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PubMed1998

cDNA sequence analysis, chromosomal assignment and expression pattern of the gene coding for integral membrane protein 2B.

The complete cDNA of the mouse integral membrane protein 2B gene (Itm2b) was determined by sequence analysis of expressed sequence tag (EST) clone L26775 and a clone isolated from a cDNA library of the osteogenic stromal cell line MN7 (Mathieu et al., 1992. Calcif. Tissue Int. 50, 362-371) and by 5' rapid amplification of cDNA ends (RACE). Alignment of different mouse ESTs confirmed the entire sequence. Northern blot analysis of different neonatal and adult mouse tissues showed that Itm2b is ubiquitously expressed. There are three mRNAs with different lengths in neonatal as well as in adult tissues, originating from alternative polyadenylation by usage of one consensus and two additional variant polyadenylation signals. The cDNA sequence of the human Itm2b homolog (ITM2B) was assembled using data from available human ESTs. Both the mouse and the human gene code for a protein of 266 amino acids (aa) that is homologous to a previously described integral membrane protein, Itm2A, of which the expression is restricted to osteo- and chondrogenic tissues. Itm2A and Itm2B belong to a family of type II integral membrane proteins, which contains a third member, Itm2C (Deleersnijder et al., 1996. J. Biol. Chem. 271, 19475-19482). The human ITM2B and mouse Itm2b genes were previously mapped as unknown ESTs to conserved syntenic regions Homo sapiens 13q12-13 and Mus musculus 14.

Adaptor Proteins, Signal Transducing↗
PubMed1989

Primary structure of cucumber (Cucumis sativus) ascorbate oxidase deduced from cDNA sequence: homology with blue copper proteins and tissue-specific expression.

cDNA clones for ascorbate oxidase were isolated from a cDNA library made from cucumber (Cucumis sativus) fruit mRNA. The library was screened with synthetic oligonucleotides that encode the NH2-terminal sequence of this enzyme. Nucleotide sequence analysis of the cloned cDNA inserts revealed a 1761-base-pair open reading frame that encoded an NH2-terminal signal peptide of 33 amino acids and a mature enzyme of 554 amino acids (Mr, 62,258). The amino acid sequence deduced from nucleotide sequence analysis agrees with the NH2-terminal amino acid sequence of the purified ascorbate oxidase, as determined by microsequencing methods. Cucumber ascorbate oxidase contained four histidine-rich regions with striking sequence homology to the corresponding parts of the other multicopper oxidases such as Neurospora crassa laccase and human ceruloplasmin and, to some extent, to a low molecular weight copper protein such as plastocyanin. Moreover, these data further support the hypothesis that the small blue copper proteins and the multicopper oxidases have evolved from the same ancestral gene. By RNA blot hybridization analysis, the mRNA for the ascorbate oxidase was found to be abundant in cucumber fruit tissue while expressed at very low levels in leaf and root tissues.

Amino Acid Sequence↗
PubMed1993

Two distinct cDNA sequences encoding the human helix-loop-helix protein Id2.

Two distinct Id2 cDNA clones, Id2A and Id2B (inhibitor of differentiation), have been isolated from a human heart cDNA library and sequenced. The deduced amino acid sequences show nearly complete identity, except for the nonsense mutation at codon 37 in Id2B. Characterization of the genomic clones revealed that Id2B is encoded by an intronless gene which probably arose after the evolutionary divergence of rats and humans.

Animals↗
PubMed1995

Baboon lipoprotein lipase: cDNA sequence and variable tissue-specific expression of two transcripts.

