Untranslated Segment Research Articles

Cloning, sequencing and heterologous expression of a cDNA encoding pigeon liver carnitine acetyltransferase.

Two overlapping cDNA clones encoding pigeon liver carnitine acetyltransferase (EC 2.3.1.7) (CAT) were isolated from a pigeon liver lambda gt11 cDNA library by gene amplification using oligonucleotide primers based on the N-terminal amino acid sequence of the enzyme. The two clones, which represent the 5' and 3' ends of the gene, were spliced together to form a single cDNA construct containing the entire coding sequence for CAT, with an in-frame TGA stop codon 42 bases before the first ATG start site and a 3'-untranslated segment of 1057 bases. The largest open reading frame of 1942 nucleotides predicted a polypeptide of 627 amino acids and a molecular mass of 71.1 kDa. The N-terminus and four internal peptides from the amino acid sequence of pigeon breast muscle CAT were identified in the predicted sequence of the liver cDNA clone. The identity of the CAT cDNA was confirmed by heterologous expression of active recombinant CAT (rCAT) in insect cells using the baculovirus expression system. Western blots of rCAT from infected insect cell lysates and immunodetection with a rabbit anti-CAT polyclonal serum showed an immunoreactive protein band similar in size to native CAT from pigeon breast muscle. Like the native enzyme, rCAT was capable of acylating carnitine with a preference for small-chain acyl-CoAs of carbon chain lengths C2-C4.

Genomic organization and structure of Bruton agammaglobulinemia tyrosine kinase: localization of mutations associated with varied clinical presentations and course in X chromosome-linked agammaglobulinemia.

X chromosome-linked agammaglobulinemia is a life-threatening disease that involves a failure in normal development of B lymphocytes and is associated with missense mutations in BTK, a gene encoding a cytoplasmic tyrosine kinase (Bruton agammaglobulinemia tyrosine kinase, EC 2.7.1.112), a member of the Tec family of protein-tyrosine kinases. The genomic organization has been determined by using conventional restriction fragment mapping, extended DNA sequencing, and PCR fragment-sizing approaches. The DNA sequences of the 18 coding exons composing BTK and their flanking-region sequences are reported; an additional exon(s) encodes a 5' untranslated segment. Single-base-pair substitutions and 4-nt deletions resulted in amino acid replacement, premature termination, frameshift, and exon deletion in a group of X chromosome-linked agammaglobulinemia patients exhibiting different clinical presentations and courses. The nature of the mutations is interpreted in terms of the genomic organization of the BTK gene and the disease course in individual patients. Several examples are found in which the same mutation occurs in unrelated patients, and one of these mutations occurs at the same codon that is substituted in the murine form of BTK, resulting in X chromosome-linked immunodeficiency disease. Considerable variation in presentation and disease course in X chromosome-linked agammaglobulinemia appears associated with the nature and position of different missense mutations.

Isolation and Characterization of Human Fast Skeletal β Troponin T cDNA: Comparative Sequence Analysis of Isoforms and Insight into the Evolution of Members of a Multigene Family

A cDNA encoding human fast skeletal beta troponin T (beta TnTf) has been isolated and characterized from a fetal skeletal muscle library. The cDNA insert is 1,000 bp in length and contains the entire coding region of 777 bp and 5' and 3' untranslated (UT) segments of 12 and 211 bp, respectively. The 3' UT segment shows the predicted stem-loop structure typical of eukaryotic mRNAs. The cDNA-derived amino acid sequence is the first available sequence for human beta TnTf protein. It is encoded by a single-copy gene that is expressed in a tissue-specific manner in fetal and adult fast skeletal muscles. Although the human beta TnTf represents the major fetal isoform, the sequence information indicates that this cDNA and the coded protein are quite distinct from the fetal and neonatal TnTf isoforms reported in other mammalian fetal muscles. The hydropathy plot indicates that human beta TnTf is highly hydrophilic along its entire length. The protein has an extremely high degree of predicted alpha-helical content involving the entire molecule except the carboxy-terminal 30 residues. Comparative sequence analysis reveals that the human beta TnTf shares a high level of sequence similarity in the coding region with other vertebrate TnTf and considerably reduced similarity with slow skeletal and cardiac TnT cDNAs. The TnT isoforms have a large central region consisting of amino acid residues 46-204 which shows a high sequence conservation both at the nucleotide and amino acid levels. This conserved region is flanked by the variable carboxy-terminal and an extremely variable amino-terminal segment. The tropomyosin-binding peptide of TnT, which is represented by amino acid residues 47-151 and also includes a part of troponin I binding region, is an important domain of this central segment. It is suggested that this conserved segment is encoded by an ancestral gene. The variable regions of vertebrate striated TnT isoforms reflect the subsequent addition and modification of genomic sequences to give rise to members of the TnT multigene family.

