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PubMed1996

Structural analysis of gamma delta TCR using a novel set of TCR gamma and delta chain-specific monoclonal antibodies generated against soluble gamma delta TCR. Evidence for a specific conformation adopted by the J delta 2 region and for a V delta 1 polymorphism.

We recently showed that secretion of non-chimeric disulfide-linked human gamma delta TCR ('soluble' TCR, sTCR) comprising V gamma 9 and V delta 2 regions could be achieved by simply introducing translational termination codons upstream from the sequences encoding TCR transmembrane region. Here we extended these findings by demonstrating efficient secretion and heterodimerization of gamma delta sTCR comprising V gamma 8, V delta 1 and V delta 3 regions, obtained via the same strategy. After immunization against immunoaffinity-purified soluble TCR, several hundreds of TCR-specific monoclonal antibodies (mAb) were generated, which fell in at least seven groups. One set of mAb was directed against a V gamma 8-specific epitope. Strikingly, despite the high degree of sequence homology between V gamma 8 and other V gamma I domains, none of these mAb were crossreactive with other members of the V gamma I family. Three other sets of mAbs were shown to recognize delta chains comprising V delta 1, V delta 2 and V delta 3 regions respectively, regardless of their junctional sequence or of the gamma chain to which they were paired. Among the V delta 1-specific mAb, some specifically recognized V delta 1D delta J delta C delta chains while others reacted with both V delta 1 D delta J delta C delta and V delta 1J alpha C alpha chains, which suggested V domain conformational alterations induced by the C region. Moreover, reactivity of one V delta 1-specific mAb (#R6.11) was affected by a polymorphic residue located on the predicted CDR4 loop of the V delta region. Two delta chain-specific mAb (#178 and #515) showed a highly unusual reactivity, which was negatively affected by particular V delta and J delta sequences: (i) mAb #515 and #178 recognized all TCR delta chains except those comprising V delta 1 or V delta 2 regions, respectively and (ii) within TCR delta chains carrying 'permissive' V delta regions, none of those comprising the J delta 2 region were recognized by #515 and/or #178 mAbs, which suggested a highly specific conformation adopted by this particular J delta sequence. Apart from its usefulness in TCR structural studies, this novel set of mAb represents an important tool for the characterization and isolation of gamma delta T cells expressing particular combinations of V gamma/V delta regions and for analysis of V alpha/V delta usage by alpha beta T cells. Moreover, since our present data strongly suggest that gamma delta TCR are easier to obtain in a soluble form than alpha beta TCR, an efficient strategy for the generation of V alpha region-specific mAb might be to immunize with chimeric gamma delta sTCR comprising particular V alpha regions.

Amino Acid Sequence↗

PubMed1984

Nuclease digestion of circular TRP1ARS1 chromatin reveals positioned nucleosomes separated by nuclease-sensitive regions.

TRP1ARS1 is a circular yeast DNA of 1453 base-pairs that contains the N-5'phosphoribosyl anthranilate isomerase (TRP1) gene and a sequence important for autonomous replication (ARS1). It exists extrachromosomally in 100 to 200 copies/cell and is presumably packed in nucleosomes. TRP1ARS1 has been partially purified as chromatin from lysed spheroplasts of yeast using gel filtration. A structural analysis of mapping micrococcal nuclease and DNAase I cutting sites with an accuracy of +/- 20 base-pairs is presented. Comparison of nuclease cleavage sites in chromatin and in purified DNA reveals that regions which are protected against nuclease attack are not distributed randomly. These regions are big enough to accommodate nucleosome cores. Three nucleosomes are positioned in the so-called ARS sequences, and are stable at low and high levels of digestion. The TRP1 gene region is covered by four nucleosomes, but they are neither randomly arranged nor precisely positioned. They are not stable and rearrange or disintegrate during digestion. The nucleosomal regions are separated by two segments of DNA (A, B), each about 180 base-pairs long, which are very sensitive to DNAase I and micrococcal nuclease and therefore presumably not packed in nucleosomes. Region B is found 5' to the TRP1 gene and might be related to transcription, whereas region A is centered around the termination codon of the TRP1 gene and the putative origin of replication.

