{"database":"JPOST Repository","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["https://storage.jpostdb.org/JPST002112/files/181008_SatoK_Rab35_KO_TMT10_bRP9.xlsx"],"Raw":["https://storage.jpostdb.org/JPST002112/files/129_Sato_Rab35_KO_TMT10_bRP9_6.raw","https://storage.jpostdb.org/JPST002112/files/138_Sato_Rab35_KO_TMT10_bRP9_1re.raw","https://storage.jpostdb.org/JPST002112/files/127_Sato_Rab35_KO_TMT10_bRP9_5.raw","https://storage.jpostdb.org/JPST002112/files/131_Sato_Rab35_KO_TMT10_bRP9_7.raw","https://storage.jpostdb.org/JPST002112/files/135_Sato_Rab35_KO_TMT10_bRP9_9.raw","https://storage.jpostdb.org/JPST002112/files/133_Sato_Rab35_KO_TMT10_bRP9_8.raw","https://storage.jpostdb.org/JPST002112/files/123_Sato_Rab35_KO_TMT10_bRP9_3.raw","https://storage.jpostdb.org/JPST002112/files/121_Sato_Rab35_KO_TMT10_bRP9_2.raw","https://storage.jpostdb.org/JPST002112/files/125_Sato_Rab35_KO_TMT10_bRP9_4.raw"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Proteomics"],"submitter":["Hidetaka Kosako"],"species":["Mus Musculus (mouse)"],"full_dataset_link":["https://repository.jpostdb.org/entry/JPST002112"],"submitter_affiliation":["Tokushima University"],"sample_protocol":[""],"repository":["jPOST"],"data_protocol":[""],"pubmed_abstract":["RAB35 is a multifunctional small GTPase that regulates endocytic recycling, cytoskeletal rearrangement, and cytokinesis. However, its physiological functions in mammalian development remain unclear. Here, we generated Rab35-knockout mice and found that RAB35 is essential for early embryogenesis. Interestingly, brain-specific Rab35-knockout mice displayed severe defects in hippocampal lamination owing to impaired distribution of pyramidal neurons, although defects in cerebral cortex formation were not evident. In addition, Rab35-knockout mice exhibited defects in spatial memory and anxiety-related behaviors. Quantitative proteomics indicated that the loss of RAB35 significantly affected the levels of other RAB proteins associated with endocytic trafficking, as well as some neural cell adhesion molecules, such as contactin-2. Collectively, our findings revealed that RAB35 is required for precise neuronal distribution in the developing hippocampus by regulating the expression of cell adhesion molecules, thereby influencing spatial memory."],"pubmed_title":["RAB35 is required for murine hippocampal development and functions by regulating neuronal cell distribution."],"pubmed_authors":["Maejima Ikuko I, Hara Taichi T, Tsukamoto Satoshi S, Koizumi Hiroyuki H, Kawauchi Takeshi T, Akuzawa Tomoko T, Hirai Rika R, Kobayashi Hisae H, Isobe Inoya I, Emoto Kazuo K, Kosako Hidetaka H, Sato Ken K"],"name_synonyms":["ammon gyrus, Horn, Cornu ammonis, Ammon, CG9575, h-ray, Peptidomics, RAY, Ammon horn fields, formatio hippocampi, Proper, ammon horn, number, Hippocampus Propers, Ammon Horn, Hippocampal Formation, hippocampus proper, DmelCG9575, presence, seahorse, AU040256, Subiculums, TPSG1, count in organism, S-adenosyl-L-methionine:thiol S-methyltransferase activity, archipallium, H-ray, Hippocampal, Formations, major hippocampus, Ammon's Horn, Cornu Ammonis, Subiculum, Hippocampus, rab35, cornu ammonis, hippocampus proprius, Ammon's, Ammon's horn, RAB1C, Propers, Hippocampus Proper., rab1c, DmRab35, CNS - Brain - Hippocampus (MMHCC), hippocampus major, Ammons Horn, dRab35, hippocampus, primal cortex, Ammons horn, DRab35, PRSS31, TMT, 9530019H02Rik, Hippocampal Formations, thiol methyltransferase activity, Formation"],"pubmed_abstract_synonyms":["Cell Adhesion Molecule, Postnidation Embryo, Intercellular, Memory, single-organism developmental process, Pre-implantation Embryo Development, RAY, Laboratory, Ammon