Showing papers on "Genome published in 1980"

Selfish genes, the phenotype paradigm and genome evolution.

Abstract: Natural selection operating within genomes will inevitably result in the appearance of DNAs with no phenotypic expression whose only ‘function’ is survival within genomes. Prokaryotic transposable elements and eukaryotic middle-repetitive sequences can be seen as such DNAs, and thus no phenotypic or evolutionary function need be assigned to them.

Codon catalog usage and the genome hypothesis.

Abstract: Frequencies for each of the 61 amino acid codons have been determined in every published mRNA sequence of 50 or more codons. The frequencies are shown for each kind of genome and for each individual gene. A surprising consistency of choices exists among genes of the same or similar genomes. Thus each genome, or kind of genome, appears to possess a "system" for choosing between codons. Frameshift genes, however, have widely different choice strategies from normal genes. Our work indicates that the main factors distinguishing between mRNA sequences relate to choices among degenerate bases. These systematic third base choices can therefore be used to establish a new kind of genetic distance, which reflects differences in coding strategy. The choice patterns we find seem compatible with the idea that the genome and not the individual gene is the unit of selection. Each gene in a genome tends to conform to its species' usage of the codon catalog; this is our genome hypothesis.

Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type.

Abstract: The poor printing of our previous Figure 2 (1) is corrected Codon usage in mRNA sequences just published is also given A new correspondence analysis is done, based on simultaneous comparison in all mRNA of use of the 61 codons This analysis reinforces our claim that most genes in a genome, or genome type, have the same coding strategy; that is, they show similar choices among synonymous codons, or among degenerate bases (2) Like analysis on frequency variation in the amino acids coded reveals an entirely different pattern

Integration of the adeno-associated virus genome into cellular DNA in latently infected human Detroit 6 cells.

Abstract: A clone of human cells (Detroit 6) latently infected by adeno-associated virus (AAV) has been characterized with regard to the status of the viral DNA. In both early (9 to 10) and late (118) passages of the clone, AAV-DNA was recombined with host DNA, at least in some cases as a head-to-tail tandem repeat, via the terminal sequences of the viral genome. However, it was not possible to distinguish between integration into chromosomal DNA and very large plasmids (< 20 x 10(6) molecular weight) which contain both viral and cellular DNA sequences. Although evidence for some modifications of the viral sequence was obtained, most of the integrated sequences appeared to be intact. In some cases sequences of undetermined origin separated adjacent copies of the viral genome. Free copies of the AAV genome were detectable in late passage cells, but not in early passage cells. The orientation of nucleotide sequences present in the free AAV DNA from late passage cells was indistinguishable from that of virion DNA. With the notable exception, the organization of the integrated AAV sequences as determined by restriction enzyme digestion remained constant with continued passage. Digestion with SmaI, which cleaves within the palindromic region of the terminal repetition in AAV DNA, produced reproducibly different patterns when early and late passage DNAs were compared. Several models for rescue of free copies of the genome from the integrated DNA are possible, all of which involve the terminal repetition.

Coding potential and regulatory signals of the polyoma virus genome.

Abstract: The complete DNA sequence of the A2 strain of polyoma virus has been determined. It consists of 5,292 base pairs. The sequence is analysed in terms of its coding potential and sites of possible functional significance or structural interest. The polyoma virus genome is compared with those of related tumour viruses, simian virus 40 and BK virus.

The molecular characterization and organization of plant chromosomal dna sequences

Abstract: INTRODUCfION ..... , 569 GENE STRUCfURE AND ARRANGEMENT ........ 571 REPLICATION ORIGINS, MEIOTIC PAIRING, AND RECOMBINATION SEQUENCES 573 CLASSIFICATION OF DNA SEQUENCES BY COpy NUMBER 575 THE LENGTH AND CHROMOSOMAL ARRANGEMENT OF SINGLE COpy SEQUENCES 578 REVERSE REPEATS 581 THE STRUCfURE OF REPEATED SEQUENCE ARRAYS 583 THE DISTRIBUTION OF FAMILIES OF REPEATED SEQUENCES IN THE GENOME 586 THE EVOLUTION OF SOME SEQUENCE ORGANIZATION PATTERNS ...... 587 SEQUENCE INTERSPERSION AND CHROMOSOME FUNCTIONS 590 SUMMARY AND CONCLUDING DISCUSSION 591

Sequence of retrovirus provirus resembles that of bacterial transposable elements

Abstract: The nucleotide sequences of the terminal regions of an infectious integrated retrovirus cloned in the modified λ phage cloning vector Charon 4A have been elucidated. There is a 569-base pair direct repeat at both ends of the viral DNA. The cell–virus junctions at each end consist of a 5-base pair direct repeat of cell DNA next to a 3-base pair inverted repeat of viral DNA. This structure resembles that of a transposable element and is consistent with the protovirus hypothesis that retroviruses evolved from the cell genome.

