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PubMed2002

Prediction of the coding sequences of mouse homologues of KIAA gene: I. The complete nucleotide sequences of 100 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries.

We have been conducting a human cDNA project to predict protein-coding sequences in long cDNAs (> 4 kb) since 1994. The number of these newly identified human genes exceeds 2000 and these genes are known as KIAA genes. As an extension of this project, we herein report characterization of cDNAs derived from mouse KIAA-homologous genes. A primary aim of this study was to prepare a set of mouse. KIAA-homologous cDNAs that could be used to analyze the physiological roles of KIAA genes in mice. In addition, comparison of the structures of mouse and human KIAA cDNAs might enable us to evaluate the integrity of KIAA cDNAs more convincingly. In this study, we selected mouse KIAA-homologous cDNA clones to be sequenced by screening a library of terminal sequences of mouse cDNAs in size-fractionated libraries. We present the entire sequences of 100 cDNA clones thus selected and predict their protein-coding sequences. The average size of the 100 cDNA sequences reached 5.1 kb and that of mouse KIAA-homologous proteins predicted from these cDNAs was 989 amino acid residues.

Animals↗

PubMed1996

Subtype 2 and atypical angiotensin receptors in the human heart.

Angiotensin receptors have been described in the human heart and are suspected to play a central role in remodeling after myocardial infarction and in cardiac hypertrophy. Two subtypes, AT1 and AT2, have so far been described in humans, with AT2 being the dominant subtype in human atria. We have now determined subtype numbers and distribution by binding in ventricular myocardium from patients with end-stage heart failure. We found about 50-80% of subtype AT2 in the right and left ventricles from patients with end-stage heart failure due to coronary artery disease and cardiomyopathy, indicating that AT2 is the dominant angiotensin receptor subtype in the whole human heart. To determine the cellular localization of angiotensin receptors in human myocardium in addition to the known localization on myocytes, smooth muscle cells and endothelial cells, we investigated cardiac fibroblasts. They express an angiotensin receptor with yet incompletely understood binding characteristics which is coupled to proliferation and DNA synthesis. As AT2 is the dominant angiotensin receptor subtype in human heart, we cloned the complete mRNA sequence by a rapid amplification of cDNA ends (RACE) procedure and thereafter the promoter sequence from a human genomic library. Once the sequence of the mRNA and thus exon 1 was obtained by the RACE-PCR, a probe was constructed for the most 5' region of exon 1 and used for screening of a human genomic DNA bank. After cutting of the positive clones with EcoR1 and Not1, a 4000 bp fragment hybridized with the probe and was further sequenced. A functional AT2 promoter, with > 90% homology with the mouse promoter and 35% homology with the human AT1 promoter containing numerous cis-acting sequences for basal (TFIID) and inducible (AP-1, PEA-3, CBF) transcription factors in the first 1000 bp was identified.

DNA↗

PubMed2005

Identification of differentially expressed genes in the developing mouse inferior colliculus.

Although injured neurons of inferior colliculus (IC) display a robust axonal outgrowth through a lesion site at postnatal day six (P6) in vitro, and are capable to re-innervate their target cells, injured neurons from P10 IC are unable to regenerate their axons across the lesion site. This axonal regenerative failure has been attributed to an increase of expression of inhibitory molecules in endogenous tissue, during development. As a first step to identify such inhibitory molecules, the present study reports the isolation of molecules differentially expressed in the IC during development. A two-directional (forward and backward) suppression subtractive hybridization (SSH) was performed on IC tissue between P6 and P10 stages. One hundred cDNAs from P6 (P6-P10) and 200 cDNAs from P10 (P10-P6)-subtracted libraries were randomly sequenced. A dot-blot screening of sequenced cDNAs revealed the differential expression for the majority of these cDNAs at their respective developmental stage. Then, the analysis of sequenced clones showed that P6 library was highly enriched in molecules expressed early in the development, such as GAP43 or vimentin proteins. By contrast, the P10 library contained mostly molecules expressed at later stages of development in the central nervous system, such as myelin-related proteins. Our results show that SSH is a suitable method for identifying differentially expressed genes in the developing IC. In addition, these results provide a foundation for further studies dealing with molecules involved in the IC development before and at the onset of hearing, some of which being probably involved in the axonal outgrowth mechanism.