We have isolated two lipoprotein lipase (LPL)-encoding cDNA (LPL) clones from a baboon cardiac cDNA library, one of which spans a region from nucleotide (nt) 705 of the coding sequence to the poly(A) tail (2.8 kb). We used reverse transcription followed by PCR (RT-PCR), and anchor-ligated rapid amplification of cDNA ends (RACE) to amplify the remaining 5' region of the LPL transcript. Sequence comparisons reveal that the baboon nt sequence is 95% identical to the human cDNA sequence (ranging from 97.5 to 92.7% in the coding and noncoding regions, respectively). Less than 2% of nt substitutions cause changes between baboon and human amino acid (aa) sequences. The aa in the catalytic triad residues, the heparin-binding site in exon 6, as well as aa in positions where missense mutations cause LPL deficiency, are identical in baboons and humans. Characterization of the tissue-specific expression of LPL using Northern blots of total RNA showed that spinal cord expressed the most LPL transcripts of all baboon tissues examined. Like humans, baboons have two transcript sizes of approx. 3.6 and 3.4 kb in most tissues that express LPL, and sequencing of the 3' untranslated region (UTR) shows this is due to two polyadenylation sites. In contrast, only the larger 3.6-kb transcript is detected in RNA isolated from central nervous system (CNS) tissues. We used RT-PCR to show that the polyadenylation signal that produces the 3.4-kb message is present in CNS LPL transcripts, but is not utilized.

Amino Acid Sequence↗
PubMed1999

The Drosophila glucose transporter gene: cDNA sequence, phylogenetic comparisons, analysis of functional sites and secondary structures.

Facilitative glucose transport is mediated by members of the glucose transporter (GLUT) protein family that belong to the large superfamily of twelve transmembrane segment transporters. We have cloned and sequenced a 2,168 base-pair cDNA from Drosophila melanogaster (termed Dmglut1: GenBank accession number AF064703) with strong homology to the mammalian Glut genes. The cDNA has an open reading frame encoding a protein of 480 amino acids which shows a similarity of 68% to the human GLUT1 protein. We have done a phylogenetic analysis of the cDNA and the deduced protein sequences and found a significant homology to a putative coding sequence (Ceglut1) in Caenorhabditis elegans. Here we report the results of analyses of functional sites and secondary structures of the proposed proteins and conclude that the Dmglut1 and Ceglut1 genes encode functional glucose transporters.

Amino Acid Sequence↗
PubMed1998

Equus caballus gelsolin--cDNA sequence and protein structural implications.

We have generated and characterized the cDNA from equine smooth muscle that encodes gelsolin, an actin-modulating protein. Overlapping cDNA clones synthesized by the reverse transcriptase/polymerase chain reaction and clones isolated from a horse genomic library provided the complete primary structure for the intracellular isoform of gelsolin, while cDNA complemented with protein sequence data produced the full-length primary transcript of the gelsolin isoform found circulating in equine plasma. The deduced amino acid sequences of the intracellular and secreted versions of equine gelsolin infer polypeptides of 731 and 755 residues with apparent molecular masses of 80.7 kDa and 83.2 kDa, respectively. Multiple sequence alignment analysis of equine, human, porcine, and murine orthologs of gelsolin demonstrates prominent similarities among all of these proteins, with the horse and human molecules exhibiting the largest degree of likeness with respect to polypeptide length and overall sequence composition. Both horse and human plasma gelsolins are comprised of 755 amino acids with 94% of the residues identical, while the degree of sequence identity in the shorter (731 residues) cytoplasmic gelsolins is 95%. Analysis of the sequences and structures of the six related domains that comprise gelsolin emphasizes the strong correlation that exists between primary structural conservation among mammalian gelsolins and maintenance of the three-dimensional domain fold characteristic of members of this protein family.

Amino Acid Sequence↗
PubMed1995

Chloroplast pentose-5-phosphate 3-epimerase from potato: cloning, cDNA sequence, and tissue-specific enzyme accumulation.

A cDNA clone encoding the chloroplast enzyme pentose-5-phosphate 3-epimerase (EC 5.1.3.1) in potato (Solanum tuberosum) was isolated and sequenced. The deduced sequence of 235 amino acids is similar to protein sequences of bacterial epimerases. Northern blot analysis showed the highest level of epimerase mRNA expression in potato leaves, whereas it was low in roots, tubers, and stems. Epimerase protein is mulated only in plant tissues possessing chloroplasts, i.e. in land to a lesser extent in stem. In contrast, transketolase, a sequential enzyme of epimerase in the reductive and oxidative pentose phosphate cycle, is accumulated in all plant tissues.

