Cloning of cDNA for the bovine IL-2 receptor (bovine Tac antigen).

We have cloned the Tac analog of the bovine IL-2 receptor (IL-2R) cDNA. Using mouse and human cDNA probes, we isolated five bovine IL-2R clones from a lambda gt11 bovine long-term lymphocyte cDNA library. Three of the clones had inserts of 2600 base pairs (bp), the same size as the bovine IL-2R mRNA visualized on Northern blots. The full-length cDNA contain a 190-bp 5' untranslated region, followed by a 825-bp coding region, and a 3' untranslated region that contain 1600 bp. Comparison of the bovine and human IL-2R-coding sequences revealed 71% homology at the nucleotide level. The 3' and 5' non-coding regions were not as homologous, apart from a specific site in the 5'-untranslated region that contained a 5'-upstream start codon. In this region, 24 of 26 nucleotides were identical for the human and bovine cDNAs. Further analysis of the bovine IL-2R sequence also revealed the following: (i) the hydrophobic domains of the IL-2R protein were more conserved between species than the hydrophilic domains, (ii) the predominant site of intracellular IL-2R phosphorylation in mouse and human was a conserved Ser which was not conserved in the bovine sequence, and (iii) there exists a statistically significant amino acid homology with the AIDS gag protein.     

cDNA clones coding for the complete murine B chain of complement Clq: nucleotide and derived amino acid sequences

We have isolated cDNA clones covering the complete B chain of the complement subunit Clq from mouse; this subunit initiates the classical complement pathway. Deoxynucleotide sequence analysis shows that these clones contain 156 nucleotides of the 5' untranslated region, followed by sequences coding for the 25 amino acids of the signal peptide; all of the 228 amino acids of the mature protein; and 140 nucleotides of the 3' untranslated region, including a poly A additional signal. The coding region for the mature protein contains 261 nucleotides for the Gly-X-Y repeat and 408 nucleotides for the globular portion of Clq. By comparing the nucleotide sequence of the mouse B chain of Clq with the human B chain (Reid, K.B.M., 1985, Biochem. J. 231, 729), we find a high homology (80%) within the mature protein, a lower homology within the signal peptide (59%) and the 3' untranslated region (47%) and no homology (26%) in the 5' untranslated region.     

cDNA clones coding for the complete murine B chain of complement C1q: nucleotide and derived amino acid sequences

We have isolated cDNA clones covering the complete B chain of the complement subunit C1q from mouse; this subunit initiates the classical complement pathway. Deoxynucleotide sequence analysis shows that these clones contain 156 nucleotides of the 5' untranslated region, followed by sequences coding for the 25 amino acids of the signal peptide, all of the 228 amino acids of the mature protein and 140 nucleotides of the 3' untranslated region, including a poly A addition signal. The coding region for the mature protein contains 261 nucleotides for the Gly-X-Y repeat and 408 nucleotides for the globular portion of C1q. By comparing the nucleotide sequence of the mouse B chain of C1q with the B chain from human (Reid, K. B. M., 1985, Biochem. J. 231, 729), we find a high homology (80%) within the mature protein, a lower homology within the signal peptide (59%) and the 3' untranslated region (47%) and no homology (26%) in the 5' untranslated region.     

Complete nucleotide sequence of the mRNA coding for the N protein of vesicular stomatitis virus (New Jersey serotype)

