GPMDB00185OtherHongtao Zhang, et al.InstrumentNot AvailableNot availableAth1hongtao.zhang@rothamsted.ac.uk257287851Biological Chemistry and Crop Protection Department, Rothamsted Research, et al.http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014401http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014402http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014403http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014404http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014405http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014406http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014395http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014396http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014398http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014377http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014399http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014400http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014378Not availableGPMDBAccording to the Arg/N-end rule pathway, proteins with basic N-termini are targeted for degradation by the Arabidopsis thaliana E3 ligase, PROTEOLYSIS6 (PRT6). Proteins can also become PRT6 substrates following post-translational arginylation by arginyltransferases ATE1 and 2. Here, we undertook a quantitative proteomics study of Arg/N-end rule mutants, ate1/2 and prt6, to investigate the impact of this pathway on the root proteome. Tandem mass tag labelling identified a small number of proteins with increased abundance in the mutants, some of which represent downstream targets of transcription factors known to be N-end rule substrates. Isolation of N-terminal peptides using terminal amine isotope labelling of samples (TAILS) combined with triple dimethyl labelling identified 1465 unique N-termini. Stabilising residues were over-represented among the free neo-N-termini, but destabilising residues were not markedly enriched in N-end rule mutants. The majority of free neo-N-termini were revealed following cleavage of organellar targeting signals, thus compartmentation may account in part for the presence of destabilising residues in the wild-type N-terminome. Our data suggest that PRT6 does not have a marked impact on the global proteome of Arabidopsis roots and is likely involved in the controlled degradation of relatively few regulatory proteins. All MS data have been deposited in the ProteomeXchange with identifier PXD001719 (http://proteomecentral.proteomexchange.org/dataset/PXD001719).Quantitative proteomics analysis of the Arg/N-end rule pathway of targeted degradation in Arabidopsis roots.Zhang Hongtao H,Deery Michael J MJ,Gannon Lucy L,Powers Stephen J SJ,Lilley Kathryn S KS,Theodoulou Frederica L FL,Zhang Hongtao H, Deery Michael J MJ, Gannon Lucy L, Powers Stephen J SJ, Lilley Kathryn S KS, Theodoulou Frederica L FLmulticellular organismal catabolic process, single-organism catabolic process, eye-lt-m03Jus-gt-, 1110033A15Rik, Edg, determination, degradation, Atr2, A., Arabidopsis thaliana, number, A. thaliana, DNB1, presence, Abll, L-(+)-arginine, count in organism, Arabidopsis thalianas, count, A. thalianas, chemical analysis, thalianas, ARG, Arg, CD105, END, AI414665, ARP, ENG, Cardaminopsis., L-Arginine, mKIAA0458, breakdown, Cresses, Gm17754, catabolism, ATN1L, Mouse-ear Cress, thaliana, eyes3, AW742570, cell surface MJ7/18 antigen, Mouse-ear Cresses, Mouse-ear, Arabidopsis, L-Arg, AA536808, Cress, assay, quantitative, Mouse ear, ORW1, Arabidopses, HHT1, presence or absence in organism, ABLL, L-Argininmulticellular organismal catabolic process, single-organism catabolic process, 1110033A15Rik, JCAP, Slf, Slpa, Eseptin, ENG., Somatomedin-C, number, FBN, Gene, FPH2, DNB1, GRO:0005338, Transcription Factor, presence, supernumerary, L-(+)-arginine, exact), reduced, ECTOL1, Gene Products, Sint1, ARG, tiny, Arg, CD105, AF17q25, WMS, ARP, study, increased, Transcription, mKIAA0458, Gm17754, catabolism, ATN1L, somatomedin-C, hypoplasia, SF, CACP, Kitl, AW742570, proteins, labeling, number of, cell surface MJ7/18 antigen, AI225793, Mast cell growth factor, OCTD, MSF, Msf, thale-cress, radix (exact), IGF1, climbing root (narrow), has or lacks parts of type, Mechano growth factor, L-Arg, Soluble KIT ligand, Sl, GPHYSD2, HHT1, thiol methyltransferase activity, SGS, ABLL, L-Arginin, small, IGF-I, radices (exact, data, SeptD1, eye-lt-m03Jus-gt-, steel factor, Edg, degradation, Arbisopsis thaliana, ra&#237z (Spanish, Atr2, hematopoietic growth factor KL, plural), Proteins, FNZ, somatomedin, aerial root (narrow), extra or missing physical or functional parts, Factor, FINC, HAPO, LETS, sKITLG, Abll, CIG, all, ACMICD, mereological quality, polypeptide, count in organism, S-adenosyl-L-methionine:thiol S-methyltransferase activity, Experiment, SINT1, count, AW547406, mechano growth factor, Protein, Arabidopsis thaliana (thale cress), PNUTL4, MFS1, ED-B, 根 (Japanese, Igf-1, END, AI414665, WMS2, ENG, L-Arginine, thale cress, NAPB, mouse-ear cress, SHEP7, breakdown, Factors, SZP, FN, mast