# Biochemistry of the lysine beta-hydroxybutyrylation pathway

> **NIH NIH R01** · UNIVERSITY OF CHICAGO · 2021 · $533,143

## Abstract

Emerging lines of evidence suggest a close link between obesity, energy metabolism, nutrients and epigenetic
mechanism. Epigenetic changes, such as dynamic histone modifications, are associated with cellular
metabolism and diabetic complications. Nevertheless, the molecular mechanisms mediating the crosstalk
between metabolism and epigenetics remain incompletely understood. We recently discovered and
comprehensively validated a new, evolutionarily-conserved lysine modification, lysine beta(β)-
hydroxybutyrylation (Kbhb), on core histones. We detected 44 non-redundant Kbhb marks on histones and
identified Sirt2 enzyme as the first enzyme to remove histone Kbhb. Levels of Kbhb are very dynamic and are
influenced by physiological conditions (e.g., starvation and type I diabetes) and nutrition sources. Increased
levels of β-hydroxybutyrate (also called 3-hydroxybutyrate) lead to increased histone Kbhb, presumably via
conversion of β-hydroxybutyrate to β-hydroxybutyryl CoA. Interestingly, histone Kbhb is enriched in active
gene promoters, and the increased H3K9bhb levels that occur during prolonged starvation are associated with
genes up-regulated in starvation-responsive metabolic pathways, thus representing a new epigenetic
regulatory mark that couples metabolism to gene expression. β-Hydroxybutyrate is a key component of
“ketone bodies” and it has been employed in dozens of anti-cancer clinical trials as a potential therapeutic in
combination with other agents. The plasma/cellular concentration of β-hydroxybutyrate can increase up to 20
mM during starvation and in pathological conditions such as diabetes mellitus (DM) and alcoholic liver damage
and this can drive histone Kbhb formation. Hyperketonemia and ketoacidosis are known to increase the risk of
morbidity and mortality in patients. Thus, molecular characterization of Kbhb pathway will not only improve our
understanding of epigenetic mechanism but also characterize functions of β-hydroxybutyrate in
physiopathology. We hypothesize that the Kbhb pathway is molecularly distinct from the lysine acetylation
pathway. We therefore propose to characterize the Kbhb pathway by defining its key regulatory elements,
including its substrates, a unique set of regulatory enzymes and direct binding proteins, thus laying a
foundation for studying its biology functions. We will use an integrated strategy in this study involving
enzymology, chemical biology, biochemistry and proteomics approaches. Our team, the Zhao laboratory and
the Cole laboratory, is well positioned to carry out this project, because of our combined expertise in these
areas and the relevant preliminary data that we have already obtained. In this proposal, we will first
comprehensively identify and quantify dynamic changes of Kbhb-containing substrates using a quantitative
proteomics approach. We will then identify and characterize Kbhb-regulatory enzymes that can add or remove
Kbhb. We will finally identify and confirm the direct protein bin...

## Key facts

- **NIH application ID:** 10210387
- **Project number:** 5R01DK118266-04
- **Recipient organization:** UNIVERSITY OF CHICAGO
- **Principal Investigator:** PHILIP A COLE
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $533,143
- **Award type:** 5
- **Project period:** 2018-07-01 → 2022-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10210387

## Citation

> US National Institutes of Health, RePORTER application 10210387, Biochemistry of the lysine beta-hydroxybutyrylation pathway (5R01DK118266-04). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10210387. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*