The nucleotide sequence of the mRNA encoding the nucleocapsid protein of the New Jersey serotype (Ogden strain) of vesicular stomatitis virus (VSV) was determined from two overlapping cDNA clones spanning almost entirely the coding region of the mRNA. The 5'-terminal noncoding sequence present in the mRNA but not in the cDNA clones was determined from a primer extended to the 5' terminus of the mRNA. The mRNA is 1329 nucleotides long (excluding polyadenylic acid) and encodes a protein of 422 amino acids. The nucleotide sequence was compared with the previously determined nucleotide sequence of the nucleocapsid protein of the Indiana serotype. An overall identity of 67.7% was found between the two serotypes. The only place where insertions and/or deletions have occurred during the evolution of the two viral genes from their presumed common ancestor is in the untranslated region. The nonidentical nucleotides are distributed throughout the length of the mRNA although not in an entirely random manner. The predicted amino acid sequence demonstrates that both proteins are initiated from the initiator codon located at the same distance from the 5' end (nucleotides 14 to 16) and contain the same number of amino acids. An overall identity of more than 80% of the amino acid sequence was observed between the two proteins when conservative replacements of amino acids were considered.     

Nucleotide sequence of the 3' terminal region of plum pox potyvirus RNA

The nucleotide sequence of the 3' terminal 2854 nucleotides of plum pox virus RNA has been determined. There is an open reading frame of 2634 nucleotides upstream from a 220 nucleotide 3' non-coding region followed by a long poly(A) tail. The gene coding for the capsid protein has been mapped adjacent to the 3' non-coding region. The predicted capsid protein is originated by a Gln-Ala cleavage and consists of 330 amino acids; the central and carboxy terminal, but not the amino terminal regions present high sequence similarity with other potyviral capsid proteins. A truncated capsid protein which is present in purified preparations of plum pox virus is originated by a Gln-Thr cleavage and contains the 260 carboxy terminal amino acids of the capsid protein. The predicted plum pox virus RNA-dependent RNA polymerase, 518 amino acids long, has been localized at the 5' end of the open reading frame.     

Both α-tubulin genes are transcriptionally active in Stylonchyia lemnae

Macronuclear DNA of the hypotrichous ciliate Stylonychia lemnae contains two size-classes of molecules coding for alpha-tubulin. Analysis of their coding regions demonstrates that these two size-classes represent two different functional alpha-tubulin genes, alpha 1 and alpha 2; a comparison of these regions shows a 97% homology in their nucleotide sequence and 98.5% in their amino acid sequence. S1-mapping experiments indicate that both alpha 1- and alpha 2-tubulin genes are transcribed. The 5' and 3' noncoding regions flanking the alpha 1- and alpha 2-tubulin genes differ in both length and nucleotide sequence within one strain. When different strains are compared, however, identical non-coding regions and slightly varying coding regions can be found in DNA molecules containing the alpha 1-tubulin genes.     

Deletion of the C-terminal end of aspartylgiucosaminidase resulting in a lysosomal accumulation disease: evidence for a unique genomic rearrangement

Aspartyiglucosaminuria (AGU) is an inborn error of glycoproteincatabolism and represents the only known human deficiency ofan amidase, aspartyiglucosaminidase (AGA, EC 3.5.1.26 [EC] ). We reporthere a detailed characterization of a unique 2 kb deletion ofthe AGA gene in a North American AGU patient. To facilitatethe characterization of the deletion, genomic lamda clones spanningthe 3' flanking region of human AGA were isolated and sequenced.The breakpoint of the deletion was determined from the patient'sDNA by sequencing the genomic region containing the novel junction.The rearrangement involved a nonhomologous recombination withonly 2 bp of homology at the deletion breakpoint. The deletion's5' breakpoint was located in the last intron of AGA, thus abolishingthe normal C-terminal exon. This is in contrast to our previousfindings indicating that the deletion in the AGA gene wouldcontain only the complete 3' untranslated region and leave thecoding region intact (1). The unique feature of this deletionis a triplication of 19 thymidine nucleotides of an invertedAlu repeat, which is located at the deletion 3' breakpoint.The analysis of the patient's AGA cONA revealed an open readingframe containing a novel C-terminal exon, coding for a 64 aminoacid sequence, which has no homology to the normal exon 9 ofAGA. This new exon has a functional splice acceptor site atits 5' end, a stop codon, and a polyadenylation signal at the3' end. Expression of the mutant AGA cDNA in COS cells showedthat mutant mRNA is synthesized in equal amounts compared withnormal. However, the mutant polypeptide precursor is not processedinto the mature subunits of AGA, and is totally degraded within24 h of synthesis.     