Animals↗

PubMedDate not supplied

Quantitative determination of single-bead metal content from a peptide combinatorial library.

An electrothermal vaporizer inductively coupled plasma mass spectrometer (ETV-ICPMS) was used to quantitatively screen metals bound to single polystyrene (TentaGel) beads with immobilized oligopeptides. Tests were performed using ETV-ICPMS to screen a series of identical beads as well as a series of combinatorial library beads exposed to a multimetal solution composed of Mg2+, Mn2+, Ni2+, Cu2+, Cd2+, Eu2+, and Pb2+. The residual metal content remaining bound to the beads after acid extractions was also analyzed by solid sampling of the entire bead using oxygen ashing in the ETV. Nine beads (80 mesh, 0.25 mmol g(-1) nominal capacity) containing covalently attached polyaspartic acid (PLAsp; n = 20) showed metal extract concentrations in the range of 4-130 ng mL(-1). After normalizing by bead volume, the precision of capacity measurements in a single bead (7-14%) was primarily dictated by analysis error and contributions from bead diameter measurement with negligible contributions, surprisingly, from variations in site density from bead to bead. A sample combinatorial library of the sequence GXXGXXGXXGXX (X = cysteine, aspartic acid, or glutamic acid and G = glycine) (60 mesh, 0.25 mmol g(-1) nominal capacity) was also used to demonstrate the utility of this method. Metal extract concentrations ranged from 1 to 1300 ng mL(-1) with significant concentration variation between beads, indicating the individual selectivity on each bead. For these larger beads, analysis precision (i.e., capacity precision) was further improved to 3-10% due to the overall increase in bead metal content. Through metal extract determinations, ETV-ICPMS was shown to be a viable nondestructive tool for full metal characterization of "hit" sequences belonging to a combinatorial library.

Binding Sites↗

PubMed1995

Conformational properties of oligonucleotides.

Vast libraries of oligonucleotide sequences can be made. Such libraries have been screened and/or selected to identify individual molecules showing various properties, including high affinity/high specificity binding (to something) or new enzymatic activity. The SELEX protocol is used to identify these interesting oligonucleotides; two recent reviews of the SELEX protocol and its power have appeared recently. Oligonucleotides derived through the SELEX process have applications in diagnostics and therapeutics, and have additional value as research reagents and compounds that provide chemical plausibility to some ideas about evolution of the biosphere. Oligonucleotide conformations are shockingly robust and potent.

Bacteriophage T4↗

PubMed1995

Molecular cloning and sequence analysis of cDNA encoding plasma alpha-1-antiproteinase from Syrian hamster: implications for the evolution of Rodentia.

Complementary DNA clones encoding plasma alpha-1-antiproteinase (also called alpha-1-antitrypsin or alpha-1-proteinase inhibitor) were isolated from Syrian hamster liver cDNA library and sequenced. The deduced amino acid sequence of putative reactive site (P3-P'3) was Ile-Pro-Met-Ser-Val-Pro, characteristic of alpha-1-antiproteinase of orthodox type (Suzuki, Y. et al. (1991) J. Biol. Chem. 266, 928-932). A molecular phylogenetic tree of all known orthologous proteins was constructed based on the synonymous substitution rate. The result shows that the hamster has branched off first before the divergence among mice, rats, and gerbils, and that the rabbit is the closest relative of the guinea pig which is separated from the rodents. Although this tree differs largely from the classical phylogeny based on the morphology (hamsters and gerbils belong to the same family, Cricetidae, and the guinea pig belongs to the order Rodentia), it lends support to recent concepts that the hamster and guinea pig differ, in a number of biochemical features, not only from each other but also from mice and rats, and that the guinea pig may belong to an order distinct from Rodentia.

Amino Acid Sequence↗

PubMed1997

Sequence analysis of the cDNA encoding the precursor of equinatoxin V, a newly discovered hemolysin from the sea anemone Actinia equina.

