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K6-Linked Ubiquitylation Signals Reactive Aldehyde-Induced RNA-Protein Crosslink Resolution

ABSTRACT: K6-Linked Ubiquitylation Signals Reactive Aldehyde-Induced RNA-Protein Crosslink Resolution

PROVIDER: PRJNA1004331 | ENA |

REPOSITORIES: ENA

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K6-Linked Ubiquitylation Signals Reactive Aldehyde-Induced RNA-Protein Crosslink Resolution

Project description:Reactive aldehydes induce the formation of RNA-protein crosslinks (RPCs), RPCs in the mRNA stall the ribosome and inhibit translation, RPCs are K6-linked ubiqutylated by RBR-type E3 ligase RNF14, RPCs are resolved in a UBXN1-VCP/p97-dependent manner

2023-11-03 | GSE240625 | GEO

Atypical K6-linked ubiquitylation marks toxic RNA-protein crosslinks induced by formaldehyde

Project description:Reactive aldehydes are produced during cellular metabolism and can accumulate in specific tissues particularly when aldehyde clearance mechanisms are impaired. Reactive aldehydes induce DNA-DNA and DNA-protein crosslinks (DPCs) that are repaired by different DNA repair pathways. Cellular toxicity of endogenous formaldehyde has been attributed to the damage of the genomic DNA and consequent inhibition of transcription. However, whether damage to other cellular macromolecules and interference with additional metabolic processes contributes to formaldehyde toxicity has not been investigated. We demonstrate that formaldehyde induces toxic RNA-protein crosslinks (RPCs) in mRNA that inhibit translation and induce a specific RPC stress response pathway that is characterized by linkage-specific ubiquitylation. RPCs in the mRNA are recognized by stalling ribosomes and marked by K6-linked ubiquitylation that promotes their clearance by the ubiquitin-dependent unfoldase VCP.

2023-09-01 | GSE225044 | GEO

K6-Linked Ubiquitylation Marks Formaldehyde-Induced RNA–Protein Crosslinks for Resolution

Project description:Reactive aldehydes are produced by normal cellular metabolism or after alcohol consumption, and accumulate in human tissues if aldehyde clearance mechanisms are impaired. Their toxicity has been attributed to the damage they cause to genomic DNA and the subsequent inhibition of transcription and replication. However, whether interference with other cellular processes contributes to aldehyde toxicity has not been investigated. We demonstrate that formaldehyde induces RNA–protein crosslinks (RPCs) that stall the ribosome and inhibit translation in human cells. RPCs in the messenger RNA are recognized by the translating ribosomes, marked by atypical K6-linked ubiquitylation catalyzed by the RING-in-Between-RING E3 ligase RNF14, and subsequently resolved by the ubiquitin- and ATP-dependent unfoldase VCP. Our findings uncover an evolutionary conserved formaldehyde-induced stress response pathway that protects cells against RPC accumulation in the cytoplasm, and suggest that RPCs contribute to the cellular and tissue toxicity of reactive aldehydes.

2023-11-13 | PXD038655 | Pride

Proteomic profiling of VCP substrates links VCP to K6-linked ubiquitylation and c-Myc function

Project description:VCP is an evolutionary conserved ubiquitin-dependent ATPase that mediates the degradation of proteins through the ubiquitin-proteasome pathway. Despite the central role of VCP in the regulation of protein homeostasis, identity and nature of its cellular substrates remain poorly defined. Here, we combined chemical inhibition of VCP and quantitative ubiquitin remnant profiling to assess the effect of VCP inhibition on the ubiquitin-modified proteome and to probe the substrate spectrum of VCP in human cells. We demonstrate that inhibition of VCP perturbs cellular ubiquitylation and increases ubiquitylation of a different subset of proteins compared to proteasome inhibition. VCP inhibition globally upregulates K6-linked ubiquitylation that is dependent on the HECT-type ubiquitin E3 ligase HUWE1. We report ~450 putative VCP substrates, many of which function in nuclear processes, including gene expression, DNA repair and cell cycle. Moreover, we identify that VCP regulates the level and activity of the transcription factor c-Myc.

2018-02-08 | GSE107313 | GEO

Atypical K6-linked ubiquitylation marks toxic RNA-protein crosslinks induced by formaldehyde

Project description:Atypical K6-linked ubiquitylation marks toxic RNA-protein crosslinks induced by formaldehyde

| PRJNA933609 | ENA

Proteomic profiling of VCP substrates links VCP to K6-linked ubiquitylation and c-Myc function

2018-02-09 | PXD003936 | Pride

Proteomic profiling of VCP substrates links VCP to K6-linked ubiquitylation and c-Myc function

Project description:Proteomic profiling of VCP substrates links VCP to K6-linked ubiquitylation and c-Myc function

| PRJNA419745 | ENA

mRNA-sequencing of 293T-no dice transfected with miR-16, miR-214, or KSHV-miR-K6-5p

Project description:The viral miRNA miR-K6-5p encoded by the DNA tumor virus Kaposi’s sarcoma-associated herpesvirus exhibits offset, sequence similarity with the tumor suppressive cellular miR-15/16 family, as well as sharing a short seed match to the cellular miR-214 (nts 2-7). We investigated how gene regulation by the viral miR-K6-5p is related to regulation by these cellular miRNAs by performing transcriptome analysis. mRNA-Seq was done in HEK 293T NoDice cells (Bogerd et al., RNA 2014) lacking Dicer which severely impaired the maturation of miRNAs thereby eliminating confounding effects of endogenously expressed miR-15/16 family. We transfected mature miRNA mimics of miR-16, miR-K6-5p wild-type, a variant of miR-K6-5p with a U at nt 1 instead of a C to control of RISC loading (miR-K6 5’U), miR-214, or a control mimic into NoDice cells, and harvested total RNA 2 days post-transfection.

2019-11-01 | GSE128576 | GEO

Oxalobacteraceae bacterium JGI 0001002-K6

Project description:Oxalobacteraceae bacterium JGI 0001002-K6

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Daphnia magna strain:K6

Project description:Daphnia magna strain:K6 Raw sequence reads

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