Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic analysis of marine nematode Litoditis marina acclimated to different salinities

ABSTRACT: We applied tandem mass tag (TMT)-based quantitative proteomic analysis to investigate the basal protein differences among worms growing under different salinity environments.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Litoditis Marina

TISSUE(S): Whole Body

SUBMITTER: Liusuo Zhang

LAB HEAD: Liusuo Zhang

PROVIDER: PXD029671 | Pride | 2022-05-20

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Transcriptomic and Proteomic Analysis of Marine Nematode <i>Litoditis marina</i> Acclimated to Different Salinities.

Xie Yusu Y Zhang Liusuo L

Genes 20220407 4

Salinity is a critical abiotic factor for all living organisms. The ability to adapt to different salinity environments determines an organism's survival and ecological niches. <i>Litoditis marina</i> is a euryhaline marine nematode widely distributed in coastal ecosystems all over the world, although numerous genes involved in its salinity response have been reported, the adaptive mechanisms underlying its euryhalinity remain unexplored. Here, we utilized worms which have been acclimated to eit ...[more]

PMID: 35456458

Similar Datasets

Quantitative proteomic analysis of pseudomonas aeruginosa samples

Project description:Ionizing irradiation kills pathogens by destroying nucleic acids while retaining the immunogenicity of pathogen proteins. However, the overall proteome of bacteria exposed to X-ray irradiation still remain unclear. This experiment was aimed to investigate the proteome changes of the laboratory Pseudomonas aeruginosa PAO1 strain after exposure to X-ray irradiation. A total of 2963 proteins were identified in this study, of which 2599 proteins contained quantitative information. If the differential expression change threshold is 2 times, and the statistical test t-test p-value <0.05 is the significance threshold, then among the quantified proteins, the expression of 48 proteins was up-regulated and 8 protein expression was down-regulated. Based on the above data, we performed a systematic bioinformatics analysis of all identified proteins, and performed functional classification, functional enrichment, and clustering analysis based on functional enrichment for all differentially expressed proteins. Combined with the above information, it provides a reference direction for further investigation in the biological effect on P. aeruginosa PAO1 and its MV formation under X-ray irradiation.

2020-12-14 | PXD019035 | Pride

TMT-Based Quantitative Proteomic Analysis Reveals the Crucial Biological Pathways Involved in Brain Injury Induced by Chest Exposure to Shock Waves

Project description:Long term chest blast exposure can lead to mental disorders, brain inflammation and oxidative stress in soldiers. However, the underlying mechanism of brain injury caused indirectly by chest blast remains unclear. It is urgent to find more potential biomarkers to reveal the deeper pathogenesis of this phenomenon. We used iTRAQ labeling combined with LC-MS/MS to screen potential differentially expressed proteins in rat brain after chest blast at different time points. Meanwhile, we also used Go, KEGG, David and Cytoscape to analyze the proteomic profile and explore its pathogenesis. Moreover, Western blotting was used to verify the target proteins. Our data showed that, a total of 6,931 proteins were identified. A total of 255 differentially expressed proteins were identified, of which 43, 84, 52, 97 and 49 proteins were identified from brain tissues at 12h, 24h, 48h, 72h, and 1w after chest blast exposure. Bioinformatics analysis, including GO, COG, KEGG and STRING, further proved that brain damage caused by chest blast exposure was involved in many important biological processes and signal pathways, such as inflammation, cell adhesion, phagocytosis, neuronal and synaptic damage, oxidative stress and apoptosis. Moreover, Western blotting further confirmed that these differentially expressed proteins and signaling pathways were associated with brain damage caused by chest blast exposure. For the first time, we screened and verified the potential protein biomarkers of brain damage caused indirectly by chest blast, and provided a new target for the treatment of this disease.

2021-12-30 | PXD025204 | Pride

Mass spectrometry analysis of RSV-induced RAW264.7 cells

Project description:In order to further explore the expression of proteins in RSV-infected macrophages, RSV type-L19 was used to stimulate RAW264.7 cells, and then mass spectrometry was conducted to detect the expression of different proteins after RSV infection. The results showed that there were different expression of proteins in RSV activated and inactive RAW264.7 cells.

