Showing papers on "Genome published in 1978"

Complete nucleotide sequence of SV40 DNA

Abstract: The determination of the total 5,224 base-pair DNA sequence of the virus SV40 has enabled us to locate precisely the known genes on the genome. At least 15.2% of the genome is presumably not translated into polypeptides. Particular points of interest revealed by the complete sequence are the initiation of the early t and T antigens at the same position and the fact that the T antigen is coded by two non-contiguous regions of the genome; the T antigen mRNA is spliced in the coding region. In the late region the gene for the major protein VP1 overlaps those for proteins VP2 and VP3 over 122 nucleotides but is read in a different frame. The almost complete amino acid sequences of the two early proteins as well as those of the late proteins have been deduced from the nucleotide sequence. The mRNAs for the latter three proteins are presumably spliced out of a common primary RNA transcript. The use of degenerate codons is decidedly non-random, but is similar for the early and late regions. Codons of the type NUC, NCG and CGN are absent or very rare.

Organization of immunoglobulin heavy chain genes and allelic deletion model

Abstract: We have assessed the number of times the gene sequence encoding constant regions of mouse immunoglobulin heavy chains gamma1, gamma2a, and gamma3 are represented in the mouse genome by hybridization kinetic analysis. All three genes are present at one copy each per haploid genome in normal tissues and myelomas producing IgM or IgG3. IgG1-producing myelomas, however, contain 1 copy each of the gamma1 and gamma2a genes and 0.5 copy of the gamma3 gene per haploid genome. IgG2b-producing myelomas contain 1 copy of the gamma2a gene and 0.5 copy each of the gamma1 and gamma3 genes per haploid genome. IgG2a-producing myelomas contain 1 copy of the gamma2a gene and 0.5 copy each of the gamma1 and gamma3 genes per haploid genome. In myelomas producing IgA, all three gamma genes are represented 0.5 times per haploid genome. In order to account for the results we propose an allelic deletion model: (i) The specific deletion of heavy chain constant region genes accompanies the recombination of a variable region gene to a constant region gene. (ii) The portion of the chromosome that resides between two joining sequences is excised out of the chromosome. (iii) The recombination occurs on one of the alleles. Based on this model we also propose that heavy chain genes are arranged on one chromosome in the following order; variable region genes, unknown spacer sequence, mu, gamma3, gamma1, gamma2b, gamma2a, and alpha.

Evolution of the bacterial genome.

Abstract: Until recently relatively few studies have been aimed directly at the subject of evolution of the bacterial genome, no doubt for the very good reason that the means to address relevant questions have not been at hand We hope to show that this situation is beginning to change We are reaching new understandings on mechanisms of gene duplications, chromosome rear­ rangements, and plasmid-promoted genetic exchange; more information is continually being amassed on new bacterial genes, on their map locations,

Multiplicity of genome equivalents in the radiation-resistant bacterium Micrococcus radiodurans.

Abstract: The complexity of the genome of Micrococcus radiodurans was determined to be (2.0 +/- 0.3) X 10(9) daltons by DNA renaturation kinetics. The number of genome equivalents of DNA per cell was calculated from the complexity and the content of DNA. A lower limit of four genome equivalents per cell was approached with decreasing growth rate. Thus, no haploid stage appeared to be realized in this organism. The replication time was estimated from the kinetics and amount of residual DNA synthesis after inhibiting initiation of new rounds of replication. From this, the redundancy of terminal genetic markers was calculated to vary with growth rate from four to approximately eight copies per cell. All genetic material, including the least abundant, is thus multiply represented in each cell. The potential significance of the maintenance in each cell of multiple gene copies is discussed in relation to the extreme radiation resistance of M. radiodurans.

Highly reiterated sequences of SIMIANSIMIANSIMIANSIMIANSIMIAN.

Abstract: A 172-base pair segment of DNA that is repeated several million times in the genome of the African green monkey has been characterized. Sequence analysis revealed that the many repeats of this complex unit are not all identical but represent a set of closely related segments: Sequence divergence occurs at various positions in the segment in a nonrandom manner. The uncloned segment obtained from monkey DNA is compared with a cloned segment of the same DNA which was recombined into the genome of simian virus 40 during permissive infection.

Low repetitive DNA content in Aspergillus nidulans.

Abstract: DNA-DNA reassociation experiments show that the genome of Aspergillus nidulans consists of approximately 97 to 98 percent unique and 2 to 3 percent reiterated sequences. The reiterated DNA sequences have a complexity of about 11,000 base pairs and are repeated approximately 60 times per haploid genome. Ribosomal RNA-DNA hybridization experiments indicate that most of the repetitive DNA codes for ribosomal RNA.