Molecular cloning of the avian erythroblastosis virus genome and recovery of oncogenic virus by transfection of chicken cells.

Abstract: Avian erythroblastosis virus (AEV) causes erythroblastosis and sarcomas in birds and transforms both erythroblasts and fibroblasts to neoplastic phenotypes in culture. The viral genetic locus required for oncogenesis by AEV is at present poorly defined; moreover, we know very little of the mechanism of tumorigenesis by the virus. To facilitate further analysis of these problems, we used molecular cloning to isolate the genome of AEV as recombinant DNA in a procaryotic vector. The identity of the isolated DNA was verified by mapping with restriction endonucleases and by tests for biological activity. The circular form of unintegrated AEV DNA was purified from synchronously infected quail cells and cloned into the EcoRI site of lambda gtWES x B. A restriction endonuclease cleavage map was established. By hybridization with complementary DNA probes representing specific parts of avian retrovirus genomes, the restriction map of the cloned AEV DNAs was correlated with a genetic map. These data show that nucleotide sequences unique to AEV comprise at least 50% of the genome and are located approximately in the middle of the AEV genome. Our data confirm and extend previous descriptions of the AEV genome obtained by other procedures. We studied in detail two recombinant clones containing AEV DNA: the topography of the viral DNA in the two clones was virtually identical, except that one clone apparently contained two copies of the terminal redundancy that occurs in linear viral DNA isolated from infected cells; the other clone probably contained only one copy of the redundant sequence. To recover infectious virus from the cloned DNA, we developed a procedure for transfection that compensated for the defectiveness of AEV in replication. We accomplished this by ligating cloned AEV DNA to the cloned DNA of a retrovirus (Rous-associated virus type 1) whose genome could complement the deficiencies of AEV. Ligation of the two viral DNAs was facilitated by using a neutral fragment of DNA as linker between otherwise noncompatible termini. Cloned AEV DNA gave rise to infectious AEV capable of transforming fibroblasts and bone marrow cells in culture and of inducing both sarcomas and erythroleukemia in chickens. We conclude that the cloned DNAs represent the authentic genome of AEV undisturbed by the cloning procedure. Molecular cloning offers a powerful approach to the identification and characterization of retrovirus genomes.

The genome of Zea mays, its organization and homology to related grasses

Abstract: The pattern of genome organization of Zea mays has been analyzed, and the relationship of maize to possible progenitor species assessed by DNA∶DNA hybridization. Reassociation of 470 and 1,350 bp fragments of maize DNA to various C0t values demonstrates that the genome is composed of 3 major kinetic classes: highly repetitive, mid-repetitive, and unique. Mini-C0t curves of the repetitive sequences at short fragment length indicate that the highly repetitive sequence class is 20% of the genome and is present at an average reiteration frequency of 800,000 copies; the mid-repetitive sequence class is 40% of the genome and is present at an average reiteration frequency of 1,000 copies. Thermal denaturation studies show that the highly repetitive sequences are 12% divergent and mid-repetitive sequences are 6% divergent. Most of the genome is organized in two interspersion patterns. One, approximately one-third of the genome, is composed of unique sequences of average length 2,100 bp interspersed with mid-repetitive sequences; the other, also one-third of the genome, is mid-repetitive sequences interspersed with highly repetitive sequences. The repetitive sequences are 500 to 1,000 bp by electron microscopic measurement. The remaining third of the genome is unique sequences farther than 5,000 bp from a palindromic or repetitive sequence. Hybridization of maize DNA from Midwestern Dent to popcorn and related grasses indicates that both the unique and repetitive sequence elements have diverged. Teosinte and popcorn are approximately equally divergent from Midwestern Dent whereas Tripsacum is much more divergent. The divergence times calculated from the depression of Tm in heterologous duplexes indicate that the divergence within Zea mays and between maize and near relatives is at least an order of magnitude greater than expected. This high degree of divergence may reflect the pressures of domestication of maize.