2023-05-26 | PXD042041 | Pride

Phosphoproteomic analysis reveals Rio1 regulated protein metabolism in response to UV irradiation and multiple cellular processes in Sulfolobus islandicus REY15A

Project description:In this study, we performed quantitative phosphoproteomic analysis on S. islandicus REY15A either treated with UV or in the absence of Rio1.

2020-11-05 | PXD021663 | Pride

Proteome-Wide Analyses Reveal Diverse Functions of Acylation Proteins in Neurospora crassa

Project description:Quantitative acetyl-proteomics, a newly identified post-translational modification, is known to regulate transcriptional activity in different organisms. Neurospora crassa is a model ascomycete fungus maintained for biochemistry and molecular biology research; however, extensive studies of the functions of its acylation proteins have yet to be performed. In this study, using LC-MS/MS qualitative proteomics strategies, we identified 1909 modification sites on 940 proteins in N. crassa and analysed the functions of these proteins using GO enrichment, KEGG pathway, and subcellular location experiments. We classified the acetylation protein involvement in diverse pathways, and protein-protein interaction (PPI) network analysis further demonstrated that these proteins participate in diverse biological processes. In summary, our study comprehensively profiles the crosstalk of modified sites, and PPI among these proteins may form a complex network with both similar and distinct regulatory mechanisms, providing improved understanding of their biological functions in N. crassa.

2021-01-26 | PXD022001 | Pride

Proteomics Study Reveals Involvement of Lysine Acetylation in Metabolic Disorder in Human Hepatocellular Carcinoma

Project description:Protein lysine acetylation is a vital post-translational modification (PTM) that plays important roles in biological processes and human diseases. However, its potential roles in hepatocellular carcinoma (HCC) development remain largely unknown. Here we performed a quantitative acetylome analysis of tumor and normal liver tissues from HCC patients. Overall, we identified 792 lysine acetylation sites in 415 proteins, and almost half of their acetylation levels were significantly changed in HCC tumor tissues. The acetylated proteins mainly consisted of metabolic enzymes, which was consistent with the subcellular location analysis that they were primarily located in mitochondria and cytoplasm. Consistently, Bioinformatics analysis showed that differently acetylated proteins were mainly involved in metabolic pathways, such as glycolysis, the tricarboxylic acid (TCA) cycle, fatty acid oxidation, and glutamine metabolism. Then we selected two down-regulated enzymes and verified their acetylation levels in HCC liver tissues. In addition, transcription factors and proteins associated with oxidative stress were identified with aberrant acetylation levels in HCC tumor tissues. Our findings illustrate abundant lysine acetylation sites in HCC liver tissues, which provides insight into the role of lysine acetylation in HCC development, and further contributes to possible implications for its use in diagnose and therapy in the future.

2021-06-14 | PXD014915 | Pride

Proteomic analyses of lysine 2-hydroxyisobutyrylation in Fusarium graminearum in response to tebuconazole and carbendazim

Project description:Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered post-translational modification in some prokaryotic and eukaryotic organisms. Here, we carried out proteome-wide analysis of Khib in Fusarium graminearum, identifying the reshaping of lysine 2-hydroxyisobutyrylome by tebuconazole or carbendazim, using the most recently-developed high-resolution LC-MS/MS in combination with high-specific affinity enrichment. In total, 3035 quantifiable Khib sites on 937 proteins were identified. With the criteria of fold changes over 1.3, normalized with total proteins, 1083 Khib sites of 509 proteins were considered as significantly affected by tebuconazole treatment, while 344 Khib sites of 227 proteins were significantly affacted by carbendazim. Furthermore, bioinformatics analysis were conducted.

2022-04-04 | PXD022499 | Pride

Genotyping, generation and lysine 2-hydroxyisobutyrylation identification of the first human autosomal dominant osteopetrosis type II specific induced pluripotent stem cells

