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Osteonectin cDNA sequence reveals potential binding regions for calcium and hydroxyapatite and shows homologies with both a basement membrane protein (SPARC) and a serine proteinase inhibitor (ovomucoid).

Osteonectin is a prominent noncollagenous protein of developing bone. A 2150-base-pair cDNA coding for osteonectin, isolated from a bovine bone cell lambda gt11 expression library, was sequenced and identified by comparison with protein sequence data. The nucleotide sequence predicts that osteonectin contains 304 amino acids, including a 17-residue signal peptide. Analysis of the deduced protein sequence suggests that the secreted protein contains at least four distinct structural domains. An acidic region at the amino terminus of the protein appears to be a potential hydroxyapatite-binding site. This is followed by a second domain, rich in cysteine, that shows sequence homology with cysteine-rich domains in turkey ovomucoid and other serine proteinase inhibitors. Two sequences homologous with central calcium-binding loops of "EF hands" and thus having potential to be high-affinity calcium-binding sites are located in two other domains within the carboxyl-terminal half of the protein. Finally, the osteonectin sequence shows near identity (greater than 90%) with another protein, SPARC (secreted protein, acidic and rich in cysteine), secreted by mouse parietal endoderm. These data suggest that osteonectin, a protein present in bone and other selected tissues, is a multifunctional protein.

Amino Acid Sequence↗

Identification, cDNA sequence and deduced amino acid sequence of the mitochondrial Rieske iron-sulfur protein from the green alga Chlamydomonas reinhardtii. Implications for protein targeting and subunit interaction.

Specific oligonucleotide probes were used to isolate a cDNA clone for the mitochondrial Rieske iron-sulfur protein of the green alga Chlamydomonas reinhardtii. The protein is synthesized as a longer precursor with a cleavable N-terminal presequence of 54 amino acids but without a C-terminal extension. Comparison of the predicted secondary structure of this N-terminal sequence with that of the targeting signal of the chloroplast Rieske protein from C. reinhardtii [de Vitry (1994) J. Biol. Chem. 269, 7603-7609] indicates that, although they both have the potential to form amphiphilic alpha helices, the mito-chondrial presequence may form a more hydrophobic helix that could penetrate deeper into the membrane. The N-terminal part of the mature mitochondrial Rieske protein is characterized by a long, strongly hydrophilic N-terminal domain and by a positive charge in the middle of the hydrophobic stretch that is presumed to interact with the bc1 complex. Thus, the protein from C. reinhardtii differs from the Rieske proteins from mammals or fungi.

Amino Acid Sequence↗

Gene expression profile and identification of differentially expressed transcripts during human intrathymic T-cell development by cDNA sequencing analysis.

The development of immature thymocytes to mature T-lymphocytes is a central process for establishing a functional immune system. The gene regulatory events involved in this process are of outstanding interest in understanding the generation of the T-cell repertoire as well as the differentiation of lineage-specific cells, such as CD4(+) helper T-cells or CD8(+) cytotoxic T-lymphocytes. While some essential genes involved in lineage decision and thymocyte differentiation have been already identified, the exact regulatory mechanisms and differential gene expressions are still unknown. The present study was performed to analyze the gene expression profile during T-cell development, in particular, during the differentiation of immature thymocytes into CD4(+) mature T-cells by analyses of expressed sequence tags (ESTs), and to elucidate novel human genes involved in this process. Based on distinct developmental stages, three PCR-based cDNA libraries from immature CD3(-),4(-),8(-) triple-negative, CD4(+),8(+) double-positive, and mature CD4(+),8(-) single-positive thymocytes were constructed. A total of 1477 randomly selected clones were analyzed by automated single-pass sequencing, and the assembly of ESTs resulted in 1027 different species of contig sequences. Among them, 392 contig sequences were matched to known genes, and several novel transcripts were discovered. The matched clones were classified into seven categories according to their functional aspects, and the gene expression profiles of the three thymocyte subsets were compared. The information obtained in current study will serve as a valuable resource for elucidating the molecular mechanism of intrathymic T-cell development.