Aldose-Ketose Isomerases↗

PubMed1984

Long range base-pairing in the leftward transcription unit of bacteriophage lambda. Characterization by electron microscopy and computer-aided sequence analysis.

Restriction fragments of bacteriophage lambda DNA corresponding to the major leftward transcription unit were purified, denatured to form single-stranded DNA, self-annealed, and examined by electron microscopy. Three intrastrand stem and loop secondary structures were observed reproducibly and the locations of the paired regions were determined. A method for computer-aided sequence analysis of these regions is presented and used to identify sets of base-pairings likely to account for the observed structures. One loop observed within gene Ea47 is postulated to involve pairing of sequences which include the polypeptide initiation and termination codons. Another loop is postulated to involve pairing of sequences in gene int with sequences located in the gam-cIII region. A third loop appears to involve sequences in and to the right of gene Ea22 paired with sequences located in the bet-gam region. A general discussion of base-pairing which gives rise to long range interactions is presented along with possible effects of the postulated models on gene expression.

Bacteriophage lambda↗

PubMed1985

Structure and expression of the cell division genes ftsQ, ftsA and ftsZ.

The essential cell division genes ftsQ, ftsA and ftsZ map in a cluster of cell envelope genes located at two minutes on the Escherichia coli genetic map and appear to constitute an atypical operon. These closely clustered genes are all transcribed in the same direction and yet each of these genes was independently cloned on a multicopy plasmid and found to be expressed. Tn5 insertion mutagenesis of this region confirmed that these genes were independently expressed, indicating that each of these genes has its own promoter. However, maximum expression of the distal ftsZ gene required the promoter for the proximal ftsQ gene. The proximal ftsZ promoter was located within the ftsA structural gene and the proximal ftsA promoter was located within the ftsQ structural gene. No transcription terminators were evident from the DNA sequence analysis of this region. The sequence analysis also revealed that the termination codon for ftsQ overlapped the initiation codon of the ftsA gene and that the ftsA and ftsZ genes were separated by 60 base-pairs. The ftsQ gene product has a calculated Mr of 31,432 and the ftsA gene product has a calculated Mr of 45,327. The structure and expression of these genes are discussed.

Autoradiography↗

PubMed1986

Complete nucleotide sequence of the topA gene encoding Escherichia coli DNA topoisomerase I.

The nucleotide sequence of a 4071 base-pair long segment containing the gene topA encoding Escherichia coli DNA topoisomerase I and its flanking regions has been determined. The gene encodes a total of 864 amino acids from the ATG start to a TAA termination codon, of which the first f-Met appears to be removed after translation; the calculated molecular weight of the translated protein is 97,413. Mapping of promoters by deletion of sequences upstream from the ATG initiation codon indicates the existence of at least two promoters that direct transcription into topA.

Amino Acid Sequence↗

PubMed1989

DNA base changes and RNA levels in N-acetoxy-2-acetylaminofluorene-induced dihydrofolate reductase mutants of Chinese hamster ovary cells.

Formerly, we isolated a series of dihydrofolate reductase-deficient Chinese hamster ovary cell mutants that were induced by N-acetoxy-2-acetylaminofluorene. Deletions and complex gene rearrangements were detected in 28% of these mutants; 72% contained putative point mutations. In the present study, we have localized the putative point mutations in the 25,000 base dhfr gene by RNase heteroduplex mapping. Assignment of a position for each mutation was successful in 16 of 19 mutants studied. We cloned DNA fragments containing the mapped mutations from nine mutants into a bacteriophage lambda vector. In the case of 11 other mutants, DNA was amplified by the polymerase chain reaction procedure. Sequence analysis of cloned and amplified DNA confirmed the presence of point mutations. Most mutants (90%) carried base substitutions; the rest contained frameshift mutations. Of the point mutations, 75% were G.C to T.A transversions in either the dhfr coding sequence or at splice sites; transition G.C to A.T mutations were found in two mutants (10%). In one of these transition mutants, the base substitution occurred at the fifth base of the third intron. Of the frameshift mutations, one was a deletion of G.C pair and the other was an insertion of an A.T pair. Of the mapped mutants, 38% exhibited greatly reduced (approximately 10-fold) steady-state levels of dhfr mRNA. All eight sequenced mutants displaying this phenotype contained premature chain termination codons. Normal levels of dhfr mRNA were observed in five missense mutants and in five mutants carrying nonsense codons in the translated portion of exon VI. Taken together with the results of other mutagens at this locus, we conclude that the low dhfr mRNA phenotype is correlated with the presence of nonsense codons in exons II to V but not in the last exon of the dhfr gene.

