histone methylation and more

Adding carbons is about the metabolic status [1]

This post is exploring methylation, acetylation, and adding ecarbons. Josua Rabinowitz’s group [1] has left us with a good starting off point. One thing they stress in their review is that the canonical post translational modification for many of us, phosphorylation is a rapid response to growth hormones binding to their receptors and such as that. Phosphorylation is, by definition, the transfer of the gamma phosphate of ATP tomino acid side chain hydroxyl groups of proteins. ADP is one of the products of this reaction. Su et al state that the 10mM concentration in the cell is more than enough to fully saturate the receptors alleviate the problem of end product inhibition. While the gamma phosphate can be put back onto ADP, this requires energy that comes from the proton gradient across the inner membrane of the mitochondria and the F_0/1-ATPase that is really an enzyme that makes ATP. This last comment was not part of the Su review.

What the Su review does stress is that end product inhibition is philosophically much more important in regulating the modifications we call acetylation and methylation. For reactants to bind to the active site of the enzyme, the products must leave.

Acetylation comments

Su and coauthors claim that hypoxia inhibits pyruvate dehydrogenase causing the accumlation of acetate. Acetyl CoA synthase, cytoplasmic (ACSC) Catalyzes the synthesis of acetyl-CoA from short-chain fatty acids with acetate the preferred substrate but also with propionate. acetate + ATP + CoA = acetyl-CoA + AMP + diphosphate. Removal of aceylation involves the sirtuins and NAD⁺.

methylation

Histone methyltransferase’s SAM affinity may determine whether histone lysines are the first recipient. It is noted that histone lysines may be mono-di- and tri-methylated. . “Histone methyltransferases may depend on local SAM production by specific associated methionine adenosyltransferase enzymes.” This statement is the cornerstone of enzyme kinetics in general. Local production increases the effective concentration and facilitates removal of the product from the active site.

• The TET family of enzymes remove DNA methylation of promotor regions of the mammalian gene. TET1, for instance, catalyzes this reaction: 2-oxoglutarate + a 5-methyl-2′-deoxycytidine in DNA + O₂ = a 5-hydroxymethyl-2′-deoxycytidine in DNA + CO₂ + succinate
• Lysine specific histone demethylase 1, LSD1, Uses FAD+ to produce an imine that is then hydrolyzed by H2O to yield FADH
• α-ketoglutarate-dependent lysine specific demethylase 2A JMJC enzymes can remove lysine tri-methylation. 2-oxoglutarate + N₆,N₆-dimethyl-L-lysyl₃₆-[histone H3] + 2 O₂ = 2 CO₂ + 2 formaldehyde + L-lysyl₃₆-[histone H3] + 2 succinate

The dependence of TET and JMJC enzymes on oxygen and α-ketoglutarate as co-substrates renders demethylation rates sensitive to both oxygenation and TCA cycle metabolism. Among TCA cycle metabolites, α-ketoglutarate promotes demethylation, whereas succinate and fumarate act as competitive inhibitors. In addition, α-ketoglutarate can undergo two-electron reduction to produce 2-hydroxyglutarate (2HG), which also competitively inhibits demethylation. Thus, methylation status is broadly sensitive to oxygen, one-carbon, and TCA-related metabolism.

Post translational histone modifications [2]

Where do these lysines “live” in the histones that are modifed? Part of the process is to negate the positive charge on lysines that are attractive to negative charges on the phosphate groups of DNA. There are four main histones: H2A, H2B, H3, and H4. They exist as an octomer. An actual X-ray crystal structure of a small piece of DNA wound around an octomer was examined because so many histone cartoons make it look like histones are spools and the DNA is the thread. Each segment of DNA is really more exposed to the environment that thread at the very center of a spool. The histone tails really don’t show up that well in this particular structure.

The Ramazi review listed other histone post translational modifications not only of lysine but also of the basic amino acid arginine. Note that lysine retains a positive charge even with three methyl groups yet it loses this positive charge with just one acetyl group.

Some of this did not make intuitive sense so peer reviewed literature was consulted and a biophysical study was found that addressed this point. [3]

Methylated histone lysine biophysics [3]

Is trimethylated lysine really charged? Maybe yes, maybe no. The point is that adding methyl groups fine tune the way that histones interact with DNA, other histones, and proteins that interact with DNA of the chromatin.

disease	enzyme	site	ref
autism mental retardation	KDM5C, X-linked intellectual disability, ASD like demethylation	H3K4	link
schizophrenia	MLL1, is essential for hippocampal synaptic plasticity and may be involved in cortical dysfunction of some cases of schizophrenia. Together, these findings emphasize the potential significance of histone, tri-methyl	H3K4	PMC
breast cancer	SETD7 monomethylation SETD7 promotes transcription of Nrf2 target genes	H3K4	PMC

The enzyme column contains fleeting remarks about the enzyme responsible for the methyaltion of lysine 4 of histone H3. UniProt was consulted to get some details as to cofactors, reaction and such as that.

