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Analysis of lactylome refines key molecular reprogramming mechanisms during oil production in Nannochloropsis oceanica

ABSTRACT: Lysine lactylation as a type of posttranslational modifications (PTMs) is recently associated with chromatin remodeling and gene transcription, but lysine lactylation of histone and non-histone proteins has not yet been studied in Nannochloropsis oceanica. To examine the prevalence and function of lactylation in N. oceanica, protein lactylation modification profiles were tracked after nitrogen deprivation for three days using 4D label-free proteome method. Under nitrogen deprivation (ND) and nitrogen repletion (NR) cultivation conditions, we mapped lactylome of proliferating microalgal cells.

INSTRUMENT(S): autoflex, timsTOF Pro

ORGANISM(S): Nannochloropsis Oceanica Strain Imet1

TISSUE(S): Cell Culture

SUBMITTER: Li Wei

LAB HEAD: Li WEI

PROVIDER: PXD038775 | Pride | 2024-07-03

REPOSITORIES: Pride

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Publications

Integration of Epigenome and Lactylome Reveals the Regulation of Lipid Production in Nannochloropsis oceanica.

Ouyang Lingyu L Wang Jiao J Zhu Han H Wu Yikai Y Wei Li L

Journal of agricultural and food chemistry 20240606

Lysine lactylation (Kla) is a kind of novel post-translational modification (PTM) that participates in gene expression and various metabolic processes. Nannochloropsis has a remarkable capacity for triacylglycerol (TAG) production under nitrogen stress. To elucidate the involvement of lactylation in lipid synthesis, we conducted chromatin immunoprecipitation sequencing (ChIP-seq) and mRNA-seq analyses to monitor lactylation modifications and transcriptome alterations in Nannochloropsis ...[more]

PMID: 38842303

Similar Datasets

Analysis of proteome refines key molecular reprogramming mechanisms during oil production in Nannochloropsis oceanica

Project description:To examine the mechanisms during oil production and integrate analysis of lactylation in N. oceanica, protein expression profiles were tracked after nitrogen deprivation for three days using 4D label-free proteome method. Under nitrogen deprivation (ND) and nitrogen repletion (NR) cultivation conditions, we mapped proteome of proliferating microalgal cells.

2024-07-03 | PXD038833 | Pride

Integration of epigenome and lactylome reveals the regulation of lipid production in Nannochloropsis oceanica [RNA-Seq]

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.

2024-06-26 | GSE260894 | GEO

Integration of epigenome and lactylome reveals the regulation of lipid production in Nannochloropsis oceanica

2024-06-26 | GSE261019 | GEO

Analysis of Lysine Lactylation in CD4+ T cells of normal and EAU mouse

Project description:Primary CD4+ T cells were isolated from normal and EAU mice spleens and used for lactylome analysis.

2023-08-29 | PXD040514 | Pride

Lysine lactylation critically regulated energy metabolism of the protozoan parasite Trypanosoma brucei

Project description:Lysine lactylation, a new post-translational modification identified on histones of human and mouse cells, stimulates gene transcription from chromatin directly. However, very little is known in the scope and cellular distribution of lactylated proteins. In the present study, we conducted the first proteome-wide survey of lactylated sites in Trypanosoma brucei, a unicellular parasite causing human African sleeping sickness and livestock nagana disease, using LC-MS/MS to identify peptides enriched by immuno-purification with an anti-lactyllysine antibody. Overall, we identified 387 unique lysine lactylated sites in 257 lactylated proteins with diverse cellular localizations and biological functions. Lactylated proteins are involved in a wide variety of cellular functions such as metabolism and gene regulation. Further, we demonstrate that the lactate-derived lactylation in trypanosome is regulated by glucose metabolism. Collectively, our findings provide the first comprehensive view of the lactylome of T. brucei and suggest that lysine lactylation in trypanosomes involves a diverse array of cellular functions.

2021-10-01 | PXD023011 | 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.

2022-06-09 | PXD031526 | Pride

Global Proteomic Analysis of Lysine lactylation in HMC3 cells under Normoxia or Hypoxia

Project description:This project carried out a quantitative study of lactylation in HMC3 Cell Line. In order to ensure a high degree of credibility of the results, we used the standard of localization probability>0.75 to filter the authentication data. In this study, a total of 3093 lactylation sites located on 1270 proteins were identified, of which 1601 sites of 751 proteins contain quantitative information. Subsequently, we carried out a systematic bioinformatics analysis of proteins containing quantitative information sites, including protein annotation, functional classification, functional enrichment and cluster analysis based on functional enrichment.

2023-03-28 | PXD028737 | Pride

Human liver cell line LO2 LC-MS/MS

Project description:A hyperlipidaemia model of L02 cells was established using free fatty acids (FFA, oleate and palmitate, 2:1; Sigma-Aldrich, USA) at a final concentration of 1 mM for 24 h. Cells were allowed to attach overnight prior to HTG-medicated serum for 24 h and then exposed to FFA during drug treatment. After treatment, LO2 cells were harvest and stored at -80 ℃, lactylation proteomics was performed by Jingjie PTM BioLabs (Hangzhou, China).

2024-01-26 | PXD045069 | Pride

Systematic profiling of lysine lactylation proteome reveals distinct changes in lactylation between the parental AGS cells and cisplatin-resistant AGS cells

Project description:Lactate enable to cause a novel post-translational modification, lactylation of proteins. We are interested in exploring whether lactate modulates DNA-damaging agents resistance in the form of lactylation. To gain a global view of DNA-damaging agents resistance-related lactylation, especially Kla of nonhistone substrates, we used 4D-Label free high-resolution LC-MS/MS, quantitative lysine lactylation analysis to investigate Kla substrates in cisplatin-resistant AGS cells.

2024-05-09 | PXD050906 | Pride

Ikzf1 lactylation regulates CD4 T cell differentiation

Project description:Dysregulation of Th17 differentiation was implicated in multiple inflammatory and autoimmune diseases including autoimmune uveitis. In the current study, we have provided evidence indicating that lactate-derived lactylation plays important roles in regulating Th17 differentiation. The lactylation level of CD4+ T cells was upregulated in EAU mice and inhibiting lactylation resulted in impaired EAU progression. We characterized the global lactylome of CD4+ T cells of normal and EAU mice. We found that the differentially lactylated proteins were enriched in pathways related to immune responses including leukocyte differentiation. Importantly, our results show that the lactylation level of Ikzf1 (K164) functions in regulating Th17 differentiation by differentially modulating gene expression patterns which are related to CD4+ T cell differentiation by CUT& Tag analysis. In view of the above mentioned well-documented evidence, Ikzf1 lactylation might represent an important regulator for Th17 differentiation in autoimmune uveitis.

2023-08-28 | GSE226678 | GEO