Cell Differentiation↗

Heparin cofactor II: cDNA sequence, chromosome localization, restriction fragment length polymorphism, and expression in Escherichia coli.

Heparin cofactor II (HCII) is an inhibitor of thrombin in plasma that is activated by dermatan sulfate or heparin. An apparently full-length cDNA for HCII was isolated from a human liver lambda gt11 cDNA library. The cDNA consisted of 2215 base pairs (bp), including an open-reading frame of 1525 bp, a stop codon, a 3'-noncoding region of 654 bp, and a poly(A) tail. The deduced amino acid sequence contained a signal peptide of 19 amino acid residues and a mature protein of 480 amino acids. The sequence of HCII demonstrated homology with antithrombin III and other members of the alpha 1-antitrypsin superfamily. Blot hybridization of an HCII probe to DNA isolated from sorted human chromosomes indicated that the HCII gene is located on chromosome 22. Twenty human leukocyte DNA samples were digested with EcoRI, PstI, HindIII, KpnI, or BamHI, and Southern blots of the digests were probed with HCII cDNA fragments. A restriction fragment length polymorphism was identified with BamHI. A slightly truncated form of the cDNA, coding for Met-Ala instead of the N-terminal 18 amino acids of mature HCII, was cloned into the vector pKK233-2 and expressed in Escherichia coli. The resultant protein of apparent molecular weight 54,000 was identified on an immunoblot with 125I-labeled anti-HCII antibodies. The recombinant HCII formed a complex with 125I-thrombin in a reaction that required the presence of heparin or dermatan sulfate.

Amino Acid Sequence↗

Frog diazepam-binding inhibitor: peptide sequence, cDNA cloning, and expression in the brain.

Three peptides derived from diazepam-binding inhibitor (DBI) were isolated in pure form from the brain of the frog Rana ridibunda. The primary structures of these peptides showed that they correspond to mammalian DBI-(1-39), DBI-(58-87), and DBI-(70-87). A set of degenerate primers, whose design was based on the amino acid sequence data, was used to screen a frog brain cDNA library. The cloned cDNA encodes an 87-amino acid polypeptide, which exhibits 68% similarity with porcine and bovine DBI. Frog DBI contains two paired basic amino acids (Lys-Lys) at positions 14-15 and 62-63 and a single cysteine within the biologically active region of the molecule. Northern blot analysis showed that DBI mRNA is expressed at a high level in the brain but is virtually absent in peripheral tissues. The distribution of DBI mRNA and DBI-like immunoreactivity in the frog brain was studied by in situ hybridization and immunocytochemistry. Both approaches revealed that the DBI gene is expressed in ependymal cells and circumventricular organs lining the ventricular cavity. Since amphibia diverged from mammals at least 250 million years ago, the data show that evolutionary pressure has acted to conserve the structure of DBI in the vertebrate phylum. The distribution of both DBI mRNA and DBI-like immunoreactivity indicates that DBI is selectively expressed in glial cells.

Amino Acid Sequence↗

Molecular cloning of cDNA sequences transcribed from mouse liver endoplasmic reticulum poly(A)mRNA.

Poly(A)mRNA was isolated from the endoplasmic reticulum (ER) of male BALB/c mice and used as the template for cDNA synthesis. Double-stranded (ds) cDNA was cloned in a bacterial plasmid and 21 clones were selected for further study. Six clones have been identified by hybrid selection of mRNA, translation of the mRNA in a template-dependent system, polyacrylamide gel electrophoresis and specific immunoprecipitation. Four code for the major urinary protein of the mouse (MUP), one for serum albumin and one for alpha 1-antitrypsin. A seventh codes for an unidentified polypeptide with Mr = 27000. Initial-rate hybridisation kinetics of immobilised cloned sequences with end-labelled mRNA showed that serum albumin mRNA is most abundant in the population of mRNA species present in the endoplasmic reticulum fraction of female BALB/c liver. MUP mRNA is also very abundant. The alpha 1-antitrypsin mRNA and the mRNA specifying the 27000-dalton protein are about 5 times less abundant than serum albumin mRNA on a molar basis.

