GPMDB00155OtherKhan MN, et al.InstrumentNot AvailableNot availableGlycine_maxmnkhan@affrc.go.jp25818724Graduate School of Life and Environmental Sciences, University of Tsukuba, et al.http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039461http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039472http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039462http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039473http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039470http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039460http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039471http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039458http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039469http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039459http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039467http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039456http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039468http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039465http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039455http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039466http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039474http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039463http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039475http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039464Not availableGPMDBThis study analyzed post-flooding recovery response mechanisms in soybean hypocotyl, which is a model organ for studying secondary growth, using a gel-free proteomic technique. Mass spectrometry analysis of proteins extracted from soybean hypocotyls identified 20 common proteins between control and flooding-stressed soybeans that changed significantly in abundance over time. The hypocotyl proteins that changed during post-flooding recovery were assigned to protein, development, secondary metabolism, and glycolysis categories. The analysis revealed that three proteins, pyruvate kinase, nucleotidylyl transferase, and beta-ketoacyl reductase, were increased in hypocotyl under flooding conditions and during post-flooding recovery. The proteins are involved in glycolysis, nucleotide synthesis and amino acid activation, and complex fatty acid biosynthesis.Soybean is a nutritionally important crop, but exhibits reduced growth and yields under flooding stress. To investigate soybean responses during post-flooding recovery, a gel-free proteomic technique was used to examine the protein profile in the hypocotyl. Two-day-old soybeans were flooded for 2 days and hypocotyl was collected under flooding and during the post-flooding recovery period. A total of 498 and 70 proteins were significantly changed in control and post-flooding recovering soybeans, respectively. Based on proteomic and clustering analyses, three proteins were selected for mRNA expression and enzyme activity assays. Pyruvate kinase was increased under flooding, but gradually decreased during post-flooding recovery period at protein abundance, mRNA, and enzyme activity levels. Nucleotidylyl transferase was decreased under flooding and increased during post-flooding recovery at both mRNA expression and enzyme activity levels. Beta-ketoacyl reductase 1 was increased under flooding and decreased during recovery at protein abundance and mRNA expression levels, but its enzyme activity gradually increased during the post-flooding recovery period. These results suggest that pyruvate kinase, nucleotidylyl transferase, and beta-ketoacyl reductase play key roles in post-flooding recovery in soybean hypocotyl by promoting glycolysis for the generation of ATP and regulation of secondary metabolic pathways.Soybean is a nutritionally important crop, but exhibits reduced growth and yields under flooding stress. To investigate soybean responses during post-flooding recovery, a gel-free proteomic technique was used to examine the protein profile in the hypocotyl. Two-day-old soybeans were flooded for 2 days and hypocotyl was collected under flooding and during the post-flooding recovery period. A total of 498 and 70 proteins were significantly changed in control and post-flooding recovering soybeans, respectively. Based on proteomic and clustering analyses, three proteins were selected for mRNA expression and enzyme activity assays. Pyruvate kinase was increased under flooding, but gradually decreased during post-flooding recovery period at protein abundance, mRNA, and enzyme activity levels. Nucleotidylyl transferase was decreased under flooding and increased during post-flooding recovery at both mRNA expression and enzyme activity levels. Beta-ketoacyl reductase 1 was increased under flooding and decreased during recovery at protein abundance and mRNA expression levels, but its enzyme activity gradually increased during the post-flooding recovery period. These results suggest that pyruvate kinase, nucleotidylyl transferase, and beta-ketoacyl reductase play key roles in post-flooding recovery in soybean hypocotyl by promoting glycolysis for the generation of ATP and regulation of secondary metabolic pathways.This study analyzed post-flooding recovery response mechanisms in soybean hypocotyl, which is a model organ for studying secondary growth, using a gel-free proteomic technique. Mass spectrometry analysis of proteins extracted from soybean hypocotyls identified 20 common proteins between control and flooding-stressed soybeans that changed significantly in abundance over time. The hypocotyl proteins that changed during post-flooding recovery were assigned to protein, development, secondary metabolism, and glycolysis categories. The analysis revealed that three proteins, pyruvate kinase, nucleotidylyl transferase, and beta-ketoacyl reductase, were increased in hypocotyl under flooding conditions and during post-flooding recovery. The proteins are involved in glycolysis, nucleotide synthesis and amino acid activation, and complex fatty acid biosynthesis.