Cloning of human papilloma virus genomic DNAs and analysis of homologous polynucleotide sequences.

Abstract: The complete DNA genomes of four distinct human papilloma viruses (human papilloma virus subtype 1a [HPV-1a], HPV-1b, HPV-2a, and HPV-4) were molecularly cloned in Escherichia coli, using the certified plasmid vector pBR322. The restriction endonuclease patterns of the cloned HPV-1a and HPV-1b DNAs were similar to those already published for uncloned DNAs. Physical maps were constructed for HPV-2a DNA and HPV-4 DNA, since these viral DNAs had not been previously mapped. By using the cloned DNAs, the genomes of HPV-1a, HPV-2a, and HPV-4 were analyzed for nucleotide sequence homology. Under standard hybridization conditions (Tm = --28 degrees C), no homology was detectable among the genomes of these papilloma viruses, in agreement with previous reports. However, under less stringent conditions (i.e., Tm = --50 degrees C), stable DNA hybrids could be detected between these viral DNAs, indicating homologous segments in the genomes with approximately 30% base mismatch. By using specific DNA fragments immobilized on nitrocellulose filters, these regions of homology were mapped. Hybridization experiments between radiolabeled bovine papilloma virus type 1 (BPV-1) DNA and the unlabeled HPV-1a, HPV-2a, or HPV-4 DNA restriction fragments under low-stringency conditions indicated that the regions of homology among the HPV DNAs are also conserved in the BPV-1 genome with approximately the same degree of base mismatch.

Replicator regions of the yeast mitochondrial DNA responsible for suppressiveness.

Abstract: Hypersuppressiveness is a heritable property of some rho- mutants (called HS) that, in crosses to rho+, give rise to about 100% rho- cells. The mtDNAs of all HS rho- mutants reveal a common organization: they all share a homologous region of about 300 base pairs (called rep) and the fragments retained are always short (ca. 1% of the wild-type genome) and tandemly repeated. Using one HS rho- mutant as an example, we show that, after crosses with rho+ strains, the mitochondrial genome of the progeny is indistinguishable from that of the HS parent. This suggests that HS mtDNA molecules have a decisive selective advantage for replication during the transient heteroplasmic stage that follows zygote formation, the rep regions playing a role in the control of replication initiation of the mtDNA molecules. The complete nucleotide sequence of one HS rho- mutant and its localization in the oli1-rib3 segment of the rho+ mitochondrial genome are presented. Comparison of the nucleotide sequences of the rep regions of two different HS rho- mutants reveals that several rep sequences must exist in the wild-type genome, probably as a result of duplications of an originally unique ancestor.

Recombinants between endogenous and exogenous avian tumor viruses: role of the C region and other portions of the genome in the control of replication and transformation.

Abstract: Endogenous retroviruses of chickens are closely related to exogenous viruses isolated from spontaneous tumors in the same species, yet differ in a number of important characteristics, including the ability to transform cells in culture, ability to cause sarcomas or leukemias, host range, and growth rate in cell culture. To correlate these differences with specific sequence differences between the two viral genomes, the genome RNA of transforming subgroup E recombinants between the Prague strain of Rous sarcoma virus, subgroup B (Pr-RSV-B), and the endogenous Rous-associated virus-0 (RAV-0), Subgroup E, and seven nontransforming subgroup E recombinants between the transformation-defective mutant of Pr-RSV-B and RAV-0 was examined by oligonucleotide fingerprinting. The pattern of inheritance among the recombinant viruses of regions of the genome in which Pr-RSV-B and RAV-0 differ allowed us to draw the following conclusions. (i) Nonselected parts of the genome were, with a few exceptions, inherited by the recombinant virus progeny randomly from either parent, with no obvious linkage between neighboring sequences. (ii) A small region in the Pr-RSV-B genome which maps in the 5' region was found in all transforming but only some of the nontransforming recombinants, suggesting that it plays a role in the control of the expression of transformation. (iii) A region of the Pr-RSV-B genome which maps between env and src was similarly linked to the src gene and may be either part of the structural gene for src or a control sequence regulating the expression of src. (iv) The C region at the extreme 3' end of the virus genome which is closely related in all the exogenous avian retroviruses but distinctly different in the endogenous viruses is the major determinant responsible for the differences in growth rate between RAV-0 and Pr-RSV-B. This latter observation allowed us to redefine the C region as a genetic locus, c, with two alleles cn (in RAV-0) and cx (in exogenous viruses).

