Proteome-wide analysis of lysine β-hydroxybutyrylation in the myocardium of diabetic rat model with cardiomyopathy

Abstract

Lysine ß-hydroxybutyrylation (kbhb), a novel modification of lysine residues with the ß-hydroxybuty group, is associated with ketone metabolism in numerous species. However, its potential role in diabetes, especially in diabetic cardiomyopathy (DCM), remains largely unexplored. In this study, using affinity enrichment and liquid chromatography-mass spectrometry (LC-MS/MS) method, we quantitatively analyze the kbhb residues on heart tissues of a DCM model rat. A total of 3,520 kbhb sites in 1,089 proteins were identified in this study. Further analysis showed that 336 kbhb sites in 143 proteins were differentially expressed between the heart tissues of DCM and wild-type rats. Among them, 284 kbhb sites in 96 proteins were upregulated, while 52 kbhb sites in 47 proteins were downregulated. Bioinformatic analysis of the proteomic results revealed that these kbhb-modified proteins were widely distributed in various components and involved in a wide range of cellular functions and biological processes (BPs). Functional analysis showed that the kbhb-modified proteins were involved in the tricarboxylic acid cycle, oxidative phosphorylation, and propanoate metabolism. Our findings demonstrated how kbhb is related to many metabolic pathways and is mainly involved in energy metabolism. These results provide the first global investigation of the kbhb profile in DCM progression and can be an essential resource to explore DCM’s pathogenesis further.

The proteomic effects of ketone bodies: implications for proteostasis and brain proteinopathies

“…The unique chemical and physical properties of β-hydroxybutyrate (BHB) enable this monocarboxylate to form covalent bonds with (Xie et al, 2016;Luo et al, 2023). The abundance of this mark changes in response to BHB levels in a dosedependent manner (Xie et al, 2016).…”

“…The unique chemical and physical properties of β-hydroxybutyrate (BHB) enable this monocarboxylate to form covalent bonds with lysine residues, resulting in a novel post-translational modification known as β-hydroxybutyrylation (Kbhb). Kbhb is a well conserved PTM, found in all the species analyzed, including the Homo sapiens , Mus musculus , Rattus norvegicus , Saccharomyces cerevisiae and Drosophila melanogaster ( Xie et al, 2016 ; Luo et al, 2023 ). The abundance of this mark changes in response to BHB levels in a dose-dependent manner ( Xie et al, 2016 ).…”

“…The β-hydroxybutyrylation of lysine 9 in histone 3 (H3K9bhb) is the most extensively studied Kbhb mark, known to be highly responsive to changes in BHB levels ( Terranova et al, 2021 ). It is enriched in response to high KBs levels in the liver, kidney, brain, heart and the cell lines HEK293T and MEF ( Xie et al, 2016 ; Huang et al, 2021 ; Koronowski et al, 2021 ; Hou et al, 2022 ; Cornuti et al, 2023 ; Luo et al, 2023 ). H3K9bhb has been related to the upregulation of a vast set of genes specific of each cell type or tissue.…”

“…The identity and number of β-hydroxybutyrylated proteins vary depending on the cell type and physiological context, highlighting the specific and dynamic nature of this post-translational modification (PTM). As seen in Table 2 , despite the diverse functions of the Kbhb proteins, there is an enrichment of β-hydroxybutyrylated proteins related to the regulation of the genome and its expression, including chromatin structure, transcript processing and DNA repair ( Xie et al, 2016 ; Huang et al, 2021 ; Cornuti et al, 2023 ) Likewise, Kbhb is enriched in proteins related to fatty acid, amino acid and pyruvate metabolism, the regulation of tricarboxylic acid cycle, oxidative phosphorylation, and detoxification pathways, among others ( Koronowski et al, 2021 ; Hou et al, 2022 ; Luo et al, 2023 ). Interestingly, 2-day starvation induced an increase in Kbhb in the cerebral cortex, mainly in proteins involved in transcription regulation, transcription dependent on RNA pol II, and morphogenesis ( Cornuti et al, 2023 ).…”

“…The cellular compartmentalization of β-hydroxybutyrylated proteins varies according to cell type or tissue ( Figure 1 ). In the heart of diabetic rats, β-hydroxybutyrylated proteins are more abundant in the cytoplasm, followed by the mitochondria, nucleus and extracellular space ( Luo et al, 2023 ). However, in HEK293T cells, proteins with Kbhb sites are more abundant in the nucleus, followed by the mitochondria, while in MEF cells most of the Kbhb proteins were located in the cytosol ( Huang et al, 2021 ; Hou et al, 2022 ).…”