Animals↗

Nonepidermal members of the keratin multigene family: cDNA sequences and in situ localization of the mRNAs.

A keratin set which consists of a type I 47kd and a type II 57kd protein occurs as a major constituent of the keratin patterns of various internal stratified epithelia of the mouse. We have isolated specific cDNA clones of the two complementary keratin subunits from a cDNA library constructed with polyA+RNA of mouse tongue epithelium and present the complete nucleotide and deduced amino acid sequences of the 57kd protein and about 75% of the corresponding data of the 47kd protein. The comparison of the sequence data with those of known epidermal keratin mRNAs coding for the two types of keratin proteins reveals a fundamentally identical and type-specific organization of the mRNAs into both highly conserved and variable domains. In order to avoid cross-reactions with other members of the keratin multigene family, appropriately taylored 35S-labeled cDNA probes comprising the low and non-homologous 3' coding and noncoding domains of the mRNAs were used for in situ hybridization to tissue sections. The localization and distribution of the corresponding transcripts indicates a strongly compartmentalized keratin expression in mouse tongue epithelium.

Amino Acid Sequence↗

Ribosomal protein L5 of Bombyx mori: cDNA sequence and tissue differences in the L5 mRNA content.

A gene encoding the ribosomal protein L5, which assembles with the 5S rRNA into one of the components of the 60S ribosomal subunit, was identified in insects for the first time. We report on the isolation of Bombyx mori cDNA, whose putative translation product is 60-76% identical with the L5 sequences known from other animals and about 50% identical with the L5 of rice and yeasts. Bombyx contains a single copy of the L5 gene, which is constitutively expressed as a 1.1 kb mRNA in all tissues. The ratio of L5 mRNA to total RNA appears to reflect the proteosynthetic tissue capacity. A very high level of L5mRNA is maintained in functional silk glands. A rapid decline of the ratio of L5mRNA to the rRNA, which occurs in the silk glands after cocoon spinning, indicates differences in the stability of these two RNA classes.

Amino Acid Sequence↗

Epitopes of human testis-specific lactate dehydrogenase deduced from a cDNA sequence.

The sequence and structure of human testis-specific L-lactate dehydrogenase [LDHC4, LDHX; (L)-lactate: NAD+ oxidoreductase, EC 1.1.1.27] has been derived from analysis of a complementary DNA (cDNA) clone comprising the complete protein coding region of the enzyme. From the deduced amino acid sequence, human LDHC4 is as different from rodent LDHC4 (73% homology) as it is from human LDHA4 (76% homology) and porcine LDHB4 (68% homology). Subunit homologies are consistent with the conclusion that the LDHC gene arose by at least two independent duplication events. Furthermore, the lower degree of homology between mouse and human LDHC4 and the appearance of this isozyme late in evolution suggests a higher rate of mutation in the mammalian LDHC genes than in the LDHA and -B genes. Comparison of exposed amino acid residues of discrete antigenic determinants of mouse and human LDHC4 reveals significant differences. Knowledge of the human LDHC4 sequence will help design human-specific peptides useful in the development of a contraceptive vaccine.

Amino Acid Sequence↗

Isolation, characterization, and cDNA sequence of a carotenoid binding protein from the silk gland of Bombyx mori larvae.