Amino Acid Sequence↗
PubMed2000

Purification, characterisation and cDNA sequencing of pyruvate decarboxylase from Zygosaccharomyces bisporus.

Cells of the wild-type yeast strain Zygosaccharomyces bisporus CBS 702 form alpha-hydroxy ketones from aromatic amino acid precursors during fermentation. Pyruvate decarboxylase (PDC, E.C. 4.1.1.1), the key enzyme of this biotransformation catalysing the non-oxidative decarboxylation of pyruvate and other 2-oxo-acids, was purified and characterised. The active enzyme is homotetrameric (alpha4) with a molecular mass of about 244 kDa. Activation of PDC by its substrate pyruvate results in a sigmoidal dependence of the reaction rate from substrate concentration (apparent Km value 1.73 mM; Hill coefficient 2.10). A cDNA library was screened using a PCR-based procedure, and a 1856 bp cDNA of PDC was identified and sequenced. The cDNA encodes a polypeptide of 563 amino acid residues (monomeric unit). Sequence alignments demonstrate high homologies (> 80%) to PDC genes from Saccharomyces cerevisiae, Kluyveromyces lactis and Kluyveromyces marxianus.

DNA, Complementary↗
PubMed1988

The amino acid sequence of the 24-kDa subunit, an iron-sulfur protein, of rat liver mitochondrial NADH dehydrogenase deduced from cDNA sequence.

Antiserum directed against bovine heart mitochondrial NADH dehydrogenase has been used to screen a rat liver cDNA expression library in lambda gt11. The insert cDNA of a positive clone was found to represent the 24-kDa subunit of NADH dehydrogenase by epitope selection using nitrocellulose filter containing the expressed proteins. The amino acid sequence deduced from the nucleotide sequence of the cloned cDNA indicated that the 24-kDa subunit is produced as a precursor with an amino-terminal extension, and that its mature form consists of 217 amino acid residues with a molecular weight of 23,933.

Amino Acid Sequence↗
PubMed1987

Nucleotide (cDNA) sequence encoding the horse gonadotrophin alpha-subunit.

Several cDNA clones corresponding to mRNA for the alpha-subunit of the horse (Equus caballus) pituitary and placental (chorionic) gonadotrophic hormones have been isolated and sequenced. Polyadenylated mRNA was purified from horse pituitary glands (the source of FSH and LH) and horse placental tissues (the source of chorionic gonadotrophin; CG). The mRNA preparations were characterized by in-vitro translation and Northern hybridization techniques using human and ovine gonadotrophin cDNA clones as probes. Complementary DNA libraries were created from the pituitary and placental mRNAs and a human CG alpha-subunit probe was used to isolate several horse alpha-subunit cDNA clones. The alpha-subunit nucleotide sequence from both sources of tissue was identical, thereby indicating that in the horse (as in man) the same gonadotrophin alpha-subunit gene is expressed in the pituitary and placenta. Our results are consistent with transcription of a single alpha-subunit gene for all the glycoprotein hormones in the horse, and we suggest that the reported differences between the horse CG and FSH alpha-subunit amino acid sequences determined by conventional peptide sequencing methods arose due to errors in the FSH alpha-subunit sequence. Comparison of the deduced amino acid sequence of the horse alpha-subunit with that of other alpha-subunit sequences indicated a number of significant differences which may be related to the unusual receptor-binding properties of the equine gonadotrophins.

Animals↗
PubMed1990

Human cytochrome P450IIA3: cDNA sequence, role of the enzyme in the metabolic activation of promutagens, comparison to nitrosamine activation by human cytochrome P450IIE1.

