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PubMed1993

Decidual prolactin-related protein. Identification, molecular cloning, and characterization.

In this report, we describe the isolation, molecular cloning, and characterization of a new member of the prolactin (PRL)-growth hormone (GH) family expressed in rat decidual tissue. A 29-kDa protein was isolated from medium conditioned by decidual explants. The protein possessed an affinity for concanavalin A and cross-reactivity with antibodies to two rat placental proteins, PRL-like protein-B (PLP-B) and PLP-C and with antibodies to human PRL. NH2-terminal sequencing of the isolated decidual protein indicated that it shared significant sequence identity with the NH2 terminus of PLP-C. The decidual protein was termed decidual prolactin-related protein (dPRP). A PLP-C cDNA was used to identify dPRP cDNAs from a rat decidual cDNA library. Nucleotide sequence analyses of the dPRP cDNAs predicted a mature protein of 239 amino acids, including a 28-amino acid signal sequence. The predicted dPRP amino acid sequence contains two putative N-linked glycosylation sites and 6 cysteine residues. The 6 cysteines are located in positions homologous to the cysteines of PLP-C and PRL. Additional sequence similarities with members of the PRL-GH family are evident. The dPRP gene was localized to rat chromosome 17, which also carries other members of the PRL gene family. Northern blot analysis showed that the dPRP cDNA clone specifically hybridized to a 1.0-kilobase mRNA. The relationship of dPRP with other members of the PRL-GH family and its putative role(s) in the physiology of pregnancy are discussed.

Amino Acid Sequence↗

PubMed1992

cDNA sequence and tissue expression of bovine vacuolar H(+)-ATPase M(r) 70,000 subunit.

cDNA clones encoding the 70,000 relative molecular weight (M(r)) subunit of the bovine vacuolar proton-adenosine triphosphatase (H(+)-ATPase) were isolated, and a total length of 3.1 kb in overlapping clones from bovine kidney and brain libraries was sequenced. The cDNA contains a 1.9-kb coding region and yields a deduced protein sequence of 618 amino acids. The subunit sequence has 50% amino acid identity with the corresponding subunit from yeast, carrot, and Neurospora vacuolar H(+)-ATPases. The internal regions of the protein are most highly conserved, whereas the NH2- and COOH-terminals exhibit variability. mRNA levels of the M(r) 70,000 subunit were examined in multiple bovine tissues and were found to be expressed at highest levels in kidney medulla and cortex, at moderate levels in brain and adrenal gland, and at low levels in liver, muscle, and heart.

Adenosine Triphosphatases↗

PubMed2005

Sequence determinants of enhanced amyloidogenicity of Alzheimer A{beta}42 peptide relative to A{beta}40.

Aggregation of proteins into insoluble deposits is associated with a variety of human diseases. In Alzheimer disease, the aggregation of amyloid beta (Abeta) peptides is believed to play a key role in pathogenesis. Although the 40-mer (Abeta40) is produced in vivo at higher levels than the 42-mer (Abeta42), senile plaque in diseased brains is composed primarily of Abeta42. Likewise, in vitro, Abeta42 forms fibrils more rapidly than Abeta40. The enhanced amyloidogenicity of Abeta42 could be due simply to its greater length. Alternatively, specific properties of residues Ile(41) and Ala(42) might favor aggregation. To distinguish between these two possibilities, we constructed a library of sequences in which residues 41 and 42 were randomized. The aggregation behavior of the resulting sequences was assessed using a high throughput screen, based on the finding that fusions of Abeta42 to green fluorescence protein (GFP) prevent the folding and fluorescence of GFP, whereas mutations in Abeta42 that disrupt aggregation produce green fluorescent fusions. Correlations between the sequences of Abeta42 mutants and the fluorescence of Abeta42-GFP fusions in vivo were confirmed in vitro through biophysical studies of synthetic 42-residue peptides. The data reveal a strong correlation between aggregation propensity and the hydrophobicity and beta-sheet propensities of residues at positions 41 and 42. Moreover, several mutants containing hydrophilic residues and/or beta-sheet breakers at positions 41 and/or 42 were less prone to aggregate than Abeta40 wherein these two residues are deleted entirely. Thus, properties of the side chains at positions 41 and 42, rather than length per se, cause Abeta42 to aggregate more readily than Abeta40.

Alzheimer Disease↗

PubMed1993

Conserved nucleotide sequences in the open reading frame and 3' untranslated region of selenoprotein P mRNA.