2-Acetylaminofluorene↗

PubMed1989

Nucleotide sequences of Caenorhabditis elegans core histone genes. Genes for different histone classes share common flanking sequence elements.

We have determined the nucleotide sequence of core histone genes and flanking regions from two of approximately 11 different genomic histone clusters of the nematode Caenorhabditis elegans. Four histone genes from one cluster (H3, H4, H2B, H2A) and two histone genes from another (H4 and H2A) were analyzed. The predicted amino acid sequences of the two H4 and H2A proteins from the two clusters are identical, whereas the nucleotide sequences of the genes have diverged 9% (H2A) and 12% (H4). Flanking sequences, which are mostly not similar, were compared to identify putative regulatory elements. A conserved sequence of 34 base-pairs is present 19 to 42 nucleotides 3' of the termination codon of all the genes. Within the conserved sequence is a 16-base dyad sequence homologous to the one typically found at the 3' end of histone genes from higher eukaryotes. The C. elegans core histone genes are organized as divergently transcribed pairs of H3-H4 and H2A-H2B and contain 5' conserved sequence elements in the shared spacer regions. One of the sequence elements, 5' CTCCNCCTNCCCACCNCANA 3', is located immediately upstream from the canonical TATA homology of each gene. Another sequence element, 5' CTGCGGGGACACATNT 3', is present in the spacer of each heterotypic pair. These two 5' conserved sequences are not present in the promoter region of histone genes from other organisms, where 5' conserved sequences are usually different for each histone class. They are also not found in non-histone genes of C. elegans. These putative regulatory sequences of C. elegans core histone genes are similar to the regulatory elements of both higher and lower eukaryotes. The coding regions of the genes and the 3' regulatory sequences are similar to those of higher eukaryotes, whereas the presence of common 5' sequence elements upstream from genes of different histone classes is similar to histone promoter elements in yeast.

Animals↗

PubMed1990

Structure and assembly of turnip crinkle virus. VI. Identification of coat protein binding sites on the RNA.

Structural studies of turnip crinkle virus have been extended to include the identification of high-affinity coat protein binding sites on the RNA genome. Virus was dissociated at elevated pH and ionic strength, and a ribonucleoprotein complex (rp-complex) was isolated by chromatography on Sephacryl S-200. Genomic RNA fragments in the rp-complex, resistant to RNase A and RNase T1 digestion and associated with tightly bound coat protein subunits, were isolated using coat-protein-specific antibodies. The identity of the protected fragments was determined by direct RNA sequencing. These approaches allowed us to study the specific RNA-protein interactions in the rp-complex obtained from dissociated virus particles. The location of one protected fragment downstream from the amber terminator codon in the first and largest of the three viral open reading frames suggests that the coat protein may play a role in the regulation of the expression of the polymerase gene. We have also identified an additional cluster of T1-protected fragments in the region of the coat protein gene that may represent further high-affinity sites involved in assembly recognition.

Base Sequence↗

PubMed1990

Analysis of ENU-induced mutations at the Adh locus in Drosophila melanogaster.

