Degenerate Oligonucleotide Probes Research Articles

Characterization of a human cDNA that encodes a functional receptor for platelet activating factor

We have cloned a cDNA for the platelet activating factor (PAF) receptor by screening an HL-60 granulocyte cDNA library with degenerate oligonucleotide probes based on conserved sequences of rhodopsin-type receptors. The 342-amino acid receptor contains 7 putative transmembrane domains, but lacks sites for N-linked glycosylation at the N-terminus. Stably transfected fibroblasts expressing the cloned cDNA responded to sub-nanomolar PAF stimulation with calcium mobilization, which could be inhibited by the PAF antagonist L-659,989. The PAF receptor message was detected as a single species of approximately 4 kb in human placenta, lung, and differentiated HL-60 granulocytes. Expression of the cloned cDNA in undifferentiated HL-60 cells devoid of endogenous PAF receptor resulted in specific and saturable binding of the PAF antagonist WEB 2086 with a dissociation constant of 30.7 nM.

Isolation and molecular characterization of the swinepox virus thymidine kinase gene

Swinepox virus (SPV), the only member of the Suipoxvirus genus, shows little antigenic relatedness or DNA homology to members of the other poxvirus genera. A SPV thymidine kinase (TK) gene was detected and mapped to the left end of the HindIII G fragment using degenerate oligonucleotide probes. Cloning and sequencing of a 1.8-kb HindIII- BamHI fragment containing the SPV TK gene revealed an open reading frame (ORF) of 181 amino acids yielding a predicted polypeptide of M r 20.6 kDa with significant homology to both poxvirus and vertebrate thymidine kinases. Comparison with other TK protein sequences showed that the SPV thymidine kinase was closely related to the TK genes from members of the ortho-, capri-, and leporipoxviruses (63.1–68.2% amino acid identity) and less so to the TK genes of avipoxviruses (52.0%) and vertebrates (57.1–59.7%). The TK gene from African swine fever virus (ASF) showed little homology (30.5%) to the SPV TK gene suggesting that these two viruses are not closely related though they share many biochemical features and infect a single, common mammalian host (swine). The SPV TK gene, like that of other poxviruses, is transcribed early, and when cloned into a TK − strain of vaccinia converted the virus to a TK + phenotype. BUdR R mutants of SPV contained frameshift, deletion, and missense mutations in the TK ORF.

A fission-yeast gene encoding a protein with features of protein-tyrosine-phosphatases.

Degenerate oligonucleotide probes encoding sequences conserved among mammalian protein-tyrosine-phosphatases (PTPases) were used to amplify DNA fragments from a Schizosaccharomyces pombe cDNA library by polymerase chain reaction (PCR) methods. A cloned PCR product predicted peptide sequences similar to those found in PTPases but not identical to any published sequences. A S. pombe gene, designated pyp1+, was identified in a cDNA library with this PCR probe, cloned, and sequenced. The sequence of the gene predicted a 550-amino acid protein with Mr 61,586, which includes amino acid sequences that are highly conserved in mammalian PTPases. Disruption of the pyp1+ gene resulted in viable cells. Overexpression of the pyp1+ gene in S. pombe permitted detection of a protein of apparent Mr 63,000.

Isolation, cloning, mapping, and nucleotide sequencing of the gene encoding flavodoxin in Escherichia coli