We report that, in a human cell line, human cytochrome P450IIA3 is capable of metabolizing aflatoxin B1, benzo[a]-pyrene, N-nitrosodimethylamine (NDMA) and N-nitrosodiethylamine (NDEA) to cytotoxic and mutagenic species. Cytochrome P450IIA3-mediated activation of NDMA and NDEA was compared with human cytochrome P450IIE1-mediated activation in the same cell system. P450IIE1 was more effective at activating NDMA than P450IIA3, while P450IIA3 was more effective at activating NDEA than P450IIE1. Whole cells and microsomal fractions obtained from control cells and from cells expressing the P450IIA3 cDNA were characterized for expression of P450IIA3. Microsomal coumarin 7-hydroxylase activity was some 40 times greater in the transfected cells than in the control cells and was catalyzed by a protein that was immunochemically related to the rat liver cytochrome P450IIA gene family. Immunoblot analysis demonstrated that this protein was readily detectable in transfected cells but barely detectable in control cells. We also report the DNA and deduced amino acid sequence of the P450IIA3 cDNA isolate used in this study. Our isolate encodes a protein 489 amino acids that is five amino acids shorter at the N terminus but otherwise identical to a previously reported human P450IIA3 cDNA sequence.

Aflatoxin B1↗
PubMed1996

Mouse annexin V chromosomal localization, cDNA sequence conservation, and molecular evolution.

A full-length cDNA encoding mouse annexin V (ANX5) was cloned, sequenced, and utilized for chromosomal mapping. The gene lies on mouse chromosome 3 in close linkage with the fibroblast growth factor 2 (basic) gene and is syntenic with other genes known to have orthologous counterparts on human chromosome 4q. The open reading frame encoded a protein of 319 amino acids (aa), with 92-96% identity to ANX5 in other species. Internal repeat 3 of mouse ANX5 exhibited the highest level of nonconservative aa replacements with respect to other annexin subfamilies, but the greatest sequence conservation among ANX5 species members. This region may thus contain features that distinguish ANX5 from other annexins in properties or function. Phylogenetic analysis and homology testing of ANX5 members indicated that the 34-kDa annexin from Torpedo marmorata may also belong to this subfamily. Comparison of nine species of ANX5 led to an estimation of the unit evolutionary mutation rate at 1% aa replacements every 8 million years, comparable to other annexins.

Amino Acid Sequence↗
PubMed1992

The complete cDNA sequence of bovine coagulation factor V.

Lack of availability of a primary structure for bovine factor V has hindered detailed analysis of a vast majority of structure-function correlations on this molecule. To determine the primary structure of bovine factor V, we used liver mRNA as a template for the synthesis of three cDNA libraries. The sequences of seven overlapping cDNA clones infer two bovine factor V variants. Variant 1 results in a 6910-basepair (bp) cDNA including 103 bp of 5'-untranslated sequence, 6633 bp of coding sequence and 171 bp of 3'-untranslated sequence with a putative polyadenylation site. Variant 2 differs only in the size of the coding sequence (6618 bp). The open reading frame translates to factor V consisting of 2211 (or 2206) amino acids including a 28-amino acid signal peptide. Comparison of the amino acid sequences with human factor Va reveals 84% identity for the heavy and 86% for the light chains. In contrast, the B domain (connecting region) exhibits only 59% identity relative to the human molecule. The bovine B domain contains two repeats of a 14-amino acid structure that is contained only once in the human sequence. Bovine factor V lacks one of the nine amino acid repeats and one of the 17 amino acid repeats present in the human B domain. Factor V has little homology to the factor VIII molecule in the B domain. The 17-amino acid repeat missing in bovine factor V allows identification of an 18-amino acid sequence that is homologous to the B domain of human factor VIII. These 18 amino acids may either constitute the unique vestige of a divergent evolution between the B domains of factors V and VIII or reveal the convergent evolution toward a critical epitope involved in the activation of both procofactors.

Amino Acid Sequence↗
PubMed1987

Chicken apolipoprotein A-I: cDNA sequence, tissue expression and evolution.

