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Directed hydroxyl radical probing reveals Upf1 binds 80S ribosomal E site rRNA at L1 stalk

ABSTRACT: Directed hydroxyl radical probing reveals Upf1 binds 80S ribosomal E site rRNA at L1 stalk

PROVIDER: PRJNA408153 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6055200.fastq.gz	Fastqsanger.gz
	SRR6055201.fastq.gz	Fastqsanger.gz
	SRR6055202.fastq.gz	Fastqsanger.gz
	SRR6055193.fastq.gz	Fastqsanger.gz
	SRR6055203.fastq.gz	Fastqsanger.gz

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Directed hydroxyl radical probing reveals Upf1 binds 80S ribosomal E site rRNA at L1 stalk

Project description:Fe-BABE probing of Upf1 binding site on yeast ribosome

2017-12-06 | GSE104072 | GEO

Directed hydroxyl radical probing reveals Upf1 binding to the 80S ribosomal E site rRNA at the L1 stalk.

Project description:Upf1 is an SF1-family RNA helicase that is essential for the nonsense-mediated decay (NMD) process in eukaryotes. While Upf1 has been shown to interact with 80S ribosomes, the molecular details of this interaction were unknown. Using purified recombinant proteins and high-throughput sequencing combined with Fe-BABE directed hydroxyl radical probing (HTS-BABE) we have characterized the interaction between Upf1 and the yeast 80S ribosome. We identify the 1C domain of Upf1, an alpha-helical insertion in the RecA helicase core, to be essential for ribosome binding, and determine that the L1 stalk of 25S rRNA is the binding site for Upf1 on the ribosome. Using the cleavage sites identified by hydroxyl radical probing and high-resolution structures of both yeast Upf1 and the human 80S ribosome, we provide a model of a Upf1:80S structure. Our model requires that the L1 stalk adopt an open configuration as adopted by an un-rotated, or classical-state, ribosome. Our results shed light on the interaction between Upf1 and the ribosome, and suggest that Upf1 may specifically engage a classical-state ribosome during translation.

| S-EPMC5829565 | biostudies-literature

Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance

Project description:Upf1, Upf2, and Upf3 are the central regulators of nonsense-mediated mRNA decay (NMD), the eukaryotic mRNA quality control pathway generally triggered when a premature termination codon is recognized by the ribosome. The NMD-related functions of the Upf proteins likely commence while these factors are ribosome-associated, but little is known of the timing of their ribosome binding, their specificity for ribosomes translating NMD substrates, or the nature and role of any ribosome:Upf complexes. Here, we have elucidated details of the ribosome-associated steps of NMD. By combining yeast genetics with selective ribosome profiling and co-sedimentation analyses of polysomes with wild-type and mutant Upf proteins, our approaches have identified distinct states of ribosome:Upf association. All three Upf factors manifest progressive polysome association as mRNA translation proceeds, but these events appear to be preceded by formation of a Upf1:80S complex as mRNAs initiate translation. This complex is likely executing an early mRNA surveillance function.

2022-10-21 | GSE186795 | GEO

Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance

Project description:Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance

| PRJNA776169 | ENA

Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance

2022-10-21 | PXD029577 | Pride

Morc2a variants cause hydroxyl radical-mediated neuropathy and are rescued by GHKL ATPase gene therapy

Project description:Mutations in the Microrchidia CW-Type Zinc Finger 2 (MORC2) GHKL ATPase module cause Charcot Marie Tooth type 2Z or a broad range of neuropathy, but etiology and therapeutic strategy are not fully defined. Previously, we reported that the Morc2a p.S87L mouse model led to neuropathy and muscular dysfunction through DNA damage accumulation. This study revealed that Morc2a p.S87L caused a protein synthesis defect, resulting in the loss of function of Morc2a and weakening its function of maintaining DNA integrity and hydroxyl radical scavenging in the GHKL ATPase domain. Morc2a GHKL ATPase domain was considered a therapeutic target based on its function of simultaneously complementing hydroxyl radical scavenging and ATPase activity. Adeno-associated virus PHP.eB serotype that has high central nervous system transduction efficiency was applied to express Morc2a or Morc2a GHKL ATPase domain protein in vivo. AAV gene therapy improved neuropathy and muscular dysfunction with single-time treatment. The loss of function characteristics due to protein synthesis defect in Morc2a p.S87L was also observed in human MORC2 p.S87L or p.R252W variant, suggesting a relevance between mouse and human pathogenesis. Here, we demonstrate Morc2a p.S87L variant causes hydroxyl radical-mediated neuropathy and could be rescued through AAV-based gene therapy.

2024-02-06 | GSE235918 | GEO

Head and Embryo 80S monosomes are much more translationally active than 80S in other tissues

Project description:Translational regulation at the stage of initiation impacts the number of ribosomes translating each mRNA molecule. For example, multiple ribosomes can engage on a single mRNA forming a polysome, resulting in highly efficient protein synthesis. However, the translational activity of single 80S ribosomes on mRNA (monosomes) is less well understood, even though these 80S monosomes represent the dominant ribosomal complexes in many tissues. Here, we used cryo-EM to determine the translational activity of 80S monosomes across different tissues in Drosophila melanogaster. We discovered that while head and embryo 80S monosomes are highly translationally active, testis and ovary 80S monosomes are translationally inactive. RNA-Seq analysis of head monosome- and polysome-translated mRNAs, revealed that head 80S monosomes preferentially translate mRNAs with TOP motifs, short 5’-UTRs, short ORFs and are enriched for uORFs. Overall, these findings highlight that regulation of translation initiation, and therefore the number of ribosomes bound per mRNA, varies substantially across tissues.

2025-03-24 | GSE267425 | GEO

Dimethylthiourea as a Quencher in Hydroxyl Radical Protein Footprinting Experiments

Project description:Hydroxyl radical protein footprinting (HRPF) is a mass spectrometry (MS)-based method for studying protein structures, interactions, conformations, and folding. We evaluated dimethylthiourea (DMTU) as a replacement for catalase in quenching HRPF reactions. We observed that the DMTU is highly effective at quenching HRPF oxidation. DMTU does not cause background protein issues like catalase, resulting in an increased number of protein identifications from complex mixtures.

2025-09-12 | PXD046435 | Pride

Hydroxyl Radical and Trifluoromethyl Carbohydrate Footprinting for Probing Protein Binding Components of Oligosaccharides

Project description:The NAG3 was modified by hydroxyl radicals and CF3 radicals and determined the end residues where these modifications occur.

2025-09-29 | PXD066426 | Pride

Gene expression of F.graminearum during maize stalk infection

Project description:Fusarium graminearum can infect maize stalk causing Gibberella stalk rot. We want to know the whole genome wide gene profiling when infecting maize stalk.

2016-02-11 | GSE53854 | GEO

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