A carotenoid binding protein (CBP) has been isolated from the silk glands of Bombyx mori larvae. The protein has an apparent molecular mass of 33 kDa and binds carotenoids in a 1:1 molar ratio. Lutein accounts for 90% of the bound carotenoids, whereas alpha-carotene and beta-carotene are minor components. Immunological analysis demonstrated the presence of CBP only in the yellow-colored tissues of the silk gland, midgut, testis, and ovary. Several phenotypes of B. mori mutants linked to carotenoid transport have been utilized to characterize CBP. The Y (yellow hemolymph) gene controls uptake of carotenoids from the midgut lumen into the midgut epithelium, and larvae with the +(Y) gene lack this property. Immunoblotting analysis confirmed the presence of CBP in mutants with the dominant Y gene only. Immunohistochemistry verified the localization of CBP in the villi of the midgut epithelium, indicating that CBP might be involved in absorption of carotenoids. A cDNA clone for CBP encoding a protein of 297 amino acids has been isolated from the B. mori silk gland cDNA library. The deduced amino acid sequence revealed that CBP is a novel member of the steroidogenic acute regulatory (StAR) protein family with its unique structural feature of a StAR-related lipid transfer domain, known to aid in lipid transfer and recognition. Lutein-binding capacity of the recombinant CBP (rCBP) determined by incubating rCBP with lutein followed by immunoprecipitation using anti-CBP IgG conjugated to protein A-Sepharose, demonstrated the formation of a lutein-rCBP complex. Sequence analyses coupled with binding specificity suggest that CBP is a new member of the StAR protein family that binds carotenoids rather than cholesterol.

Amino Acid Sequence↗

Characterization of multiple metalloproteinases with fibrinogenolytic activity from the venom of Taiwan habu (Trimeresurus mucrosquamatus): protein microsequencing coupled with cDNA sequence analysis.

Three fibrinogenolytic proteases were isolated and purified from the venom of Taiwan habu (Trimeresurus mucrosquamatus) using anion-exchange and gel-filtration chromatographies followed by cation-exchange HPLC. Further characterization of these purified fractions with fibrinogenase activity indicated that they are single-chain proteases of approximately 24 kDa, possessing strong cleaving activity mainly on the A alpha and less on B beta and gamma chains of fibrinogen subunit chains. Enzyme activities were strongly inhibited by EDTA or 1,10-phenanthroline and not by phenylmethanesulfonyl fluoride, suggesting that these fibrinogenases belong to the family of metalloproteinases and not thrombin-like serine proteases. N-Terminal sequence analysis of these proteases failed to show any free amino-terminal residues, thus hampering the sequence determination by conventional sequencing strategy. Microsequencing on the electroblotted fragments of CNBr-treated proteases separated on SDS-PAGE was then used to determine the partial sequences. Sequence comparison of the determined partial sequences of these proteins with published sequences of the protein data bank revealed that they showed sequence homology with H2-protease. HR2a and protrigramin, which were all shown to belong to metalloproteinases present in various snake venoms. Polymerase chain reaction (PCR) was employed to amplify cDNAs constructed from the poly(A)+RNA of fresh venom glands of the same snake species to facilitate cloning and sequencing of these proteases. Sequencing several positive clones containing amplified cDNAs revealed the existence of one fibrinogenase in the Taiwan habu, which was contained within one complete cDNA encoding the preproproteinase precursor of hemorrhagic metalloproteinases.

Amino Acid Sequence↗

Complete cDNA sequence of rat atrial myosin light chain 1: patterns of expression during development and with hypertension.

Distinct atrial and ventricular isoforms of myosin light chain 1 (LC1) exist in mammals. The atrial LC1 is also expressed in fetal ventricular and skeletal muscle. Here we present a full length cDNA encoding a rat atrial LC1, based upon homology with previously reported LC1 sequences and its atrial-specific pattern of RNA hybridization in adult cardiac muscle. Atrial and ventricular RNA expression were studied during rat development and with chronic hypertension. Atrial LC1 mRNA was expressed in rat atria throughout development, and was coexpressed with ventricular LC1 mRNA in the hearts of 12-day and 16-day embryos, and in the ventricles of newborn rats (less than 24 hours). In 9 day-old neonates, atrial LC1 mRNA expression was restricted to rat atrium. In adult rats exhibiting renovascular hypertension, the expression of the atrial and ventricular LC1 mRNAs was unchanged from that seen in normal control animals.