Using an antibody against chicken apolipoprotein (apo) A-I, we identified multiple cDNA clones for the protein in two intestinal cDNA libraries in lambda gt11. The complete nucleotide sequence of chicken apoA-I cDNA was determined. The sequence predicts a mature protein of 240 amino acids, a 6-amino acid propeptide and an 18-amino acid signal peptide. Using a 32P-cDNA probe, we detected the presence of apoA-I mRNA in 21 day old chicken intestine, liver, kidney, spleen, breast muscle and brain. The primary sequence of apoA-I contains numerous tandem repeats of 11 and 22 residues in a manner similar to the mammalian proteins. Our analysis of apoA-I sequences from human, rabbit, dog, rat, and chicken indicates that the rate of amino acid substitution is considerably faster in the rat lineage than in other mammalian lineages.

Amino Acid Sequence↗
PubMed1990

Primary structure of mouse proacrosin deduced from the cDNA sequence and its gene expression during spermatogenesis.

In the present study, we identified cDNA clones of mouse acrosin from a testis lambda gt11 library. The deduced amino acid sequence indicates that mouse acrosin is initially synthesized as a single-chain polypeptide with a 16-residue signal peptide followed by a 23-residue light chain and then a 394-residue heavy chain; mouse acrosin zymogen contains 417 amino acid residues with a calculated molecular mass of 46,993 Da. The cDNA-derived sequence of mouse proacrosin shows a high degree of similarity with human and porcine proacrosins and major portions of bovine trypsin, including the active site residues, the recognition site for substrate, the location of 12 cysteine residues, and two potential N-glycosylation sites. The sequence homology suggests that mouse proacrosin is converted to a mature acrosin, which consists of the light and heavy chains with a combined molecular mass of 35,587 Da, by cleavage of the peptide bond between Arg23 and IIe24, and sequential removal of 23-, 26-, and 50-residue COOH-terminal segments. Using Northern blot analysis of RNAs from various mouse tissues, the acrosin gene transcript was present only in testis. The 1,800-base acrosin message was first detectable in 18-day-old testis. At the same time of testicular development, some of the acrosin mRNA was actually associated with polysomes. Also, in situ hybridization analysis suggests that the acrosin gene is expressed only in the round spermatid. Therefore, it is most likely that transcription of the mouse acrosin gene and subsequent translation of its mRNA first occur in the early stages of the round spermatid, and that the acrosin message is not under translational control.

Acrosin↗
PubMed1987

Gene family of male-specific testosterone 16 alpha-hydroxylase (C-P-450(16) alpha) in mouse liver: cDNA sequences, neonatal imprinting, and reversible regulation by androgen.

The cDNA clone p16 alpha-1 for the male-specific isozyme (C-P-450(16) alpha)1 of testosterone 16 alpha-hydroxylase in livers of 129/J mice [Harada, N., & Negishi, M. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 2024-2028] and two additional full-length cDNAs overlapping with p16 alpha-1 (p16 alpha-2 and p16 alpha-16) were sequenced. p16 alpha-2 contained a single open reading frame of 1512 nucleotides, consisting of 71 base pairs of the 5'-noncoding region and 63 base pairs of the 3'-noncoding region with an additional poly(A) tract. From this DNA sequence, C-P-450(16) alpha was deduced to contain 504 amino acids with a calculated molecular mass of 56,948 daltons. p16 alpha-1 showed a nucleotide sequence identical with that of p16 alpha-2 but lacked nine amino acid residues from the N-terminus. Another cDNA clone, p16 alpha-16, also exhibited the same coding sequence with the exception of a 142 base pair deletion spanning from nucleotide 853 to nucleotide 994 of p16 alpha-2. This deletion seems to be a whole exon of this gene, resulting in a shift of reading frame and an early termination codon at 10 amino acid residues from the deletion. The expected translation product of this mRNA is calculated to be 294 amino acids and 33,300 daltons. The putative poly(A) addition signal AATAAA is present for all three clones, but there are polymorphisms in the start sites of polyadenylation.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1987

Hybridization and partial cDNA sequence analyses of bovine lung angiotensin I-converting enzyme.

