1. Class I histone deacetylases (HDAC1-3) are histone lysine delactylases
Carlos Moreno-Yruela, Di Zhang, Wei Wei, Michael Bæk, Wenchao Liu, Jinjun Gao, Daniela Danková, Alexander L Nielsen, Julie E Bolding, Lu Yang, Samuel T Jameson, Jiemin Wong, Christian A Olsen, Yingming Zhao Sci Adv. 2022 Jan 21;8(3):eabi6696. doi: 10.1126/sciadv.abi6696. Epub 2022 Jan 19.
Lysine L-lactylation [K(L-la)] is a newly discovered histone mark stimulated under conditions of high glycolysis, such as the Warburg effect. K(L-la) is associated with functions that are different from the widely studied histone acetylation. While K(L-la) can be introduced by the acetyltransferase p300, histone delactylases enzymes remained unknown. Here, we report the systematic evaluation of zinc- and nicotinamide adenine dinucleotide-dependent histone deacetylases (HDACs) for their ability to cleave ε-N-L-lactyllysine marks. Our screens identified HDAC1-3 and SIRT1-3 as delactylases in vitro. HDAC1-3 show robust activity toward not only K(L-la) but also K(D-la) and diverse short-chain acyl modifications. We further confirmed the de-L-lactylase activity of HDACs 1 and 3 in cells. Together, these data suggest that histone lactylation is installed and removed by regulatory enzymes as opposed to spontaneous chemical reactivity. Our results therefore represent an important step toward full characterization of this pathway's regulatory elements.
2. Quantification of N6-formylated lysine in bacterial protein digests using liquid chromatography/tandem mass spectrometry despite spontaneous formation and matrix effects
Jacob S Folz, Jenelle A Patterson, Andrew D Hanson, Oliver Fiehn Rapid Commun Mass Spectrom. 2021 Mar 15;35(5):e9019. doi: 10.1002/rcm.9019.
Rationale: N6-Formyl lysine is a well-known modification of histones and other proteins. It can also be formed as a damaged product from direct formylation of free lysine and accompanied by other lysine derivatives such as acetylated or methylated forms. In relation to the activity of cellular repair enzymes in protein turnover and to lysine metabolism, it is important to accurately quantify the overall ratio of modified lysine to free lysine. Methods: N6-Formyl lysine was quantified using liquid chromatography/tandem mass spectrometry (LC/MS/MS) with data collected in a non-targeted manner using positive mode electrospray ionization on a Q-Exactive HF+ Orbitrap mass spectrometer. Studies were performed with lysine and deuterated lysine spiked into protein digests and solvents to investigate the extent of spontaneous formation and matrix effects of formation of N6-formyl lysine. Results: We show that N6-formyl lysine, N2-formyl lysine, N6-acetyl lysine, and N2-acetyl lysine are all formed spontaneously during sample preparation and LC/MS/MS analysis, which complicates quantification of these metabolites in biological samples. N6-Formyl lysine was spontaneously formed and correlated to the concentration of lysine. In the sample matrix of protein digests, 0.03% of lysine was spontaneously converted into N6-formyl lysine, and 0.005% of lysine was converted into N6-formyl lysine in pure run solvent. Conclusions: Spontaneous formation of N6-formyl lysine, N6-acetyl lysine, N2-formyl lysine, and N2-acetyl lysine needs to be subtracted from biologically formed lysine modifications when quantifying these epimetabolites in biological samples.
3. Theoretical and experimental study of the infrared and Raman spectra of L-lysine acetylation
Guohua Yao, Qing Huang Spectrochim Acta A Mol Biomol Spectrosc. 2022 Oct 5;278:121371. doi: 10.1016/j.saa.2022.121371. Epub 2022 May 12.
Acetylation is a common and extremely important protein modification in biology, referring to the covalent attachment of an acetyl group to the amino group. There are two forms of protein acetylation, which are lysine Nε-acetylation and N-terminal Nα-acetylation, respectively. Protein lysine Nε-acetylation is a globally important post-translational modification which plays a critical regulatory role in almost all aspects of cell metabolism. In addition, whether lysine on the N-terminal of protein can undergo Nα-acetylation is still a controversial viewpoint. Carrying out further molecular study of the role of acetylation is also the one of challenges. In order to investigate the protein acetylation more effectively, it is thus necessary to have a thorough and comprehensive understanding of lysine acetylation. In this work, both Raman and infrared (IR) spectra of L-lysine Nε-Ace-Lys, Nα-Ace-Lys, and NαNε-Ace-Lys were explored through both experimental experiment and theoretical computation based on density function theory (DFT). Vibration assignments and geometry structures of three acetylated lysines were therefore obtained for the first time in this work. The IR or Raman spectra of four molecules are very different from each other, which can be easily distinguished from the characteristic bands at 1500-1700 cm-1 and 3200-3400 cm-1 regions. Therefore, this work may provide the guide for probing the protein acetylation by Raman and IR spectroscopy.