Inducible nitric-oxide-synthase mRNA is transiently expressed and destroyed by a cycloheximide-sensitive process.

Nitric oxide is a mediator of a wide range of physiological processes. It is produced by an enzyme family, the nitric-oxide synthases, one form of which is induced in many cells following stimulation with cytokines and lipopolysaccharide. The aim of the experiments reported in this study was to investigate the regulation of mRNA expression for this inducible nitric-oxide synthase in smooth muscle cells and macrophages. Stimulation of these cells with cytokines and lipopolysaccharide results in a marked elevation of nitric-oxide-synthase mRNA levels, which however do not remain elevated, but reach a maximum at 3-6 h after stimulation before returning to baseline levels over the next 20 h. Enzyme activity, however, remained virtually constant for 48 h following stimulation. Inspection of the 3' untranslated segment of both murine and human inducible nitric-oxide-synthase mRNAs showed the presence of a conserved AU-rich octanucleotide sequence, previously identified in cytokine and oncogene mRNAs and shown to mediate mRNA instability. A particular feature of the breakdown of mRNAs bearing this sequence is that degradation is prevented by protein-synthesis inhibition. We show in this study that the half-life of inducible nitric-oxide-synthase mRNA is 6 h and that in the presence of an inhibitor of protein synthesis this breakdown is prevented. Thus, the mRNA for inducible nitric-oxide synthase shares some features in common with cytokines such as the transient expression and decay of its mRNA which can be prevented by protein-synthesis inhibition.

Human factor B Complete cDNA sequence of the BF ∗S allele

The gene of human complement factor B (BF) is located within the class III region of the major histocompatibility complex. The knowledge of the coding sequence of the BF gene rests on a set of partial sequence studies reported by various sources, and full-length sequences ascribed to specific alleles of this polymorphic complement component have not yet been published. Now, we have isolated and sequenced a collection of cDNA clones derived from BF ∗S , the major BF allele. We present an uninterrupted, allele-specific sequence of the entire coding region and the 3′ untranslated segment of the cDNA. Extensive comparison of this and previously available sequence data was carried out, and a number of base substitutions were observed in relation to some of the earlier sequences. The possibility that these differences arise from polymorphism in the BF gene is discussed.

The human peripheral renzodiazepine receptor gene: Cloning and characterization of alternative splicing in normal tissues and in a patient with congenital lipoid adrenal hyperplasia

The mitochondrial benzodiazepine receptor (mBzR)appears to be a key factor in the flow of cholesterol into mitochondia to permit the initiation of steroid hormone synthesis. The mBzR consists of three components; the 18-kDa component on the outer mitochondrial membrane appears to contain the benzodiazepine binding site, and is hence often termed the peripheral benzodiazepine receptor (PBR). Using a cloned human PBR cDNA as probe, we have cloned the human PBR gene. The 13-kb gene is divided into four exons, with exon 1 encoding only a short 5′ untranslated segment. The 5′ flanking DNA lacks TATA and CAAT boxes but contains a cluster of SP-1 binding sites, typical of “housekeeping” genes. The encoded PBR mRNA is alternately spliced into two forms: “authentic” PBR mRNA retains all four exons, while a short form termed PBRS lacks exon 2. While PBR-S contains a 102-codon open reading frame with a typical initiator sequence, the reading frame differs from that of PBR, so that the encoded protein is unrelated to PBR. RT-PCR and RNase protection experiments confirm that both PBR and PBR-S are expressed in all tissues examined and that expression PBR-S is about 10 times the level of PBR. Expression of PBR cDNA in pCMV5 vectors transfected into COS-1 cells resulted in increased binding of [3H]PK11195, but expression of PBR-S did not. It has been speculated that patients with congenital lipoid adrenal hyperplasia, who cannot make any steroids, might have a genetic lesion in mBzR. RT-PCR analysis of testicular RNA from such a patient, sequencing of the cDNA, and blotting analysis of genomic DNA all indicate that the gene and mRNA for the PBR component of mBzR are normal in this disease.