Rat liver selenoprotein P contains 10 selenocysteine residues in its primary structure (deduced). It is the only selenoprotein characterized to date that has more than one selenocysteine residue. Selenoprotein P cDNA has been cloned from human liver and heart cDNA libraries and sequenced. The open reading frames are identical and contain a signal peptide, indicating that the protein is secreted by both organs and is therefore not exclusively produced in the liver. Ten selenocysteine residues (deduced) are present. Comparison of the open reading frame of the human cDNA with the rat cDNA reveals a 69% identity of the nucleotide sequence and 72% identity of the deduced amino acid sequence. Two regions in the 3' untranslated portion have high conservation between human and rat. Each of these regions contains a predicted stable stem-loop structure similar to the single stem-loop structures reported in 3' untranslated regions of type I iodothyronine 5'-deiodinase and glutathione peroxidase. The stem-loop structure of type I iodothyronine 5'-deiodinase has been shown to be necessary for incorporation of the selenocysteine residue at the UGA codon. Because only two stem-loop structures are present in the 3' untranslated region of selenoprotein P mRNA, it can be concluded that a separate stem-loop structure is not required for each selenocysteine residue.

Amino Acid Sequence↗

PubMed1999

Development of Polymorphic EST Markers Suitable for Genetic Linkage Mapping of Catfish.

: Expressed sequence tag (EST) markers are important for gene mapping and for marker-assisted selection (MAS). To develop EST markers for use in catfish gene mapping, 100 randomly picked complementary DNAs from the channel catfish (Ictalurus punctatus) pituitary library were sequenced. The EST sequences were used to design primers to amplify channel catfish and blue catfish (I. furcatus) genomic DNAs. Polymerase chain reaction products of the ESTs were analyzed to determine length polymorphism between the channel catfish and blue catfish. Eleven polymorphic EST markers were identified. Five of the 11 EST markers were from known genes and the other six were from unidentified ESTs. Seven ESTs were found to be associated with microsatellite sequences. Analysis of channel catfish gene sequences indicated highly biased codon usage, with 16 codons being preferably used. These codons were more preferably used in highly expressed ribosomal protein genes and in highly expressed pituitary hormone genes. G/C-rich codons are less used in channel catfish than those in other vertebrates suggesting AT-richness of the channel catfish genome.

Journal Article↗

PubMed2006

Large-scale identification of genes implicated in kidney glomerulus development and function.

To advance our understanding of development, function and diseases in the kidney glomerulus, we have established and large-scale sequenced cDNA libraries from mouse glomeruli at different stages of development, resulting in a catalogue of 6053 different genes. The glomerular cDNA clones were arrayed and hybridized against a series of labeled targets from isolated glomeruli, non-glomerular kidney tissue, FACS-sorted podocytes and brain capillaries, which identified over 300 glomerular cell-enriched transcripts, some of which were further sublocalized to podocytes, mesangial cells and juxtaglomerular cells by in situ hybridization. For the earliest podocyte marker identified, Foxc2, knockout mice were used to analyze the role of this protein during glomerular development. We show that Foxc2 controls the expression of a distinct set of podocyte genes involved in podocyte differentiation and glomerular basement membrane maturation. The primary podocyte defects also cause abnormal differentiation and organization of the glomerular vascular cells. We surmise that studies on the other novel glomerulus-enriched transcripts identified in this study will provide new insight into glomerular development and pathomechanisms of disease.

Animals↗

PubMed1986

Structure and expression of a second sea urchin U1 RNA gene repeat.

There are two tandemly repeated sets of U1 RNA genes in the sea urchin L. variegatus. Each of these genes is present in a 1.4 kb repeat defined by a HindIII site about 450 bases 5' to the gene. The sequences of a member of both repeating units (U1.1 and U1.2) has been determined. The repeats are nearly identical for 550 nucleotides 5' to the gene but show great divergence starting 30 nucleotides 3' to the gene, just after the CAAAGAAAGAAAA sequence thought to be required for 3' end formation. The other boundary between the conserved and non-conserved sequences is a polypyrimidine sequence (on the strand which codes for U1 RNA). Both of these repeats are expressed in blastula stage embryos, as judged by transcription of unique sequences 3' to the gene in nuclei isolated from blastula stage embryos. At least some of the two types of repeats are interspersed, since representatives of both repeat types on a single gamma phage isolated from a gene library. The sequence of the U1 RNA in L. variegatus eggs and embryos corresponds to the sequence of the U1 repeat.