cell growth factor, underdeveloped, increased number, Tails, Stem cell factor, eyes3, root, MASS, STAT5, Protein Gene Products, Gene Proteins, present in greater numbers in organism, stem cell factor, KL-1, ligase, MGF, c-Kit ligand, SSKS, cardinality, KITLG, AA536808, GFND2, GFND, MSF1, quantitative, SCF, ORW1, E430016J11Rik, TMT, Proteomes, RWDD5, accessory, presence or absence in organismmulticellular organismal catabolic process, single-organism catabolic process, eye-lt-m03Jus-gt-, 1110033A15Rik, Edg, determination, degradation, Atr2, A., Arabidopsis thaliana, number, A. thaliana, DNB1, presence, Abll, L-(+)-arginine, count in organism, Arabidopsis thalianas, count, A. thalianas, chemical analysis, thalianas, ARG, Arg, CD105, END, AI414665, ARP, ENG, Cardaminopsis., L-Arginine, mKIAA0458, breakdown, Cresses, Gm17754, catabolism, ATN1L, Mouse-ear Cress, thaliana, eyes3, AW742570, cell surface MJ7/18 antigen, Mouse-ear Cresses, Mouse-ear, Arabidopsis, L-Arg, AA536808, Cress, assay, quantitative, Mouse ear, ORW1, Arabidopses, HHT1, presence or absence in organism, ABLL, L-Argininmulticellular organismal catabolic process, single-organism catabolic process, 1110033A15Rik, AI461847, A., number, cleavage, FBN, A4, Gene, DNB1, GRO:0005338, Transcription Factor, presence, supernumerary, TYPE, Cardaminopsis, L-(+)-arginine, DAGA4, Polypeptides, Arabidopsis thalianas, exact), reduced, isolation, ECTOL1, A. thalianas, Gene Products, thalianas, Pgi, ARG, tiny, Arg, MAM, Gpi-1, CD105, SCG3, WMS, ARP, study, increased, Transcription, mKIAA0458, reference sample, Cresses, Gm17754, catabolism, Gpi-1r, Nlk, ATN1L, Gpi-1s, Mouse-ear Cress, Phi, hypoplasia, Gpi-1t, AW742570, proteins, labeling, purification, number of, cell surface MJ7/18 antigen, AI225793, free, Mouse-ear, OCTD, isolation and purification, thale-cress, radix (exact), climbing root (narrow), has or lacks parts of type, L-Arg, Cress, Mouse ear, GPHYSD2, Arabidopses, HHT1, SGS, Controlled, ABLL, L-Arginin, small, Data Set., Gpi, radices (exact, data, Controlling, eye-lt-m03Jus-gt-, Edg, degradation, Arbisopsis thaliana, ra&#237z (Spanish, Atr2, plural), Proteins, Arabidopsis thaliana, aerial root (narrow), A. thaliana, extra or missing physical or functional parts, Factor, MF, Amf, Abll, LGMD2C, all, ACMICD, mereological quality, polypeptide, count in organism, count, mOC-X, AW547406, Protein, Arabidopsis thaliana (thale cress), MFS1, 根 (Japanese, NK|GPI, END, AI414665, WMS2, NK, ENG, L-Arginine, thale cress, mouse-ear cress, Org, ORG, breakdown, Factors, DMDA1, underdeveloped, increased number, Tails, thaliana, Gpi1-r, Gpi1-s, eyes3, root, MASS, Mouse-ear Cresses, Gpi1-t, Protein Gene Products, Gene Proteins, present in greater numbers in organism, Arabidopsis, DMDA, ligase, SSKS, cardinality, SCARMD2, AA536808, quantitative, ORW1, E430016J11Rik, Proteomes, RWDD5, Bglap-rs1, accessory, Gpi1s, presence or absence in organism1805http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014396dbgap_ncbi~0patentfamilies~0rfam~0merops~0complex-portal~0uniprot~0wormbaseparasite~0embl-covid19~0reactome~0emdb~0wgs_masters~0ebiweb_resources~0opentargets_genetics~0biomodels_all~0ipd-mhc~0ebiweb_teams~0taxonomy~0genome_assembly~0sc-experiments~0ebiweb_people~0enzymeportal_enzymes~0ipd-nhkir~0cellosaurus~0pdbe~0chebi~0patentproteins~0interpro7~0uniref~0chembl~0pdbekb~0gpcrdb~0hgnc~0sc-genes~0intact~0rhea~0ebiweb_training~0alphafold~0imgt-hla~0patentnucleotides~0ensemblroot~0eva_studies~0non-coding~0europepmc~0pubmed~1identifiers_registry~0pdbechem~0hpa-covid19~0eva-variants-covid19~0biosamples~0gwas_catalog~0biotools~0tls_masters~0mesh~0coding~0sra~0opentargets~0efo~0embl-pathogen~0project~0pride~1human_diseases~0geo_datasets~0embl~0treefam~0uniparc~0ols~0dgva~0intenz~0go~0tsa_masters~0biosamples-covid19~0ebiweb_corporate~0omim~0lrg~0earlycause-molecular-sequences~0ipd-kir~0empiar~0rnacentral~0orcid_data_claims~0gpmdb~2lineage-covid19~0metagenomics~0pfam~0pride archive~1varsite~00Resource Reanalysis0.00.00.0055521283158544110.01.0falseQuantitative proteomics analysis of the Arg/N-end rule pathway of targeted degradation in Arabidopsis roots.Data from ProteomeXchange, PXD ID: PXD001719. Experiment: TAILS_freeNt, file: TAILS_B_freeNt.msf.mgf. Published as part of Proteomics. 2015 Feb 27 . From the Abstract: {{i}} According to the Arg/N-end rule pathway, proteins with basic N-termini are targeted for degradation by the Arabidopsis thaliana E3 ligase, PROTEOLYSIS6 (PRT6). Proteins can also become PRT6 substrates following post-translational arginylation by arginyltransferases ATE1 and 2. Here, we undertook a quantitative proteomics study of Arg/N-end rule mutants, ate1/2 and prt6, to investigate the impact of this pathway on the root proteome. Tandem mass tag (TMT) labelling identified a small number of proteins with increased abundance in the mutants, some of which represent downstream targets of transcription factors known to be N-end rule substrates ... {{/i}}2015-03-27GPM3232001439625728785PXD001719PXD001719