Characterization of the mouse gene that encodes the delta/YY1/NF-E1/UCRBP transcription factor.

The mouse gene that encodes the delta transcription factor has been cloned and characterized. This gene spans 23 kb and is composed of five exons and four introns. The first exon consists of a long (431 bp), (C+G)-rich, untranslated segment and a 679-bp coding segment, which specifies the unusual tracts of consecutive acidic residues and histidines and the long alanine-glycine stretches. The sequence that encodes the four zinc-finger motifs of this protein is interrupted by two introns. Nuclease protection experiments revealed a major transcriptional start point and several additional start points distributed over a 28-bp segment. Transfection experiments with 5' and 3' deletion mutants localized the promoter to a (C+G)-rich region that is < 700 bp upstream and no more than 32 bp downstream of the major start point. An especially critical promoter element lies between -58 and -18 and contains a high-affinity Sp1 binding site, as demonstrated by electrophoretic mobility-shift experiments with nuclear extract and recombinant Sp1 proteins. Several striking similarities between the delta gene and genes encoding other transcription factors and regulatory proteins are noted and discussed with respect to their possible biological significance.

Cloning, sequencing, and expression of a cDNA encoding rat liver carnitine palmitoyltransferase I. Direct evidence that a single polypeptide is involved in inhibitor interaction and catalytic function.

We report the isolation and characterization of a full-length cDNA encoding rat liver carnitine palmitoyltransferase I (CPT I). Oligonucleotides corresponding to two tryptic peptides derived from the malonyl-CoA/etomoxir-CoA-binding protein of rat liver mitochondria (Esser, V., Kuwajima, M., Britton, C. H., Krishnan, K., Foster, D. W., and McGarry, J. D. (1993) J. Biol. Chem. 268, 5810-5816) were used to screen a rat liver cDNA library constructed in the plasmid cloning vector, pcDV. The clone obtained consisted of a 102-nucleotide 5'-untranslated region, a single open reading frame of 2,319 bases predicting a protein of 773 amino acids (M(r) = 88,150), and a 3'-untranslated segment of 1,957 nucleotides followed by the poly(A)+ tail. A 0.9-kilobase fragment of the cDNA recognized a single species of mRNA (approximately 4.7 kilobases in size) in rat liver. The identity of the cDNA was confirmed by the findings that (i) the open reading frame encoded all four peptides found in the original protein; (ii) transfection of COS cells with the cDNA subcloned into the expression vector, pCMV6, resulted in a selective and 10-20-fold induction of a malonyl-CoA- and etomoxir-CoA-sensitive CPT activity; and (iii) the overexpressed product was readily detected on Western blots by an antibody raised against the starting material. It seems likely that the de novo synthesized enzyme is targeted to the mitochondrial outer membrane via a leader peptide and that the mature protein achieves membrane anchoring through a stretch of 20 amino acids present near its amino terminus. The predicted amino acid sequence of the protein shows regions of strong identity with those of three other rat acyltransferases, namely, liver CPT II, liver carnitine octanoyltransferase, and brain choline acetyltransferase. The findings provide the first insight into the structure of a CPT I isoform. They also establish unequivocally that CPT I and CPT II are distinct proteins and that inhibitors of CPT I interact within its catalytic domain, not with an associated regulatory component.