The flavodoxins constitute a highly conserved family of small, acidic electron transfer proteins with flavin mononucleotide prosthetic groups. They are found in prokaryotes and in red and green algae, where they provide electrons at low potentials for the reduction of nitrogen by nitrogenase, for the light-dependent reduction of NADP+ in photosynthesis, and for the reduction of sulfite. Proteins with the physical characteristics of flavodoxins have been implicated in the reductive activation of pyruvate formate-lyase and cobalamin-dependent methionine synthase in Escherichia coli. We have purified flavodoxin to homogeneity from E. coli, determined its N-terminal amino acid sequence, and used this sequence to construct a 64-fold degenerate oligonucleotide probe for the flavodoxin gene. Because the phenotype of a flavodoxin mutant is not known, we used this degenerate probe to screen the phages of the Kohara library and identified two phages, with inserts mapping at approximately 16 min, that hybridized to the probe. The flavodoxin gene, designated fldA, was subcloned from the DNA in the overlap region of these two clones. The deduced amino acid sequence, determined by nucleotide sequencing of the flavodoxin gene, shows strong homology with flavodoxins from nitrogen-fixing bacteria and cyanobacteria. The fldA gene maps at 15.9 min on the E. coli chromosome and is transcribed in a counterclockwise direction.

Borrowed proteins in bacterial bioluminescence.

A library of Photobacterium phosphoreum DNA was screened in lambda 2001 for the lumazine protein gene, using two degenerate 17-mer oligonucleotide probes that were deduced from a partial protein primary sequence. The lumazine protein gene was localized to a 3.4-kilobase BamHI/EcoRI fragment in one clone. The fragment contained an open reading frame, encoding a 189-residue protein, that had a predicted amino acid sequence that concurred with the partial sequence determined for lumazine protein. Considerable sequence similarity was detected between lumazine protein, the yellow fluorescence protein from Vibrio fischeri, and the alpha subunit of riboflavin synthetase (EC 2.5.1.9). A highly conserved sequence in lumazine protein corresponds to the proposed lumazine binding sites in the alpha subunit of riboflavin synthetase. Several secondary structure programs predict the conformation of this site in lumazine protein to be a beta-sheet. A minimal model with three interactions between the ligand and this beta-sheet structure is proposed, which is consistent with the results of NMR and ligand binding studies.

Expression and characterization of the thymidine kinase gene of African swine fever virus

The thymidine kinase (TK) gene of African swine fever virus (ASFV) was located within the viral genome by using two degenerate oligonucleotide probes derived from sequences of the vaccinia virus and cellular TK genes. The TK gene was mapped within a 0.72-kbp BglII-XhoI fragment (0.242 to 0.246 map units) derived from a 23.9-kbp SalI-B fragment of the ASFV genome. Identification of this region as the ASFV TK gene was confirmed by expression of TK in Escherichia coli and by the synthesis of active TK in a cell-free system programmed with RNA synthesized in vitro. The sequenced gene for TK includes an open reading frame of 588 nucleotides encoding a protein of 196 amino acids. The deduced amino acid sequence shows 32.4% identity with the TK of vaccinia virus.

Identification and sequencing of theChoristoneura biennisentomopoxvirus DNA polymerase gene

A degenerate oligonucleotide probe corresponding to a highly conserved amino acid sequence in several DNA polymerases was used to locate the DNA polymerase gene in the Choristoneura biennis entomopoxvirus. Southern blot analysis of the entomopoxvirus genome using the degenerate oligonucleotide probe showed specific interaction between the probe and an eight kilobasepair EcoRI fragment from the entomopoxvirus genome. Sequencing this EcoRI fragment revealed an open reading frame 2892 nucleotides in length, capable of encoding a protein about 115 kilodaltons. Homology search of this open reading frame against other proteins indicated a high degree of homology in four distinct regions with DNA polymerases from other organisms. The highest degree of homology (24.9% at the amino acid level) was found between the vaccinia DNA polymerase gene and the entomopoxvirus open reading frame.

Cloning of the cDNA encoding an RNA regulatory protein--the human iron-responsive element-binding protein.