Animals↗

PubMed1994

Cloning, sequencing and comparison of three lactococcal L-lactate dehydrogenase genes.

The conversion of pyruvate to lactate is a key feature of lactococcal strains. The enzyme which facilitates this conversion, L-lactate dehydrogenase (LDH), and the gene which encodes it (Idh), are therefore of great significance. This paper presents the cloning and DNA sequence analysis of three further lactococcal genes which are of key importance in the genetic manipulation of commercial starter strains. The Idh gene from Lactococcus lactis subsp. Lactis biovar diacetylactis BU2-60 has been isolated from a lambda library and sequenced. The Idh gene from L. lactis subsp. cremoris NCDO 762 and that from L. lactis subsp. Lactis IL1403 have been amplified by the polymerase chain reaction (PCR) and sequenced. These DNA sequences and deduced amino acid sequences have been compared with those from L. lactis subsp. Lactis MG1363. The LDHs from L. lactis subsp. Lactis MG1363 and L. lactis subsp. cremoris NCDO 762 are 99.4% homologous. The LDHs from L. lactis subsp. lactis MG1363 and L. lactis subsp. Lactis IL1403 are 96.4% homologous. The LDHs from L. lactis subsp. lactis IL1403 and L. lactis subsp. lactis biovar diacetylactis BU2-60 are 99.9% homologous. Our results provide further evidence that L. lactis subsp. Lactis MG1363 and other L. lactis subsp. Lactis NCDO 712 derived strains should be reclassified as Lactococcus lactis subsp. cremoris.

Amino Acid Sequence↗

PubMed2005

PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information.

BACKGROUND: Phages, viruses that infect prokaryotes, are the most abundant microbes in the world. A major limitation to studying these viruses is the difficulty of cultivating the appropriate prokaryotic hosts. One way around this limitation is to directly clone and sequence shotgun libraries of uncultured viral communities (i.e., metagenomic analyses). PHACCS http://phage.sdsu.edu/phaccs, Phage Communities from Contig Spectrum, is an online bioinformatic tool to assess the biodiversity of uncultured viral communities. PHACCS uses the contig spectrum from shotgun DNA sequence assemblies to mathematically model the structure of viral communities and make predictions about diversity. RESULTS: PHACCS builds models of possible community structure using a modified Lander-Waterman algorithm to predict the underlying contig spectrum. PHACCS finds the most appropriate structure model by optimizing the model parameters until the predicted contig spectrum is as close as possible to the experimental one. This model is the basis for making estimates of uncultured viral community richness, evenness, diversity index and abundance of the most abundant genotype. CONCLUSION: PHACCS analysis of four different environmental phage communities suggests that the power law is an important rank-abundance form to describe uncultured viral community structure. The estimates support the fact that the four phage communities were extremely diverse and that phage community biodiversity and structure may be correlated with that of their hosts.

Algorithms↗

PubMed1993

A survey of the Mycoplasma genitalium genome by using random sequencing.

A total of 508 random clones from five Mycoplasma genitalium genomic libraries were partially sequenced and analyzed. This resulted in the identification of 291 unique contigs. Sequence information from these clones (100,993 nucleotides), representing approximately 17% of this pathogen's genome, was analyzed by comparison to the DNA and protein sequence data bases. The frequency with which clones could be identified, by virtue of possessing homology to another data base entry, was 46%. Sequence analysis indicated the following. (i) The M. genitalium genome contains many genes involved in various metabolic processes. (ii) Repetitive DNA may comprise as much as 4% of this genome. (iii) The MgPa adhesin gene may be the result of horizontal transfer from an unknown origin. (iv) Not all dinucleotide pairs are present in this genome at the expected frequency. (v) This genome potentially encodes approximately 390 proteins and makes very efficient use of its limited amount of DNA. In addition, this study allowed us to estimate the number of genes involved with various cellular functions.

Amino Acid Sequence↗

PubMed1985

Human c-f gr gene does not contain coding sequence for actin-like protein.

f gr is a member of the protein kinase oncogene family and was found to have the highest homology to yes gene among the members of the family. Using a v-yes probe, a molecular clone of human c-f gr locus was isolated from a genomic library. Nucleotide sequence determination revealed that the actin gene-like sequence found in v-f gr gene was absent at the corresponding position of the c-f gr gene. Thus, the v-f gr gene product is considered to be a tri-chimeric gene product consisting of viral gag gene and two distinct cellular genes, actin gene and the proto-f gr gene.

