{"database":"GPMDB","file_versions":[],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":30,"searchCount":5},"additional":{"omics_type":["Other"],"submitter":["Kershaw CJ, et al."],"instrument_platform":["Instrument"],"disease":["Not Available"],"brenda_tissue":["Not available"],"species":["Yeast"],"submitter_mail":["chris.grant@manchester.ac.uk"],"publication":["25569619"],"submitter_affiliation":["Faculty of Life Sciences, The University of Manchester, Manchester"],"model":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018405","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018415","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018407","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018418","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018406","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018417","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018409","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018419","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018408","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018410","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018421","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018420","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018423","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018412","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018411","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018422","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018414","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018424","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018413"],"cell_type":["Not available"],"repository":["GPMDB"],"pubmed_abstract":["The mechanisms by which RNA-binding proteins control the translation of subsets of mRNAs are not yet clear. Slf1p and Sro9p are atypical-La motif containing proteins which are members of a superfamily of RNA-binding proteins conserved in eukaryotes. RIP-Seq analysis of these two yeast proteins identified overlapping and distinct sets of mRNA targets, including highly translated mRNAs such as those encoding ribosomal proteins. In paralell, transcriptome analysis of slf1Δ and sro9Δ mutant strains indicated altered gene expression in similar functional classes of mRNAs following loss of each factor. The loss of SLF1 had a greater impact on the transcriptome, and in particular, revealed changes in genes involved in the oxidative stress response. slf1Δ cells are more sensitive to oxidants and RIP-Seq analysis of oxidatively stressed cells enriched Slf1p targets encoding antioxidants and other proteins required for oxidant tolerance. To quantify these effects at the protein level, we used label-free mass spectrometry to compare the proteomes of wild-type and slf1Δ strains following oxidative stress. This analysis identified several proteins which are normally induced in response to hydrogen peroxide, but where this increase is attenuated in the slf1Δ mutant. Importantly, a significant number of the mRNAs encoding these targets were also identified as Slf1p-mRNA targets. We show that Slf1p remains associated with the few translating ribosomes following hydrogen peroxide stress and that Slf1p co-immunoprecipitates ribosomes and members of the eIF4E/eIF4G/Pab1p 'closed loop' complex suggesting that Slf1p interacts with actively translated mRNAs following stress. Finally, mutational analysis of SLF1 revealed a novel ribosome interacting domain in Slf1p, independent of its RNA binding La-motif. Together, our results indicate that Slf1p mediates a translational response to oxidative stress via mRNA-specific translational control."],"pubmed_title":["The yeast La related protein Slf1p is a key activator of translation during the oxidative stress response."],"pubmed_authors":["Kershaw Christopher J CJ,Costello Joseph