CDNA sequence and alternative mRNA splicing of surfactant-associated protein C (SP-C) in rabbit lung

An 784 base pair (bp) copy DNA (cDNA) for the low molecular weight hydrophobic surfactant-associated protein C (SP-C) has been isolated from a λgt11 cDNA library constructed from fetal rabbit lung mRNA. The cDNA, which coded for a 193 amino-acid proprotein with 6 bp 5′ and 193 bp 3′ untranslated segments, possesses considerable nucleic acid and predicted amino-acid homology with previously reported SP-C cDNAs. The predicted amino-acid sequence of the 35 amino-acid mature polypeptide shares 94–97% identity with human, rat and mouse SP-C and is 88–91% homologous to the mature proteins from bovine, porcine and canine lung. The last 12 amino acids of mature SP-C are highly hydrophobic and invariant. Alignment of the rabbit and human nucleic acid sequences required introduction of a 27 bp gap in the rabbit sequence at a site corresponding to the exon-intron junction of the 5th exon of the human genomic sequence. Since previous studies have identified differential splicing at the 5′ and 3′ ends of the human 5th exon, we investigated the potential existence of alternative splicing of rabbit SP-C mRNA. Reverse transcription (RT) of total RNA followed by polymerase chain reaction (PCR) was used to establish the relative abundance of alternative splicing products from fetal and adult lung and from rabbit kidney, placenta and liver. The relative abundance of the 250, 280 and 350 bp bands observed was the same in lung and other tissues. PCR amplification of genomic rabbit DNA indicated that the 350 bp fragment corresponds to the unspliced nascent transcript. The lack of developmental or tissue-specific abundance patterns implies the absence of secondary influences on SP-C mRNA polymorphism. Indeed, free energy of formation calculations predicted the presence of hairpin structures favouring formation of the more abundant 250 bp form. These observations plus the absence of any effect of alternative splicing on SP-C protein structure led us to conclude a physiological role is unlikely.

Recognition of UGA as a selenocysteine codon in Type I deiodinase requires sequences in the 3′ untranslated region

Selenocysteine is incorporated cotranslationally at UGA codons, normally read as stop codons, in several bacterial proteins and in the mammalian proteins glutathione peroxidase (GPX), selenoprotein P and Type I iodothyronine 5' deiodinase (5'DI). Previous analyses in bacteria have suggested that a stem-loop structure involving the UGA codon and adjacent sequences is necessary and sufficient for selenocysteine incorporation into formate dehydrogenase and glycine reductase. We used the recently cloned 5'DI to investigate selenoprotein synthesis in eukaryotes. We show that successful incorporation of selenocysteine into this enzyme requires a specific 3' untranslated (3'ut) segment of about 200 nucleotides, which is found in both rat and human 5'DI messenger RNAs. These sequences are not required for expression of a cysteine-mutant deiodinase. Although there is little primary sequence similarity between the 3'ut regions of these mRNAs and those encoding GPX, the 3'ut sequences of rat GPX can substitute for the 5'DI sequences in directing selenocysteine insertion. Computer analyses predict similar stem-loop structures in the 3'ut regions of the 5'DI and GPX mRNAs. Limited mutations in these structures reduce or eliminate their capacity to permit 5'DI translation. These results identify a 'selenocysteine-insertion sequence' motif in the 3'ut region of these mRNAs that is essential for successful translation of 5'DI, presumably GPX, and possibly other eukaryotic selenocysteine-containing proteins.

Hepatitis C virus.

