Biomedical subjects

Masuko Katoh

Publications and source records attributed to Masuko Katoh.

99 records · Page 6Linked to original sources

PubMed2003

Identification and characterization of TPARM gene in silico.

Several tumor suppressor genes are located within human chromosome 11q23 region. We have cloned and characterized MFRP and RNF26 genes at 11q23.3. We also identified and characterized KIAA1735/MTHDIX gene at 11q23.1 and CLDN24 gene at 11q23.2 by using bioinformatics. Here, a novel human gene corresponding to a 5'-truncated FLJ20535 cDNA was identified. FLJ20535 corresponded to nucleotide position 55-2255 of FLJ13859, and nucleotide position 52-2169 of FLJ13859 was the coding region. Because of tetratricopeptide repeat (TPR) and armadillo repeat (ARM) domains within its gene product, the novel human gene was designated TPARM. Mouse E330017O07Rik cDNA was derived from mouse Tparm gene. Human TPARM (705 aa) and mouse Tparm (704 aa), showing 75.4% total-amino-acid identity, consist of TPR domain and three ARM domains. TPR domain of TPARM was most homologous to that of SMAP1, while ARM1-ARM3 domains of TPARM were most homologous to ARM7-ARM9 domains of CTNNB1 (also known as beta-catenin). TPARM might be implicated in the WNT-beta-catenin signaling pathway. TPARM mRNA was expressed in testis, prostate, lung, germinal center B-cells, and also in neuroblastoma, teratocarcinoma, colon cancer, and gastric cancer. Human TPARM gene was found to consist of 22 exons. TPARM gene, located between NCAM1 and DRD2 genes, was mapped to human chromosome 11q23.2. TPARM as well as NCAM1 and DRD2 were predicted to be candidate tumor suppressor genes within the commonly deleted region of malignant melanoma on 11q23.1-q23.2 (between microsatellite markers D11S1347 and D11S4122).

Amino Acid Sequence↗

PubMed2003

Identification and characterization of FLJ10737 and CAMTA1 genes on the commonly deleted region of neuroblastoma at human chromosome 1p36.31-p36.23.

Tumor suppressor genes of neuroblastoma are located at human chromosome 1p36, 4p16, 11q23.3, and 14q32. We have previously cloned and characterized MFRP and RNF26 genes at 11q23.3. Here, we searched for genes within the 1p36.31-p36.23 commonly deleted region between microsatellite markers D1S2731 and D1S2666 by using bioinformatics. D1S2731 was located within FLJ10737 gene, consisting of 16 exons. D1S2666 was located within CAMTA1 gene, consisting of 23 exons. FLJ10737 and CAMTA1 genes were located in the head-to-head manner with an interval of about 83 kb. Exons 1-10 of FLJ10737 gene as well as exons 1-5 of CAMTA1 gene were located within the 1p36.31-p36.23 commonly deleted region. FLJ10737 (559 aa) was found to consist of the DnaJ domain, bipartite nuclear localization signal (NLS), FADH domain, and FEMCA domain. Mouse E030019A03, zebrafish MGC55845, Drosophila CG8531 and Arabidopsis At2g35720 were homologs of human FLJ10737. FADH domain was conserved among vertebrate FLJ10737 orthologs as well as human AD-015, mouse Histocompatibility 47, and rat Ratsg2. KIAA0833 was the representative human CAMTA1 cDNA. Nucleotide sequence of mouse Camta1 cDNA was determined in silico by assembling nucleotide sequences of BY733411, BU610694 ESTs and AK122383 cDNA. Human CAMTA1 (1673 aa) and mouse Camta1 (1682 aa) showed 94.1% total-amino-acid identity. CAMTA1 was a Calmodulin-binding transcription activator (CAMTA) family protein, consisting of CG-1 domain, TIG domain, ankyrin repeats, and IQ motifs. FLJ10737 and CAMTA1 genes on 1p36.31-p36.23 are candidate tumor suppressor genes of neuroblastoma.

Amino Acid Sequence↗

PubMed2003

Identification and characterization of human BCL9L gene and mouse Bcl9l gene in silico.