Iron-responsive elements (IREs) are stemloop structures found in the mRNAs encoding ferritin and the transferrin receptor. These elements participate in the iron-induced regulation of the translation of ferritin and the stability of the transferrin receptor mRNA. Regulation in both instances is mediated by binding of a cytosolic protein to the IREs. High-affinity binding is seen when cells are starved of iron and results in repression of ferritin translation and inhibition of transferrin receptor mRNA degradation. The IRE-binding protein (IRE-BP) has been identified as an approximately 90-kDa protein that has been purified by both affinity and conventional chromatography. In this report we use RNA affinity chromatography and two-dimensional gel electrophoresis to isolate the IRE-BP for protein sequencing. A degenerate oligonucleotide probe derived from a single peptide sequence was used to isolate a cDNA clone that encodes a protein containing 13 other sequenced peptides obtained from the IRE-BP. Consistent with previous characterization of the IRE-BP, the cDNA encodes a protein of 87 kDa with a slightly acidic pI, and the corresponding mRNA of approximately 3.6 kilobases is found in a variety of cell types. The encoded protein contains a nucleotide-binding consensus sequence and regions of cysteine and histidine clusters. This mRNA is encoded by a single gene on human chromosome 9, a finding consistent with previous localization by functional mapping. The protein contains no previously defined consensus motifs for either RNA or DNA binding. The simultaneous cloning of a different, but highly homologous, cDNA suggests that the IRE-BP is a member of a distinct gene family.

Cloning and expression of eukaryotic initiation factor 4B cDNA: sequence determination identifies a common RNA recognition motif.

Eukaryotic protein synthesis initiation factor 4B (eIF-4B) is an 80,000 dalton polypeptide which is essential for the binding of mRNA to ribosomes. A highly purified preparation of eIF-4B from HeLa cells was subjected to enzymatic cleavage and amino-terminal amino acid sequence analysis. Degenerate oligonucleotide probes were used to isolate a 3851 bp cDNA encoding eIF-4B from a human cDNA library. The DNA encodes a protein comprising 611 residues with a mass of 69,843 daltons. The amino-terminal domain of eIF-4B contains a consensus RNA binding domain present in a number of other RNA binding proteins. Expression of eIF-4B in transfected COS-1 cells yielded a polypeptide which reacted with anti-eIF-4B antiserum and comigrated with purified eIF-4B. Expression of eIF-4B in COS-1 cells resulted in a general inhibition of translation, possibly due to a 50-fold eIF-4B overproduction.

Characterization of a beta subunit of the gastric H+/K(+)-transporting ATPase.

The catalytic subunit of the H+/K(+)-transporting ATPase (EC 3.6.1.3) has 62% identity to the alpha, or catalytic subunit, of the Na+/K(+)-transporting ATPase (EC 3.6.1.37); however, a homologous beta subunit was unknown until recently. Removal of the carbohydrate from purified hog H+/K(+)ATPase vesicles reveals a 35-kDa peptide that, when fragmented with protease V8, gives sequences homologous to both beta 1 and beta 2 subunits of the Na+/K(+)-ATPase. cDNA clones for a beta subunit of the gastric H+/K(+)-ATPase were isolated from a rabbit stomach cDNA library by using degenerate 17-mer oligonucleotide probes made to the protease V8-treated peptides. An open reading frame (54-926) encodes a predicted 291-amino acid peptide with Mr = 33,320, which exhibits 31% and 44% homologies to the Na+/K+)-ATPase beta 1 and Na+/K(+)-ATPase beta 2 proteins, respectively. A Kyte-Doolittle hydropathy plot predicts a single N-terminal transmembrane domain with a small hydrophobic region near the C terminus. The presumed extracytosolic domain contains seven potential N-linked glycosylation sites and six out of nine cysteines. Northern (RNA) blot analysis of stomach RNA with the rabbit H+/K(+)-ATPase beta probe identifies a single mRNA of 1.3-1.5 kilobases, similar in concentration to the alpha subunit mRNA. The presence of a defined gastric H+/K(+)-ATPase beta subunit extends the homology between H+/K(+)-ATPase and the Na+/K(+)-ATPase subclass of phosphoenzyme transport ATPases and distinguishes them from the monomeric Ca2+ and proton pump subclasses.