SummaryHepCV is the major cause of NANB PT hepatitis and is also implicated as the cause in a large proportion of sporadic cases of NANBH. Chronic infection with HepCV has also been linked to the development of hepatocellular carcinoma. Chimpanzees and marmosets are the only animals found to be experimentally infectable and the virus has not been propagated in any cell culture system.HepCV is an enveloped virus with a diameter of 30–60 nm and a 10-kb positive-stranded RNA genome. Its genome organization resembles that of the flaviviruses and pestiviruses. A 5′-untranslated segment of 341 nucleotides precedes a continuous ORF of 9030/9033 nucleotides which is followed by a 54 nucleotides long 3′-non-coding segment. Further work is required to resolve the question of whether the genomic RNA possesses a 3′-poly(U) or poly(A) tail. The genome also carries an internal poly(A) segment towards the 5′-end of its ORF. Genomic RNA is probably translated into a single polyprotein of 3010/3011 amino acids which is processed into functional proteins. The viral proteins have not been identified, but on the basis of the predicted amino acid sequences, hydrophobicity plots, location of potential glycosylation sites and similarities of these properties to those of pesti- and flaviviruses, the following genome organization has been predicted. The predicted viral structural proteins, a nucleocapsid protein and two envelope glycoproteins are located at the aminoterminal end of the polyprotein. They are followed by a highly hydrophobic protein and proteins that exhibit proteinase, helicase and replicase domains and thus are probably involved in RNA replication and protein processing. The replicase domain is located close to the carboxy terminus of the polyprotein.Although the overall nucleotide and amino acid homologies between HepCV and pestiviruses are low, a number of similarities exist that point to a closer ancestral relationship to the latter than the flaviviruses. First, the 5′-untranslated segment of the HepCV genome resembles that of the pestivirus genomes in size and presence of several short ORFs and it contains several segments with high nucleotide homology. Second, the two putative envelope glycoproteins of HepCV resemble two of the three putative envelope glycoproteins of the pestiviruses. Because its genome organization and predicted virion structure closely resemble those of the flaviviruses and pestiviruses, HepCV has been proposed to be placed in the familyFlaviviridae. It has been suggested to be classified as a new third genus in this family because it is only remotely related to the pestiviruses and flaviviruses in nucleotide sequence of its genome and the amino acid sequences of the predicted viral proteins.On the basis of genomic sequence information, an immunoprobe has been devised for screening blood supplies and donors for anti-HepCV antibodies to a non-structural protein of HepCV. The immuno-assay exhibits a high efficiency in detecting infected donors, though one caveat is that antibodies to the test antigen develop in infected individuals only between 2 and 8 months post infection. On the other hand, viral RNA can be detected in plasma by reverse transcription and amplification of the cDNA by PCR within a few days post infection. Thus the latter technique may become more important in the detection of HepCV in blood and tissues once the technique becomes more widely established as a diagnostic tool.The untranslated 5′-segment has been found to be highly conserved in the genomes of different HepCV isolates from various parts of the world. The replicase domain is also highly conserved, but considerable amino acid and nucleotide differences exist in other segments of the long ORFs of various HepCV isolates. Divergence among different isolates is particularly great (up to 30%) in the segment encoding the two putative envelope glycoproteins and the upstream hydrophobic protein. The variability in envelope glycoproteins needs to be considered in the development of immuno-probes and of vaccines for HepCV.

The cDNA sequence and the deduced amino acid sequence of human transcobalamin II show homology with rat intrinsic factor and human transcobalamin I.

The cellular uptake of cobalamin (Cbl, vitamin B12) is mediated by transcobalamin II (TCII), a plasma protein that binds Cbl and is secreted by human umbilical vein endothelial (HUVE) cells. These cells synthesize and secrete TCII and, therefore, served as the source of the complementary DNA (cDNA) library from which the TCII cDNA was isolated. This full-length cDNA consists of 1866 nucleotides that code for a leader peptide of 18 amino acids, a secreted protein of 409 amino acids, a 5'-untranslated segment of 37 nucleotides, and a 3'-untranslated region of 548 nucleotides. A single 1.9-kilobase species of mRNA corresponding to the size of the cDNA was identified by Northern blot analysis of the RNA isolated from HUVE cells. TCII has 20% amino acid homology and greater than 50% nucleotide homology with human transcobalamin I (TCI) and with rat intrinsic factor (R-IF). TCII has no homology with the amino-terminal region of R-IF that has been reported to have significant primary as well as secondary structural homology with the nucleotide-binding domain of NAD-dependent oxidoreductases. The regions of homology that are common to all three proteins are located in seven domains of the amino acid sequence. One or more of these conserved domains is likely to be involved in Cbl binding, a function that is common to all three proteins. However, the difference in the affinity of TCII, TCI, and R-IF for Cbl and Cbl analogues indicates, a priori, that structural differences in the ligand-binding site of these proteins exist and these probably resulted from divergence of a common ancestral gene.

Structure of the gene for rat nucleolar protein B23.