N-Ethyl-N-nitrosourea (ENU) was used to induce mutations in the Drosophila melanogaster, alcohol dehydrogenase (Adh) gene. Flies were treated with ENU and mated to homozygous intragenic Adh null mutants; Adh null mutations were selected by exposure of the F1 generation to 1-penten-3-ol. Fourteen Adh null mutations were recovered which included 11 from spermatozoa, 2 from oocytes and 1 from a premeiotic spermatocyte. 2 mutations from spermatozoa and 1 of the mutations from oocytes were multilocus deficiencies which included the Adh locus as determined by complementation tests. The remaining 11 intragenic Adh null mutations were sequenced using the Sanger dideoxy method. One Adh null mutation induced in an oocyte was an AT to TA transversion and the mutation induced in a premeiotic spermatocyte was a GC to AT transition, both of which resulted in a single amino acid substitution. The 11 null mutations induced in spermatozoa were a data set in which both the dose of ENU and the treated germ-cell stage were held constant; therefore, only these 11 mutations were used to calculate the mutation frequency and compare the mutations at the Adh locus with those recovered in other studies. The dose of ENU induced a sex-linked recessive lethal frequency approximately 300 times that of the spontaneous frequency; therefore, these mutations were assumed to have been induced by ENU. 2 of the 11 mutations induced in spermatozoa were multilocus deficiencies and 9 were intragenic mutations. 7 of the 9 intragenic mutations were GC to AT transitions which resulted in 5 single amino acid substitutions, 1 premature translation termination codon, and 1 splice site mutation.(ABSTRACT TRUNCATED AT 400 WORDS)

Alcohol Dehydrogenase↗

PubMed1991

The cDNA sequence of a depressant insect selective neurotoxin from the scorpion Buthotus judaicus.

A 400 nucleotide cDNA clone encoding the depressant insect toxin of the scorpion Buthotus judaicus (BjIT2), was isolated. DNA sequence analysis suggests that the toxin is a processed product of a precursor composed of: (1) a 21 amino acid residue signal peptide; (2) a 61 amino acid region of the mature toxin; and (3) an additional Arg-Lys-Lys tail at the carboxy terminus prior to a termination codon. Comparison between the precursor polypeptides of BjIT2 and another depressant insect toxin derived from the scorpion Leiurus quinquestriatus hebraeus (LqhIT2) shows similarities in their hydropathic profiles.

Amino Acid Sequence↗

PubMed1983

Nonsense mutations affecting the lengths of the NS1 nonstructural proteins of influenza A virus isolates.

The proteins from cells infected with influenza A virus field isolates were labeled with [35S]methionine and analyzed by SDS-polyacrylamide gel electrophoresis. By screening more than 100 field isolates, it was found that the NS1 proteins had the greatest mobility differences, far exceeding those observed among other corresponding viral polypeptides. Partial sequence determination of RNA segment eight from 12 viruses revealed the existence of nonsense mutations at six different positions in their NS1 coding regions. The termination codons consisted of opal, ochre, and amber mutations. The sizes predicted from these sequences of 202, 217, 219, 220, 230, and 237 amino acids were in agreement with the observed mobilities of the viral polypeptides on SDS-polyacrylamide gels. The observation of large deletions in the carboxy termini of the NS1 proteins of field virus isolates would suggest that a high degree of variation can be tolerated in this polypeptide without affecting its functional capability.

Base Sequence↗

PubMed1985

Sites of recombination between the transforming gene of avian myeloblastosis virus and its helper virus.

The sites of recombination between the transforming gene of avian myeloblastosis virus (AMV) and its natural helper myeloblastosis-associated virus (MAV) have been determined. In AMV, the cellular sequence substituting for the viral envelope (env) gene gives rise to a different carboxyl terminus of the DNA polymerase. The 5'-recombination site coincides with the RNA splice acceptor site for the production of env mRNA in MAV-infected cells. The 3'-recombination site reveals that the last 11 amino acids including the termination codon are shared by the env protein and AMV transforming protein. The RNA splice acceptor site for the generation of subgenomic v-myb mRNA is located 84 nucleotides downstream from the 5'-recombination site. The AMV transforming protein consists of helper virus-related sequences at both of its amino and carboxyl termini, and all but 84 nucleotides of the cell-derived v-myb sequence. The comparison of MAV gp85 amino acid sequence with those of subgroups B, C, and E indicates that the MAV present in clone lambda 10A2-1 belongs to subgroup B. The high degree of homology among different avian retroviruses of the same subgroup indicates that the amino acid sequence of gp85 is important in determining the conformation of the envelope glycoprotein.

Amino Acid Sequence↗

PubMed1985

Nucleotide sequence analysis of the chicken gene c-mil, the progenitor of the retroviral oncogene v-mil.