horn fields, BAA88244, supply, postnatal development, Mus domesticus, Post-implantation, Monomeric G-Protein, growth and development, CASP-14, Anxiety, Pre implantation Embryo Development, House Mouse, Divisions, Embryonic Programming, Cytokineses, AU040256, Small, ras Related GTP Binding Proteins, Embryo Development, Leukocyte Adhesion Molecules, GTPases, Small GTPases, cortical plate (areas), DmelCG3664, Formations, symptoms, Molecule, GTP-Binding Protein, synganglion, Leukocyte Adhesion Molecule, Fs(3)Hor, cortex cerebralis, Archipallium, ras Related G Proteins, Paleocortices, multicellular organismal biosynthetic process, small G-protein, single-organism biosynthetic process, DmelCG2684, AU045498, Cortex Cerebrus, ras-Related, Swiss Mice, NTef2, suprasegmental levels of nervous system, Angst, Ammons Horn, Small G Proteins, Social Anxieties, Social Anxiety, Preimplantation Embryo Development, Social, cytokinesis involved in cell cycle, Contactin-2, Rab-5, Ammons horn, l(2)k08232, Plate, Anxiousness, Anxieties, Nerve Cell, HRB, Hrb, 9530019H02Rik, ammon gyrus, screening, RAB5, Cell Adhesion Molecules, NCAM, GTP Binding Proteins, embryonal development, suprasegmental structures, Nervousness, Ammon, h-ray, formatio hippocampi, Paleocortex, CG3664, CASP14, mouse, Ammon Horn, small GTPase activity, hippocampus proper, small monomeric GTPase activity, Memories, seahorse, ras-Related GTPases, Fs(3)Sz11, retrograde transport of endocytic vesicles, dRab5, Subiculums, cortical plate (CTXpl), Anxiety disease, Dm Rab5, Hippocampal, Cell Adhesion, Mini-ICE, anxiety, ras-Related G-Proteins, major hippocampus, embryo Ce, Ammon's Horn, rab5, Subiculum, Mus musculus, Ammon's, cell cycle cytokinesis, Ammon's horn, Nerve Cells, Intercellular Adhesion Molecule, Caspase-14 subunit p10, mice, Encephalon, Swiss Mouse, Archipalliums, Molecules, signs, Caspase-14 subunit p19, Small G-Proteins, MICE, early, domesticus, loss of, dRab35, G Proteins, primal cortex, Horka, Cells, Monomeric, CG2684, Hypervigilance, Fs(3)Horka, Mouse, pallium of the brain, Allocortex, RIP, Rip, cortex cerebri, AAF51265, Postimplantation, DmRab5, Embryonic Programmings, the brain, Saccharide Mediated Cell Adhesion Molecules, heterotrimeric G-protein GTPase activity, 3.4.22.-, DRab5, CG9575, Intercellular Adhesion Molecules, Peptidomics, Adhesion Molecules, Nerve, ammon horn, number, small monomeric G protein activity, embryogenesis, Gene, mini-ICE, large G-protein GTPase activity, Monomeric G Protein, Development, Saccharide-Mediated Cell Adhesion Molecules, ras-Related GTP-Binding Proteins, presence, Prenidation Embryo Development, H-ray, Ras superfamily protein, House, Embryonic Developments, Gene Products, Mus musculus domesticus, DmF2, Drab5, Animal, Mice, Cerebral, Cornu Ammonis, Intercellular Adhesion, GTP-Binding Proteins, D730048C23Rik, Hippocampus, Neural, lod, Postnidation, cortex of cerebral hemisphere, Allocortices, Swiss, distribution, Cortical, ras Related GTPase, Small G Protein, Postnidation Embryo Development, ras-Related GTP-Binding, DmRab35, Pre-implantation, Division, hippocampus major, small GTPase, RAB5a, Cytoplasmic, Adhesion Molecule, embryogenesis and morphogenesis, DRab35, Leukocyte Adhesion, G-Proteins, Monomeric G Proteins, Neuron, Monomeric GTP Binding Proteins, Cortex Cerebri, ras Related GTP Binding Protein, GTPase, G-Protein, Horn, ras Related GTPases, Cornu ammonis, Leukocyte, findings, large G-protein activity, Cerebral Cortices, Proper, Proteins, Cortical Plates, Post implantation Embryo Development, Hippocampus Propers, Post-implantation Embryo Development, Preimplantation, Hippocampal Formation, DmelCG9575, Spatial