Protein B23 is an abundant RNA-associated nucleolar phosphoprotein involved in the ribosome assembly process. Previous studies showed that two forms of the protein (B23.1 and B23.2) are generated from a single gene via alternative splicing of 3' exons at the mRNA level (Chang, J. H., and Olson, M. O. J. (1989) J. Biol. Chem. 264, 11732-11737). We now report the structure of the complete B23 gene which spans 11-kilobases of DNA and contains 12 exons coding for the 294 amino acid residues. B23.1 mRNA is encoded by exons 1-9, 11, and 12, whereas exons 1-10 code for the B23.2 mRNA. Each exon codes for a relatively short segment of the protein (2-40 amino acid residues). The exons, which are distributed unevenly over the length of the gene, are separated by introns varying in size between 122 base pairs and 2.2 kilobases. Southern blot analyses using a probe derived from the untranslated segment of exon 10 suggests that a single expressed gene is present in the rat genome. Additional genomic clones contained apparent processed pseudogenes for protein B23. Primer extension studies and comparison with a processed pseudogene reveal a probable transcription initiation site at position -96 from the first ATG. The 5' region of the gene contains several possible regulatory elements. Three GC boxes which are potential binding sites for transcription factor Sp1 were found, including one within the first intron. A segment of about 1500 base pairs in the 5' region is unusually rich in the dinucleotide CpG. Although no CCAAT box was found a well-defined TATA box is present at position -126. The latter feature suggests that the B23 gene has some properties of tissue-specific genes in addition to the predominant characteristics of housekeeping genes.

Cloning, sequencing, and expression of a cDNA encoding rat liver mitochondrial carnitine palmitoyltransferase II.

We report the isolation and characterization of a full-length cDNA encoding rat liver carnitine palmitoyltransferase II (CPT II). Beginning with the purified protein CNBr fragments were generated and sequenced. Corresponding oligonucleotides were used to screen a rat liver cDNA library constructed in the plasmid cloning vector, pcDV. The clone ultimately obtained consisted of a 62 nucleotide 5'-untranslated region, a single open reading frame of 1,974 bases predicting a protein of 658 amino acids (Mr = 74,119), and a 3'-untranslated segment of 260 nucleotides followed by the poly (A) tail. The identity of the cDNA was confirmed by the findings that (a) the open reading frame encoded all three peptides found in the original protein; (b) a fourth peptide synthesized from a portion of the deduced amino acid sequence and used to immunize a rabbit resulted in the generation of an antibody that recognized pure CPT II on a Western blot; (c) in vitro transcription and translation of the cDNA (ligated into pBlue-script KS (+] generated a protein that was specifically immunoprecipitated by anti-CPT II antibody and having a Mr slightly greater than that of mature CPT II; (d) transfection of COS cells with the cDNA subcloned into the expression vector, pCMV4, resulted in a 6-fold induction of mitochondrial CPT II catalytic activity. It seems likely that the de novo synthesized enzyme gains entry into the mitochondrion via a targeting peptide that is subsequently cleaved. The mature protein probably associates (relatively loosely) with the inner membrane through a limited number of membrane spanning domains. The predicted amino acid sequence of CPT II shows strong identity with those of two other acyltransferases, namely, rat liver peroxisomal carnitine octanoyltransferase and porcine choline acetyltransferase.

Regulated expression of nuclear protein(s) in myogenic cells that binds to a conserved 3' untranslated region in pro alpha 1 (I) collagen cDNA.

We describe the identification and DNA-binding properties of nuclear proteins from rat L6 myoblasts which recognize an interspecies conserved 3' untranslated segment of pro alpha 1 (I) collagen cDNA. Levels of the two pro alpha 1 (I) collagen RNAs, present in L6 myoblasts, decreased drastically between 54 and 75 h after induction of myotube formation in serum-free medium. Both mRNAs contained a conserved sequence segment of 135 nucleotides (termed tame sequence) in the 3' untranslated region that had 96% homology to the human and murine pro alpha 1 (I) collagen genes. The cDNA of this tame sequence was specifically recognized by nuclear protein(s) from L6 myoblasts, as judged by gel retardation assays and DNase I footprints. The tame-binding protein(s) was able to recognize its target sequence on double-stranded DNA but bound also to the appropriate single-stranded oligonucleotide. Protein that bound to the tame sequence was undetectable in nuclear extracts of L6 myotubes that did not accumulate the two collagen mRNAs. Therefore, the activity of this nuclear protein seems to be linked to accumulation of the sequences that it recognizes in vitro. The collagen RNAs and the nuclear tame-binding proteins reappeared after a change of medium, which further suggests that the RNAs and the protein(s) are coordinately regulated.

