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Structure of the plant 80S ribosome.

ABSTRACT: The 80S ribosome was purified from tobacco (Nicotiana tabacum) leaves. part of the extract was analysed by mass spectrometry and the rest was used for cryo-EM investigations of the structure of the 80S ribosome.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Nicotiana Tabacum (common Tobacco)

TISSUE(S): Leaf

SUBMITTER: Etienne Meyer

LAB HEAD: Christian Spahn

PROVIDER: PXD032330 | Pride | 2023-07-20

REPOSITORIES: Pride

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Structure of the actively translating plant 80S ribosome at 2.2 Å resolution.

Smirnova Julia J Loerke Justus J Kleinau Gunnar G Schmidt Andrea A Bürger Jörg J Meyer Etienne H EH Mielke Thorsten T Scheerer Patrick P Bock Ralph R Spahn Christian M T CMT Zoschke Reimo R

Nature plants 20230508 6

In plant cells, translation occurs in three compartments: the cytosol, the plastids and the mitochondria. While the structures of the (prokaryotic-type) ribosomes in plastids and mitochondria are well characterized, high-resolution structures of the eukaryotic 80S ribosomes in the cytosol have been lacking. Here the structure of translating tobacco (Nicotiana tabacum) 80S ribosomes was solved by cryo-electron microscopy with a global resolution of 2.2 Å. The ribosome structure includes two tRNAs ...[more]

PMID: 37156858

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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

Initiation Pausing of 80S Ribosome on mRNA Is Governed by 5'UTR and Responsive to mTORC1 Signaling (RNA-Seq)

Project description:Recent studies have revealed that the mRNA translation is punctuated by ribosomal pauses through the body of transcripts. However, little is known about its physiological significance and regulatory aspects. Here we present a multi-dimensional ribosome profiling approach to quantify the dynamics of initiation and elongation of 80S ribosomes across the entire transcriptome in mammalian cells. We show that a subset of transcripts have a significant pausing of 80S ribosome around the start codon, creating a major barrier to the commitment of translation elongation. Intriguingly, genes encoding ribosome proteins themselves exhibit an exceptionally high initiation pausing on their transcripts. Our studies also reveal that the initiation pausing is dependent on the 5M-bM-^@M-^Y untranslated region (5M-bM-^@M-^Y UTR) of mRNAs and subject to the regulation of mammalian target of rapamycin complex 1 (mTORC1). Thus, the initiation pausing of 80S ribosome represents a novel regulatory step in translational control mediated by nutrient signaling pathway. Monitor the translational status of transcriptome in mammalian cells under different conditions

2011-11-12 | E-GEOD-25626 | biostudies-arrayexpress

Initiation Pausing of 80S Ribosome on mRNA Is Governed by 5’UTR and Responsive to mTORC1 Signaling (Microarray)

Project description:Recent studies have revealed that the mRNA translation is punctuated by ribosomal pauses through the body of transcripts. However, little is known about its physiological significance and regulatory aspects. Here we present a multi-dimensional ribosome profiling approach to quantify the dynamics of initiation and elongation of 80S ribosomes across the entire transcriptome in mammalian cells. We show that a subset of transcripts have a significant pausing of 80S ribosome around the start codon, creating a major barrier to the commitment of translation elongation. Intriguingly, genes encoding ribosome proteins themselves exhibit an exceptionally high initiation pausing on their transcripts. Our studies also reveal that the initiation pausing is dependent on the 5’ untranslated region (5’ UTR) of mRNAs and subject to the regulation of mammalian target of rapamycin complex 1 (mTORC1). Thus, the initiation pausing of 80S ribosome represents a novel regulatory step in translational control mediated by nutrient signaling pathway. Untreated TSC2 WT MEFs, TSC2 KO MEFs and TSC2 WT MEFs, TSC2 KO MEFs treated with 20nM rapamycin for 30 minutes or 3hours were harvested for ribosme profiling. The fraction samples were pooled into three groups based on velocity sedimentation: single ribosome fraction (Small group), fractions with 2 ~ 4 ribosomes (Medium group), and the one with ≥5 ribosomes (Large group). RNA were extracted from the whole cell lysis and each fraction group.

2011-11-12 | E-GEOD-25331 | biostudies-arrayexpress

Initiation Pausing of 80S Ribosome on mRNA Is Governed by 5’UTR and Responsive to mTORC1 Signaling (Microarray)

Project description:Recent studies have revealed that the mRNA translation is punctuated by ribosomal pauses through the body of transcripts. However, little is known about its physiological significance and regulatory aspects. Here we present a multi-dimensional ribosome profiling approach to quantify the dynamics of initiation and elongation of 80S ribosomes across the entire transcriptome in mammalian cells. We show that a subset of transcripts have a significant pausing of 80S ribosome around the start codon, creating a major barrier to the commitment of translation elongation. Intriguingly, genes encoding ribosome proteins themselves exhibit an exceptionally high initiation pausing on their transcripts. Our studies also reveal that the initiation pausing is dependent on the 5’ untranslated region (5’ UTR) of mRNAs and subject to the regulation of mammalian target of rapamycin complex 1 (mTORC1). Thus, the initiation pausing of 80S ribosome represents a novel regulatory step in translational control mediated by nutrient signaling pathway.

2011-11-12 | GSE25331 | GEO

Initiation Pausing of 80S Ribosome on mRNA Is Governed by 5'UTR and Responsive to mTORC1 Signaling (RNA-Seq)

Project description:Recent studies have revealed that the mRNA translation is punctuated by ribosomal pauses through the body of transcripts. However, little is known about its physiological significance and regulatory aspects. Here we present a multi-dimensional ribosome profiling approach to quantify the dynamics of initiation and elongation of 80S ribosomes across the entire transcriptome in mammalian cells. We show that a subset of transcripts have a significant pausing of 80S ribosome around the start codon, creating a major barrier to the commitment of translation elongation. Intriguingly, genes encoding ribosome proteins themselves exhibit an exceptionally high initiation pausing on their transcripts. Our studies also reveal that the initiation pausing is dependent on the 5’ untranslated region (5’ UTR) of mRNAs and subject to the regulation of mammalian target of rapamycin complex 1 (mTORC1). Thus, the initiation pausing of 80S ribosome represents a novel regulatory step in translational control mediated by nutrient signaling pathway.

2011-11-12 | GSE25626 | GEO

mRNA regions where 80S ribosomes pause during translation elongation in vivo interact with protein uS19, a component of the decoding site

Project description:80S-ribosome bound uS19 translatome-wide crosslinking sites in human mRNAs revealed by PAR-CLIP

2019-03-14 | GSE128265 | GEO

Redefining the translational status of 80S monosomes

2016-02-11 | GSE76117 | GEO

Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1 at the A site

Project description:In response to environmental changes, cells flexibly and rapidly alter gene expression, through translational controls. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is upregulated through upstream open reading frames (uORFs) that comprise only AUG and stop codons, in response to a shortage of boric acid in the environment. However, the molecular details of how the minimum uORF controls the translation of the downstream main ORF, in a boric acid concentration-dependent manner, have remained unclear. Here, combining ribosome profiling, TCP-Seq, structural analysis with cryo-electron microscopy, and biochemical assays, we showed that the 80S ribosome (80S) assembled at AUG-stop migrates into the subsequent RNA segment, followed by downstream translation initiation, and that boric acid impedes this process by the stable confinement of eukaryotic release factor 1 (eRF1) on the 80S on AUG-stop. Our results provide molecular insight into translation regulation by a minimum and environment-responsive uORF.

2023-09-19 | GSE223755 | GEO

Boric acidon intercepts 80S ribosome migration from AUG-stop by stable eRF1 immobilization

Project description:Upon the environmental changes, cells flexibly and rapidly alter the gene expression by the translation control. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is upregulated through the upstream open reading frame (uORF), which comprises only AUG and stop codons, in response to the shortage of boric acid. However, the molecular details of how the minimum uORF controls the translation of downstream main ORF depending on the boric acid concentration remained unclear. Here we showed that the 80S ribosome (80S) assembled at AUG-stop migrates into the subsequent RNA segment for downstream translation initiation and that the presence of boric acid impedes the process by stable confinement of eukaryotic release factor 1 (eRF1) on 80S on AUG-stop. Ribosome profiling along the in vitro-translated reporter mRNA revealed that the number of the ribosomes on AUG-stop and that along the downstream are anti-correlated in response to boric acid, reflecting the 80S scanning leaving AUG-stop for translation initiation from downstream ORF. Moreover, cryo-electron microscopy (cryo-EM) analysis revealed that, in the presence of boric acid, the initiator methionyl-tRNA (Met-tRNAi) in the P site stably contacts eRF1 in the A site on AUG-stop. In contrast, the absence of boric acid led to weaker eRF1 density, suggesting that eRF1 cannot be stably positioned without boric acid. Consistent with the structural features, the hydrolysis of Met-tRNAi on AUG-stop was accelerated by boric acid, which is likely to be the checkpoint for the subsequent 80S scanning of the downstream. Our results provide a molecular insight into the translation regulation by a minimum and environment-responsive uORF.

2023-09-20 | GSE189222 | GEO

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

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