Human BCL9 gene is over-expressed in some cases of acute lymphoblastic leukemia (ALL) with t(1;14)(q21;q32). Drosophila segment polarity gene legless (lgs), encoding wingless-armadillo (WNT - beta-catenin) signaling molecule, is the homolog of human BCL9. Here, we identified and characterized human BCL9-like (BCL9L) gene as well as mouse Bcl9-like (Bcl9l) gene by using bioinformatics. Uncharacterized DLNB11 cDNA (AB094091.1) was derived from human BCL9L gene. Nucleotide sequence of mouse Bcl9l cDNA was determined in silico by assembling mouse ESTs BF464707, BQ258167, 5'-truncated BC003321 cDNA, and mouse genome clone RP24-308H8 (AC125129.5). Human BCL9L and mouse Bcl9l genes were found to consist of eight exons. Exon-intron structure was well conserved between human BCL9L and mouse Bcl9l genes. Human BCL9L (1499 aa) showed 94.0% and 34.8% total-amino-acid identity with mouse Bcl9l (1494 aa) and human BCL9, respectively. Six domains (B9H1-B9H6) were conserved among mammalian BCL9 family proteins. B9H1 and B9H2 domains, and N-terminal part of B9H3 domain were identical to HD1, HD2, and HD3 domains conserved between human BCL9 and Drosophila lgs. B9H4, B9H5 and B9H6 were novel domains. B9H4 domain was characterized by multiple Ser-Pro repeats. Human BCL9L mRNA was expressed in fetal brain, adult lung, amygdala, eye, prostate, and also in several types of tumors including pancreatic cancer, prostate cancer, head and neck tumor and embryonal tumor. BCL9L gene was located between BLR1 and UPK2 genes within the commonly deleted region of neuroblastoma at human chromosome 11q23.3. This is the first report on human BCL9L and mouse Bcl9l.

Amino Acid Sequence↗

PubMed2003

Identification and characterization of human FNBP3 gene in silico.

FMNL1, FMNL2, FMNL3, DAAM1, DAAM2, DIAPH1 and DIAPH2 constitute the Formin-homology subfamily with FDD, FH1 and FH2 domains. FMNL2 gene is linked to FNBP3 (also known as HYPA) gene on human chromosome 2q23.3, while FMNL3 gene to FNBP3L (also known as HYPC) gene on 12q13. Because human FNBP3 cDNA (NM_017892.2) was a 5'-truncated partial clone, we identified and characterized human FNBP3 gene by using bioinformatics. Human FNBP3 gene, consisting of 26 exons, was located within human genome sequences AC079344.5, AC012443.8, and human chromosome 2 genomic contig NT_005403.13. Nucleotide sequence of human FNBP3 cDNA was determined in silico by assembling nucleotide sequences of 26 exons of FNBP3 gene. HYPA cDNA and IMAGE cDNA clones 3356968, 4026200, 4733897 were 3'-truncated partial FNBP3 cDNAs, while FNBP3 (NM_017892.2), FLJ11559, NY-REN-6, and FLJ20585 were 5'-truncated partial FNBP3 cDNAs. Two FNBP3 isoforms with or without 126-bp region in the 3'-part of exon 1 were transcribed due to alternative splicing. FNBP3 isoform 2 without the 126-bp region was the major FNBP3 transcript. Two WW domains, two FF domains, two bipartite nuclear localization signals, FB3HM and FB3HC domains were conserved among vertebrate FNBP3 homologs, including human FNBP3, FNBP3L, mouse Fnbp3, Fnbp3l, chicken fnbp3 and zebrafish fnbp3. FNBP3, binding to TNFSF6 (Fas ligand), Huntingtin and Formin proteins, might transduce extracellular signals to the Rho-related signaling pathway. On the other hand, FNBP3 with nuclear localization signals and two tyrosine phosphorylation sites might transduce extracellular signals to the nucleus. This is the first report on comprehensive characterization of human FNBP3 gene.

Alternative Splicing↗

PubMed2003

Identification and characterization of human KIAA1391 and mouse Kiaa1391 genes encoding novel RhoGAP family proteins with RA domain and ANXL repeats.