Actins↗

PubMed2002

Cloning and functional characterization of the mouse fructose transporter, GLUT5.

Mouse GLUT5 cDNA and a 7.7-kb genomic fragment have been isolated and characterized. The cDNA sequence suggests mouse GLUT5 is composed of 501 amino acids, and has 69-88% amino acid identity with human, rat, and rabbit GLUT5. Expression of mouse GLUT5 cRNA in Xenopus laevis oocytes showed that GLUT5 mediated fructose transport, with a K(t) of 13 mM. Northern blot studies detected GLUT5 mRNA expression in mouse small intestine, kidney, and testis, with transcript sizes of approximately 2.1, 2.1, and 2.8 kb, respectively. 5'Rapid Amplification of cDNA Ends (5'RACE) determined that the differences in transcript sizes occurred because GLUT5 possessed alternative transcriptional initiation sites in somatic and germ cells. In agreement with studies in rats and rabbits, mouse small intestinal GLUT5 mRNA expression levels were increased following exposure to a 65% fructose-enriched diet. In addition, developmental studies showed a significant increase in GLUT5 mRNA expression levels in adult mouse testis when compared to prepubertal mouse testis. To begin to identify the cis-acting domains responsible for GLUT5 expression characteristics, a 7.7-kb GLUT5 genomic fragment was isolated from a mouse lambda fix11 library and sequenced. The clone contained exons 1-4 and 5' flanking regions. Moreover, caudal homeobox gene (CdxA), upstream stimulatory factor (USF), and sex-determining region of Y (SRY) binding sites were identified in the 5' flanking region that may be responsible for GLUT5's expression characteristics: tissue distribution, sensitivity to dietary fructose in the small intestine, and developmental expression in the testis.

Amino Acid Sequence↗

PubMed1994

Two-stage selection of sequences from a random phage display library delineates both core residues and permitted structural range within an epitope.

Libraries of random peptides can be screened to identify species which interact with antibodies or receptors. Similarly, maps of native molecular interactions can frequently be deduced by screening a limited set of peptide fragments derived from sequences within a native antigen or ligand. However, the existence of cross-reactive sequences that mimic original epitopes and the limited replaceability of amino acid residues suggest that the sequence space accessible by a receptor can be much broader. Definition of this space is of particular importance where structural information is required for peptidomimetic or drug design. We have used a two-stage selection scheme to expand the sequence space accessible by a phage display library and to define peptide epitopes of the anti-FLAG octapeptide monoclonal M2 antibody. Affinity selection of a primary library of 2 x 10(6) random decapeptides identified a non-contiguous core of three residues in the binding motif Tyr-Lys-Xaa-Xaa-Asp. A second stage library with 2 x 10(7) individual clones bearing the core motif but with the remaining flanking and internal residues re-randomized permitted access to a broader sequence space represented in a library equivalent to several orders of magnitude larger. Data here demonstrate that extended access to binding sequence space permitted by multi-stage screening of phage display libraries can reveal not only essential residues required for ligand binding, but also the ligand structural range permitted within the receptor binding pocket.

Amino Acid Sequence↗

PubMed1989

Molecular cloning, cDNA structure and predicted amino acid sequence of bovine 3 beta-hydroxy-5-ene steroid dehydrogenase/delta 5-delta 4 isomerase.

We have used our recently characterized human 3 beta-hydroxy-5-ene steroid dehydrogenase/delta 5-delta 4-isomerase (3 beta-HSD) cDNA as probe to isolate cDNAs encoding bovine 3 beta-HSD from a bovine ovary lambda gtll cDNA library. Nucleotide sequence analysis of two overlapping cDNA clones of 1362 bp and 1536 bp in length predicts a protein of 372 amino acids with a calculated molecular mass of 42,093 (excluding the first Met). The deduced amino acid sequence of bovine 3 beta-HSD displays 79% homology with human 3 beta-HSD while the nucleotide sequence of the coding region shares 82% interspecies similarity. Hybridization of cloned cDNAs to bovine ovary poly(A)+ RNA shows the presence of an approximately 1.7 kb mRNA species.

3-Hydroxysteroid Dehydrogenases↗

PubMed1991

Cloning and sequence analysis of complementary DNA encoding a precursor for chicken natriuretic peptide.