Nucleotide and deduced amino acid sequence of the 3′ end of the BYMV-MI genome

Summary We have cloned and sequenced cDNA transcribed from the 3 1239 nucleotides of the genomic RNA of a Western Australian isolate (MI) of bean yellow mosaic potyvirus (BYMV). This sequence contains 246 nucleotides of the NIb (replicase) gene and 819 nucleotides representing the entire coding region of the viral coat protein gene, followed by a 3 non-coding region of 174 nucleotides. The coding region of the coat protein gene is identical in length (273 amino acids) to that already reported for other isolates of this virus. The sequence identities obtained for BYMV-MI and published sequences of BYMV isolates range between 85% and 92% for the coding region of the coat protein and 90% to 98% for the 3 non-coding region. Likewise, the region of the NIb gene sequenced shows 99% and 97% sequence identity in the deduced amino acid and the nucleotide sequences, respectively.     

Molecular cloning of hepatitis C virus genome from a single Japanese carrier: sequence variation within the same individual and among infected individuals.

A hepatitis C virus (HCV) genome was isolated and sequenced from a single Japanese patient with chronic non-A, non-B hepatitis. The genome (HCV-JT), which was constructed with 23 cDNA clones, consisted of 9436 nucleotides with a long open reading frame which could encode a sequence of 3010 amino acid residues. To study the sequence variation of the HCV genome in an individual, we analyzed another sequence of the HCV genome (HCV-JT') constructed with different cDNA clones derived from the same patient. The nucleotide variation between HCV-JT and -JT' was less than 1%, and was distributed throughout the genome except in the 5' non-coding region, where no variation was observed. The diversity was higher (1.6%) in the putative envelope protein region than in other regions. The nucleotide and deduced amino acid sequences of HCV-JT showed homologies of about 91 and 95%, respectively, with those of other Japanese HCV isolates. The nucleotide diversity was high in the gp 70 region (corresponding to the NS 1 region of flaviviruses) and low in the 5' non-coding and p22 (putative core protein) regions. A similar pattern of distribution of nucleotide changes was observed on comparison of HCV-JT with an American isolate HCV-US, where the homologies in nucleotide and amino acid sequences were about 79 and 85%, respectively. Base transversions contributed about 50% of the total base exchanges between the Japanese and American HCV sequences, but only 20% or less of those among Japanese HCV or among American HCV sequences. Thus, the Japanese and American HCVs are genetically distinguishable, supporting our earlier prediction that these two HCVs could be classified as different subtypes.     

Major sperm protein genes from Onchocerca volvulus

Nematode spermatozoa, unlike their mammalian counterparts, are nonflagellated crawling cells. The pseudopod of these cells contains the major sperm protein (MSP) which comprises more than 15% of the protein in the sperm. MSP is presumed to function as a cytoskeletal element involved in motility. An Ascaris MSP cDNA sequence was used as a probe to identify and isolate Onchocerca volvulus MSP clones from a lambda gt11 genomic library. Two clones, OVGS-1 (765 bp) and OVGS-2 (1765 bp), were characterized by restriction endonuclease mapping and sequence analysis. Both genomic clones contain MSP protein coding regions of 99 and 282 bp separated by an intervening sequence of 153 bp. The genes OVGS-1 and OVGS-2 are 95% similar in nucleotide sequence in the protein coding regions, but only 79% similar in their intron sequences. A number of potential regulatory sequences in the flanking regions and at the exon/intron junctions of the O. volvulus MSP genes are in good agreement with consensus sequences in other eukaryotic cells. The nucleotide sequence of the O. volvulus MSP genes were over 80% similar to the Ascaris MSP cDNA sequence and 79% similar to the Caenorhabditis MSP-3 cDNA. The predicted amino acid sequence of the O. volvulus MSPs were 96% similar to each other, 90-91% similar to Ascaris MSP and 81-82% similar to Caenorhabditis MSP-3. These results offer evidence that the MSP sequences have been highly conserved throughout nematode evolution but are variable in their genomic organization and the presence of introns.     