Regulated expression of nuclear protein(s) in myogenic cells that binds to a conserved 3' untranslated region in pro alpha 1 (I) collagen cDNA.

We describe the identification and DNA-binding properties of nuclear proteins from rat L6 myoblasts which recognize an interspecies conserved 3' untranslated segment of pro alpha 1 (I) collagen cDNA. Levels of the two pro alpha 1 (I) collagen RNAs, present in L6 myoblasts, decreased drastically between 54 and 75 h after induction of myotube formation in serum-free medium. Both mRNAs contained a conserved sequence segment of 135 nucleotides (termed tame sequence) in the 3' untranslated region that had 96% homology to the human and murine pro alpha 1 (I) collagen genes. The cDNA of this tame sequence was specifically recognized by nuclear protein(s) from L6 myoblasts, as judged by gel retardation assays and DNase I footprints. The tame-binding protein(s) was able to recognize its target sequence on double-stranded DNA but bound also to the appropriate single-stranded oligonucleotide. Protein that bound to the tame sequence was undetectable in nuclear extracts of L6 myotubes that did not accumulate the two collagen mRNAs. Therefore, the activity of this nuclear protein seems to be linked to accumulation of the sequences that it recognizes in vitro. The collagen RNAs and the nuclear tame-binding proteins reappeared after a change of medium, which further suggests that the RNAs and the protein(s) are coordinately regulated.

The laminin B2 chain promoter contains unique repeat sequences and is active in transient transfection.

We previously isolated cDNA clones coding for the entire murine laminin B2 chain. In this report, we have screened a mouse genomic library with a 5' portion of the laminin B2 chain cDNA and isolated two genomic clones which contain the first and second exons. The transcription initiation site was determined by primer extension and S1 nuclease mapping. Exon 1 contained 641 bp (base pairs) including 229 bp of 5'-untranslated segment, sequences coding for the signal peptide and the N-terminal portion of the protein, while exon 2 contained 305 bp. Nucleotide sequencing of 830 bp of the 5'-flanking region of the gene showed several interesting features including the presence of 9 "GC" boxes, a stretch of 9 nearly identical repeats of 11 nucleotides between -200 and -450, and a sequence which is similar to the cAMP consensus sequence. There was no TATA box or CAAT box. A recombinant plasmid containing the 830 bp promoter segment coupled to the chloramphenicol acetyltransferase gene was constructed and transfected into various cells. Differentiated F9 cells transfected with this construct showed twice as much chloramphenicol acetyltransferase activity as the undifferentiated cells. The 830-bp B2 laminin promoter was also active in NIH-3T3 cells which produce little laminin, but was not active in human HT-1080 cells. These results indicate that this structurally unique promoter contains DNA sequences that help regulate the gene during differentiation.

The structure of anchorin CII, a collagen binding protein isolated from chondrocyte membrane.

cDNA clones for anchorin CII (Mr = 34,000), a collagen-binding protein, were isolated from a lambda gt 11 cDNA library prepared from chick cartilage mRNA. Several overlapping clones were characterized which gave rise to an open reading frame coding for 329 residues and a 3'-untranslated segment of 500 base pairs. The clones were identified as coding for anchorin by hybrid select translation analysis and by comparing the deduced amino acid sequence with the sequence of 10 tryptic peptides of the protein. A hydrophobic domain of 25 residues interrupted with 3 polar residues was identified with the carboxyl-terminal portion. There was no evidence for an aminoterminal signal peptide. Northern analysis revealed that the 5' probe hybridizes to a single 1.7-kilobases (kb) mRNA species, whereas the 3' probe hybridizes to two mRNA species of 1.7 kb and 5 kb, which are present in many cells including chondrocytes, crop cells, and fibroblasts. The level of anchorin mRNA in chick embryo fibroblasts was increased by infection with Rous sarcoma virus.