A cDNA encoding the 214-amino-acid (aa) precursor of equinatoxin V (EqtV) has been isolated from an Actinia equina cDNA library. The sequence of the mature toxin is preceded, as that of EqtII, by a signal peptide of 19 aa and a hydrophilic propeptide of 16 aa ending with a pair of basic residues. This is similar to the precursors of calitoxins from another sea anemone Calliactis parasitica and to those of some antimicrobial peptides of the magainin and dermaseptin families from vertebrates. The deduced aa sequence of the potential cell attachment Arg-Gly-Asp motif-containing EqtV shows 82% identity to that of EqtII.

Amino Acid Sequence↗

PubMed1998

Isolation and sequencing of a second Rhizobium tropici CFN299 genetic locus that contains genes homologous to amino acid sulphate activation genes.

A Rhizobium tropici CFN299 DNA region, homologous to genes involved in Nod factor synthesis and amino acid sulphate activation, was isolated from a genome library. DNA sequence analysis revealed two open reading frames, orf1 and orf2. orf1 showed highest sequence similarity to the Escherichia coli cysD gene while orf2 is closely related to Rhizobium sp. N33 nodQ. However, the orf2 deduced peptide is 152 amino acids shorter than Rhizobium sp. N33 NodQ, and lacks the 3'-phosphoadenosine 5'-phosphosulphate-binding motif. A dendrogram based on the alignment of the deduced amino acid sequences of orf2/nodQ/cysN genes separated Escherichia coli cysN and orf2 from the nodQ cluster. Upstream of orf1, partial sequence analysis revealed the 3' part of an orf that is highly similar to E. coli cysH. The G + C content of orf1 and orf2 differs significantly from the G + C content of R. tropici symbiotic sulphate activation nodPQ genes. This data suggests that the isolated R. tropici CFN299 locus contains housekeeping genes for amino acid sulphate activation.

Amino Acids↗

PubMed1996

Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs.

Nearly 7000 Arabidopsis thaliana-expressed sequence tags (ESTs) from 10 cDNA libraries have been sequenced, of which almost 5000 non-redundant tags have been submitted to the EMBL data bank. The quality of the cDNA libraries used is analysed. Similarity searches in international protein data banks have allowed the detection of significant similarities to a wide range of proteins from many organisms. Alignment with ESTs from the rice systematic sequencing project has allowed the detection of amino acid motifs which are conserved between the two organisms, thus identifying tags to genes encoding highly conserved proteins. These genes are candidates for a common framework in genome mapping projects in different plants.

Amino Acid Sequence↗

PubMed2003

Large-scale sequencing analysis of the full-length cDNA library of human hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is one of the human cancers clearly linked to viral infections. Although the major risk factors for HCC development have been elucidated, the hepatocellular carcinogenesis pathway resulting in malignant transformation of liver cells remains to be clarified. Recently, some results of microarray and comparative genomic hybridization analysis have been provided as comprehensive studies of genomic instability in HCC, including mutation, deletion and DNA copy losses. In this work, the full-length cDNA library has been constructed and sequenced, and the sequencing results have been further clustered and analyzed. The results show that 1,342 genes have been found, and about 300 of these genes may be important in e.g. cell proliferation, DNA repair and apoptosis. After further analysis of DNA sequences, the deletion genotypes of at least 24 genes have been found. However, the functional changes of these deletion mutants and their significance in hepatocellular carcinogenesis remain to be clarified. This research may be one of the best to obtain the candidate genes for hepatocellular carcinogenesis.

Aged↗

PubMed2003

Cloning and characterization of a Schistosoma mansoni 1H and 30S clones as two tegumental vaccine candidate antigens.