The commonly deleted region of breast cancer at human chromosome 11q23.1 is located between microsatellite markers D11S927 and D11S1347. We have previously identified and characterized the KIAA1735 gene, encoding MTH and DIX domain protein, within the 11q23.1 commonly deleted region. The BTG4 gene, encoding BTG/TOB family protein, as well as the SIK2 gene, encoding salt-inducible serine/threonine kinase 2, were also located within the 11q23.1 region. We identified and characterized the KIAA1391 gene within the 11q23.1 commonly deleted region by using bioinformatics. The nucleotide position 11-3586 of human KIAA1391 cDNA was predicted as the coding region of human KIAA1391 gene. Mouse Kiaa1391 gene was located within mouse genome sequences RP23-95E13 (AC102770.4), RP23-212M11 (AC140363.1), and mouse chromosome 9 genomic contig NT_039473.1. Exon-intron structure was well conserved between human KIAA1391 gene and mouse Kiaa1391 gene. Nucleotide sequence of mouse Kiaa1391 cDNA was determined in silico by assembling nucleotide sequences of exon 1-15 of mouse Kiaa1391 gene. Human KIAA1391 protein (1191 aa) and mouse Kiaa1391 protein (1182 aa) showed 79.1% total-amino-acid identity. RA domain (codon 198-274), RhoGAP domain (codon 363-546), and two Annexin-like (ANXL) repeats (codon 657-767 and 796-909) of human KIAA1391 protein were conserved in mouse Kiaa1391 protein. This is the first report on the comprehensive characterization of human KIAA1391 gene and mouse Kiaa1391 gene, encoding RhoGAP proteins with RA domain and two ANXL repeats.

Amino Acid Sequence↗

PubMed2003

Identification and characterization of human LL5A gene and mouse Ll5a gene in silico.

ARCN1, KIAA0638, TREH, DDX6, BLR1, BCL9L, UPK2, DLNB13, DLNB14, RPS25, SBDN, G6PT1, HYOU1, VPS11, HMBS, H2AFX, DPAGT1, KIAA0285, MIZF, ABCG4, NOD9, PDZK2, CBL, MCAM, RNF26, C1QTNF5, MFRP, USP2, THY1, and PVRL1 genes are located within the commonly deleted region of neuroblastoma at human chromosome 11q23.3. Here, we characterized the KIAA0638 gene within the 11q23.3 region by using bioinformatics. Because human KIAA0638 gene was homologous to human LL5B gene encoding LL5beta protein, KIAA0638 was designated LL5A gene encoding LL5alpha protein. LL5A isoform 1 (FLJ00141 type) consists of exons 1-12, 14-21 and 23, while LL5A isoform 2 (KIAA0638 type) consists of exon 1-23. LL5A isoform 1 was the major transcript among LL5A isoforms generated due to alternative splicing. Nucleotide sequence of mouse Ll5a cDNA was determined by assembling CB522359 EST and 5'-truncated mKIAA0638 cDNA. Human LL5alpha isoform 2 showed 94.4 and 35.9% total-amino-acid identity with mouse Ll5alpha and human LL5beta, respectively. LL5alpha proteins consist of Forkhead associated (FHA) domain, bipartite nuclear localization signal (NLS), Chromosome segregation ATPases (SMC) domain, and Pleckstrin homology (PH) domain. LL5alpha proteins were homologous to PtdIns(3,4,5)P3 sensor protein LL5beta in the SMC and PH domains, and were also homologous to KIF1A, KIF1B, KIF13A, KIF13B, KIF14, and SNX23 proteins in the FHA domain. LL5alpha protein might be a transducer of PtdIns(3,4,5)P3 levels to the intracellular trafficking system.

Alternative Splicing↗

PubMed2003

Identification and characterization of TRIP8 gene in silico.

TRIP1-TRIP15 genes encode thyroid hormone receptor beta (TR beta)-binding proteins. TRIP10 gene encodes FNBP1 family protein with FCH, FBH, and SH3 domains. Among 15 TRIP genes, TRIP8 gene remained uncharacterized except TRIP8 partial cDNA (L40411). Here, we determined the complete coding sequence of TRIP8 gene by using bio-informatics. Nucleotide sequence of full-length TRIP8 cDNA was determined in silico by assembling nucleotide sequences of FLJ14374 and DKFZp761F0118 cDNAs. TRIP8 protein (2540 aa) was found to consist of two bipartite nuclear localization signals (codon 352-368 and 2365-2381), TRI8H1 domain (codon 1697-1873), TRI8H2 domain (codon 2057-2351), and JMJC domain (codon 2387-2486). TRI8H1, TRI8H2 and JMJC domains were conserved among TRIP8, 5qNCA (C5orf7) and TSGA proteins. TR beta-binding domain was overlapped with N-terminal part of TRI8H2 domain, and C2HC4-type zinc finger-like motif was located within C-terminal part of TRI8H1 domain. Because JMJC domain proteins are implicated in chromatin remodeling, TRIP8 was predicted to be a transcriptional regulator associated with nuclear hormone receptors. Human TRIP8 gene, consisting of 26 exons, was about 300 kb in size. Intra-species comparative genomics revealed that TRIP8-EGR2 locus at human chromosome 10q21.3 and 5qNCA-EGR1 locus at human chromosome 5q31 are paralogous regions within human genome. Microsatellite marker D10S1225, associated with Alzheimer's disease, non-syndromic congenital retinal non-attachment (NCRNA) and non-syndromic autosomal recessive persistent hyperplastic primary vitreous (arPHPV), was located within the TRIP8-EGR2 locus. This is the first report on comprehensive characterization of the TRIP8 gene.