L JL,Castelli Lydia M LM,Talavera David D,Rowe William W,Sims Paul F G PF,Ashe Mark P MP,Hubbard Simon J SJ,Pavitt Graham D GD,Grant Chris M CM,","Kershaw Christopher J CJ, Costello Joseph L JL, Castelli Lydia M LM, Talavera David D, Rowe William W, Sims Paul F G PF, Ashe Mark P MP, Hubbard Simon J SJ, Pavitt Graham D GD, Grant Chris M CM"],"name_synonyms":["Saccharomyces oviformis, protein translation, reactivity, Yeast, protein anabolism, protein biosynthetic process, baker's yeast, Saccharomyes cerevisiae, responsivity., proteins, Saccharomyces uvarum var. melibiosus, Saccaromyces cerevisiae, Saccharomyces italicus, Stresses, Sccharomyces cerevisiae, polypeptide, Oxidative Stresses, Candida robusta, protein synthesis, Saccharomyces capensis, Oxidative, yeast, Stress, protein formation, protein biosynthesis, response, brewer's yeast, lager beer yeast"],"description_synonyms":["protein translation, atypia, data, Controlling, protein anabolism, protein biosynthetic process, aberrant, determination, Proteins, Gene, baker's yeast, defective, Double-Stranded, Saccaromyces cerevisiae, Saccharomyces italicus, eukaryotes, polypeptide, Sccharomyces cerevisiae, Double Stranded RNA Binding Proteins, Double-Stranded RNA-Binding Proteins, Protein, chemical analysis, yeast, protein formation, Gene Products, INSDC_feature:mRNA, protein biosynthesis, Ribosomal Protein., atypical, RNA-Binding Protein, lager beer yeast, RNA Binding Proteins, Saccharomyces oviformis, Yeast, Ribosomal, RIP-seq, protein_coding_transcript, reference sample, distinct, mRNA, RNA-Binding Proteins, Eukarya, Saccharomyes cerevisiae, messenger RNA, proteins, Eucarya, Saccharomyces uvarum var. melibiosus, eucaryotes, Protein Gene Products, Gene Proteins, Eukaryotae, template RNA, Candida robusta, clear, protein synthesis, Saccharomyces capensis, ds RNA-Binding Proteins, assay, Eucaryotae, brewer's yeast, RNA Binding Protein, RIP-seq assay, euk-, Controlled"],"pubmed_title_synonyms":["Saccharomyces oviformis, protein translation, reactivity, Yeast, protein anabolism, protein biosynthetic process, baker's yeast, Saccharomyes cerevisiae, responsivity., proteins, Saccharomyces uvarum var. melibiosus, Saccaromyces cerevisiae, Saccharomyces italicus, Stresses, Sccharomyces cerevisiae, polypeptide, Oxidative Stresses, Candida robusta, protein synthesis, Saccharomyces capensis, Oxidative, yeast, Stress, protein formation, protein biosynthesis, response, brewer's yeast, lager beer yeast"],"pubmed_abstract_synonyms":["protein translation, Materials, determination, H2O2, Gene Expression Profile, A4, Oxydol, ribosomal RNA, Ribosomal Protein, Profiles, dihydrogen dioxide, eIF-4F 25 kDa subunit, Double Stranded RNA Binding Proteins, Oxidative, responsivity, Analysis, InChI=1/H2O2/c1-2/h1-2H, Effect, RNA Binding Proteins, Mass Spectrum Analysis, H(2)O(2), Ribosomal, Gene Expressions, reference sample, Hydroperoxide, Analyses, EIF4EL1, Saccharomyes cerevisiae, proteins, number of, Eucarya, Saccharomyces uvarum var. melibiosus, Signatures, free, eucaryotes, Oxidative Stresses, Saccharomyces capensis, Expression Signature, Antioxidant, ds RNA-Binding Proteins, Anti-Oxidant Effect, Transcriptomes, Strains, brewer's yeast, associated, RNA Binding Protein, protein anabolism, Eif4e-ps, protein biosynthetic process, aberrant, Oxidizing Agents, If4e, Expression Profiles, extra or missing physical or functional parts, Double-Stranded, Spectrum Analysis, results, Spectroscopy, Gene Expression, poly-A RNA binding, Perhydrol, Double-Stranded RNA-Binding Proteins, Expression Signatures, protein formation, Genetic Materials, Expression Profile, Genetic Material, RNA-Binding Protein, Transcriptome Profiles, Yeast, antioxidants, Superoxol, protein_coding_transcript, Hydrogen peroxide (H2O2), dioxidane, RNA-Binding Proteins, Eukarya, Spectrometry, AUTS19, [H]OO[H], loss