Two Schistosoma mansoni cDNA clones 30S and 1H were identified by immunoscreening of sporocyst lambdagt11 library and by random sequencing of clones from lambdaZap libraries, respectively. Clone 30S was one of 30 clones identified by an antibody raised against tegument of 3-h schistosomules. The clone was found to encode an 81 amino-acid protein fragment. It was expressed in Escherichia coli as a fusion protein of calculated molecular mass of about 35 kDa with C-terminus of Schistosoma japonicum glutathione-S-transferase (Sj26; about 26 kDa). The recombinant fusion protein was specifically recognized by serum of rabbits immunized with irradiated cercariae. Clone 1H is one of 76 expressed sequence tags derived from an adult worm library. It encodes the complete sequence of a tegumental membrane protein, Sm13. The 104 amino-acid open reading frame encodes a protein with a calculated molecular mass of about 11.9 kDa. Clone 1H was expressed in E. coli as an insoluble fusion protein with Sj26 of about 40 kDa. In Western blots, the fusion protein was recognized by serum from rabbits vaccinated with irradiated cercariae but not by preimmune rabbit sera. The cloning, characterization and expression of those proteins are therefore potentially usefull for vaccine development.

Amino Acid Sequence↗

PubMed1990

The gene encoding SMR1, a precursor-like polypeptide of the male rat submaxillary gland, has the same organization as the preprothyrotropin-releasing hormone gene.

SMR1 is a precursor-like polypeptide of the submaxillary glands of rats. Sequence analysis predicts that it could be processed by maturation enzymes to release a small peptide resembling the thyrotropin-releasing hormone. The SMR1 gene was isolated from a rat genomic library and sequenced. The SMR1 gene spans 4.7 kb and consists of three exons. The two introns occur a few nucleotides before the initiation codon in the 5' untranslated region, and a few nucleotides before the first predicted processing site, respectively. Such a structure is reminiscent of that of the preprothyrotropin-releasing hormone gene. The site of transcriptional initiation of the SMR1 gene was determined and 1.4 kb of 5'-flanking sequence was sequenced. The sequence analysis revealed the presence of alternating purine-pyrimidine tracts and of purine-rich sequences. In addition, some sequences which could be involved in the regulation of SMR1 gene expression were identified.

Amino Acid Sequence↗

PubMed2005

Diversity of functional genes of methanogens, methanotrophs and sulfate reducers in deep-sea hydrothermal environments.

To contribute to the identification of methanogens, methanotrophs and sulfate-reducing bacteria (SRB) in microbial communities from the 13 degrees N (East Pacific Rise) and Rainbow (Mid-Atlantic Ridge) hydrothermal vent fields, we investigated the diversity of mcrA, pmoA and dsrAB genes sequences. Clone libraries were obtained using DNA isolated from fragments of diffuse vents, sediment and in situ samplers. The clones were categorized by restriction fragment length polymorphism, and representatives of each group were sequenced. Sequences were related to that of hyperthermophilic (order Methanopyrales and family Methanocaldococcaceae), thermophilic and mesophilic (family Methanococcaceae) methanogens, thermophilic (proposed genus 'Methylothermus') and mesophilic type I methanotrophs, and hyperthermophilic (order Archaeoglobales), thermophilic (order Thermodesulfobacteriales) and mesophilic (family Desulfobulbaceae) SRB. Several of the obtained sequences were distantly related to the genes of cultivated organisms, providing evidence of the existence of novel lineages in the three functional groups. This study provides for the first time an insight into the diversity of several functional genes of deep-sea hydrothermal system microorganisms.

Archaeal Proteins↗

PubMed1993

Molecular cloning and sequence analysis of two porcine seminal proteins, PSP-I and PSP-II: new members of the spermadhesin family.

Two full-length cDNAs encoding porcine seminal proteins, PSP-I and PSP-II, have been isolated from a porcine seminal vesicle cDNA library. Nucleotide sequence analysis of the 706-bp PSP-I cDNA predicts a precursor protein of 133 amino acid residues, which includes a 21-residue signal peptide and a 112-residue secreted protein. On the other hand, the complete sequence of the 686-bp PSP-II cDNA reveals a coding sequence for a 21-residue signal peptide and a 116-residue secreted protein. The predicted amino acid sequences agree very well with those determined by conventional amino acid sequence analysis. Alignment of the two cDNA sequences shows an overall 66% sequence homology throughout their entire length. However, the sequence homology is much higher in the 3' untranslated region (72%) than in the coding region (61%). This suggests that these two genes evolved by duplication and divergence from a common ancestral gene. They share about 50% amino acid sequence homology and a similar overall structure with three members of the spermadhesin family.