Sequence and evolutionary relationships of African swine fever virus thymidine kinase

The thymidine kinase gene of African swine fever virus was mapped in a 1.4-kb EcoRl- PstI fragment located in the left half of the EcoRI K fragment of African swine fever virus DNA by using degenerate oligonucleotide probes derived from regions of the thymidine kinase sequence conserved in several poxviruses, man, mouse, and chicken. The nucleotide sequence of this region revealed an open reading frame of 196 codons, whose translated amino acid sequence showed significant similarity to the thymidine kinases of vaccinia virus, variola virus, monkeypox virus, shope fibroma virus, fowlpox virus, capripox virus, man, mouse, and chicken. The similarity scores obtained after comparison of known thymidine kinase sequences indicated that the African swine fever virus thymidine kinase is more distantly related than the poxvirus thymidine kinases to their cellular homologs. The evolutionary implications of these findings are discussed.

Analysis of naturally occurring deletion variants of african swine fever virus: Multigene family 110 is not essential for infectivity or virulence in pigs

A comparison of uncloned African swine fever virus isolates with their cloned counterparts revealed the presence of genetic variants in three out of seven uncloned field virus populations tested. Five different virus clones were isolated from the uncloned KIR69 virus stock by limit dilution. Structural analysis of the variants showed that they differed by single deletions of 10–16 kilobases in the region located between 6.8 and 27 kilobases from the left DNA terminus. There was no homology between DNA sequences immediately to the left and right of the deletions indicating that the mechanism generating deletion variants was not homologous recombination. The alignment of the restriction maps of the variants with those of other virus isolates indicated that two of the variants lacked the whole multigene family 110. This was confirmed by hybridization of the viral DNA with a degenerate oligonucleotide probe. Each virus variant replicated to high titer and was virulent in domestic pigs. Therefore, the multigene family 110 was not required for viral replication or virulence in domestic pigs. The virus variants were stable upon repeated passage in swine macrophages, indicating that the generation of variants is not a frequent genetic event in vitro.

Isolation, Characterization, and Mapping of a Human Acid β-Galactosidase cDNA

A lambda gt11 human testicular cDNA library was screened with degenerate oligonucleotide probe mixtures based on amino acid sequence data generated from cyanogen bromide fragments and tryptic fragments of purified human beta-galactosidase. Six positive clones were identified after screening 2 x 10(6) plaques. The sequences of these six clones were determined and found to be derived from two different cDNAs. The sequence of the longest of these cDNAs is nearly identical to that recently determined by Oshima et al. (1988). It codes for a 76-kD protein and all 11 peptides that were generated from the purified enzyme. The second clone is shorter by 393 bp in the central portion of the coding region. Analysis by Northern blotting revealed the presence of a single mRNA species of 2.45 kb in lymphoblasts and testicular tissue. It is deduced from the amino acid sequence data that proteolytic processing of the precursor form of beta-galactosidase must occur by cleavage in the carboxy-terminal portion of the polypeptide perhaps around amino acid 530 at a uniquely hydrophilic sequence. Using a probe generated from the 3' region of the cDNA, we have mapped the locus coding for human beta-galactosidase to chromosome 3p21-3pter.

Putative N-terminal sequence of murine soluble immune response suppressor (SIRS): significant homology with short neurotoxin 1

Soluble immune response suppressor (SIRS) is a low-molecular-weight protein (approximately 10,000 daltons) produced by mitogen- or interferon-activated T lymphocytes that can block development of humoral or cell-mediated immune responses in vivo or in vitro. As previously reported, murine SIRS is heterogeneous, eluting in two broad peaks on high performance reverse phase chromatography as well as displaying several broad isoelectric point forms. A putative N-terminal 21 amino acid sequence has been obtained for one of the less hydrophobic isoforms, SIRS-alpha 7. The sequence of SIRS-alpha 7 is unique in mammals but shows a remarkable homology to the family of short neurotoxins (short neurotoxin 1) found in sea snake, adder, and cobra species. A degenerate oligonucleotide probe based on the protein sequence was synthesized and was shown to hybridize to SIRS messenger RNA as measured by SIRS synthesis in a rabbit reticulocyte lysate system. A synthetic polypeptide based on the 21-residue sequence was also prepared and coupled to thyroglobulin or keyhole limpet hemocyanin. These were used to prepare rabbit antisera that neutralize SIRS bioactivity and precipitate authentic SIRS.