of, DMDA, Agents, protein synthesis, Material, Cistron, E430016J11Rik, Strains and Sprains, Proteomes, bis(hydridooxygen)(O--O), EG668879, HOOH, atypia, mRNA cap-binding protein, Transcriptome Profile, Effects, number, Oxidizing, Gene, baker's yeast, antioxydant, Spectrum Analyses, Hydrogen Peroxide (H2O2), Saccharomyces italicus, TYPE, Stresses, DAGA4, sensitive, Anti-Oxidant, yeast, Gene Products, Mass, antoxidant role, atypical, Anti-Oxidant Effects, MAM, Sprains, SCG3, attenuated, lager beer yeast, Mass Spectroscopy, reactivity, RIP-seq, Genetic, poly(A) RNA binding, Profile, messenger RNA, Peroxide, blocked, EIF4GI, dihydrogen peroxide, Expressions, EIF-4G1, InChIKey=MHAJPDPJQMAIIY-UHFFFAOYAL, template RNA, Candida robusta, poly(A)-RNA binding, [OH(OH)], has or lacks parts of type, Expression, Controlled., base pairing with RNA, Controlled, eIF-4E, Controlling, P220, Transcriptome, Proteins, Sprain, dihydrogen(peroxide), defective, Cistrons, Saccaromyces cerevisiae, Cell, Anti Oxidant Effect, LGMD2C, eukaryotes, whole transcriptome, mereological quality, polypeptide, Sccharomyces cerevisiae, Antioxidant Effect, Protein, chemical analysis, Gene Expression Signatures, Strain, PARK18, INSDC_feature:mRNA, protein biosynthesis, Gene Expression Signature, membrane bound ribosome, Mass Spectrum Analyses, EIF4E1, free ribosome, Saccharomyces oviformis, Anti Oxidant Effects, Mass Spectrum, Ribosome, Hydrogen, distinct, DMDA1, mRNA, CBP, Translatings, EIF4F, EIF4G, EIF4E, Protein Gene Products, Gene Proteins, Antioxidant Effects, eIF4E, Eukaryotae, clear, Gene Expression Profiles, Stress, SCARMD2, cardinality, assay, Eucaryotae, response, Signature, RIP-seq assay, RWDD5, euk-"],"view_count":["30"],"citation_count":["0"],"search_count":["5"],"full_dataset_link":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310018418"],"search_domains":["dbgap_ncbi~0","patentfamilies~0","rfam~0","merops~0","complex-portal~0","uniprot~0","wormbaseparasite~0","embl-covid19~0","reactome~0","emdb~0","wgs_masters~0","ebiweb_resources~0","opentargets_genetics~0","biomodels_all~0","ipd-mhc~0","ebiweb_teams~0","taxonomy~0","genome_assembly~0","sc-experiments~0","ebiweb_people~0","enzymeportal_enzymes~0","ipd-nhkir~0","cellosaurus~0","pdbe~0","chebi~0","patentproteins~0","interpro7~0","uniref~0","chembl~0","pdbekb~0","gpcrdb~0","hgnc~0","sc-genes~0","intact~0","rhea~0","ebiweb_training~0","alphafold~0","imgt-hla~0","patentnucleotides~0","ensemblroot~0","eva_studies~0","non-coding~0","europepmc~0","pubmed~1","identifiers_registry~0","pdbechem~0","hpa-covid19~0","eva-variants-covid19~0","biosamples~0","gwas_catalog~0","biotools~0","tls_masters~0","mesh~0","coding~0","sra~0","opentargets~0","efo~0","embl-pathogen~0","project~0","pride~1","human_diseases~0","geo_datasets~0","embl~0","treefam~0","uniparc~0","ols~0","dgva~0","intenz~0","go~0","tsa_masters~0","biosamples-covid19~0","ebiweb_corporate~0","omim~0","lrg~0","earlycause-molecular-sequences~0","ipd-kir~0","empiar~0","rnacentral~0","orcid_data_claims~0","gpmdb~2","lineage-covid19~0","metagenomics~0","pfam~0","pride 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File: 20131025_GP_CK_S2_1in10_01.mzml. Published as part of PLoS Genet. 2015 Jan 8;11(1):e1004903  . From the Abstract: {{i}} The mechanisms by which RNA-binding proteins control the translation of subsets of mRNAs are not yet clear. Slf1p and Sro9p are atypical-La motif containing proteins which are members of a superfamily of RNA-binding proteins conserved in eukaryotes. RIP-Seq analysis of these two yeast proteins identified overlapping and distinct sets of mRNA targets, including highly translated mRNAs such as those encoding ribosomal proteins ... {{/i}}","dates":{"submission":"2015-03-13"},"accession":"GPM32310018418","cross_references":{"pubmed":["25569619"],"Pride":["PXD000887"],"pride":[],"Pride Archive":["PXD000887"]}}