Rat complement factor H: molecular cloning,sequencing and quantification with a newly established ELISA

Factor H (FH) is the predominant soluble regulatory protein of the complement system. With a concentration of 300-600 microg/ml in human plasma it acts as a cofactor for the FI-mediated cleavage of the component C3b to iC3b. Furthermore, it competes with factor B for binding to C3b and C3(H2O) and promotes the dissociation of the C3bBb complex (i.e. it has decay accelerating activity). FH is a monomer of about 155 kDa which comprises 20 short consensus repeats (SCR), each of which is composed of nearly 60 amino acid residues. For the screening of a rat liver cDNA library, we used two hybridization probes which had been produced by polymerase chain reaction (PCR). The probes were generated using degenerated primers which corresponded to conserved parts of the human and the murine factor H nucleotide sequences. The entire rat sequence spanned 4240 nucleotides with an open reading frame of 3708 nucleotides. These were preceded by 23 nucleotides of the 5' untranslated region, followed by a stop codon and a 3' untranslated region of 478 nucleotides including the polyadenylation-signal up to the beginning of the poly A tail. Comparison of the rat cDNA-derived coding sequence revealed identities of 74% to the human and 87% to the mouse FH nucleotide sequence. The translation product of rat FH mRNA was 1236 aa in length (leader sequence included) with an identity of 63% to the human and 81.5% to the murine protein. The degree of glycosylation of rat FH-Mr is about 9.5%. To quantitate FH in rat serum and supernatants of primary cultures of rat hepatocytes (HC), a reliable and sensitive sandwich-enzyme-linked immunosorbent assay (ELISA) was established. The concentration of FH in rat serum was calculated to be 238 microg +/- 21 microg/ml (mean +/- SD). Its concentration in the culture supernatants of HC was upregulated about three-fold by interferon (IFN)-gamma (100 U/ml).     

Structure and chromosomal localization of the human 2',3'-cyclic nucleotide 3'-phosphodiesterase gene

Human brain cDNA clones for the myelin associated enzyme 2' 3' -cyclic nucleotide 3' -phosphodiesterase (CNPase) have been isolated and sequenced. The only 5' untranslated region (UTR) sequence found was that of a human CNPII mRNA, with no direct evidence for a CNPI mRNA. Human CNPase cDNAs were used to isolate genomic clones containing the human CNPase gene which is 9 kb long. Four exons were identified, separated by three introns, and the sequence of each exon and intron/exon boundary has been established.
The polymerase chain reaction (PCR) was used to detect the presence of the human CNPase gene in DNA from a panel of rodent/human somatic cell hybrids. By this means the human CNPase gene was mapped to chromosome 17. In situ hybridization of a human CNPase genomic clone to metaphase chromosomes further localized this gene to chromosomal band 17q21.     

Two species of the phosphoprotein mRNA with differently edited reading frames discovered in measles virus infected Vero cells. Brief report

One cDNA clone representing the phosphoprotein mRNA sequence of the Edmonston strain of measles virus contained 4 G nucleotides at a particular position. Two other clones contained 3 G nucleotides at the same position. Otherwise the nucleotide sequence were identical. The mRNA with 3 G nucleotides codes for the 70 kD phosphoprotein. The mRNA with 4 G nucleotides may code for a putative new peptide with 231 aminoterminal amino acids in common with the P protein whereas the 68 carboxyterminal amino acids are different from any amino acid sequence of the phosphoprotein. Thus the consequence of the insertion of one additional G is a translational shift to a shorter open reading frame. There are several indications that the observation is of biological significance.