Cloning and Sequencing of a Complementary Deoxyribonucleic Acid Coding for a Bovine αs1-Casein A from Mammary Tissue of a Homozygous B Variant Cow

A cDNA clone for bovine αs1-casein variant A was isolated from a mammary gland cDNA library using a synthetic degenerate oligonucleotide probe. The largest Pst I insert containing an EcoR I site was sequenced. It contained 1090 base pairs, 47 in the 5′ noncoding region, 603 in the coding region and 440 in the 3′ noncoding region. The nucleotide sequence was compared with three published cDNA sequences for αs1-casein variant B. The most obvious difference was the absence of the 39 bases encoding the 13 amino acids that are present in die B variant but absent from the A variant. In addition, five other single base positions differed within individual codons among the four sequences at the third base for each codon, but this did not change the amino acids encoded. There were, however, a number of differences found in the 3′ noncoding region. The isolated cDNA was subjected to site-directed mutagenesis to replace a Val-Ile dipeptide with Phe-Phe to increase the chymosin sensitivity of the protein. When the milk proteins from mammary gland tissue extracts were typed, the αs1-casein A gene product was not detected.

Identification of the thymidine kinase gene of feline herpesvirus: use of degenerate oligonucleotides in the polymerase chain reaction to isolate herpesvirus gene homologs.

Feline herpesvirus 1 (FHV) is the causative agent of viral rhinotracheitis in cats. Current vaccination programs employing attenuated live and killed FHV vaccines have been effective in reducing the incidence of this disease. As an initial step in the development of recombinant FHVs for use in the vaccination of cats, we have identified the thymidine kinase (TK) gene of this feline-specific alphaherpesvirus. Comparisons of the amino acid sequences of other herpesvirus TK proteins have shown that these proteins are highly divergent, sharing only short regions of imperfect amino acid identity. We have used the polymerase chain reaction method of DNA amplification to increase the specificity associated with the use of short, highly degenerate oligonucleotide probes derived from regions of imperfect amino acid conservation. These methods were used to isolate the TK gene of FHV and should prove to be useful in the identification of new members of other viral and cellular gene families. A recombinant FHV bearing a deletion in the identified TK gene was constructed and shown to possess the expected TK- phenotype. The FHV TK gene is located at a position of approximately 40% in the long unique component of the FHV genome. The location of the TK gene and the location and orientation of flanking FHV genes, homologs of herpes simplex virus type 1 UL24 and UL22, are conserved among alphaherpesviruses.

GABAA receptor beta subunit heterogeneity: functional expression of cloned cDNAs.

Cloned cDNAs encoding two new beta subunits of the rat and bovine GABAA receptor have been isolated using a degenerate oligonucleotide probe based on a highly conserved peptide sequence in the second transmembrane domain of GABAA receptor subunits. The beta 2 and beta 3 subunits share approximately 72% sequence identity with the previously characterized beta 1 polypeptide. Northern analysis showed that both beta 2 and beta 3 mRNAs are more abundant in the brain than beta 1 mRNA. All three beta subunit encoding cDNAs were also identified in a library constructed from adrenal medulla RNA. Each beta subunit, when co-expressed in Xenopus oocytes with an alpha subunit, forms functional GABAA receptors. These results, together with the known alpha subunit heterogeneity, suggest that a variety of related but functionally distinct GABAA receptor subtypes are generated by different subunit combinations.

