Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA118545 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:RNA extracted at 240min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.
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Project description:The post-translational modification of lysine acetylation is related to hepatocellular carcinoma (HCC), and understanding this relationship requires detailed knowledge about the acetylated proteome in HCC tissue and about differences in protein acetylation between cirrhosis and liver cancer. Here we characterized the acetylome in three paired sets of cirrhotic tissue and hepatitis B-related HCC tissue. Combining affinity-based enrichment of acetylated peptides with highly sensitive mass spectrometry, we identified 1493 acetylation sites in 777 proteins and quantified 1040 acetylation sites in 587 proteins. We discovered that the histone acetyltransferases p300 and CBP were hyperacetylated in HCC and cirrhosis but not in normal liver tissue. We also identified several proteins acetylated at more than 10 lysines in HCC and cirrhosis. In addition, our results revealed that HCC was associated with up-regulation of acetylation at 353 sites in 237 proteins and down-regulation of acetylation at 209 sites in 122 proteins. We validated our results using western blotting and immunohistochemistry. Validation with an independent set of clinical samples confirmed our initial screening result that acetylation of lysine 120 in histone H2B type 1-C/E/F/G/I and lysine 18 in histone H3.3 was significantly associated with survival of HCC patients. Acetylation of lysine 77 in histone H4 was associated with survival as well as recurrence. Our study provides numerous new leads to examine the role of acetylation in HCC and its potential as a prognostic marker as well as therapeutic target.
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Project description:Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal 5'-phosphate (PLP) dependent enzymes known as the aspartate aminotransferase superfamily or alpha-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-l-kynurenine to produce 3-hydroxyanthranilate and l-alanine, while l-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km of 28.3 +/- 1.9 microM and a specific activity of 1.75 micromol min-1 mg-1 for 3-hydroxy-dl-kynurenine. Crystals of recombinant kynureninase that diffracted to 2.0 A were obtained, and the atomic structure of the PLP-bound holoenzyme was determined by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB entry 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the "open" and "closed" conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins' small domains and reveals a role for Arg-434 similar to its role in other AAT alpha-family members. Docking of 3-hydroxy-l-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates.
| S-EPMC2531291 | biostudies-literature