Memories, encephalon, Cell, development, count in organism, ras-Related GTP-Binding Protein, archipallium, Cortex, Mus, C130049H11Rik, Neural Cell Adhesion Molecule, Cytoplasmic Division, Protein, Spatial, Small GTPase, supply and distribution, Postimplantation Embryo Development, ras-Related GTPase, Hippocampus Proper, embryonic stage, Embryonic, rab35, Spatial Memories., Embryo, cornu ammonis, brain cortex, Monomeric G-Proteins, hippocampus proprius, RAB1C, Propers, rab1c, postnatal growth, Embryogenesis, Small G-Protein, House Mice, C85612, CNS - Brain - Hippocampus (MMHCC), Lds, Laboratory Mice, Protein Gene Products, Gene Proteins, hippocampus, Periallocortex, Periallocortices, Cytoplasmic Divisions, RAB, Rab, growth, Laboratory Mouse, Hippocampal Formations, Severe, Formation, Cortical Plate"],"pubmed_title_synonyms":["rab35, AU040256, development, dRab35, nerve cell, RAB1C, neuronal cell, CG9575, H-ray, single-organism developmental process, h-ray, DRab35, RAY, distribution, supply., postnatal development, rab1c, postnatal growth, DmRab35, growth and development, supply and distribution, DmelCG9575, 9530019H02Rik, growth"],"description_synonyms":["Methane, MeCN, Raw, Lysine Hydrochloride, RAY, Laboratory, TFA, l(2)Sos, House Mouse, heavy chain disease, prevention, trichloro-, Long Term, nodus primitivus., AU040256, 5730420M11Rik, Trifluoroacetate, Polypeptides, DmelCG11081, KL receptor activity, Lysine Acetate, hydrogen chloride, dorsal marginal zone, Method, DPlexA, CH3-C#N, SCO5, SEC, 2, SCO1, 2-amino-3-mercaptopropanoic acid, Gsfsow3, WMS, L Lysine, C79691, SET, C, Divorced, C79325, K, E(var)189, M, sec, Salt, Divorces, W, T6G21.3, CG17245, AI047805, DmelCG4299, Lccp, isolation and purification, set, Wasserstoffchlorid, LYS, scientific observation, ACN, Lysin, sample, Acn, Bs, Half Cystine, 9530019H02Rik, SGS, LC-MS2, preventive therapy, Stars, h-ray, Zinc Cysteinate, Trypsin/K, CASP14, Longterm Effect, Guanidine Monohydroiodine, Procedure, DmelCG7793, not genetically inherited, ACMICD, PBT, TPSG1, Dm1, Chlorwasserstoff, dme-SOS, Methionin, Hmet, (2R)-2-amino-3-sulfanylpropanoic acid, BcDNA:GM05237, Acid, pbt, HLA-DR-associated protein II, Caspase-14 subunit p10, DI-2, I-2Dm, Swiss Mouse, pooled, Guanidine Phosphate, reagent, Caspase-14 subunit p19, MASCOT, Methodological, alpha, sodium hydrate, beta Trypsin, I-2PP1, dRab35, TAF-IBETA, spirit of wood, liquid chromatography-tandem mass spectroscopy, Indicator, PRSS31, DMZ, Mouse, TAF-Ibeta, methyl cyanide, chlorane, STARS, TMT, Liquimeth, Methyl Alcohol, krk1, Hydroxylamine Hydrochloride, 3.4.22.-, 2-amino-4-(methylsulfanyl)butanoic acid, Effects, chlorure d'hydrogene, Biocatalysts, number, Pierce, L-Zystein, mini-ICE, CH3OH, EK2-8, precursor, thomson, 17alpha)-isomer, CG7826, mass-to-charge ratio, Guanidium, H-ray, isolation, LC-MSMS, CG7835, Gene Products, Mus musculus domesticus, CG42273, Lysine, Half-Cystine, Technique, Cesium Trifluoroacetate, T6K12_14, Monohydroiodine, Acinus, Hydrogen chloride, Longterm, L Cysteine, E-920, plex A, Monosodium Salt, beta-Trypsin, plex B, 2pp2a, DmRab35, Sciences, Hcys, Long-Term, CG10574, Genotypes, DmelCG17245, acinusL, Study, Injectable, mKIAA0989, Enzyme, Monohydrobromide, Guanidinium Chloride, 2PP2A, 2-amino-4-(methylthio)butanoic acid, acinusS, CYSTEINE, dSET, dSet, FREE CYSTEINE, peptidos, SOS, 2.3, (2R)-2-amino-3-mercaptopropanoic acid, metionina, 4-(2-hydroxyethyl)-, measuring, proto-oncogene c-Kit, Guanidine Monohydrate, Guanidine Nitrate, 1-(14)C-labeled, Proteins, Methyl alcohol, sos, chloridohydrogen, backward, acetonitrile, L-Isomer, buffer, mKIAA0670, Engine, CD142, polypeptide, I-2PP2A, KIT ligand receptor activity, Acetate, chemical