Project description:Background: Autosomal dominant osteopetrosis type II (ADO2) is a rare human genetic disease that has been broadly studied as an important osteopetrosis model; however, there are no disease-specific induced pluripotent stem cells (ADO2-iPSCs) that may be valuable for understanding the pathogenesis and may be a potential source of cells for autologous cell therapy. Methods: To generate the first human ADO2-iPSCs from a Chinese family with ADO2 and to identify their characteristics, blood samples were collected from the proband and his parents and were used for genotyping by whole-exome sequencing (WES); the urine-derived cells of the proband were reprogrammed with episomal plasmids that contained transcription factors, such as KLF4, OCT4, c-MYC, and SOX2. The proteome-wide analysis of lysine 2-hydroxyisobutyrylation in the ADO2-iPSCs and control cell lines was performed by high-resolution LC-MS/MS and a bioinformatics analysis. Results: WES with filtering strategies identified a mutation in CLCN7 (R286W) in the proband and his father, which was absent in the proband’s mother and the healthy controls; this was confirmed by Sanger sequencing. The ADO2-iPSCs were successfully generated, which carried the normal male karyotype (46, XY) and carried the mutation of CLCN7 (R286W); the ADO2-iPSCs positively expressed alkaline phosphatase and other surface markers; and no vector and transgene was detected. The ADO2-iPSCs could differentiate into all three germ cell layers, both in vitro and in vivo. Our proteomic profiling detected 7, 405 proteins and revealed 3,684 2-hydroxyisobutyrylated sites in 1,036 proteins in the ADO2-iPSCs. Conclusions: Our data indicated that mutation CLCN7 (R286W) may be a cause of the osteopetrosis family. The generated vector-free and transgene-free ADO2-iPSCs with identified lysine 2-hydroxyisobutyrylation may be valuable for personalized and cell-based regenerative medicine in the future.

2022-02-15 | PXD014227 | Pride

Crotonylome profiling reveals extensive lysine crotonylation in common wheat

Project description:Histone lysine crotonylation (Kcr) is a newly discovered protein post-translational modification (PTM), which was detected from yeast to humans and is mainly related with active transcription. With the development of proteomics technologies, high abundance of non-histone proteins modified by Kcr was also found recently. Here, we first report that lysine Kcr also occurs on cytoplasmic and mitochondrial proteins in common wheat (Triticum aestivum L.). We identified 4,696 Lys-acetylated sites on 1,726 proteins which involved in a wide variety of biological processes, such as chromatin-associated processes, Calvin-Benson cycle, glycolysis, protein metabolism and transport, which representing the largest dataset of lysine acylation proteome reported in the plant kingdom. Interestingly, 98 proteins were involved in multiple processes of photosynthesis, suggesting an important role of lysine Kcr in processes. In addition, 21 potentially specific Kcr motifs in wheat were detected. The protein interaction network analysis revealed that diverse interactions are modulated by protein Kcr. The overlap between Kcr and acetylation (Kac) indicated that they may coordinately regulate the function of some proteins in common wheat. Futhermore, comparative analysis indicated that lysine Kcr is conserved between common wheat and Nicotiana tabacum. Taken together, this study provided the first global survey of Kcr in wheat, making a promising starting point for further functional analysis of Kcr in plants.

2023-07-20 | PXD008483 | Pride

Systematic analysis of the lysine malonylome in Sanghuangporus sanghuang

Project description:Background: Sanghuangporus sanghuang is a well-known traditional medicinal mushroom associated with mulberry, which has enormous economic and medical value. Despite being known for many years, the regulatory mechanisms of bioactive compounds biosynthesis in this medicinal mushroom are still unclear.Lysine malonylation is one of a post-translational modifications that has many critical functions in various aspects of cell metabolism. However, at present we do not know its role in S. sanghuang. In this study, a global investigation of lysine malonylome in S. sanghuang was therefore carried out. Results: In total, 714 malonyl modification sites were matched to 255 different proteins. The analysis indicated that malonyl modifications were involved in a wide range of acellular functions and displayed a distinct subcellular localization. Bioinformatics analysis indicated that malonylated proteins were engaged in different metabolic pathways, including glyoxylate and dicarboxylate metabolism, glycolysis/gluconeogenesis, and the tricarboxylic acid (TCA) cycle. Notably, a total of 26 enzymes related to triterpene and polysaccharide biosynthesis were found to be malonylated, indicating an indispensable role of lysine malonylation in bioactive compounds biosynthesis in S. sanghuang. Conclusions: These findings suggest that malonylation is associated with many metabolic pathways, particularly the metabolism of bioactive compounds triterpene and polysaccharide. This paper represents the first comprehensive survey of malonylation in S. sanghuang and provides an important data for further study on the physiological function of lysine malonylation in S. sanghuang and other medicinal mushrooms.

2022-02-17 | PXD025835 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data