Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA322081 | ENA |
REPOSITORIES: ENA
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Project description:NAD(P)H:quinone Oxidoreductase (NQO1) is essential for cell defense against reactive oxidative species, cancer, and metabolic stress. Recently, NQO1 was found in ribonucleoprotein (RNP) complexes, but NQO1-interacting mRNAs and the functional impact of such interactions are not known. Here, we used ribonucleoprotein immunoprecipitation (RIP) and microarray analysis to identify comprehensively the subset of NQO1 target mRNAs in human hepatoma HepG2 cells. One of its main targets, SERPINA1 mRNA, encodes the serine protease inhibitor α-1-antitrypsin, A1AT, which is associated with disorders including obesity-related metabolic inflammation, chronic obstructive pulmonary disease (COPD), liver cirrhosis and hepatocellular carcinoma. Biotin pulldown analysis indicated that NQO1 can bind the 3’ untranslated region (UTR) and the coding region (CR) of SERPINA1 mRNA. NQO1 did not affect SERPINA1 mRNA levels; instead, it enhanced the translation of SERPINA1 mRNA, as NQO1 silencing decreased the size of polysomes forming on SERPINA1 mRNA and lowered the abundance of A1AT. Luciferase reporter analysis further indicated that NQO1 regulates SERPINA1 mRNA translation through the SERPINA1 3’UTR. Accordingly, NQO1-KO mice had reduced hepatic and serum levels of A1AT and increased activity of neutrophil elastase, one of the main targets of A1AT. We propose that this novel mechanism of action of NQO1 as RNA-binding protein may help to explain its pleiotropic biological effects.
2017-05-22 | GSE81614 | GEO
Project description:Novel RNA-binding activity of MYF5 enhances Ccnd1/Cyclin D1 mRNA translation during myogenesis
| PRJNA297693 | ENA
Project description:Tristetraprolin family of proteins regulate mRNA stability by binding to specific AU-rich elements in transcripts. This binding promotes the shortening of the mRNA poly(A) tail, or deadenylation, initiating mRNA degradation. The CCR4-NOT complex plays a central role in deadenylation, while the cytoplasmic poly(A)-binding protein PABPC1 typically protects mRNAs from decay. Here, we investigate how tristetraprolin interacts with CCR4-NOT and PABPC1 to control mRNA stability. Using purified proteins and in vitro assays, we find that tristetraprolin engages CCR4-NOT through multiple interaction sites and promotes its activity, emphasizing the importance of multivalent binding for efficient deadenylation. Phosphorylation of tristetraprolin does not affect its interaction with CCR4-NOT or its deadenylation activity, but is essential for tristetraprolin binding to PABPC1. We propose that tristetraprolin promotes the processive deadenylation activity of CCR4-NOT on mRNAs containing AU-rich elements, with phosphorylation-dependent interactions with PABPC1 potentially enhancing deadenylation and promoting regulated mRNA decay.
2025-06-30 | MSV000098386 | MassIVE
Project description:The RNA-binding protein eIF2A has been implicated in a variety of cellular processes including tumorigenesis. This role has been attributed to its function as alternative translation initiation factor. However, the mechanisms by which eIF2A regulates translation and its contribution to oncogenic transformation are unclear. Here, we shed light on these aspects using a melanoma cell model consisting of the non-tumoral melanocytic cell line MelST and its metastatic counterpart obtained by RasV12 overexpression (MelSTR). Depletion of eIF2A from MelST and MelSTR cells revealed acquired dependencies upon Ras transformation for migration. Surprisingly, analysis of the transcriptome (RNA-Seq) and translatome (ribosome profiling) upon eIF2A depletion showed minor to no changes in translation. RIP-Seq and RT-qPCR furthermore indicate that eIF2A binds mRNA targets in a translation-independent manner. Interestingly, protein interactome analyses point towards a function of eIF2A in cytoskeletal remodeling and indeed we can show that eIF2A localizes to the centrosome and affects its composition and orientation, linking eIF2A with migration. In addition, eIF2A promotes migration in a manner that depends on its RNA-binding activity. Together, these results indicate that eIF2A does not function as a translation factor in melanoma cells, but through a novel function which is based on its RNA-binding activity and its connections to the centrosome.
2025-06-27 | GSE279657 | GEO
Project description:The RNA-binding protein eIF2A has been implicated in a variety of cellular processes including tumorigenesis. This role has been attributed to its function as alternative translation initiation factor. However, the mechanisms by which eIF2A regulates translation and its contribution to oncogenic transformation are unclear. Here, we shed light on these aspects using a melanoma cell model consisting of the non-tumoral melanocytic cell line MelST and its metastatic counterpart obtained by RasV12 overexpression (MelSTR). Depletion of eIF2A from MelST and MelSTR cells revealed acquired dependencies upon Ras transformation for migration. Surprisingly, analysis of the transcriptome (RNA-Seq) and translatome (ribosome profiling) upon eIF2A depletion showed minor to no changes in translation. RIP-Seq and RT-qPCR furthermore indicate that eIF2A binds mRNA targets in a translation-independent manner. Interestingly, protein interactome analyses point towards a function of eIF2A in cytoskeletal remodeling and indeed we can show that eIF2A localizes to the centrosome and affects its composition and orientation, linking eIF2A with migration. In addition, eIF2A promotes migration in a manner that depends on its RNA-binding activity. Together, these results indicate that eIF2A does not function as a translation factor in melanoma cells, but through a novel function which is based on its RNA-binding activity and its connections to the centrosome.