analysis, Long Term Effects, Dm I-2, Nitrate, 5alpha, MFS1, Sodium, MIXL, MeOH, soda lye, L-Lysine, Sos1, Met, XKrk1, T6K12.14, Guanidine Monohydrobromide, AU020952, Guanidine, RAB1C, Col4a-1, Guanidine Sulfate, ensemble, prophylaxis, Separations, Striated muscle activator of Rho-dependent signaling, Chloride, House Mice, (R)-2-amino-3-mercaptopropanoic acid, ethanenitrile, muscle, CD117, 2-Amino-3-mercaptopropionic acid, Longterm Effects, ME-IV, plan specification, Gene Proteins, Genogroups, C-Kit, control, Ssm, xkl-1, Aetznatron, liquid chromatography tandem mass spectrometry, E920, Sulfate, Enisyl, hydrochloric acid, Methoxide, reversed, liquid chromatography tandem mass spectroscopy, IPP2A2, Bru, BG:DS00941.4, E 920, NCMe, CG7793, determination, Mus domesticus, classic hairy cell leukaemia, Monohydrate, Guanidine Sulfate (2:1), HEPES Monosodium Salt, CASP-14, Hydrogenchlorid, Xkl-1, peptide, Techniques, L-Isomer Methionine, Gsfsco1, Methionine, peptido, BANF, Min, Cystein, prevention and control, Gsfsco5, Injectables, Effect, E(sev)2A, DmelCG42273, MIX, wood alcohol, SOW3, Svc, HEPES Monosodium, 3-hydroxy-5-estrane-17-carbonitrile, LCMSMS, reference sample, peptides, TAF-I, cisteina, 2610036I19Rik, 2610510L13Rik, min, epsilon-diaminocaproic acid, Swiss Mice, mAPC, Phosphate, purification, preventive measures, reaction, Hydroxylammonium Chloride, IGAAD, fSAP152, Methodological Studies, 1-Piperazineethanesulfonic acid, DmelCG10574, ppm, trifluoro-, TF, Guanidine Sulfate (1:1), TEAB, Sodium Methoxide, Reagents, Natriumhydroxid, hydroxyde de sodium, Sl, GPHYSD2, Racemethionine, Long-Term Effects, reagents, phapii, Monohydrochloride, Alcohol, mouse, LC-MS/MS, 2-Amino-4-(methylthio)butyric acid, Dmel_CG7826, StF-IT-1, Tr-kit, Th, Search, classic hairy cell leukemia, Cys, S-adenosyl-L-methionine:thiol S-methyltransferase activity, HCD, Mini-ICE, lysine, kl1-A, Henson's node, KIT, reactif, Carbinol, PlexA1, fixed, Dmel_CG7835, Acetic acid, br24, dSos, br25, carbinol, Mnb, MNB, parent ion, tyrosine-protein kinase Kit, Mus musculus, MILD1, NaOH, PlexB, 34Ea, PlexA, MS/MS, mice, Xylella fastidiosa str. Temecula1, Sonications, HCl, Trifluoroacetic, Guanidine Monohydrochloride, L-Cysteine, kit, MASS, CG4299, AW124434, MICE, Plex1, Methodological Study, muscle element, L-Cystein, domesticus, Trichloromethane, chloracetamide, nanospray, Wood, precursor ion, Cesium, Biocatalyst, Polypeptide, HEPES, PLEXB, i2pp2a, Cysteine Hydrochloride, CG9575, Procedures, AW549739, Reagent, SCF receptor activity, L Isomer, FBN, Gene, Methyl, CG11081, ACINUS, Methylalkohol, presence, PHAPII, LC-MS-MS, Buffer, method, scfr, House, Ms1, ECTOL1, Injection, method used in an experiment, Studies, L-Methionine, Wood Alcohol, D-Plex A, Del(8)44H, Mice, SCFR, Separated, cloruro de hidrogeno, Reagents and Indicators, l(2)br25, Pedameth, Pro-Mega, l(2)br24, Guanidium Chloride, Nestin, Search Engines, Fdc, reactivo, MS1, Swiss, MS2, Selb, l(2)k06321, ipp2a2, soude caustique, Indicators, Xylella fastidiosa (strain Temecula1 / ATCC 700964), OCTD, 10^[-6], wood naphtha, taf-ibeta, DRab35, stem node, male sterility 1, musculus, N-2-Hydroxyethylpiperazine-N'-2'-ethanesulfonic Acid, Long-Term Effect, l(2)34Ea, Guanidine Hydrochloride, TCEP, thiol methyltransferase activity, Controlled, Controlling, DYRK1, 3H-labeled, DL-Methionine, igaad, DmelCG9575, plex, Guanidinium, Peptide, group, [HCl], count in organism, LC/MS/MS, secret agent, Genogroup, Mus, l(2)k05224, Protein, caustic soda, I2PP2A, Hydrochloride, Guanidine Sulfite (1:1), Dyrk1, (3alpha, ACETONITRILE, tandem MS, Zystein, cyanomethane, WMS2, Data Base, DDA, rab35, Separation, c-KIT, PRSS, nodal stem, MALE STERILITY 