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UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER

ABSTRACT: Supporting MS data for paper (doi: 10.1038/s41586-024-07073-0) by DaRosa P.A., Penchev I. et al., titled "UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER". Index of MS supporting files uploaded: - Related to Fig. 1a and Extended Data Fig. 1a (AO3435-AO3440: TMT proteomics (Unimod: 35; 737; 4)). - Related to Fig. 1b, c (see MSV000093721).

INSTRUMENT(S): Orbitrap Fusion Lumos, Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Alban Ordureau Joao A. Paulo

PROVIDER: MSV000093510 | MassIVE | Mon Nov 27 07:56:00 GMT 2023

REPOSITORIES: MassIVE

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UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER.

DaRosa Paul A PA Penchev Ivan I Gumbin Samantha C SC Scavone Francesco F Wąchalska Magda M Paulo Joao A JA Ordureau Alban A Peter Joshua J JJ Kulathu Yogesh Y Harper J Wade JW Becker Thomas T Beckmann Roland R Kopito Ron R RR

Nature 20240221 8003

Reversible modification of target proteins by ubiquitin and ubiquitin-like proteins (UBLs) is widely used by eukaryotic cells to control protein fate and cell behaviour<sup>1</sup>. UFM1 is a UBL that predominantly modifies a single lysine residue on a single ribosomal protein, uL24 (also called RPL26), on ribosomes at the cytoplasmic surface of the endoplasmic reticulum (ER)<sup>2,3</sup>. UFM1 conjugation (UFMylation) facilitates the rescue of 60S ribosomal subunits (60S) that are released aft ...[more]

PMID: 38383785

Similar Datasets

UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER

Project description:Supporting MS data for paper (doi: 10.1038/s41586-024-07073-0) by DaRosa P.A., Penchev I. et al., titled "UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER". Index of MS supporting files uploaded: Related to Related to Fig. 1b, c (xb01004(UFM1), xb01005(SBP-UFM1): LFQ IP-MS (Unimod: 35; 4)). See also MSV000093510

2023-12-22 | MSV000093721 | MassIVE

Recycling of autophagosomal components from autolysosomes by the recycler complex

Project description:The autophagic SNARE protein STX17 is recruited to autophagosomes and translocated to autolysosome after fusion of autophagosomes with lysosomes 30-32. We observed that the number of autophagic vacuoles with STX17 significantly increased after 2 hours of starvation. However, the number of STX17 puncta significantly decreased during prolonged starvation of 5 hours (Fig. 1a). Interestingly, no obvious degradation of STX17 was observed after prolonged starvation (Fig. 1b)

2022-01-24 | PXD031183 |

Human cerebrospinal fluid autoantibody lipid microarray profiling

Project description:This SuperSeries is composed of the following subset Series: GSE37664: Human cerebrospinal fluid autoantibody lipid microarray profiling (Fig. 1A) GSE37670: Human cerebrospinal fluid autoantibody lipid microarray profiling (Fig. 2A) GSE37826: Human cerebrospinal fluid autoantibody lipid microarray profiling (Fig. 2C) Refer to individual Series

2012-05-08 | E-GEOD-37830 | biostudies-arrayexpress

Hcr1/eIF3j is a 60S ribosomal subunit recycling accessory factor in vivo

Project description:Hcr1/eIF3j is a sub-stoichiometric subunit of eukaryotic initiation factor 3 (eIF3) that can dissociate the post-termination 40S ribosomal subunit from mRNA in vitro. We examined this ribosome recycling role in vivo by ribosome profiling and reporter assays and found that loss of Hcr1 led to reinitiation of translation in 3’UTRs, consistent with a defect in recycling. However, the defect appeared to be in recycling of the 60S subunit, rather than the 40S subunit, because reinitiation did not require an AUG codon and was suppressed by overexpression of the 60S dissociation factor Rli1/ABCE1. Consistent with a 60S recycling role, overexpression of Hcr1 could not compensate for loss of 40S recycling factors Tma64/eIF2D and Tma20/MCT-1. Intriguingly, loss of Hcr1 triggered higher expression of RLI1 via an apparent feedback loop. These findings suggest Hcr1/eIF3j is recruited to ribosomes at stop codons and may coordinate the transition to a new round of translation.

2019-05-23 | GSE124204 | GEO

Quantitative Proteome Remodeling Characterization of Two Human Reference Pluripotent Stem Cell Lines During Neurogenesis and Cardiomyogenesis

Project description:Supporting raw MS data for paper (doi: 10.1002/pmic.202100246) by Nam K.H. et al, titled "Quantitative Proteome Remodeling Characterization of Two Human Reference Pluripotent Stem Cell Lines During Neurogenesis and Cardiomyogenesis". Index of RAW files uploaded: - Related to Figure 1 (KN97-120: whole proteome (Unimod: 35; 2016; 4)). - Related to Figure 2 (KN121-126: phospho proteome (Unimod: 35; 21; 2016; 4)) - Related to Figures 3 and 4 (KN205-228: whole proteome (Unimod: 35; 2016; 4))