Chicken alpha-natriuretic peptide (alpha-chNP) has been identified in chicken heart, which showed higher homology to brain natriuretic peptide (BNP) than to atrial natriuretic peptide (ANP). Complementary DNA (cDNA) clone encoding a chNP precursor (pre-chNP) was isolated from cardiac cDNA library and sequenced. Pre-chNP was 140-residue peptide carrying a 24-residue signal peptide at the N-terminus and alpha-chNP at the C-terminus, and did not exhibit high homology to porcine BNP except for the C-terminal region. However, a characteristic AT-rich nucleotide sequence commonly found in mammalian BNPs was also present in the 3'-untranslated region. Thus, chNP is concluded to be classified into the BNP-type.

Amino Acid Sequence↗

PubMed2003

dffA gene from Aspergillus oryzae encodes L-ornithine N5-oxygenase and is indispensable for deferriferrichrysin biosynthesis.

We identified and analyzed the dffA gene from Aspergillus oryzae which encodes L-ornithine N5-oxygenase involved in the biosynthesis of deferriferrichrysin, a type of siderophore which is a low-molecular-weight iron chelating compound. From among more than 20,000 clones in an A. oryzae EST (expressed sequence tag) library, we found only one clone encoding a protein that exhibited homology to theUstilago maydis sid1 protein (Sid1) and Pseudomonas aeruginosa pvdA protein (PvdA), both known as the only examples of L-ornithine N5-oxygenase. The complete gene sequence shows that the dffA gene includes a 1575-bp open reading frame (ORF), one 66-bp intorn, which is a typical intorn length inA. oryzae, and encodes 502 amino acids with putative FAD-binding, NADP-binding, and 'FATGY' motifs, which are conserved inN-hydroxylating enzymes. As well as that of the U. maydis sid1 gene,dffA gene expression was induced under iron-limited conditions, and the promoter region has several GATA-type transcription regulator binding motifs. When the dffA gene was expressed under the control of the a-amylase promoter in A. oryzae, transformants revealed inducible high L-ornithine N5-oxygenase activities. In addition, a dffA gene disruptant showed no deferriferrichrysin production even under iron-limited conditions. These results clearly suggest that the dffA gene is indispensable for deferriferrichrysin biosynthesis in A. oryzae.

Journal Article↗

PubMed1992

Structurally and functionally conserved regions of cytochrome P-450 reductase as targets for DNA amplification by the polymerase chain reaction. Cloning and nucleotide sequence of the Schizosaccharomyces pombe cDNA.

1. Alignments of the available cytochrome P-450 reductase amino acid sequences, and comparison with the crystal structure of ferredoxin-NADP reductase, indicate that two highly conserved regions are of functional importance. 2. Degenerate oligonucleotide primers, based on these sequences, were used in the polymerase chain reaction to amplify a 309 bp fragment of the cytochrome P-450 reductase gene from Schizosaccharomyces pombe for use as an homologous probe. 3. A 2.6 kb cDNA was cloned from a lambda library, and sequencing revealed an open-reading frame of 2034 bp encoding a protein of M(r) 76774. This protein shares 38-41% identity with other eukaryotic cytochrome P-450 reductases, and 30% identity with that of Bacillus megaterium. 4. Comparison of the N-terminal FMN-binding domain with flavodoxin, and the C-terminal FAD- and NADP-binding domain with ferredoxin-NADP reductase, indicates the presence of several functionally conserved regions. 5. The Sc. pombe cytochrome P-450 reductase gene was shown to contain no introns.

Amino Acid Sequence↗

PubMed1987

Relationship of an unstable argG gene to a 5.7-kilobase amplifiable DNA sequence in Streptomyces lividans 66.

The relationship between an unstable argG gene and a 5.7-kilobase (kb) amplifiable DNA sequence in Streptomyces lividans 66 was investigated. Spontaneous, high-frequency Arg mutants deleted for this gene typically contain 200 to 300 copies of the tandemly reiterated sequence. A library of S. lividans 66 (strain 1326) wild-type genomic DNA was prepared in the vector lambda Charon 35. Chromosome walking over 44 kb established that argG is located 25 kb distant from a duplicated amplifiable DNA structure. A sequence was characterized, located farther distal from the amplifiable structure, containing strong homology with an internal sequence of the amplifiable DNA, which may have a role in the deletion of argG. Genetic mapping showed that argG and the 5.7-kb amplifiable sequence are linked to another unstable gene, determining chloramphenicol resistance (Camr) and that together these genes may be located in a silent chromosomal arc.

Argininosuccinate Synthase↗