2025-06-27 | GSE279472 | GEO
Project description:The RNA-binding protein eIF2A has been implicated in a variety of cellular processes including tumorigenesis. This role has been attributed to its function as alternative translation initiation factor. However, the mechanisms by which eIF2A regulates translation and its contribution to oncogenic transformation are unclear. Here, we shed light on these aspects using a melanoma cell model consisting of the non-tumoral melanocytic cell line MelST and its metastatic counterpart obtained by RasV12 overexpression (MelSTR). Depletion of eIF2A from MelST and MelSTR cells revealed acquired dependencies upon Ras transformation for migration. Surprisingly, analysis of the transcriptome (RNA-Seq) and translatome (ribosome profiling) upon eIF2A depletion showed minor to no changes in translation. RIP-Seq and RT-qPCR furthermore indicate that eIF2A binds mRNA targets in a translation-independent manner. Interestingly, protein interactome analyses point towards a function of eIF2A in cytoskeletal remodeling and indeed we can show that eIF2A localizes to the centrosome and affects its composition and orientation, linking eIF2A with migration. In addition, eIF2A promotes migration in a manner that depends on its RNA-binding activity. Together, these results indicate that eIF2A does not function as a translation factor in melanoma cells, but through a novel function which is based on its RNA-binding activity and its connections to the centrosome.
2025-06-27 | GSE279471 | GEO
Project description:The initiation of translation begins with formation of a ribosome-mRNA complex. In bacteria, the 30S ribosomal subunit is recruited to many mRNAs through both base pairing with the Shine Dalgarno (SD) sequence and RNA-binding by ribosomal protein bS1. Translation can initiate on mRNAs that are being transcribed, and RNA polymerase (RNAP) can promote recruitment of the pioneering 30S. Here we have examined ribosome recruitment to mRNAs using cryogenic electron microscopy (cryo-EM), single-molecule fluorescence co-localization, and whole-cell cross-linking mass spectrometry. Structures of 30S-mRNA complexes show that bS1 delivers the mRNA to the ribosome for SD duplex formation and initial 30S subunit activation. RNAP associates flexibly with the 30S platform during nascent mRNA delivery and accelerates their association in a bS1-dependent manner in vitro. Collectively, our data provide a mechanistic framework for how the SD duplex, ribosomal proteins and RNAP cooperate in 30S recruitment to mRNAs and thereby establish transcription-translation coupling.
2024-11-15 | PXD048229 | JPOST Repository
Project description:The emergence and spread of Plasmodium falciparum human malaria parasites resistant to antimalarial drugs, including artemisinin, a first line antimalarial drug, is threatening malaria treatment and prompting fears of a resurgence of the disease. New drugs with novel mode of actions are thus urgently required. Several compounds with antimalarial activity are known to target protein translation, although few of these targets have been validated. Translation initiation in eukaryotes is known to require eukaryotic translation initiation factor 4F (eIF4F) complex, which binds to the 5′-cap structure on mature mRNA and recruits other proteins for translation of mRNA. The putative components of the eIF4F complex in P. falciparum have been identified in the genome including PfeIF4E, a 5′-cap-binding protein; PfeIF4A, a helicase protein for unwinding mRNA, and PfeIF4G, a PfeIF4E/PfeIF4A scaffold protein, which could constitute a novel antimalarial target. However, it is not known if these proteins constitute a P. falciparum eIF4F complex in vivo, nor what other proteins interact with the mRNA 5′-cap to control translation initiation in this species. Here, we investigated P. falciparum proteins that interact with the mRNA 5′-cap. Native protein extract from P. falciparum parasites was applied to m7GTP agarose beads and specific binding proteins eluted using m7GTP. LC-MS/MS based proteomic analysis of the m7GTP-eluted proteins demonstrated the presence of PfeIF4E, which was not found in control experiments with non-methylated GTP beads, verifying the native cap-binding function of PfeIF4E. PfeIF4A, PfeIF4G, and a putative polyadenylate-binding protein-interacting protein were present among m7GTP-eluted proteins but in low abundances. Interestingly, proteomics data clearly demonstrated P. falciparum enolase (Pfeno) in the m7GTP-eluted proteins.
2022-04-23 | PXD025583 | JPOST Repository
Project description:The emergence and spread of Plasmodium falciparum human malaria parasites resistant to antimalarial drugs, including artemisinin, a first line antimalarial drug, is threatening malaria treatment and prompting fears of a resurgence of the disease. New drugs with novel mode of actions are thus urgently required. Several compounds with antimalarial activity are known to target protein translation, although few of these targets have been validated. Translation initiation in eukaryotes is known to require eukaryotic translation initiation factor 4F (eIF4F) complex, which binds to the 5′-cap structure on mature mRNA and recruits other proteins for translation of mRNA. The putative components of the eIF4F complex in P. falciparum have been identified in the genome including PfeIF4E, a 5′-cap-binding protein; PfeIF4A, a helicase protein for unwinding mRNA, and PfeIF4G, a PfeIF4E/PfeIF4A scaffold protein, which could constitute a novel antimalarial target. However, it is not known if these proteins constitute a P. falciparum eIF4F complex in vivo, nor what other proteins interact with the mRNA 5′-cap to control translation initiation in this species. Here, we investigated P. falciparum proteins that interact with the mRNA 5′-cap. Native protein extract from P. falciparum parasites was applied to m7GTP agarose beads and specific binding proteins eluted using m7GTP. LC-MS/MS based proteomic analysis of the m7GTP-eluted proteins demonstrated the presence of PfeIF4E, which was not found in control experiments with non-methylated GTP beads, verifying the native cap-binding function of PfeIF4E. PfeIF4A, PfeIF4G, and a putative polyadenylate-binding protein-interacting protein were present among m7GTP-eluted proteins but in low abundances. Interestingly, proteomics data clearly demonstrated P. falciparum enolase (Pfeno) in the m7GTP-eluted proteins.
2022-04-22 | PXD025553 | JPOST Repository