Recombinants between herpes simplex virus types 1 and 2: analyses of genome structures and expression of immediate early polypeptides.

Abstract: Recombinants between temperature-sensitive mutants of herpes simplex virus types 1 (HSV-1) and 2 (HSV-2) were constructed. Using restriction endonucleases, we analyzed the genome composition of 17 intertypic recombinants and detected crossovers in every region of the genome. The virion DNA of one recombinant appeared to be largely "frozen" in two of the four possible genome arrangements of HSV. Knowledge of the genome structures of recombinants enabled us to physically map immediate early polypeptides. We present evidence that the immediate early polypeptide Vmw IE 110 of HSV-1 and its functionally equivalent polypeptide, Vmw IE 118, of HSV-2 may map in the repetitive sequences bounding the long unique region of HSV.

Homology between human and simian repeated DNA.

Abstract: A RELATIVELY small proportion of the total DNA of eukaryotic cells has been considered to be transcribed and translated; the rest of the genome may be variously categorised into several subsets such as spacer and repeated DNAs. Such nontranslated sequences presumably have a role in the modulation of transcription and in the organisation of chromosomes. Some satellite DNAs may be extremely simple in sequence1, even in human DNA2. Other repeated DNAs showing greater sequence complexity have been considered to form a separate subset of repeated DNAs2,3. Very recently, the exact base sequence of such complex repeats has been determined in a few organisms4,5. The conservation of such sequences between related species, and even more extensively in the evolutionary tree, is not known. We report here data which indicate the base order of a subset of human repeated DNA which is fairly complex in sequence. We have shown that such human DNA repeats are quite well conserved both in nucleotide sequence order and in nominal repeat length between human and lower primates.

Multiple related immunoglobulin variable-region genes identified by cloning and sequence analysis.

Abstract: We have identified at least six EcoRI fragments of mouse DNA that encode variable-region gene sequences closely related to the mouse kappa light chain, MOPC-149. Two of these fragments have been cloned, and the entire nucleotide sequence of the variable-region genes encoded on each has been determined. Both genes encode closely related variable-region sequences extending from codon position 1 through position 97. Neither fragment encodes a constant-region sequence. Although both genes are closely related, they differ from one another and from the sequence expressed in the MOPC-149 cell from which they were cloned. These few differences cluster within the complementarity-determining regions although several occur in framework sequences as well. We therefore conclude that an antibody-producing cell contains genetic information corresponding to its expressed sequence and several other closely related but silent sequences. These initial results raise the possibility that similar sets of genes might exist corresponding to each of the many subgroups already identified among mouse kappa light chains. If true, this would further suggest that the mouse genome might be rich enough in variable-region genes so as to encode a major portion of the variable-region repertoire.

Negative strand viruses and the host cell.

Abstract: Aug ust/September 1978, xxiv + 848pp., £22.50/$46.50 0.12.465350.2 Based on a meeting held at Cambridge in August 1977, this book provides a comprehensive account by contributors from all over the world of the current knowledge of the molecular and cellular biology of negative strand viruses. In the three years since the publication of Negative Strand Viruses (Academic Press, 1975) the understanding of the biology of this type of virus has increased enormously. In particular, the close relationships between negative strand virus replication and normal cell processes have become more apparent, and have increased our understanding of several aspects of cell function.

Evolution of overlapping genes.

Abstract: THE nucleotide sequence of the DNA of φX174 phage established by Sanger's group1,2 has revealed that this phage has two overlapping genes in which the same stretch of DNA can code for two proteins which are translated in different reading frames. That two overlapping genes occur in the same DNA genome suggests that this overlapping expression is not unique to φX174 but of more general significance, at least in organisms with small DNA molecules. Once the overlapping expression is established, all mutations in one gene would also alter the other gene within the region of overlap. Some of these mutations, however, may affect one protein but not the other because of codon degeneracy. In general, the evolutionary constraints on a sequence representing both proteins must be very severe. In this report we estimate the extent to which the evolution of a gene is reduced by the acquisition of overlapping expression.

Determination of capsid size by satellite bacteriophage P4.

Abstract: Satellite bacteriophage P4 requires all morphogenic gene products provided by a helper phage, such as coliphage P2, to assemble its own capsid, which is one-third the volume of the larger helper capsid. We have isolated a satellite phage P4 sid (size determination) mutant that is unable to direct the assembly of the small wild-type-size P4 capsid. Instead, this mutant produces P4 plaque-forming units with large P2-size capsids which contain two or three copies of the P4 sid1 genome. P4 sid1 is evidently mutated in a protein that is specifically responsible for determining the precise size and symmetry of the structure into which the helper P2 gene products will assemble. In addition, we have found that the physical size of the genome does not appear to play an essential role in the proper assembly of the icosahedral capsid, since the majority of the P4 sid1 plaque-forming units do not contain a complete capsidful of DNA.