• KDM5C Fe and α-ketoglutarate are cofactors in this enzyme. Histone demethylase that specifically demethylates ‘Lys-4’ of histone H3, thereby playing a central role in histone code (PubMed:28262558). Does not demethylate histone H3 ‘Lys-9’, H3 ‘Lys-27’, H3 ‘Lys-36’, H3 ‘Lys-79’ or H4 ‘Lys-20’. Demethylates trimethylated and dimethylated but not monomethylated H3 ‘Lys-4’. Participates in transcriptional repression of neuronal genes by recruiting histone deacetylases and REST at neuron-restrictive silencer elements. Represses the CLOCK-BMAL1 heterodimer-mediated transcriptional activation of the core clock component PER2 (By similarity).
• MLL1 catalyzes methyl group transfer from S-adenosyl-L-methionine to the epsilon-amino group of ‘Lys-4’ of histone H3 (H3K4) via a non-processive mechanism. Part of chromatin remodeling machinery predominantly forms H3K4me1 and H3K4me2 methylation marks at active chromatin sites where transcription and DNA repair take place. L-lysyl₄-[histone H3] + S-adenosyl-L-methionine = H⁺ + N₆-methyl-L-lysyl₄-[histone H3] + S-adenosyl-L-homocysteine
• SETD7 “specifically” monomethylates ‘Lys-4’ of histone H3. L-lysyl₄-[histone H3] + S-adenosyl-L-methionine = H⁺ + N₆-methyl-L-lysyl₄-[histone H3] + S-adenosyl-L-homocysteine. UniProt gives PubMed references of other enzymes methylated by SETD7, Recruited by IPF1/PDX-1 to the insulin promoter, leading to activate transcription (PubMed:16141209).
  Has also methyltransferase activity toward non-histone proteins such as CGAS, p53/TP53, TAF10, and possibly TAF7 by recognizing and binding the [KR]-[STA]-K in substrate protein.

Have several enzymes evolved to methylate one specific lysine in one of four core histones? Or do these enzymes have other functions? How are these enzyme regulated?

The Liu review of histone modifications

These authors had three very colorful renditions of post translational modifications of histones. Figure 2 brought home the concept that there are many reasons why DNA might need to go onto or come off of a histone. Figure 3 brought home the concept that there are many enzymes involved with acetelating and deacetylating histones.

2.1. Histone methylation

• Histone methylation 17 were located in lysin e and seven in arginine. Much of the discussion related to histone methylation in cancer.
• Histone acetylation weakens the binding to negatively charged DNA.
• Histone phosphorylation is necessary for cell division. DNA double strand breaks can initiate histone phosphorylation.
• Histone ubiquitination does not target histones for dgradation unlike other proteins. Ubiquitination requires three types of enzyme catalysis: ubiquitin activator enzyme E1, ubiquitin‐binding enzyme estradiol (E2), and ubiquitin‐protein ligase E3. This modification seems to play a role in DNA damage repair.
• Histone porpionyl and butanylation are derived from the acylCoA carriers. H3K14 is the site of Kpr and Kbu in vivo, and HAT and HDAC can catalyze the addition and removal of propionyl and butyryl groups. [4] Sirt1/2/3 of the HDAC class can remove the propionyl and butyryl groups.
• Histone malonylation is the process of covalently binding malonyl groups to histone lysine residues under the catalysis of enzymes. Sirt5 may deacetylation.
• Histone crontonylation refers to the attachement of crotonyl

Postscipt on histone propionylation [5]

Coming full circle Jo and co authors raised antibodies against various acylated forms o H3k23 and established a metabolic role of acylation. This study used cultured myotubles. Starved cultures exhibited less acetylation, proponylation, butylation and crotonation. Histone modification increased upon refeeding. [5] H3K23 “marks” were associated with gene transcription.

References

1. Su X, Wellen KE, Rabinowitz JD. Metabolic control of methylation and acetylation. Curr Opin Chem Biol. 2016 Feb;30:52-60. PMC free article
2. Ramazi S, Allahverdi A, Zahiri J. Evaluation of post-translational modifications in histone proteins: A review on histoneT modification defects in developmental and neurological disorders. J Biosci. 2020;45:135. free paper
3. Luo M. Chemical and Biochemical Perspectives of Protein Lysine Methylation. Chem Rev. 2018 Jul 25;118(14):6656-6705. PMC free paper
4. Liu R, Wu J, Guo H, Yao W, Li S, Lu Y, Jia Y, Liang X, Tang J, Zhang H. Post-translational modifications of histones: Mechanisms, biological functions, and therapeutic targets. MedComm (2020). 2023 May 20;4(3):e292. PMC free articlePM
5. Jo C, Park S, Oh S, Choi J, Kim EK, Youn HD, Cho EJ. Histone acylation marks respond to metabolic perturbations and enable cellular adaptation. Exp Mol Med. 2020 Dec;52(12):2005-2019. PMC free article