ATPases Associated with Diverse Cellular Activitie↗

PubMed2003

Identification and characterization of human PPFIA4 gene in silico.

Human PPFIA1 (also known as LIP.1 or Liprin alpha1) gene, located within CCND1-FGF4-EMS1 amplicon at human chromosome 11q13.3, encodes KIF1A-binding protein, which is implicated in trafficking of LAR subfamily PTPases and AMPA-type glutamate receptors. Human PPFIA4 (AF034801) and rat Ppfia4 (AY057064) are 5'-truncated partial cDNAs, and the complete coding sequence of PPFIA4 ortholog of any species remained to be identified. Here, we determined the complete coding sequence of human PPFIA4 gene by using bioinformatics. Exons 1-12 of PPFIA4 gene were located within human genome sequence AC096632.3, while exons 11-29 within AL451082.6. PPFIA4-MYOG locus (human chromosome 1q32.1) was paralogous to PPFIA2-LIN7A-MYF5-MYF6 locus (12q21.31), which was also paralogous to PPFIA3-LIN7B locus (19q13.41). PPFIA4 (1186 aa) showed 70.9%, 67.1%, and 61.8% total-amino-acid identity with PPFIA2, PPFIA1, and PPFIA3, respectively. PPFIA family members consist of PFIH1, PFIH2, PFIH3, PFIH4 domains and three SAM (Sterile alpha motif) domains. C-terminal binding domain for GRIP proteins (VRTYSC motif) was present in PPFIA1, PPFIA2 and PPFIA3, but not in PPFIA4. Bipartite nuclear localization signal was included within PFIH4 domain. PFIH2 domain was identical to ERM or Smc domain. The region spanning PFIH2-PFIH3 domains is the binding domain for KIF1A. The region spanning SAM1-SAM3 domains is the binding domain for LAR subfamily PTPases and PPFIBP (Liprin beta) family proteins. This is the first report on comprehensive characterization of PPFIA4 belonging to the PPFIA family of kinesin-cargo linkers.

Adaptor Proteins, Signal Transducing↗

PubMed2003

Identification and characterization of human GRID2IP gene and rat Grid2ip gene in silico.

Formin-homology proteins are implicated in the cell polarity control through the assembly of specific actin structures. FMNL1/KW-13/FMNL, FMNL2/KIAA1902/FHOD2, FMNL3/KIAA2014, DAAM1, DAAM2, DIAPH1 and DIAPH2 are Formin-homology proteins with the FDD domain, while Fmn1, Fmn2, FHOD1 and Grid2ip/Delphilin are Formin-homology proteins without the FDD domain. Mouse Grid2ip links glutamate receptor delta2 subunit with actin cytoskeleton and various signaling molecules. Here, we identified and characterized human GRID2IP gene as well as rat Grid2ip gene by using bioinformatics. Human GRID2IP gene was identified within human genome sequence CTD-2195F21 (AC072052.6). Human GRID2IP gene, consisting of 21 exons, was mapped to human chromosome 7p22.1. Rat Grid2ip gene, consisting of 21 exons, was identified within rat genome sequence CH230-82F18 (AC126572.3). Human GRID2IP (1020 aa) showed 91.7% total-amino-acid identity with rat Grid2ip (1024 aa), and 92.7% total-amino-acid identity with mouse Grid2ip. Human GRID2IP protein was found to consist of PDZ domain (codon 94-166), GRCAH domain (codon 204-269), FH1 domain (codon 559-621), and FH2 domain (codon 640-1005). GRCAH domain identified in this study was conserved among mammalian GRID2IP orthologs and mammalian CIP98/KIAA1526 orthologs. This is the first report on comprehensive characterization of human GRID2IP gene as well as on identification of GRCAH domain.

Amino Acid Sequence↗