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SILAC experiment quantifying the proteomics of WT and HBO1-KO HeLa

ABSTRACT: Lysine lactylation (Kla) links metabolism and gene regulation and plays a key role in multiple biological processes. We report that HBO1 functions as a lysine lactyltransferase to regulate transcription. Quantitative proteomic analysis further revealsed 95 endogenous Kla sites targeted by HBO1, with the majority located on histones.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Cervix Squamous Epithelium

DISEASE(S): Cervix Carcinoma

SUBMITTER: siyu wang

LAB HEAD: Kai Zhang

PROVIDER: PXD051415 | Pride | 2024-04-13

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	HeLa-Histone-La.raw	Raw
	HeLa-Histone-LactylationSites.txt	Txt
	HeLa-Kla-1.raw	Raw
	HeLa-Kla-2.raw	Raw
	HeLa-Kla-3.raw	Raw

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Lysine lactylation regulates biofilm formation of streptococcus mutans

Project description:Lactate produced in glycolysis has recently been discovered to modify lysine residues on eukaryotic proteins, a post-translational modification (PTM) called lysine lactylation (Kla). This modification not only participates in regulating gene expression through lactylation of histones, but also impacts the function of non-histone proteins. However, lactylation in prokaryotes has not been reported. Here, we report the identification of 1869 lysine lactylation sites in 465 proteins in the cariogenic organism Streptococcus mutans using a newly developed 4-dimensional label-free quantitative proteomic approach, representing the first Kla dataset in prokaryotes. Combining quantitative analysis, we report that the modification levels of 282 sites from 124 proteins increased by over 1.5-fold, and 80 sites from 52 proteins decreased by over 0.67-fold in the biofilm growth state. These results provide a systematic perspective of the distribution and function of Kla and improve our understanding of the role of lactate in the metabolic regulation of prokaryotes.

2023-08-24 | PXD037027 | Pride

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2022-08-11 | PXD033991 | Pride

HBO1 catalyzes lysine lactylation and mediates histone H3K9la to regulate gene transcription

Project description:Lysine lactylation (Kla) links metabolism and gene regulation and plays a key role in multiple biological processes. However, the regulatory mechanism and functional consequence of Kla remain to be explored. Here, we report that HBO1 functions as a lysine lactyltransferase to regulate transcription. Interestingly, CUT&Tag assays demonstrate that HBO1 is required for histone H3K9la on TSSs and the regulated Kla can facilitate in signaling pathways and progress of tumorigenesis. Our study reveals HBO1 serves as a lactyltransferase to mediate a histone Kla-dependent gene transcription.

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Project description:Protein lactylation is a newly discovered posttranslational modification (PTM) and involved in multiple biological processes both in mammalian cells and rice grains. However, the function of lysine lactylation remains unexplored in wheat. In this study, we performed the first comparative proteomes and lysine lactylomes during seed germination of wheat. In total, 8,000 proteins and 927 lactylated sites in 394 proteins were identified at 0 and 12 hour after imbibition (HAI). Functional enrichment analysis showed that glycolysis and the TCA cycle related proteins were significantly enriched, and more differentially lactylated proteins were enriched in up-regulated lactylated proteins at 12 HAI vs 0 HAI through KEGG pathway and protein domain enrichment analysis compared to down-regulated lactylated proteins. Meanwhile, ten particularly preferred amino acids near lactylation sites were found in the embryos of germinated seeds: AA*KlaT, A***KlaD********A, KlaA**T****K, K******A*Kla, K*Kla********K, KlaA******A, Kla*A, KD****Kla, K********Kla and KlaG. These results supplied a comprehensive profile of lysine lactylation of wheat and indicated that protein lysine lactylation played important functions in several biological processes.