Involvement of phage Mu-1 early functions in Mu-mediated chromosomal rearrangements.

Abstract: THE temperate iphage Mu-1 not only integrates at any location in the chromosome of its host Escherichia coli1 but also provokes different types of chromosomal aberrations: insertions of extrachromosomal circular DNA2–4, translocations, deletions and inversions of chromosomal segments (refs 5, 6, Howe and Bukhari, unpublished results and M.F., in preparation). Immunity to phage Mu prevents the induction of such events, indicating that Mu gene expression is required for these rearrangements. Furthermore, the direct participation of Mu DNA in the generation of chromosomal aberrations is demonstrated by the observations that one entire Mu genome is always adjacent to the site of the deletions, two entire Mu genomes in the same orientation flank the inserted and translocated DNA fragments, and inverted chromosomal segments are surrounded by two entire Mu genomes in opposite orientations (ref. 22 and M.F., in preparation). Dependence of such Mu-induced alteration on the A and B early phage functions was investigated. A− mutants of Mu are unable to mediate all the events tested, while B− mutants still promote deletion. Based on the results presented here, and on other data, we propose that the A function directly concerns the insertion of the phage and that the B gene codes for a replication function.

Studies on the single-stranded diseontinuities of the cauliflower mosaic virus genome

Abstract: The Cauliflower Mosaic Virus (CaMV) genome is a double-stranded DNA molecule of about 5 million daltons. Native DNA molecules appear heterogeneous when analysed by gel electrophoresis. We have examined the nature of this apparent heterogeneity. Besides, this genome is shown here to contain three single-stranded breaks, as revealed by different denaturation experiments: heating at 75 degrees C, treatment with NaOH or dimethyl sulfoxide (DMSO). Labelling with terminal transferase proves that the 3' ends at these interruptions all have free hydroxyl groups. Electron microscopy and alkaline gel electrophoresis indicate that these three discontinuities are shared by both strands, and that they are not randomly located. S1 nuclease is active on CaMV DNA and generates three fragments. The comparison between the sizes of these fragments and of the products of denaturation leads us to consider that S1 acts at the level of the interruptions. We have determined that two of them, distant by one third genome unit, are in the same strand; the other is in the opposite strand, distant by one sixth genome unit from the nearest other one. The combined use of restriction enzymes and S1 nuclease has enabled us to locate these three discontinuities on the restriction map of the CaMV genome that we have otherwise established.

Gene K, a new overlapping gene in bacteriophage G4.

Abstract: A third overlapping gene in the isometric bacteriophages has been identified by nucleotide sequence analysis of the G4 genome and by isolation and microsequence analysis of the new protein. Five nucleotides are used in all three translational reading frames of the DNA.

Nucleotide sequence relationships between the genomes of an endogenous and an exogenous avian tumor virus.

Abstract: We have used mapping of large T1 oligonucleotides to examine the genome of Rous-associated virus-O (RAV-O), an endogenous virus of chickens, and to compare it with that of Prague strain Rous sarcoma virus, subgroup B, (Pr-RSV-B), an exogenous sarcoma virus. To extend the sensitivity of such comparisons, we have developed a system of nucleic acid hybridization and hybridization-competition combined with fingerprinting. This method allows us to estimate the relative degree of relatedness of various portions of the viral genomes. From the results of this study, we have concluded that the genomes of Pr-RSV-B and RAV-O are related in the following way. The 5'-terminal half of the genomes (corresponding to the gag and pol regions) is virtually identical, with only scattered single nucleotide differences. This region is followed by a region comprising 25 to 30% of the genome (the env region) which contains substantial nucleotide sequence differences, most or all of which are due to single base changes. The env-coding region can be further subdivided into three regions: a more variable region probably containing sequences coding for subgroup specificity, flanked by relatively common sequences on each side. To the 3' side of the env region, the RAV-O genome contains a very short sequence not found in Pr-RSV-B, whereas the Pr-RSV-B genome contains a much longer unrelated sequence. The central portion of this sequence comprises the src gene as defined by transformation-defective mutants. Particularly striking is the absence, in the RAV-O genome, of any nucleotide sequence related to the "c region" found very near the 3' end of all exogenous tumor viruses. Both the Pr-RSV-B and RAV-O genomes contain the identical terminally redundant sequence of 21 nucleotides near each end of the genome.