Crotonylation: Biochemical Traits, Enzymes, and Chromatin Roles

Post-translational modifications (PTMs) regulate protein function, with lysine crotonylation emerging as a key player in gene expression and cellular processes. Unlike well-studied modifications such as acetylation or methylation, crotonylation introduces distinct chemical properties that influence chromatin dynamics and transcriptional regulation.

Recent research links crotonylation to metabolism, enzyme activity, and tissue-specific functions. Understanding its biochemical traits, regulatory enzymes, and chromatin roles provides insight into how cells fine-tune gene expression and respond to environmental cues.

Biochemical Characteristics of Lysine Crotonylation

Lysine crotonylation involves the addition of a crotonyl group (-CO-CH=CH-CH3) to the ε-amino group of lysine residues. This modification introduces a planar, unsaturated four-carbon moiety, altering the electrostatic and steric properties of lysine. Unlike acetylation, which neutralizes lysine’s positive charge, crotonylation also adds a bulkier, more hydrophobic structure. This affects protein-protein and protein-DNA interactions, particularly in chromatin-associated proteins, influencing nucleosome stability and transcriptional activity.

The rigidity of the crotonyl group, due to its conjugated double bond, affects the spatial arrangement of modified proteins. Studies show crotonylated histones are recognized differently by bromodomain-containing proteins compared to acetylated ones, suggesting crotonylation plays a distinct regulatory role in chromatin dynamics.

Structurally, crotonylation alters the local microenvironment of lysine, impacting hydrogen bonding and hydrophobic interactions. This can change protein stability and function, as seen in histones where crotonylation enhances transcriptional activation. Nuclear magnetic resonance (NMR) and X-ray crystallography studies reveal that crotonylation disrupts local secondary structures, exposing or occluding interaction surfaces critical for protein function.

Enzymes Involved in Crotonylation and Decrotonylation

Lysine crotonylation is dynamically regulated by enzymes that add or remove crotonyl groups. Lysine crotonyltransferases (KCTs) catalyze crotonylation, while decrotonylases reverse it, maintaining a balance that impacts chromatin structure and protein function.

Histone acetyltransferases (HATs), particularly p300/CBP, act as key mediators of crotonylation. Structural studies show p300 accommodates crotonyl-CoA similarly to acetyl-CoA, though the unsaturated crotonyl group alters substrate affinity and enzymatic kinetics. Crotonylation levels are influenced by crotonyl-CoA availability, which fluctuates with metabolic activity.

Histone deacetylases (HDACs), especially sirtuins like SIRT1, SIRT2, and SIRT3, mediate crotonyl removal. SIRT3, in particular, shows strong preference for histone substrates and links crotonylation dynamics to metabolic conditions. Given SIRT3’s role in mitochondrial function, crotonylation likely extends beyond nuclear chromatin regulation to influence oxidative metabolism.

Beyond histones, crotonylation affects non-histone proteins, including transcriptional regulators. Some KCTs and decrotonylases exhibit substrate selectivity beyond histones, broadening the functional scope of this modification.

Roles in Chromatin Regulation

Lysine crotonylation influences chromatin architecture, shaping genetic accessibility and transcription. Unlike acetylation, which weakens histone-DNA interactions through charge neutralization, crotonylation adds a bulkier, hydrophobic moiety that uniquely alters nucleosome dynamics. This modification is enriched at active enhancers and promoters, marking transcriptionally engaged chromatin states. Genome-wide studies show crotonylation is associated with gene loci involved in rapid transcriptional responses.

Bromodomain-containing proteins, which typically recognize acetylated lysines, exhibit differential affinities for crotonylated histones. Structural analyses suggest certain bromodomains selectively bind crotonylated histones, influencing transcriptional complex assembly. This indicates crotonylation functions as a distinct epigenetic marker rather than a simple alternative to acetylation.

Crotonylation also maintains open chromatin states necessary for processes like embryonic development and cellular differentiation. It is particularly enriched in germ cells, where it coexists with other activating histone marks to promote lineage-specific gene expression. Its persistence at certain genomic regions after transcriptional cues subside suggests a role in epigenetic memory, allowing cells to retain transcriptional competence.

Associations With Cellular Metabolism

Lysine crotonylation is tightly linked to cellular metabolism, dependent on crotonyl-CoA availability, which is derived from fatty acid oxidation and amino acid catabolism. Crotonyl-CoA levels fluctuate with metabolic states, directly influencing crotonylation levels. In nutrient-rich conditions, increased fatty acid oxidation raises crotonyl-CoA concentrations, enhancing crotonylation. Under metabolic stress or energy deprivation, crotonyl-CoA availability declines, shifting the balance toward decrotonylation and altering gene expression.

This metabolic sensitivity suggests crotonylation regulates energy-responsive transcriptional programs. Some mitochondrial enzymes, such as succinate dehydrogenase, exhibit crotonylation-dependent activity changes, indicating a feedback loop between cellular energy production and protein function. Metabolic disorders like diabetes and obesity have been linked to abnormal crotonyl-CoA levels, hinting that dysregulated crotonylation may contribute to disease pathology.

Tissue-Specific Distribution in Organisms

Lysine crotonylation varies across tissues, reflecting its role in specialized cellular functions. It is particularly enriched in metabolically active tissues such as the liver, muscle, and brain, suggesting a connection to energy-demanding physiological processes.

In the liver, crotonylation is prominent due to the high availability of crotonyl-CoA from lipid oxidation, potentially influencing metabolic enzyme activity and transcriptional programs related to lipid homeostasis. In the brain, crotonylation has been detected in neuronal chromatin, where it may regulate gene expression linked to synaptic plasticity and cognitive function. Given the brain’s reliance on oxidative metabolism, fluctuations in crotonyl-CoA availability could impact neuronal activity.

Muscle tissue also exhibits a distinct crotonylation profile, with modifications observed in contractile proteins and metabolic enzymes. This suggests crotonylation may influence muscle adaptation to energy demands, endurance, and recovery. The tissue-specific nature of crotonylation underscores its functional diversity, with each organ utilizing this modification to fine-tune physiological processes.