2024-01-26 | PXD046488 | Pride

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Project description:Toxoplasma gondii, a single-celled protozoan parasite (phylum Apicomplexa) and remains the causative pathogen of one of the most wide-spread infectious diseases, toxoplasmosis. To continuously proliferate in warm-blooded animals, this parasite undergoes repeated cycles of invasion, division and induction of host cell rupture. Lactate, which is derived from cellular metabolic pathways, is widely considered not only an energy source in organisms but also a regulatory molecule that participates in gene activation. Lysine lactylation is a new type of protein posttranslational modification (PTM) that was recently associated with chromatin remodeling, but the lysine lactylation of histone and nonhistone proteins has not yet been studied in parasites. To examine the prevalence and function of lactylation in T. gondii parasites, we mapped the lactylation proteome of proliferating tachyzoite cells and found 1,964 lactylation sites on 955 proteins in the T. gondii RH strain. The lactylated proteins were distributed in multiple subcellular compartments and were closely related to a wide variety of biological processes, including mRNA splicing, the citrate cycle (TCA cycle), aminoacyl-tRNA biosynthesis, glyoxylate and dicarboxylate metabolism, glycolysis/gluconeogenesis, oxidative phosphorylation, RNA transport and the HIF-1 signaling pathway. Lysine lactation might regulate numerous cellular processes to aid the establishment of a hospitable environment that allows the survival, replication and dissemination of the parasite. These study offers the first data of the global lactylation proteome and provides a basis for further functional dissection of important proteins associated with T. gondii development and pathogenicity.

2024-04-07 | PXD022700 | Pride

Systematic Identification of the Lysine lactylation in the Protozoan Parasite Toxoplasma gondii

Project description:Lysine lactylation (Kla) is a new posttranslational modification (PTM) identified in histone and nonhistone proteins of several eukaryotic cells that directly activate gene expression and DNA replication. However, very little is known about their scope and cellular distribution in apicomplexan parasites that are important to public and animal health. Toxoplasma gondii, the agent of toxoplasmosis, is one of obligate intracellular apicomplexan parasite that can infect all kinds of nucleated cells of animals and humans. Using this parasite as model organism, herein, we produced the first global lysine lactylome profile through LC-MS/MS. Overall, a total of 983 Kla sites occurred on 523 lactylated proteins were identified in Toxoplasma tachyzoites, the acute toxoplasmosis-causing stage. Bioinformatics analysis revealed that these lactylated proteins are evolutionarily conserved and involved in a wide variety of cellular functions such as energy metabolism, gene regulation and protein biosynthesis. Moreover, the results from subcellular localization analysis and IFA showed that the majority of lactylated T. gondii proteins localized in the nucleus, indicating a potential impact of Kla on gene regulation. Notably, an extensive batch of parasite-specific proteins unique to Apicomplexa is lactylated in T. gondii. Our findings revealed that Kla was widespread in the early branching eukaryotic cell, and that lactylated proteins, including a crowd of unique parasite proteins, were involved in a remarkably diverse array of cellular functions. These valuable data will improve our understanding of the evolution of Kla while potentially providing novel therapeutic avenues.

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Dynamic profiling of histone Kcr and Kla during neural differentiation in P19 embryonal carcinoma cells

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Project description:Lysine lactylation (Kla) is a kind of novel post-translational modification (PTM), which participates in gene expression and various metabolic processes. Nannochloropsis, a significant oleaginous microalgae of economic significance, demonstrates a remarkable capacity for triacylglycerol (TAG) production under nitrogen stress. To elucidate the involvement of lactylation in lipid synthesis, we conducted ChIP-seq and mRNA-seq analyses to monitor lactylation modifications and transcriptome alterations in Nannochloropsis oceanica. In all, 2,057 genes showed considerable variation between nitrogen deprivation (ND) and nitrogen repletion (NR) conditions, comprising 853 upregulated genes and 1,204 downregulated genes. Moreover, a total of 5,375 differential Kla peaks were identified, including 5,331 gain peaks and 44 loss peaks under ND vs NR. The differential Kla peaks were primarily distributed in the promoter (<= 1 kb) (71.07%), 5’UTR (22.64%), and exon (4.25%). Integrative analysis of ChIP-seq, transcriptome, and previous proteome and lactylome data elucidates the potential mechanism by which lactylation promotes lipid accumulation under ND. Lactylation facilitates autophagy and protein degradation, leading to the recycling of carbon into the tricarboxylic acid (TCA) cycle, thereby providing carbon precursors for lipid synthesis. Additionally, lactylation induces the redirection of carbon from membrane lipids to TAG by upregulating lipases and enhancing the TCA cycle and β-oxidation pathways. This research reveals the regulatory functions of lactylation in lipid metabolism and gene expression in Nannochloropsis, offering a new perspective for the investigation of lipid biosynthesis.

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