<h4>Unlabelled</h4>Soybean is a nutritionally important crop, but exhibits reduced growth and yields under flooding stress. To investigate soybean responses during post-flooding recovery, a gel-free proteomic technique was used to examine the protein profile in the hypocotyl. Two-day-old soybeans were flooded for 2 days and hypocotyl was collected under flooding and during the post-flooding recovery period. A total of 498 and 70 proteins were significantly changed in control and post-flooding recovering soybeans, respectively. Based on proteomic and clustering analyses, three proteins were selected for mRNA expression and enzyme activity assays. Pyruvate kinase was increased under flooding, but gradually decreased during post-flooding recovery period at protein abundance, mRNA, and enzyme activity levels. Nucleotidylyl transferase was decreased under flooding and increased during post-flooding recovery at both mRNA expression and enzyme activity levels. Beta-ketoacyl reductase 1 was increased under flooding and decreased during recovery at protein abundance and mRNA expression levels, but its enzyme activity gradually increased during the post-flooding recovery period. These results suggest that pyruvate kinase, nucleotidylyl transferase, and beta-ketoacyl reductase play key roles in post-flooding recovery in soybean hypocotyl by promoting glycolysis for the generation of ATP and regulation of secondary metabolic pathways.<h4>Biological significance</h4>This study analyzed post-flooding recovery response mechanisms in soybean hypocotyl, which is a model organ for studying secondary growth, using a gel-free proteomic technique. Mass spectrometry analysis of proteins extracted from soybean hypocotyls identified 20 common proteins between control and flooding-stressed soybeans that changed significantly in abundance over time. The hypocotyl proteins that changed during post-flooding recovery were assigned to protein, development, secondary metabolism, and glycolysis categories. The analysis revealed that three proteins, pyruvate kinase, nucleotidylyl transferase, and beta-ketoacyl reductase, were increased in hypocotyl under flooding conditions and during post-flooding recovery. The proteins are involved in glycolysis, nucleotide synthesis and amino acid activation, and complex fatty acid biosynthesis.Proteomic analysis of soybean hypocotyl during recovery after flooding stress.Khan Mudassar Nawaz MN,Sakata Katsumi K,Komatsu Setsuko S,Khan Mudassar Nawaz MN, Sakata Katsumi K, Komatsu Setsuko Ssoybean, cv. Wye, Glycine max, proteomic analysis, soybeans, Hypocotyls.IGF-I, data, SHEP7, steel factor, mast cell growth factor, Soybean, Slf, hematopoietic growth factor KL, Stem cell factor, soybeans, Bean, Soy Beans, Somatomedin-C, somatomedin-C, SF, somatomedin, Kitl, FPH2, time., proteins, STAT5, Mast cell growth factor, free, sKITLG, soybean, Soy Bean, cv. Wye, polypeptide, period, stem cell factor, Menstrual period, KL-1, Period, IGF1, MGF, mechano growth factor, Glycine max, c-Kit ligand, Mechano growth factor, KITLG, Hypocotyls, Beans, Soluble KIT ligand, SCF, Igf-1, Sl, Soysoybean, cv. Wye, Glycine max, proteomic analysis, soybeans, Hypocotyls.secondary metabolite metabolic process, R-Type Pyruvate Kinase, single-organism developmental process, determination, Effects, Metabolisms, fatty acid formation., Gene, Embden-Meyerhof, Embden Meyerhof Parnas Pathway, supernumerary, Long Term, element, secondary metabolite metabolism, period, Transferase, Metabolism, responsivity, Gene Products, Embden-Meyerhof Pathway, Effect, organ, study, reactivity, increased, nucleotide anabolism, reference sample, Soybean, Longterm, soybeans, Soy Beans, nucleotide formation, Pathways, proteins, Long-Term, Pyruvate Kinase L, M Type Pyruvate Kinase, free, soybean, L-Type Pyruvate Kinase, L-Type, anatomical unit, body organ, nucleotide synthesis, Beans, Long-Term Effect, fatty acid synthesis, R-Type, Long-Term Effects, Soy, modifed Embden-Meyerhof pathway, M1-Type, Controlled, cambial secondary growth, M-Type Pyruvate Kinase, Controlling, Pathway, Embden Meyerhof Pathway, nucleotide biosynthesis, Proteins, fatty acid anabolism, Longterm Effect, anaerobic glycolysis, M2-Type, Embden-Meyerhof-Parnas, Pyruvate Kinase, Soy Bean, Secondary Metabolisms, polypeptide, development, Embden-Meyerhof-Parnas Pathway, L Type Pyruvate Kinase, M1 Type Pyruvate Kinase, Protein, Long Term Effects, chemical analysis, Hypocotyls, secondary metabolism, M2-Type Pyruvate Kinase, R Type Pyruvate Kinase, increased number, Bean, Embden-Meyerhof-Parnas pathway, Embden-Meyerhof pathway, M-Type, Longterm Effects, M1-Type Pyruvate Kinase, Protein Gene Products, cv. Wye, Gene Proteins, Secondary, present in greater numbers in organism, glycolysis, Glycine max, M2 Type Pyruvate Kinase, assay, response, fatty acid biosynthesis, time, Embden-Meyerhof Pathways, accessory1505http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210039463dbgap_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 Reanalysis0.00.00.00462677359654534250.01.0falseProteomic analysis of soybean hypocotyl during recovery after flooding stress.Data from ProteomeXchange, PXD ID: PXD001567. File: 423.mgf. Published as part of . From the Abstract: {{i}} ... To investigate soybean responses during post-flooding recovery, a gel-free proteomic technique was used to examine the protein profile in the hypocotyl. Two-day-old soybeans were flooded for 2days and hypocotyl was collected under flooding and during the post-flooding recovery period ... {{/i}}2015-05-26GPM1121003946325818724PXD001567PXD001567