A rapid enzymatic DNA sequencing technique: determination of sequence alterations in early simian virus 40 temperature sensitive and deletion mutants

Plasmacytomas with more than one immunoglobulin kappa mRNA: implications for allelic exclusion

Although only one allele of an immunoglobulin gene is thought to be expressed as a polypeptide by a given lymphocyte ("allelic exclusion"), three murine plasmacytomas were found to contain more than one kappa light chain mRNA species, as evidenced by the sequences of distinct kappa cDNA clones. Two different kappa cDNA sequences were cloned from BFPC 61 microsomal mRNA, two from MOPC 173, and three from S107. One cDNA sequence from each tumor matches the known secreted polypeptide, while the variant sequences differ in the variable (V) region. Hence fusion of a V kappa gene to a joining (J kappa) gene has occurred independently on separate homologous chromosomes and each allele is transcriptionally competent. The BFPC 61 variant sequence contained a normal V kappa sequence linked out of phase to J kappa 2; hence allelic exclusion in this line is accounted for by an error in DNA rearrangement. One S107 variant cDNA has an untranslatable sequence linked to J kappa--C kappa and may derive from a non-V kappa or pseudo-V kappa gene fused to J kappa. Another S107 variant cDNA, however, has a proper V kappa linked in phase to J kappa (albeit missing the first two germ-line J kappa codons) and the MOPC 173 variant sequence also contains a proper V kappa--J kappa join, although it does not encode a tryptophan residue common to all immunoglobulin chains. The presence of two potentially expressible kappa mRNAs in both S107 and MOPC 173 suggests that allelic exclusion does not hold in all lymphocytes, or that it sometimes reflects events subsequent to mRNA production, such as inability of certain kappa chains to assemble properly with the heavy chain. These observations are compatible with a stochastic model for allelic exclusion in which productive and nonproductive V--J recombination events occur at a certain frequency for each allele.

DNA sequences of polyoma virus early deletion mutants

The DNA sequences of four "early" viable deletion mutants of polyoma virus have been determined. Two of these (dl-8 and dl-23) are mutants with deletions in the region of the genome that codes for parts of both large and middle T-antigens, and two (dl-6 and dl-28) are mutants with deletions around the viral origin of replication. The former mutants have altered transformation properties relative to wild-type virus, and dl-8 appears to be replication deficient (B. E. Griffin and C. Maddock, J. Virol. 31:645-656, 1979). Sequences are discussed in terms of the altered phenotypes observed for the various mutants, the DNA structures and protein sequences that are affected by the deletions, and how these might affect the biological properties of the mutants.

Control region for adenovirus VA RNA transcription

Plasmids containing the VA RNA genes of adenovirus are faithfully transcribed by a crude cytoplasmic extract containing DNA-dependent RNA polymerase III [Wu, G.-J. (1978) Proc. Natl. Acad. Sci. USA 75, 2175-2179]. By subjecting these DNA templates to in vitro site-directed mutagenesis with a novel enzyme of Pseudomonas and recloning in pBR322, we have constructed an ordered series of deletions which affect the in vitro transcription of the major RNA polymerase III viral product, VAI RNA. Three regions that are required for specific synthesis of VAI RNA can be defined. One, inside the gene at nucleotides +10 to +76, affects the transcription in an all-or-none fashion. Transcription is initiated on plasmid sequences that replace up to 10 nucleotides downstream from the 5' end of the gene. Variants with deletions past nucleotide +15 do not support the transcription of VAI RNA. Removal of 3'-end sequences downstream from +76 allows correct initiation. A second region, upstream from the initiation site, affects the exact alignment of the first nucleotide of the transcript [Thimmapaya, B., Jones, N. & Shenk, T. (1979) Cell 18, 947-959]. A third region, downstream from +76, encodes signals for termination of transcription, and new signals were brought in with other viral DNA sequences. Transcription competition experiments indicate that the primary site for binding of a transcriptional regulation factor is located between nucleotides +55 and +70 and suggest that the control region is bifunctional. An internal control region for VAI RNA, approximately 60 bases long and 11 bases downstream from the 5' end of the gene, can be defined.

Characterization of a cloned histone gene cluster of the newt Notophthalamus viridescens

We report the cloning and characterization of a histone gene cluster of the newt Notophthalamus viridescens. Fragments containing newt histone genes were identified in whole genome Southern blots; these fragments were cloned into a bacteriophage lambda cloning vector constructed for this purpose. The positions of most of the histone genes were determined by hybridizing subcloned sea urchin histone genes to digests of the cloned newt gene cluster. The position of each gene was verified, and its polarity determined by sequencing a portion of each. The order of the genes in the cloned segment is H1-H3-H2B-H2A-H4, with each of the genes but H2B being transcribed in the same direction. Subcloned segments of the histone gene repeat were used to determine the size of each newt oocyte histone mRNA.

Nucleotide sequence changes in polyoma virus A gene mutants

The mutational alterations in polyoma virus mutants ts-a and ts-25E which cause their large T-antigens to be thermolabile have been identified. In ts-a, a G leads to A transition at nucleotide 2193 causes the replacement of Ala (GCT) by Thr (ACT). In ts-25E, a G leads to T transversion at nucleotide 2883 causes the replacement of Gly (GGC) by Cys (TGC). Revertants of both mutants have been isolated and shown to have the original nucleotides restored at these positions.