2022-02-14 | MSV000088833 | MassIVE

CTLH E3 Ligase Regulates the Degradation of HMG-CoA Synthase 1 Through the Pro/N-end Rule Pathway

Project description:Supporting raw MS data for paper (doi: 10.1016/j.molcel.2024.04.026) by Yi S.A. et al, titled "CTLH E3 Ligase Regulates the Degradation of HMG-CoA Synthase 1 Through the Pro/N-end Rule Pathway". Index of RAW files uploaded: - Related to Supplementary Table 1 (HA-9-81-X | WT (1), ATG7KO (2), RB1CC1 (3): whole proteome (Unimod: 35; 2016; 4)). - Related to Supplementary Table 2 - Proteome (HA-1-50: whole proteome (Unimod: 35; 2016; 4)). - Related to Supplementary Table 2 - PhosphoSites (HA-1-50_Phos: phospho proteome (Unimod: 35; 21; 2016; 4)) - Related to Supplementary Table 3 (Yis-1-49: whole proteome (Unimod: 35; 2016; 4))

2022-11-29 | MSV000090814 | MassIVE

NAK-associated protein 1/NAP1 activates TBK1 to ensure accurate mitosis and cytokinesis.

Project description:Supporting raw MS data for paper (DOI:10.1083/jcb.202303082) by Paul S. et al., titled "NAK-associated protein 1/NAP1 activates TBK1 to ensure accurate mitosis and cytokinesis". Index of MS supporting files uploaded: - Related to Figure 6A;S4A (AO3556-AO3579: whole proteome (Unimod: 35; 2016; 4)). - Related to Figure 6A-D;S4B-D (AO3580-AO3603: phospho proteome (Unimod: 35; 21; 2016; 4)). TMTpro channel: WT-UT (126, 127n, 127c, 128n), WT-MRT (128c, 129n, 129c, 130n), TBK1_KO-UT (130c, 131n, 131c, 132n), TBK1_KO-MRT (132c, 133n, 133c, 134n).

2023-11-01 | MSV000093220 | MassIVE

Differentially expressed genes in B-1b compared to B-1a

Project description:B-1b cells are known to produce higher IgM level compared to B-1a cells. This study aims to identify differentially expressed genes and pathways that might enrich in B-1b cells and contribute to higher IgM production.

2022-06-30 | GSE207011 | GEO

Two isoforms of the essential C. elegans Argonaute CSR-1 differentially regulate sperm and oocyte fertility through distinct small RNA classes

Project description:The C. elegans genome encodes nineteen functional Argonaute proteins that utilize 22G-RNAs, 26G-RNAs, miRNAs, or piRNAs to regulate their target transcripts. Only one of these proteins is essential under normal laboratory conditions: CSR-1. While CSR-1 has been studied in various developmental and functional contexts, nearly all studies investigating CSR-1 have overlooked the fact that the csr-1 locus encodes two isoforms. These isoforms differ by an additional 163 amino acids present in the N-terminus of CSR-1a. Using CRISPR-Cas9 genome editing to introduce GFP::3xFLAG epitopes into the long (CSR-1a) and short (CSR-1b) isoforms of CSR-1, we identified differential expression patterns for the two isoforms. CSR-1a is expressed specifically during spermatogenesis and in select somatic tissues, including the intestine. In contrast, CSR-1b, is expressed constitutively in the germline. Essential functions of csr-1 described in the literature coincide with CSR-1b. In contrast,CSR-1a plays tissue specific functions during spermatogenesis, where it integrates into a spermatogenesis sRNA regulatory network including ALG-3, ALG-4, and WAGO-10 that is necessary for male fertility. CSR-1a is also required in the intestine for the silencing of repetitive transgenes. Sequencing of small RNAs associated with each CSR-1 isoform reveals that CSR-1a engages with 22G- and 26G-RNAs, while CSR-1b interacts with only 22G-RNAs to regulate distinct groups of germline genes and regulate both sperm and oocyte-mediated fertility.

2020-07-19 | GSE154678 | GEO

CSR-1A post-translational modification

Project description:CSR-1 is an essential Argonaute protein that binds to a subclass of 22G-RNAs targeting most germline-expressed genes. Here we show that the two isoforms of CSR-1 have distinct expression patterns; CSR-1B is ubiquitously expressed throughout the germline and during all stages of development while CSR-1A expression is restricted to germ cells undergoing spermatogenesis. Furthermore, CSR-1A associates preferentially with 22G-RNAs mapping to spermatogenesis-specific genes whereas CSR-1B-bound small RNAs map predominantly to oogenesis-specific genes. Interestingly, the exon unique to CSR-1A contains multiple dimethylarginine modifications, which are necessary for the preferential binding of CSR-1A to spermatogenesis-specific 22G-RNAs. Thus, we have discovered a regulatory mechanism for C. elegans Argonaute proteins that allows for specificity of small RNA binding between similar Argonaute proteins with overlapping temporal and spatial localization.

2021-06-17 | PXD021227 | Pride

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