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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

2022-10-21 | PXD029577 | Pride

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

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

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

stalk biogenesis phosphorelay

Project description:mutants in the stalk biogenesis and sigma-54 pathways Keywords: mutant expression patterns

2006-04-06 | GSE3328 | GEO

Redefining the translational status of 80S monosomes

Project description:Fully assembled ribosomes exist in two populations: polysomes and monosomes. While the former has been studied extensively, to what extent translation occurs on monosomes and its importance for overall translational output remains controversial. Here, we used ribosome profiling to examine the translational status of 80S monosomes in Saccharomyces cerevisiae. We found that the vast majority of 80S monosomes are elongating, not initiating. Further, most mRNAs exhibit some degree of monosome occupancy, with monosomes predominating on nonsense-mediated decay (NMD) targets, upstream open reading frames (uORFs), canonical ORFs shorter than ~590 nucleotides and ORFs for which the total time required to complete elongation is substantially shorter than that required for initiation. Importantly, mRNAs encoding low-abundance regulatory proteins tend to be enriched in the monosome fraction. Our data highlight the importance of monosomes for the translation of highly regulated mRNAs.Â We examined the translational status of single 80S ribosomes using ribosome profiling, and compared these monosome footprints to both polysome ribosome footprints and general ribosome profiling. RNASeq libraries were also prepared from the overall sample input.

2016-02-11 | E-GEOD-76117 | biostudies-arrayexpress

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. Using lasr capture microdisecction, we captured 8 time points infecting hyphae samples for maize stalk and after two-round amplification, we hybrid the aRNA to Affymetrix array.

2016-02-11 | E-GEOD-53854 | biostudies-arrayexpress

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