Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1282644 | ENA |
REPOSITORIES: ENA
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Project description:Whole proteome and ribosome-nascent-chain complex (RNC) changes of A549 cisplatin-resistant cells after treated with aurintricarboxylic acid
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Project description:The cancer cells selectively promote translation of specific oncogenic transcripts to facilitate cancer survival and progression, while the underlying mechanisms are poorly understood. N7-methylguanosine (m7G) tRNA modification and its methyltransferase complex METTL1/WDR4 are significantly up-regulated in intrahepatic cholangiocarcinoma (ICC) and associated with poor prognosis. We developed tRNA reduction and cleavage sequencing (TRAC-Seq) to reveal the m7G tRNA methylome inICC cell line and ribosome nascent-chain complex-bound mRNAs sequencing(RNC-seq) and ribosome profiling(Ribo-seq) to study the differential translated genes and reveal the ribosome pausing. A subset of 22 tRNAs is modified at a ‘RAGGU’ motif within the variable loop. We observe increased ribosome occupancy at the corresponding codons in the Mettl1 knockdown ICC cell line implying widespread effects on tRNA function, ribosome pausing, and mRNA translation. Translation of cell cycle genes and EGFR signaling pathway genes is particularly affected. Our study uncovers the important physiological function and mechanism of METTL1-mediated m7G tRNA modification in the regulation of cancer progression.
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Project description:The human mitochondrial genome encodes thirteen subunits of the oxidative phosphorylation system essential for energy metabolism to drive cellular activities. Translation of eleven mRNAs by membrane-bound ribosomes is coupled to insertion of the nascent polypeptides into the inner membrane aided by the OXA1L insertase. To this end, the mechanism of membrane insertion of nascent polypeptides and the functional link to the translation process are not understood. Here we applied ribosome profiling to assess translation dynamics in combination with cryo-EM analyses of a COX1 ribosome nascent chain complex to visualize co-translational folding of the nascent chain. We find that the membrane topology of the translation product impacts translation speed and that positioning of amphipathic helices in the ribosome vestibule induces structural changes, correlating with translation stalling events. Thus, our findings reveal a tight link between translation process and folding and membrane insertion of nascent polypeptides at the inner mitochondrial membrane.
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Project description:In order to explore the effect of betaine on NAFLD and its mechanism, we divided mice into high-fat diet (HF) and high-fat diet with betaine (HB) groups, and used N6-methyladenosine sequence (m6A-seq), RNA-seq and mRNAs bound to ribosome-nascent chain complex sequencing (RNC-seq) to evaluate the gene expression levels in the liver of each group.
2021-05-20 | GSE174550 | GEO
Project description:To investigate the role of METTL3-mediated m6A modification and mRNA translation, we performed m6A-sequencing and Ribosome-nascent chain (RNC)-RNA sequencing in high glucose treated control or METTL3 knockdown HTR8/SVneo cells.
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Project description:Various proteins in the cell begin to fold during synthesis at the ribosome, many with the assistance of molecular chaperones. While the cotranslational activity of ribosome-associated chaperones and Hsp70 is frequently studied, the role of Hsp60 chaperonins during protein synthesis remains poorly understood. Here, we studied the binding of E. coli chaperonin GroEL to ribosome-nascent chain complexes (RNCs), to understand GroEL activity during nascent chain (NC) synthesis and folding. Using biochemical reconstitution, structural proteomics and electron microscopy we describe the physical architecture of GroEL:RNC and ATP/BeFx-GroEL/ES:RNC complexes. We show that GroEL engages destabilised nascent chains on the inside of its cavity via the apical domains and disordered C-terminal tails. This GroEL:RNC complex can be capped by GroES on the NC-bound ring, with GroEL but not GroEL/ES binding promoting nascent chain destabilisation. Lastly, we observe that GroEL directly competes with Hsp70 for nascent chain binding. Our findings thus show that GroEL is a versatile chaperone which in addition to its well characterised post-translational activity can affect folding of nascent chains undergoing synthesis.
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Project description:Various proteins in the cell begin to fold during synthesis at the ribosome, many with the assistance of molecular chaperones. While the cotranslational activity of ribosome-associated chaperones and Hsp70 is frequently studied, the role of Hsp60 chaperonins during protein synthesis remains poorly understood. Here, we studied the binding of E. coli chaperonin GroEL to ribosome-nascent chain complexes (RNCs), to understand GroEL activity during nascent chain (NC) synthesis and folding. Using biochemical reconstitution, structural proteomics and electron microscopy we describe the physical architecture of GroEL:RNC and ATP/BeFx-GroEL/ES:RNC complexes. We show that GroEL engages destabilised nascent chains on the inside of its cavity via the apical domains and disordered C-terminal tails. This GroEL:RNC complex can be capped by GroES on the NC-bound ring, with GroEL but not GroEL/ES binding promoting nascent chain destabilisation. Lastly, we observe that GroEL directly competes with Hsp70 for nascent chain binding. Our findings thus show that GroEL is a versatile chaperone which in addition to its well characterised post-translational activity can affect folding of nascent chains undergoing synthesis.
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Project description:Various proteins in the cell begin to fold during synthesis at the ribosome, many with the assistance of molecular chaperones. While the cotranslational activity of ribosome-associated chaperones and Hsp70 is frequently studied, the role of Hsp60 chaperonins during protein synthesis remains poorly understood. Here, we studied the binding of E. coli chaperonin GroEL to ribosome-nascent chain complexes (RNCs), to understand GroEL activity during nascent chain (NC) synthesis and folding. Using biochemical reconstitution, structural proteomics and electron microscopy we describe the physical architecture of GroEL:RNC and ATP/BeFx-GroEL/ES:RNC complexes. We show that GroEL engages destabilised nascent chains on the inside of its cavity via the apical domains and disordered C-terminal tails. This GroEL:RNC complex can be capped by GroES on the NC-bound ring, with GroEL but not GroEL/ES binding promoting nascent chain destabilisation. Lastly, we observe that GroEL directly competes with Hsp70 for nascent chain binding. Our findings thus show that GroEL is a versatile chaperone which in addition to its well characterised post-translational activity can affect folding of nascent chains undergoing synthesis.
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