Is There a Histone Code in Bacteria? Valerie Carabetta’s Search for Epigenetic Regulation in Bacillus subtilis
- Ray Sullivan
- May 14
- 3 min read
At the 2025 Theobald Smith Society Spring Symposium, Valerie Carabetta—Associate Professor at Cooper Medical School of Rowan University—delivered a captivating talk that challenged our understanding of bacterial gene regulation. Her central question: could bacteria possess something akin to the eukaryotic "histone code"?
Valerie’s lab focuses on post-translational modifications of bacterial chromatin-like proteins, particularly the HU-family protein HBsu in Bacillus subtilis. Her team’s findings suggest that lysine acetylation of HBsu may play a regulatory role similar to histone modifications in eukaryotes—governing DNA compaction, gene expression, sporulation, and even antibiotic persistence.
Chromosome Compaction and the “Histone-like” HBsu Protein
While eukaryotes use histones to compact their long, linear chromosomes, bacteria face a similar challenge—fitting a large circular chromosome into a small cell. Valerie described the structural organization of the bacterial nucleoid, where DNA loops are compacted with the help of nucleoid-associated proteins. Chief among them is the HU-family protein HBsu in B. subtilis.
Her lab has identified seven acetylation sites on HBsu. Through site-directed mutagenesis, they created “acetylation-mimic” (lysine-to-glutamine) and “deacetylation-mimic” (lysine-to-arginine) mutants to study their roles in DNA binding and nucleoid architecture. Six out of the seven sites showed clear effects on chromosome compaction, strongly suggesting these modifications regulate HBsu-DNA interactions. Notably, K37, the one site with no compaction phenotype, faces away from DNA in structural models—supporting the theory that acetylation impacts direct DNA contacts.
Acetylation in Sporulation and Gene Regulation
Sporulation—a last-resort survival strategy for B. subtilis—also appears to be governed by HBsu acetylation. Using time-course RNA analysis, Dr. Carabetta's team showed that acetylation at lysine 41 (K41) upregulates key sporulation genes like sigF and spoIIQ, suggesting K41 acts as a developmental switch. In K41Q mutants, spores form earlier than in wild-type, but they are less stress-resistant, indicating that premature or dysregulated sporulation is detrimental.
This led to a provocative hypothesis: K41 acetylation serves as a switch between early and late sporulation stages, fine-tuning the transition through regulatory gene expression. Other sites, in contrast, appear to suppress sporulation when acetylated, suggesting a complex interplay of modifications—not unlike a histone code.
Antibiotic Stress, Persistence, and Chromatin Remodeling
Dr. Carabetta also explored how HBsu acetylation influences bacterial responses to antibiotic stress. Under kanamycin treatment, wild-type B. subtilis compacted its nucleoid. However, mutants mimicking constant acetylation at K3 and K75 failed to compact their chromosomes, while K41Q mutants showed increased nucleoid size. This implies that nucleoid structure may shift in response to stress, potentially influencing survival.
When tested for persistence—a dormant state that allows survival during antibiotic treatment—these same mutants showed delayed recovery after antibiotic removal. Dr. Carabetta proposed a model where stress-induced deacetylation triggers compaction and survival, while subsequent re-acetylation, particularly at K41, enables recovery and regrowth.
Enzymes Regulating HBsu Acetylation
To support the idea of a regulatory “code,” there must be enzymes that dynamically add and remove acetyl groups. Dr. Carabetta’s lab identified at least four acetyltransferases—YfmK, YdgE, YdhI, and YokD—that modify HBsu, with YdgE showing a strong preference for K41. These enzymes may be differentially expressed depending on environmental conditions like nutrient stress or antibiotic exposure.
They are now investigating SrtN, a NAD⁺-dependent deacetylase, as the potential HBsu deacetylase. Preliminary mass spectrometry and in vitro assays suggest it can remove acetyl groups from histone-like peptides. One exciting avenue is exploring these enzymes as targets for novel antimicrobial development, a project being advanced by Dr. Carabetta’s student Maxwell Akantibila.
Toward a Bacterial Epigenetic Paradigm
Dr. Carabetta’s talk built a compelling case for epigenetic-like regulation in bacteria, where reversible modifications to chromatin proteins influence stress responses and cell fate decisions. Her work challenges the long-held view that bacteria lack complex gene regulation and highlights how post-translational modification of chromatin proteins like HBsu may serve as a bacterial “histone code.”
As she and her team continue to map out this code and the enzymes that regulate it, their findings could open new avenues in antimicrobial therapy, synthetic biology, and our understanding of microbial cell biology.
You can watch Professor Carabetta’s talk at: https://youtu.be/Nq_CMZ-wh3U
References
Carr RA, Tucker T, Newman PM, Jadalla L, Jaludi K, Reid BE, Alpheaus DN, Korrapati A, Pivonka AE, Carabetta VJ. Nε-lysine acetylation of the histone-like protein HBsu influences antibiotic survival and persistence in Bacillus subtilis. Front Microbiol. 2024 May 21;15:1356733. doi: 10.3389/fmicb.2024.1356733. PMID: 38835483; PMCID: PMC11148388.
Popova L, Carr RA, Carabetta VJ. Recent Contributions of Proteomics to Our Understanding of Reversible Nε-Lysine Acylation in Bacteria. J Proteome Res. 2024 Aug 2;23(8):2733-2749. doi: 10.1021/acs.jproteome.3c00912. Epub 2024 Mar 5. PMID: 38442041; PMCID: PMC11296938.
Carabetta VJ, Hardouin J. Editorial: Bacterial Post-translational Modifications. Front Microbiol. 2022 Mar 22;13:874602. doi: 10.3389/fmicb.2022.874602. PMID: 35391732; PMCID: PMC8983106.
Luu J, Mott CM, Schreiber OR, Giovinco HM, Betchen M, Carabetta VJ. Nε-Lysine Acetylation of the Histone-Like Protein HBsu Regulates the Process of Sporulation and Affects the Resistance Properties of Bacillus subtilis Spores. Front Microbiol. 2022 Jan 17;12:782815. doi: 10.3389/fmicb.2021.782815. PMID: 35111139; PMCID: PMC8801598.
Wonderful science and summary.