Aging↗

Isolation of an Arabidopsis cDNA sequence encoding a 22 kDa calcium-binding protein (CaBP-22) related to calmodulin.

Complementary DNA sequences were isolated from a library of cloned Arabidopsis leaf mRNA sequences in lambda gt10 that encoded a 21.7 kDa polypeptide (CaBP-22), which shared 66% amino acid sequence identity with Arabidopsis calmodulin. The putative Ca(2+)-binding domains of CaBP-22 and calmodulin, however, were more conserved and shared 79% sequence identity. Ca2+ binding by CaBP-22, which was inferred from its amino acid sequence similarity with calmodulin, was demonstrated indirectly by Ca(2+)-induced mobility shifting of in vitro translated CaBP-22 during SDS-polyacrylamide gel electrophoresis. CaBP-22 is encoded by a ca. 0.9 kb mRNA that was detected by northern blotting of leaf poly(A)+ RNA; this mRNA was slightly larger than the 809 bp CaBP-22 cDNA insert, indicating that the deduced amino acid sequence of CaBP-22 is near full-length. CaBP-22 mRNA was detected in RNA fractions isolated from leaves of both soil-grown and hydroponically grown Arabidopsis, but below the limits of detection in RNA isolated from roots, and developing siliques. Thus, CaBP-22 represents a new member of the EF-hand family of Ca(2+)-binding proteins with no known animal homologue and may participate in transducing Ca2+ signals to a specific subset of response elements.

Amino Acid Sequence↗

HSP90 homologue from Madagascar periwinkle (Catharanthus roseus): cDNA sequence, regulation of protein expression and location in the endoplasmic reticulum.

We describe cDNAs for a HSP90 homologue from Catharanthus roseus and studies on the regulation of expression. The largest cDNA (2670 bp) coded for a protein of 817 amino acids with a calculated size of 93,491 Da and a pI of 4.61. It contained a eucaryotic secretory signal, the endoplasmic reticulum (ER) targeting and retention signal (Lys-Asp-Glu-Leu), and the HSP90 protein family signature with one conservative exchange (Asn-Lys-Asp-Ile-Phe-Leu instead of Asn-Lys-Glu-Ile-Phe-Leu). RNA blots revealed a transcript of 2.8-2.9 kb, and genomic DNA blots suggested a single gene. The expression was analysed with antiserum against a fusion protein expressed in Escherichia coli. Immunoblots revealed a protein of 93 +/- 1.5 kDa (often a doublet) only in the membrane fraction, and sucrose density gradients suggested association with the ER. The protein was constitutively expressed in C. roseus cell cultures grown at 25 degrees C, and expression was apparently unaffected by various stress conditions, such as heat, high sucrose, elicitor from Phytophthora megasperma or yeast extract. It was not detectable in young C. roseus plants at room temperature, and heat shock for several hours at 37 degrees C was necessary to obtain detectable expression. In maize (Zea mays), a cross-reacting protein was detectable in cell cultures, but not in young plants. The results suggested that the cloned protein is not a major component in the heat shock response. We propose a chaperone role in the assembly and processing of cell wall components and other secreted proteins, i.e. functions that are very active in cells with a high rate of growth and division.

Amino Acid Sequence↗

The cDNA sequence encoding bovine pregastric esterase.

The polymerase chain reaction (PCR) was used to amplify specific parts of the gene encoding calf pregastric esterase (PGE). Primers based on conserved regions in human gastric lipase (HGL) and rat lingual lipase (RLL) were used to screen a cDNA library prepared from calf tongue tissue. This resulted in the cloning of the entire coding sequence for PGE, which exists as a mature 378-amino-acid (aa) polypeptide with a molecular mass of 42,960 Da. The PGE, HGL and RLL genes all share a high degree of identity at both the nucleotide and amino-acid sequence levels. Except for the Gly-Xaa-Ser-Xaa-Gly sequence containing the active site Ser, there is little identity with non-preduodenal lipases.

