmed using a semisynthetic biotinylated p300 HAT domain that could be physically separated from the catalytically defective p300 HAT by avidin affinity chromatography. Autoacetylation catalyzed by p300 HAT was approximately 1000-fold more efficient than PCAF (p300/CREB-binding protein-associated factor)-mediated acetylation of catalytically defective p300 HAT. Using a novel tandem mass spectrometric approach, it was found to be possible to observe up to 17 autoacetylation events within the intact p300 regulatory loop. Kinetic analysis of the site specificity of p300 autoacetylation reveals a class of rapid events followed by a slower set of modifications. Several of these rapid autoacetylation sites correlate with an acetyltransferase-activating function based on prior mutagenesis analysis.

Inhibition of histone deacetylases

Reversible histone acetylation, governed dynamically by histone acetyltransferases (HATs) and histone deacetylases (HDACs), plays a pivotal role in regulation of gene expression through remodeling chromatin structure. Manipulation of the equilibrium between acetylation and deacetylation of histones by specific HDAC inhibitors is thus a useful tool to study functional role(s) for histone hyper-/hypoacetylation in controlling gene transcription and many other cellular activities. By using the trans-activating effect of trichostatin A (TSA), a widely used HDAC inhibitor, on the telomerase reverse transcriptase (hTERT) gene as an example, we summarize various aspects of HDAC inhibitors and provide a general strategy for their in vitro application in studies of gene regulation.