Genome organization and expression in plants

Abstract: Organization of the Nuclear Genome.- Contrasting Patterns of DNA Sequence Organisation in Plants.- On the Evolution and Functional Significance of DNA Sequence Organisation in Vascular Plants.- Plant DNA: Long, Pure and Simple.- The Evolution of Plant Genome Structure.- Cloning and Analysis of Plant DNA.- Chromosome and Gene Structure in Plants: A Picture Deduced from Analysis of Molecular Clones of Plant DNA.- A Model for a Molecular Cloning System in Higher Plants: Isolation of Plant Viral Promotors.- Transcription of the Nuclear Genome.- Purification, Structures and Functions of the Nuclear RNA Polymerases from Higher Plants.- RNA Polymerases and Transcription During Developmental Transitions in Soybean.- Nuclear Genome Expression.- Analysis and Resolution of mRNA Populations.- Structural Gene Expression in Tobacco.- The Regulation of Nuclear Genome Expression.- Messenger RNA Domains in the Embryogenesis and Germination of Cotton Cotyledons.- Hormonal and Genetic Regulation of ?-Amylase Synthesis in Barley Aleurone Cells.- Auxin-Regulated Cell Enlargement: Is there Action at the Level of Gene Expression?.- The Effects of Auxin on the Polyadenylated RNA of Soybean Hypocotyls.- The Role of Light in the Induction of mRNAs for Phenylalanine Ammonia-Lyase and Related Enzymes in Plant Cell Cultures.- Functional Characterization of some Ribosomal Proteins from Wheat Germ.- Macromolecular Properties, Biosynthesis and Genetic Regulation of Cereal Storage Proteins.- Maize Storage Proteins: Characterization and Biosynthesis.- Recent Evidence Concerning the Genetic Regulation of Zein Synthesis.- The Cloning of Zein Sequences and an Approach to Zein Genetics.- The Synthesis of Barley Storage Proteins.- Macromolecular Properties, Biosynthesis and Genetic Regulation of Legume Seed Storage Proteins.- Biosynthesis of Pea Seed Proteins: Evidence for Precursor Forms from in vivo and in vitro Studies.- Bean Seed Globulin mRNA: Translation, Characterization, and its Use as a Probe Towards Genetic Engineering of Crop Plants.- The mRNAs that Code for Soybean Seed Proteins.- Developmental Regulation of Seed Protein Synthesis in Seeds.- Organization and Expression of the Chloroplast Genome.- Organisation and Transcription of Maize Chloroplast Genes.- The Organisation in Higher Plants of the Genes Coding for Chloroplast Ribosomal RNA.- Transfer RNAs and Aminoacyl-tRNA Synthetases in Plant Organelles.- Synthesis, Transport and Assembly Of Chloroplast Proteins.- Synthesis, Transport and Assembly of Chloroplast Proteins.- In vitro Synthesis, Transport, and Assembly of the Constituent Polypeptides of the Light-Harvesting Chlorophyll a/b Protein Complex.- Synthesis, Processing and Functional Probing of P-32000, The Major Membrane Protein Translated Within the Chloroplast.- The Characterisation of Leaf Messenger RNAs and Their Use in the Synthesis of Complementary DNAs.- Sites of Synthesis and Codification of Chloroplast Elongation Factors.- Nuclear Genes Controlling Chloroplast Development.- Mitochondrial Genome Organization and Expression in Higher Plants.- Physico-Chemical and Restriction Endonuclease Analysis of Mitochondrial DNA from Higher Plants.- Mitochondrial Genome Expression in Higher Plants.- The Molecular Biology of Nitrogen Fixation.- Genetics of Nitrogen Fixation In The Bacterium Klebsiella Pneumoniae.- Expression of Host Genes During Symbiotic Nitrogen Fixation.- The Ti-Plasmid of Agrobacterium Tumefaciens.- The Ti-Plasmid of Agrobacterium tumefaciens its role in Crown-Gall Formation.- Location and Fate of pTi T37 DNA in Reversion of Crown Gall Teratoma.- Crown Gall Transcription of Ti Plasmid - