Metabolic regulation of gene expression through histone acylations

Abstract

Eight types of short-chain Lys acylations have recently been identified on histones: propionylation, butyrylation, 2-hydroxyisobutyrylation, succinylation, malonylation, glutarylation, crotonylation and β-hydroxybutyrylation. Emerging evidence suggests that these histone modifications affect gene expression and are structurally and functionally different from the widely studied histone Lys acetylation. In this Review, we discuss the regulation of non-acetyl histone acylation by enzymatic and metabolic mechanisms, the acylation 'reader' proteins that mediate the effects of different acylations and their physiological functions, which include signal-dependent gene activation, spermatogenesis, tissue injury and metabolic stress. We propose a model to explain our present understanding of how differential histone acylation is regulated by the metabolism of the different acyl-CoA forms, which in turn modulates the regulation of gene expression.

Figure 1. Discovering Lys acylations

(a) An antibody against a certain Lys acylation (for example, acetylation) can be used to enrich for peptides with structurally-related acylations, for example, that differ in only one (propionylation) or two (butyrylation) hydrocarbon groups. (b) Alternatively, spectra obtained by tandem mass spectrometry can be unbiased analyzed using a nonrestrictive protein-sequence alignment algorithm to detect a mass shift in a substrate peptide, which is in turn used to locate a new modification in the peptide. In the left panel, the top diagram represents the peptide backbone cleavage; blue-colored bars represent peaks from a theoretical peptide, and red-colored bars represent peaks from an experimentally-detected peptide with a mass shift; the y-axis represents the relative abundance of peptide ions; and the m/z ratio at x-axis represents mass-to-charge ratio of peptide ions. The accurate molecular weight of a modification is used to deduce its theoretical chemical structures (middle panel). The candidate peptides with such modifications are synthesized and used to validate the in vivo-derived peptides by high performance liquid chromatography (HPLC) -coelution and tandem mass spectrometry (right panel; HPLC peaks from an in vivo peptide (blue), synthetic peptide (red) and their mixture (green) are illustrated).

Figure 2. Chemical structures of nine Lys acylations and their distributions on histones

a) Illustration of Lys acetylation and eight new types of short-chain Lys acylations, clustered into three groups according to their chemical properties. b) A map of histone sequences showing the distributions of Lys acylations on the different histones from mouse. Sequences in boxes refer to the global domains of the five histones. Modified with permission from REF. . Ac, acetylation; Bhb, β-hydroxybutyrylation; Bu, butyrylation; Cr, crotonylation; Glu, glutarylation; Hib, 2-hydroxyisobutyrylation; Ma, malonylation; Pr, propionylation; Succ, succinylation.

Figure 3. Writers and erasers for Lys acylations

a) Illustration of the structures of acyl-Coenzyme A (acyl-CoA) and of the enzymatic reactions of adding or removing acyl-lysine by two groups of enzymes. b) A table showing the enzymatic activities of Lys acyltransferases (writers) and deacylases (erasers). CBP, CREB-binding protein; GNATs, Gcn5-related N-acetyltransferases; HAT, histone acetyltransferase; HDAC, histone deacetylase; Kbhb, Lys β-hydroxybutyrylation; Kbu, Lys butyrylation; Kcr, Lys crotonylation; Kglu, Lys glutarylation; Khib, Lys 2-hydroxyisobutyrylation; Kma, Lys malonylation; Kpr, Lys propionylation; Ksucc, Lys succinylation; MYSTs, MOZ, Ybf2, Sas2, Tip60; NA, not available; NAD⁺, nicotinamide adenine dinucleotide; p300, E1A binding protein p300; sirtuins, Sir2 (silent information regulator 2)-related enzymes.