Amino Acid Sequence↗

PubMed1990

Deduced amino acid sequence of heme binding region of chicken cholesterol side chain cleavage cytochrome P450.

The primary structure of the carboxy terminal 296 amino acids of chicken cholesterol side chain cleavage cytochrome P450 (P450scc) was deduced from a partial cDNA clone isolated from a chicken ovarian cDNA library. The sequence contained putative steroid binding and heme binding regions. Comparison of this sequence with the corresponding sequences of three mammalian forms of P450scc shows greater than 50% homology. The heme binding region of the avian P450scc shows 76% homology with the heme binding regions of rat and human P450scc and 81% homology with that of bovine P450scc.

Amino Acid Sequence↗

PubMed2004

Highly diverse heparan sulfate analogue libraries: providing access to expanded areas of sequence space for bioactivity screening.

Structurally diverse heparan sulfate analogue libraries were produced chemicoenzymatically from heparin. They possess vastly more heterogeneity than tissue heparan sulfates, expand the sequence space available for screening, and can help identify minimal structural features associated with activity. Library components are likely to exhibit fewer nonspecific interactions and side-effects than heparin or simple chemically modified heparin. A strategy for their use is illustrated for the fibroblast growth factor-receptor tyrosine kinase signaling system.

Cell Line↗

PubMed1995

Isolation of a kidney-specific peptide recognized by alloreactive HLA-A3-restricted human CTL.

The molecular nature of tissue-specific Ags involved in MHC-restricted CTL responses is as yet undefined. To determine the specificity of these peptides, their function, and their possible relationship to allograft rejection, we have utilized human kidney-specific CD8+ CTL clones to screen reversed-phase HPLC (RP-HPLC)-separated self peptides presented by allo-class I molecules. One of these clones is HLA-A3-restricted and the other HLA-B62-restricted, lysing human kidney cell lines but not MHC identical B lymphoblastoid cells which express the appropriate HLA molecules. We have identified a biologically active RP-HPLC fraction containing self peptides eluted from affinity-purified MHC molecules from HLA-A3+ kidney. This peptide is not expressed in HLA-A3+ spleen. Similarly, a HLA-B62-associated peptide fraction was identified in kidney but not in spleen using the HLA-B62-restricted CTL clone. Sequence analysis of the biologically active fraction from HLA-A3 kidney revealed multiple peptides. Because of the ambiguity of the peptide sequence, a mixed peptide library corresponding to this sequence was synthesized that included the HLA-A3 binding motif. The biologically active peptide library was RP-HPLC fractionated and the fraction containing HLA-A3-restricted CTL activity was sequenced. The resulting sequence of the alloreactive HLA-A3-restricted peptide epitope is GPPGVTIVK. By using this unique strategy, we describe the successful isolation and sequencing of an antigenic peptide that is recognized by a human alloreactive kidney-specific CTL clone.

Amino Acid Sequence↗

PubMed1999

Minimal promoter components of the human growth/differentiation factor-5 gene.

Growth/differentiation factor-5 (GDF-5) is a new member of the BMP family supposed to be involved in chondrogenesis. We cloned the human GDF-5 gene from lambda phage library and sequenced its 3.5-kb 5'-flanking region. The transcription start site was mapped by 5'-RACE to the sequence that coincides with the initiator element. Electrophoresis mobility shift assays (EMSA) demonstrated a zinc finger transcription factor, YY1, to bind to the sequence surrounding the transcription start site. To localize positive and negative regulatory elements in the GDF-5 5'-upstream region, we constructed a series of progressively deleted promoter-reporter plasmids. The transient transfection assay with human osteoblastic Hos cells indicated that a minimal enhancer element resides within -117 to -27 relative to the transcription initiation site. Since the GDF-5 promoter was active even in fibroblastic L cells, a mechanism governing its chondrocyte-restrictive expression needs to be explored.

5' Untranslated Regions↗