Amino Acid Sequence↗

Adhalin mRNA and cDNA sequence are normal in the cardiomyopathic hamster.

Adhalin is deficient in two forms of human muscular dystrophy, one due to mutations in the adhalin gene and one linked to an unidentified gene on chromosome 13. Because adhalin is deficient in skeletal and cardiac muscles of BIO 14.6 hamsters, which experience both myopathy and cardiomyopathy, cDNA encoding adhalin from BIO 14.6 hamster skeletal muscle was cloned and sequenced. Adhalin mRNA was expressed at normal levels in BIO 14.6 hamster cardiac muscle, and no mutation in adhalin coding sequence was found, indicating that the inherited myopathy and cardiomyopathy of the BIO 14.6 hamster are most likely not due to mutations in the adhalin gene.

Amino Acid Sequence↗

cDNA sequencing confirms HTLV-I expression in adult T-cell leukemia/lymphoma and different sequence variations in vivo and in vitro.

Human T-lymphotropic virus type I (HTLV-I) is the etiological agent of adult T-cell leukemia/lymphoma (ATL) and of tropical spastic paraparesis/HTLV-I-associated myelopathy (TSP/HAM). In both diseases, expression of viral message can generally only be demonstrated by the reverse transcriptase-polymerase chain reaction (RT-PCR) technique. We have previously reported on the the expression of at least four types of alternatively spliced pX mRNAs in vitro and in vivo (1). The sequence variation between HTLV-I pX cDNAs cloned from two different HTLV-I-infected cell lines and from uncultured primary peripheral blood mononuclear cells (PBMC) from two ATL patients was examined. None of the cDNA clones from one of the ATL samples was completely identical to any of the previously cloned cell line messages, establishing that the demonstration of HTLV-I mRNA in ATL is not the result of PCR contamination. Sequence analysis showed that differences between samples can be clustered according to their geographic origin. Cell line cDNAs showed a more marked sequence drift than ATL cDNAs, especially in the long terminal repeat (LTR), demonstrating association of intrastrain variability with culture in vitro. Intrastrain cDNA variability in vivo also suggests ongoing viral replication in infected individuals. A premature stop codon in the pX-II open reading frame (orf) was a common finding, suggesting that the complete putative pX-II protein is not essential for T-cell immortalization or HTLV-I replication.

Base Sequence↗

cDNA sequence, tissue-specific expression, and chromosomal mapping of the human slow-twitch skeletal muscle isoform of troponin I.

Troponin I (TnI) is a myofibrillar protein involved in the calcium-mediated regulation of striated muscle contraction. Three isoforms of TnI are known and each is expressed in a muscle fiber-type-specific manner. TnI-fast and TnI-slow are expressed exclusively in fast-twitch and slow-twitch skeletal muscle myofibers, respectively, while a third isoform, TnI-card, is expressed in both the atrium and the ventricle of the heart. An explanation of the myofiber-type-restricted expression of the troponin I multigene family will further aid in understanding how various types of striated muscle fibers are established. To initiate the study of TnI isoform gene expression, we have isolated a full-length cDNA representing the human slow-twitch skeletal muscle isoform of troponin I. Sequence comparisons demonstrate that the TnI-slow protein is highly conserved between species. Therefore, the cDNA was used as a probe to investigate the tissue-specific and developmental regulation of the TnI-slow gene in both rodent and human myogenic cells. TnI-slow message appears to be restricted to muscle tissue containing slow-twitch skeletal muscle myofibers. TnI-slow gene expression is induced in differentiated cultures of primary human muscle cells and several (but not all) myogenic cell lines. In addition, a human-specific probe prepared from the 3' untranslated region of the cDNA has been used to probe a panel of human/mouse somatic cell hybrid lines, resulting in the assignment of the human TnI-slow gene to the q12----qter region of chromosome 1. The locus is designated TNNI1.

Amino Acid Sequence↗