Figure 4. Co-Crystal structures of the YEATS domain bound to crotonyl-Lys reveal a common mechanism for crotonyl-Lys preference

The YEATS (Yaf9, ENL, AF9, Taf14, and Sas5) domain binds with higher affinity to histone Lys crotonylation compared to histone Lys acetylation. Crystal structures of three different YEATS domains reveal a conserved mechanism for Lys crotonylation recognition and preference. a) Close-up of the AF9-YEATS (purple) binding pocket bound to an acetylated histone h3 Lys 9 (H3K9ac) peptide (PDB: 4TMP). b) Close-up of the AF9-YEATS binding pocket bound to a crotonylated H3K9 (H3K9cr) peptide. The extended hydrocarbon chain of the crotonyl group is accommodated within the YEATS binding pocket (PDB: 5HJB). c-e) Co-crystal structures of the YEATS domain of (c) AF9 (purple), (d) YEATS2 (pink) and (e) Taf14 (grey) bound to the indicated crotonylated histone peptides (orange) reveal a common aromatic-sandwich that clamps the crotonylamide by π-aromatic interactions. Each structure reveals the use of a different combination of two aromatic residues to sandwich Kcr: F59 and Y78 for AF9 (c), Y262 and W282 for YEATS2 (d), and F62 and W81 for Taf14 (e). This π -stacking exploits the unique double bond of crotonyl and explains the preference of the YEATS domain for Lys crotonylation over Lys acetylation. (c) PDB: 5HJB, (d) PDB: 5IQl, (e) PDB: 5IOK.

Figure 5. Metabolic regulation of histone acylation

The levels of any particular histone acylation depend on the relative concentration of its respective acyl-CoA (R-CoA) and of the other acyl-CoAs. For simplicity, this is represented here as the ratio between R-CoA and the most abundant acyl-CoA, acetyl-CoA (AcCoA). This ratio will determine how much of a particular acyl-CoA will be used by promiscuous histone acyl-transferases (writers) to acylate histone Lys residues. Acyl-CoAs can be generated through various intermediate metabolic pathways. Here we highlight pathways discussed in this review, which contribute either to R-CoA (non-acetyl CoAs) or AcCoA. For a more comprehensive discussion of these pathways see REF. . In metazoans, Acetyl-CoA used for histone acetylation is synthesized from citrate (derived from glucose through the tricarboxylic acid (TCA) cycle) by ATP-citrate lyase (ACL). Many acyl-CoAs can be derived from their cognate short-chain fatty acid (SCFA) by Acyl-CoA Synthetase 2 (ACSS2), including acetate and its CoA form. The pathway generating the SCFA β-hydroxybutyrate (bhb) involves the breakdown of long-chain fatty acids (LCFA) through β-oxidation and subsequent ketogenesis. Malonyl-CoA (Mal-CoA) is generated as the first step in LCFA synthesis. It is still unclear what other cytoplasmic or nuclear pathways exist that generate the acyl-CoAs needed for the diversity of the observed histone acylations (represented as a question mark).

Figure 6. The functions of differential histone acylation

Examples of how different histone acylations are involved in various biological processes. a) Signal-dependent gene activation. Lys crotonylation (Kcr) and Lys acetylation by the histone acyl transferase p300 are induced by the inflammatory signal lipopolysaccharide (not shown) at target genes. Increasing the concentration of crotonyl-CoA (CrCoA) leads to an increase in the levels of p300-catalyzed Kcr, leading to increased recruitment of AF9 and enhanced gene expression. b) Spermatogenesis. Kcr marks X-linked genes that escape meiotic sex chromosome inactivation (MSCI). Histone butyrylation (Kbu) disrupts BRDT binding to chromatin, thereby preventing the histone-to-protamine transition in specific loci in elongating spermatids. c) Metabolic-induced stress. During prolonged starvation, when glucose molecules are scarce, fatty acids replace glucose as the major energy source in the liver. Through the process of ketogenesis, acetyl-CoAs (AcCoA) are converted to ketone bodies, such as β-hydroxybutyrate. β-hydroxybutyrate can then be charged to free coenzyme A to form β-hydroxybutyrate-CoA (bhb-CoA), the high energy donor for the histone modification β-hydroxybutyrylation (Kbhb) is induced in response to ketogenesis and marks a class of activated starvation-response genes.