1 PROTEIN, 2-amino-3-sulfanylpropanoic acid, Nestin Protein, CC1, rab1c, EY2-3, Tripcellim, N 2 Hydroxyethylpiperazine N' 2' ethanesulfonic Acid, L-2-Amino-3-mercaptopropionic acid, sample population, Laboratory Mice, Protein Gene Products, Trypure, dSET/TAF-Ibeta, Su(tor)2-2, c-kit, 2610030F17Rik, wood spirit, SSKS, alpha-amino-gamma-methylmercaptobutyric acid, Peptid, assay, SCH, AA407739, 6-diaminohexanoic acid, Laboratory Mouse, 3-OHECN"],"additional_accession":[]},"is_claimable":false,"name":"TMT-based quantitative proteomics in Rab35 cKO P0 hippocampus","description":"The hippocampi from the control (Rab35flox/+; Nestin-Cre) and Rab35 cKO mice groups at P0 (n = 5 biological replicates per genotype) were lysed in a buffer containing 6 M guanidine hydrochloride, 100 mM HEPES-NaOH (pH 8.0), 10 mM TCEP, and 40 mM chloroacetamide. The lysates were dissolved through heating and sonication, followed by centrifugation at 15,000 rpm for 15 min at 4°C. Proteins (100 μg each) were purified using methanol/chloroform precipitation and solubilized through the addition of 20 μL of 0.1% RapiGest SF (Waters) in 50 mM triethylammonium bicarbonate. After repeated sonication and vortexing, the proteins were digested with 1 μg of trypsin/Lys-C mix (Promega) for 16 h at 37°C. The peptide concentrations were determined using the Pierce quantitative colorimetric peptide assay (Thermo Fisher Scientific). Approximately 25 μg of peptides for each sample was labeled with 0.2 mg of TMT10-plex reagents (Thermo Fisher Scientific) for 1 h at 25°C. After the reaction was quenched with hydroxylamine, all the TMT-labeled samples were pooled, acidified with trifluoroacetic acid (TFA), and fractionated using the Pierce high pH reversed-phase peptide fractionation kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. Nine fractions were collected using 5%, 10%, 12.5%, 15%, 17.5%, 20%, 22.5%, 25%, and 80% acetonitrile (ACN). Each fraction was evaporated in a SpeedVac concentrator and dissolved in 0.1% TFA and 3% ACN. LC-MS/MS analysis of the resultant peptides (1 μg each) was performed on an EASY- nLC 1200 UHPLC connected to a Q Exactive Plus mass spectrometer through a nanoelectrospray ion source (Thermo Fisher Scientific). The peptides were separated with a linear gradient from 4–20% ACN for min 0–180 and 20–32% ACN for min 180–220, followed by an increase to 80% ACN during min 220–230. The mass spectrometer was operated in a data-dependent acquisition mode with a top 15 MS/MS method. MS1 spectra were measured with a resolution of 70,000, an automatic gain control (AGC) target of 3e6, and a mass range of 375–1,400 m/z. HCD MS/MS spectra were acquired at a resolution of 35,000, an AGC target of 1e5, an isolation window of 0.4 m/z, a maximum injection time of 100 msec, and a normalized collision energy of 34. Dynamic exclusion was set to 30 sec. Raw data were directly analyzed against the SwissProt database restricted to M. musculus using Proteome Discoverer version 2.3 (Thermo Fisher Scientific) with Mascot search engine version 2.5 (Matrix Science) for identification and TMT quantification. The search parameters were as follows: (a) trypsin as an enzyme with up to two missed cleavages; (b) precursor mass tolerance of 10 ppm; (c) fragment mass tolerance of 0.02 Da; (d) TMT of lysine and peptide N-terminus and carbamidomethylation of cysteine as fixed modifications; and (e) oxidation of methionine as a variable modification. Peptides were filtered at a false-discovery rate (FDR) of 1% using the percolator node.","dates":{"publication":"Fri Apr 07 00:00:00 BST 2023"},"accession":"PXD041290","cross_references":{"TAXONOMY":["10090"],"pubmed":["37085665"]}}