<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
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<CvList>
<Cv fullName="PSI-MS" uri="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" id="MS"/>
<Cv fullName="PSI-MOD" uri="https://raw.githubusercontent.com/MICommunity/psidev/master/psi/mod/data/PSI-MOD.obo" id="MOD"/>
<Cv fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" id="UNIMOD"/>
</CvList>
<ChangeLog>
<ChangeLogEntry date="2023-11-14">Updated project metadata.</ChangeLogEntry>
</ChangeLog>
<DatasetSummary announceDate="2023-11-14" hostingRepository="PRIDE" title="Identification of nascent peptides of peptidyl-tRNA dissociated from ribosome in the early elongation stage in Escherichia coli pthts cells">
<Description>Accurate translation of mRNAs into functional proteins is a fundamental process in all living organisms. In bacteria, in the early stage of translation elongation, peptidyl-tRNAs (pep-tRNAs) with short nascent chains frequently dissociate from the ribosome (pep-tRNA drop-off). The dissociated pep-tRNAs are deacylated and recycled by peptidyl-tRNA hydrolase (PTH), which is an essential enzyme in bacteria. Here, we establish a highly sensitive method for direct profiling of pep-tRNAs using RNA isolation method and mass spectrometry. We isolated each tRNA species with peptide from Escherichia coli pthts cells using reciprocal circulating chromatography and precisely analyzed their nascent peptides. As a result, we successfully detected 703 peptides consisted of 402 cognate peptides and 301 non-cognate peptides with single amino-acid substitution. Detailed analysis of individual pep-tRNAs revealed that most of the substitutions in the miscoded peptides take place at the C-terminal drop-off site. We further examined this observation using a reporter construct and found that the non-cognate pep-tRNAs produced by mistranslation rarely participate in the next round of elongation but dissociate from the ribosome, suggesting that pep-tRNA drop-off is an active mechanism by which the ribosome rejects miscoded pep-tRNAs in the early elongation, thereby contributing to quality control of protein synthesis after peptide bond formation.</Description>
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<cvParam cvRef="MS" accession="MS:1002854" name="Peer-reviewed dataset"/>
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<cvParam cvRef="MS" accession="MS:1002856" name="Supported dataset by repository"/>
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<DatasetIdentifierList>
<DatasetIdentifier>
<cvParam cvRef="MS" accession="MS:1001919" name="ProteomeXchange accession number" value="PXD030805"/>
<cvParam cvRef="MS" accession="MS:1001921" name="ProteomeXchange accession number version number" value="2"/>
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<DatasetIdentifier>
<cvParam cvRef="MS" accession="MS:1001922" name="Digital Object Identifier (DOI)" value="10.6019/PXD030805"/>
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<DatasetOriginList>
<DatasetOrigin>
<cvParam cvRef="MS" accession="MS:1002868" name="Original data"/>
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</DatasetOriginList>
<SpeciesList>
<Species>
<cvParam cvRef="MS" accession="MS:1001469" name="taxonomy: scientific name" value="Escherichia coli"/>
<cvParam cvRef="MS" accession="MS:1001467" name="taxonomy: NCBI TaxID" value="562"/>
</Species>
</SpeciesList>
<InstrumentList>
<Instrument id="Instrument_1">
<cvParam cvRef="MS" accession="MS:1001910" name="LTQ Orbitrap Elite"/>
</Instrument>
</InstrumentList>
<ModificationList>
<cvParam cvRef="MOD" accession="MOD:00394" name="acetylated residue"/>
<cvParam cvRef="MOD" accession="MOD:00425" name="monohydroxylated residue"/>
<cvParam cvRef="MOD" accession="MOD:00397" name="iodoacetamide derivatized residue"/>
</ModificationList>
<ContactList>
<Contact id="project_submitter">
<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Asuteka Nagao"/>
<cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="tasuteka@g.ecc.u-tokyo.ac.jp"/>
<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="The university of Tokyo"/>
<cvParam cvRef="MS" accession="MS:1002037" name="dataset submitter"/>
</Contact>
<Contact id="project_lab_head">
<cvParam cvRef="MS" accession="MS:1002332" name="lab head"/>
<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Tsutomu Suzuki"/>
<cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="ts@chembio.t.u-tokyo.ac.jp"/>
<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan."/>
</Contact>
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<Publication id="DOI-10_6019_PXD030805">
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<cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="translation"/>
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<FullDatasetLink>
<cvParam cvRef="MS" accession="MS:1001930" name="PRIDE project URI" value="http://www.ebi.ac.uk/pride/archive/projects/PXD030805"/>
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</FullDatasetLinkList>
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