The mRNA encoding angiotensin I-converting enzyme, a zinc-metallo dipeptidyl carboxyhydrolase, has been identified in extracts prepared from bovine lung tissue. Bovine lung poly(A) + mRNAs were subjected to electrophoresis and northern blot hybridization analysis using a radiolabeled synthetic 24-deoxyoligonucleotide probe complementary to eight codons for amino acids at the active-site of the enzyme (Harris, R.B. & Wilson, I.B., J. Biol. Chem. 260, 2208-2211, 1985). This amino acid sequence contains the catalytic glutamic acid residue. A single RNA species (approximately equal to 4 kb) was detected which is 1 kb larger than predicted from the molecular weight of the enzyme. The excess nucleic acid composition may be due to leader and/or trailer sequences or the RNA may encode a high molecular weight precursor form of the enzyme. We have cloned an EcoR1-HindIII digest fragment (1400 bp) of the duplex cDNA derived from the bovine lung converting enzyme poly(A) + mRNA and also Bal31 deletion fragments generated from the 1400 bp clone. Several of the Bal31 clones contain the active-site sequence codons of the enzyme and the complete cDNA sequence of one of these (72 bp) has been determined. We found the amino acid sequence at the active site to be -Phe-Thr-Glu-Leu-Ala-Asn-Ser-, containing the catalytic Glu residue. This sequence is identical with the sequence that we previously determined by manual Edman degradation analysis of the appropriate active-site peptide except that we now find Asn instead of Asp. We have sequenced 670 bp of the 1400 bp clone but have not yet overlapped the active-site sequence.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed2002

Exploration of novel motifs derived from mouse cDNA sequences.

We performed a systematic maximum density subgraph (MDS) detection of conserved sequence regions to discover new, biologically relevant motifs from a set of 21,050 conceptually translated mouse cDNA (FANTOM1) sequences. A total of 3202 candidate sequences, which shared similar regions over >20 amino acid residues, were screened against known conserved regions listed in Pfam, ProDom, and InterPro. The filtering procedure resulted in 139 FANTOM1 sequences belonging to 49 new motif candidates. Using annotations and multiple sequence alignment information, we removed by visual inspection 42 candidates whose members were found to be false positives because of sequence redundancy, alternative splicing, low complexity, transcribed retroviral repeat elements contained in the region of the predicted open reading frame, and reports in the literature. The remaining seven motifs have been expanded by hidden Markov model (HMM) profile searches of SWISS-PROT/TrEMBL from 28 FANTOM1 sequences to 164 members and analyzed in detail on sequence and structure level to elucidate the possible functions of motifs and members. The novel and conserved motif MDS00105 is specific for the mammalian inhibitor of growth (ING) family. Three submotifs MDS00105.1-3 are specific for ING1/ING1L, ING1-homolog, and ING3 subfamilies. The motif MDS00105 together with a PHD finger domain constitutes a module for ING proteins. Structural motif MDS00113 represents a leucine zipper-like motif. Conserved motif MDS00145 is a novel 1-acyl-SN-glycerol-3-phosphate acyltransferase (AGPAT) submotif containing a transmembrane domain that distinguishes AGPAT3 and AGPAT4 from all other acyltransferase domain-containing proteins. Functional motif MDS00148 overlaps with the kazal-type serine protease inhibitor domain but has been detected only in an extracellular loop region of solute carrier 21 (SLC21) (organic anion transporters) family members, which may regulate the specificity of anion uptake. Our motif discovery not only aided in the functional characterization of new mouse orthologs for potential drug targets but also allowed us to predict that at least 16 other new motifs are waiting to be discovered from the current SWISS-PROT/TrEMBL database.

1-Acylglycerol-3-Phosphate O-Acyltransferase↗