Cloning and Sequence Analysis of a Rat Liver cDNA Encoding Acyl-peptide Hydrolase

Acyl-peptide hydrolase catalyzes the removal of an N alpha-acetylated amino acid residue from an N alpha-acetylated peptide. Two overlapping degenerate oligonucleotide probes based on the sequence of a CNBr tryptic peptide, derived from purified rat acyl-peptide hydrolase, were synthesized and used to screen a rat liver lambda gt11 cDNA library. A 2.5-kilobase cDNA was cloned and sequenced. This clone contained 2364 base pairs of rat acyl-peptide hydrolase sequence but lacked a translational initiation codon. Using a 220-base pair probe derived from near the 5'-end of this almost full-length cDNA to rescreen the library, full-length clones were isolated, which contained an in-frame ATG codon at nucleotides 6-8 and encoded the NH2-terminal sequence, Met-Glu-Arg-Gln.... The DNA sequence encoded a protein of 732 amino acid residues, 40% of which were confirmed by protein sequence data from 19 CNBr or CNBr tryptic peptides. The isolated enzyme is NH2-terminally blocked (Kobayashi, K., and Smith, J. A. (1987) J. Biol. Chem. 262, 11435-11445), and based on the NH2-terminal protein sequence deduced from the DNA sequence and the sequence of the most NH2-terminal CNBr peptide, it is likely that the NH2-terminal residue is an acetylated methionine residue, since such residues are frequently juxtaposed to glutamyl residues (Persson, B., Flinta, C., von Heijne, G., and Jornvall, H. (1985) Eur. J. Biochem. 152, 523-527). The RNA blot analysis revealed a single message of 2.7 kilobases in various rat tissues examined. Although this enzyme is known to be inhibited by diisopropyl fluorophosphate and acetylalanine chloromethyl ketone (Kobayashi, K., and Smith, J. A. (1987) J. Biol. Chem. 262, 11435-11445), no strong similarity in protein sequence has been found with other serine proteases. This result suggests that acyl-peptide hydrolase may be a unique serine protease.

Two putative protein-tyrosine kinases identified by application of the polymerase chain reaction.

The pivotal role that protein-tyrosine kinases (PTKs) play in the growth regulation of eukaryotic cells is manifest in the frequent appearance of members of the PTK family as growth factor receptors or as the transforming agents of acutely transforming retroviruses. A feature common to all members of the PTK family is a highly conserved catalytic domain which is characteristic of the group as a whole and whose activity appears to be tightly regulated within the cell by other domains of the PTK. Degenerate oligonucleotide probes corresponding to two invariant amino acid sequence motifs within the catalytic domains of all PTK family members were synthesized and employed in the polymerase chain reaction (PCR) to amplify cDNA sequences between them. An M13 PCR library was produced in this way from cDNA prepared against mRNA from the murine hemopoietic cell line FDC-P1. The PCR library was then screened by DNA sequencing for PTK-related sequences. Two sequences were identified that, on the basis of sequence comparison with known PTKs, may encode representatives of a new class of PTK.

5-Carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenases of Escherichia coli C and Klebsiella pneumoniae M5a1 show very high N-terminal sequence homology

5-Carboxymethyl-2-hydroxymuconic semialdehyde (CHMS) dehydrogenase from Escherichia coli C and Klebsiella pneumoniae M5a1 have been purified and some of their properties studied. The apparent Km values for NAD and CHMS were 11.7 ± 1.5 μM and 5.2 ± 1.9 μM. respectively, for the K. pneumoniae enzyme, and 19.5 ± 2.7 μM and 9.2 ± 1.4 μM, respectively, for the E. coli enzyme. Both enzymes were optimally active at pH 7.5 in sodium phosphate buffer. They had subunit molecular weights of 52 000 (± 1000) and the native enzymes appeared to be dimers of identical subunits. The first 20 residues of their N-terminal amino acid sequences were 90% homologous. A degenerate oligonucleotide probe constructed to a six amino acid sequence common to both enzymes gave strong hybridization with DNA from E. coli strains B and W as well as with E. coli C and K. pneumoniae but little or no hybridization to DNA from E. coli K12 or Pseudomonas putida.