The nucleotide sequence of the chicken gene c-mil was determined within and around all regions homologous to the oncogene v-mil of avian retrovirus MH2. The regions of homology to the previously determined v-mil sequence, ranging in size from 28 to 177 base pairs (bp), are distributed over 14 kilobase pairs (kbp) of the chicken genome and are organized in 11 exons. All exon-intron boundaries of c-mil, except the 5' boundary of exon 1 and the 3' boundary of exon 11, were unambiguously defined by the identification of consensus splice donor and acceptor sites precisely at positions where homology to v-mil ceases or resumes. The homology to v-mil starts within the coding sequence of exon 1 and ends within the 3' untranslated region of exon 11, 12 nucleotides downstream from the nonsense codon terminating the large open reading frame shared between c-mil and v-mil. The c-mil and v-mil sequences differ at only 7 out of 1153 nucleotide positions, and the predicted sequences of v-mil and c-mil proteins differ by one conservative and four nonconservative substitutions among 379 amino acid residues. Hence, the carboxy-terminal domains of the MH2 gag-mil hybrid protein and of the putative c-mil protein are very similar. However, the amino-terminal domain of the cellular protein is possibly encoded by additional 5' c-mil sequences not present in the transduced v-mil oncogene, while that of the MH2 hybrid protein is encoded by viral gag sequences. The sequence analysis also revealed that c-mil and c-myc derived sequences are immediately adjacent on the MH2 genome carrying both the v-mil and the v-myc oncogene. Hence, transduction of c-mil into MH2 involved recombination, at the 3' site, with either the c-myc locus or a previously transduced v-myc gene, and, at the 5' site, with gag sequences of the transducing virus. At both sites, no significant homologies were found between the sequence elements involved in the recombination.

Amino Acid Sequence↗

PubMed1986

Nucleotide sequence of the glycoprotein gene and intergenic region of the Lassa virus S genome RNA.

Two overlapping cDNA clones corresponding to the 5' region of the Lassa virus S genome RNA were isolated and their nucleotide sequences determined. Similar to Pichinde and lymphocytic choriomeningitis viruses (LCMV), Lassa virus has an ambisense S RNA. The precursor to the viral glycoproteins (GPC) is encoded in viral RNA sequence originating at position 56 and terminating at position 1529 from the 5' terminus of the S RNA. A short, noncoding, intergenic region capable of forming a hairpin structure separates the termination codons of the nucleoprotein (N) and GPC genes. Hydropathic analysis of the GPC gene product of Lassa virus indicates the presence of hydrophobic domains near the amino and carboxy termini as previously noted in the corresponding proteins of Pichinde and LCM viruses. A comparison of the nucleotide sequences on the 3' termini of the viral and viral-complimentary S RNA species of Lassa, LCM, and Pichinde viruses reveals slight sequence differences that may possibly be involved in the regulation of RNA synthesis and gene expression.

Amino Acid Sequence↗

PubMed1988

A unique amino-terminal sequence predicted for the chicken proto-ets protein.

Avian cellular sequences homologous to the ets domain of the avian leukemia retrovirus, E26, have been characterized, and shown to contain nine discrete regions within a single locus of about 60 kb. The structure of the viral homologous and nonhomologous domains of this chicken ets-1 gene is characterized and seen to define the unique amino acid sequences of the ets protein. We have isolated and sequenced an avian ets-1 cDNA clone obtained from chicken thymus. This cDNA clone contains an open reading frame (ORF) encoding the normal cellular product of 441 amino acids. This product is significantly smaller than that encoded by the v-ets domain of the E26 transforming protein, p135, which contains 491 amino acids. The open reading frame predicted by our sequence data results in a protein calculated to be 50 kDa, which is slightly smaller than that actually observed in chicken cells. The presence of termination codons 5' to this ORF demonstrates that the cDNA characterized contains the entire coding region for the chicken ets gene.

Amino Acid Sequence↗

PubMed1988

Selective inhibition of formation of suppressor glutamine tRNA in Moloney murine leukemia virus-infected NIH-3T3 cells by Avarol.

