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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

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 | GSE261019 | GEO

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

2024-06-26 | GSE260894 | GEO

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

Staphylococcus aureus LC-MSMS lactylation

Project description:To extensively elucidate protein lactylation (Kla), a proteome-wide analysis of lactylation was carried out in Staphylococcus aureus. Proteins extracted from Staphylococcus aureus were digested by trypsin and anti-lactyl lysine antibody was used to enrich the lactylated peptides, which were determined by following LC-MS/MS analysis.

2024-10-08 | PXD046022 | Pride

Proteome and Crotonylome of normal and leucine deprivation treated AML12 cells

Project description:Leucine, as a branched amino acid, is not only a substrate for protein synthesis, but also a signaling molecule that affects many biological processes. Lysine crotonylation is a novel post-translational modification in both histone and non-histone proteins. What effect amino acids have on crotonylation remains unclear. Here, we identified a large number of crotonylated proteins and sites affected by leucine deprivation for 2 hours in AML12 cells.

2023-05-10 | PXD018118 | Pride

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

Toxoplasma gondii; protein posttranslational modification; lactylation; metabolism; function

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

Genome-wide maps of histone modifications in response to nitrogen deprivation in Nannochloropsis oceanica.

Project description:Epigenetic regulation in response to nitrogen stress for one ant two days, and epigenome-association with phenotypic plasticity of lipid metabolism are firstly uncovered in marine microalga Nannochloropsis oceanica IMET1. The result showed that H3K27ac, Kcr, Kbu and H3K36me2 histone modifications were present in N. oceanica IMET1. Moreover, they regulated gene expression.

2023-08-23 | GSE224086 | GEO

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