Simian virus 40 tandem repeated sequences as an element of the early promoter

On the late side of the simian virus 40 (SV40) DNA replication origin are several sets of tandem repeated sequences, the largest of which is 72 base pairs long. The role of these sequences was examined through construction of deletion mutants of SV40. A mutant from which one of the 72-base-pair repeated units was removed is viable upon transfection of monkey kidney cells with viral DNA. Extension of this deletion into the second repeated unit, however, leads to nonviability, as recognized by the absence of early transcription and of tumor antigen production. These observations indicate that the 72-base-pair repeated sequences form an essential element in the early viral transcriptional promoter and explain the inability of such a deleted genome to complement an early temperature-sensitive mutant of SV40, tsA, as well as the failure to replicate its DNA. In a parallel experiment it was found that the extended deletion mutant was also unable to complement a late temperature-sensitive mutant of SV40, tsB. This suggests that the extended mutant is also defective in DNA replication or late transcription (or both).

Complete nucleotide sequence of the influenza A/PR/8/34 virus NS gene and comparison with the NS genes of the A/Udorn/72 and A/FPV/Rostock/34 strains

The nucleotide sequence of the NS gene of the human influenza virus A/PR/8/34 was determined and found to be the same length (890 nucleotides) as the NS gene of another human influenza virus A/Udorn/72 and of the avian isolate A/FPV/Rostock/34. Comparison of the sequences of the NS genes of the two human influenza viruses shows an 8.9% difference whereas the NS gene of the avian isolate differs by only 8% from that of the human strain A/PR/8/34. The extensive sequence similarity among these three genes does not support the notion of species specific homology groups among NS genes of avian and human influenza virus strains. The primary sequence of the A/PR/8/34 NS gene is consistent with the findings that the influenza virus NS gene may code for two overlapping polypeptides. In addition, an open reading frame potentially coding for a polypeptide 167 amino acids in length was found in the negative strand RNA of the A/PR/8/34 virus NS gene.

Simian virus 40-associated small RNA: mapping on the simian virus 40 genome and characterization of its synthesis

The simian virus 40 (SV40)-associated small RNA (SAS-RNA) has previously been shown to arise late in SV40 lytic infection and to bear homology with the SV40 early mRNA's, or the SV40 genome, at map position 0.21. By using hybridization analysis, we determined that the SAS-RNA is between 62 and 65 nucleotides in length and its homology region lies between nucleotides 2760 and 2825 of the SV40 late(+) DNA strand. Viable deletion mutants which lacked part or all of this region made no SAS-RNA, strongly indicating that this is the coding region of the SAS-RNA. The expected sequence for the SAS-RNA, determined from the DNA sequence between nucleotides 2760 and 2825, appeared to be very pyrimidine rich (76% uridine and cytidine). Deletion or alteration of sequences immediately preceding the SAS-RNA coding region (approximately nucleotides 2716 to 2748) resulted in the loss of SAS-RNA production. These sequences may be part of a promotor for SAS-RNA synthesis or a processing site for its excision from long nuclear late transcripts. Under growth conditions where late transcription was not fully initiated (tsA58 at 41 degrees C; wild-type SV40 in the presence of 1-beta-D-arabinofuranosylcytosine), no SAS-RNA was produced, indicating that the expression of the SAS-RNA is regulated by a mechanism related to the control of late transcription.

Exons encode functional and structural units of chicken lysozyme

The nucleotide sequence was determined for the chicken egg white lysozyme mRNA and for the exons of the gene together with their flanking intron regions. The exon pattern is to some degree related to the structural subdivision of the final protein product. However, the relationship of exons to functional units of the enzyme is better established. Exon 2 codes for amino acids 28-82, which include the catalytically active residues and a cluster of amino acids which bind rings C, D, E, and F of the oligosaccharide substrate. Exon 3 codes for amino acids 82-108, which give additional substrate specificity, determine the cleavage frame for the alternating N-acetylglucosamine/N-acetylmuramic acid chain, and increase the catalytic efficiency of the active center. Exons 1 and 4, respectively, code for translational signal sequences on the mRNA, for the signal peptide of prelysozyme, and for the amino- and carboxy-terminal regions of the enzyme. These regions increase the stability of the molecule but are not directly involved in the catalytic function.

Nonviral oligonucleotides at the 5' terminus of cytoplasmic influenza viral mRNA deduced from cloned complete genomic sequences

We obtained influenza viral DNA clones containing sequences derived from cytoplasmic viral mRNA and genomic viral RNA. Sequence analysis of terminal nucleotides of five independentlyisolated viral DNA segments showed that additional oligonucleotides were covalently linked to the 5' terminus of viral mRNA transcripts. The sequences of these additional nucleotides varied among DNA clones of the same gene and of different genes as well. These inserts also varied in length, ranging from 6 to 14 nucleotides. The heterogeneity of these sequences suggests that they were derived originally from cellular RNA molecules. These findings provide evidence that cellular RNA sequences are used to prime influenza viral mRNA transcription in infected cells. In addition, the sequences at both termini of vRNA were fully represented in clone pFV 88, indicating that the cloned DNA contained the complete viral gene coding for the hemagglutinin.