Isolation and characterization of a soybean (Glycine max) lipoxygenase-3 gene

cDNA and genomic DNA clones for a soybean (Glycine max) seed lipoxygenase-3 (lox-3) isozyme have been isolated and characterized by molecular cloning and sequence analysis. The cDNA clone p3H9 was identified as encoding a lipoxygenase isozyme based on hybridization selection and immunoprecipitation assays. The insert from p3H9 was used to screen 700,000 recombinants in a phage genomic library. Two overlapping genomic clones were isolated. After localizing the mRNA coding region to the midportion of one of these clones, nucleotide sequence analysis was performed. The structure of the gene was deduced following the additional cloning and sequencing of nearly full length cDNAs. Primer extension and S1 protection experiments were used to define the 5′ boundary of the gene. The gene is encoded by nine exons interrupted by eight introns. All exon-intron junctions conform to the GT-AG rule. The deduced amino acid sequence consists of 857 amino acids with a molecular weight of 96,663 daltons. The 5′ untranslated segment contains approximately 46 nucleotides before the first methionine (ATG) codon. A typical TATA box occurs some 30 nucleotides upstream of the message start site while a CAAG sequence occurs in place of a CAAT box some 80 nucleotides upstream of the start of transcription. Four polyadenylation signals are present in the 3′ untranslated region. At least two of these are used, giving rise to cDNA clones bearing 3′ untranslated segments of 148 and 196 nucleotides. To identify which member of the lox gene family had been isolated, a gene-specific probe from the 3′ untranslated region of p3H9 was hybridized to dot blots of soybean embryo RNAs derived from lox-1,-2, or-3 null mutants. No hybridization to RNA from the lox-3 null mutant was seen, while the remaining mutant RNAs showed no reduction in hybridization. Further confirmation that the gene encodes a lox-3 isozyme was obtained by a comparison of deduced and determined amino acid sequence data. An analysis of the lox-3 sequence and a comparison to other available soybean lox sequences is also presented.

Molecular analysis of human and rat calmodulin complementary DNA clones. Evidence for additional active genes in these species.

A cDNA clone, lambda rCB1, encoding calmodulin was isolated from a rat brain expression library. The sequence was determined and compared to the structures of the previously described rat genes, lambda SC4 and lambda SC8 (Nojima, H., and Sokabe, H. (1986) J. Mol. Biol. 190, 391-400). Faithful sequence conservation is observed in the coding regions of lambda rCB1 and lambda SC4, the bona fide gene. Both cDNAs encode identical amino acid sequence. Very limited sequence homology, however, is noted in the 3'-untranslated segments of these clones. Surprisingly, when the lambda rCB1 nucleotide structure is compared to the processed intronless gene, lambda SC8, extensive sequence homology is found both in the coding and noncoding regions. The inferred protein sequences of lambda SC8 and lambda rCB1, however, are divergent. Using a fragment of lambda rCB1 to screen an expression library derived from a human embryonic cell line, a calmodulin cDNA clone, lambda hCE1, was isolated and characterized. Comparison of the sequence of lambda hCE1 to the cDNA from human liver, hCWP (Wawrzynczak, E. J., and Perham, R. N. (1984) Biochem. Int. 9, 177-185), reveals substantial structural divergence. Strikingly poor homology is seen in the 5'- and 3'-noncoding segments, but the coding regions were 85% homologous. Both lambda hCE1 and hCWP encode proteins of identical primary structure which is equivalent to the protein sequence deduced from lambda rCB1 and lambda SC4. Taken together these results suggest the existence of an additional actively transcribed calmodulin gene, not previously identified, in each of the human and rat genomes. Transcripts of lambda rCB1 and lambda hCE1 were observed in all tissues examined indicating the absence of tissue-specific expression. Calmodulin gene polymorphisms were detected using TaqI, HindIII, and MspI.