Avarol is a sesquiterpenoid hydroquinone, which displays no inhibitory potencies on mammalian DNA polymerases alpha, beta, and gamma, on mammalian RNA polymerases I, II, and III, or on reverse transcriptases from Moloney murine leukemia virus (Mo-MuLV) and from HIV. For a further elucidation of the antiviral effect of Avarol, we used NIH-3T3 cells infected with Mo-MuLV as a model system. The results show that in uninfected NIH-3T3 cells Avarol (i) causes a 50% reduction of the growth rate only at the high concentration of 29.6 microM and (ii) is accumulated in the cytoplasm close to the nucleus. At the much lower concentrations of 1-3 microM, Avarol causes an almost complete inhibition of viral progeny release. Moreover, it is shown that at 3 microM Avarol, the increase of the Mo-MuLV-induced UAG suppressor glutamine tRNA (tRNA(UmUGGln) was reduced to the normal level. Dot blot hybridization studies revealed that Avarol displays no inhibitory activity on cellular and viral mRNA synthesis. Taking the processing pathway of viral polyprotein Pr180gag,pol to p80 (reverse transcriptase) as an example, our Western blotting experiments showed that the final maturation process, conversion of p110 to p80, is inhibited in Avarol-treated cells. From these data we conclude that Avarol prevents the suppression of the UAG termination codon at the gag-pol junction of the retroviral genome. The functional consequence of this event is very likely an inhibition of the readthrough of the retroviral protease gene which overlaps the pol and gag genes, resulting in the reduction of the protease synthesis which is necessary for the viral proliferation.

Animals↗

PubMed1989

The genome structure of turnip crinkle virus.

The nucleotide sequence of turnip crinkle virus (TCV) genomic RNA has been determined from cDNA clones representing most of the genome. Segments were confirmed using dideoxynucleotide sequencing directly from viral RNA, and the 3' terminal sequence was confirmed by chemical sequencing of end-labeled genomic RNA. Three open reading frames (ORFs) have been identified by examination of the deduced amino acid sequences and by comparison with the ORFs found in the genome of carnation mottle virus. ORF 1 initiates near the 5' terminus of the genome and is punctuated by an amber termination codon. Translation of ORF 1 would yield a 28-kDa protein and an 88-kDa read-through product. The read-through domain possesses amino acid sequence similarities with putative viral RNA polymerases. ORFs 2 and 3 encode products of 38 (coat protein) and 8 kDa, respectively, which are expressed from subgenomic mRNAs. The organization of the TCV genome suggests that TCV is closely related to carnation mottle virus and distinct from members classified in other small RNA virus groups, such as the tombus- and sobemoviruses.

Amino Acid Sequence↗

PubMed1989

Herpes simplex virus alpha protein ICP27 can inhibit or augment viral gene transactivation.

Three of the five alpha (immediate early) gene products of herpes simplex virus, infected cell proteins (ICPs) 4, 0, and 27 play a role in the control of expression of viral beta (delayed-early) and gamma (late) genes. We report here that ICP27 can inhibit or augment the individual or combined abilities of ICP4 and ICP0 to stimulate expression of chimeric genes containing viral gene promoters in a transient expression system. The specific effect of ICP27 was dependent on the viral gene promoter in the chimeric gene. ICP27 inhibited the ability of ICP4 and ICP0 to activate some beta gene promoters but augmented their ability to activate other beta or gamma 1 gene promoters when they were used in the target genes. Activation of the target genes by adenovirus E1A was not affected by ICP27 under the same conditions. ICP27 also repressed the ability of ICP0 to stimulate expression of a chimeric gene containing an alpha gene promoter. Insertion of a termination codon in the middle of the ICP27 coding region severely reduced the inhibitory effect of the plasmid, indicating that this activity requires expression of functional ICP27 polypeptide. This report focuses on the ICP27 activity that negatively regulates ICP4 transactivation of a chimeric gene containing the upstream sequences of the HSV beta gene ICP8. ICP27 decreased the level of mRNA initiated at the transcriptional start site of the ICP8 gene. The level of expression of the ICP4 gene was not changed by ICP27 but an alteration in the electrophoretic mobility of ICP4 expressed was observed. The modulatory effect of ICP27 on HSV transactivators may control the progress of the lytic cycle or provide a balance that varies in different cell types to affect whether lytic or latent infection ensues.

Animals↗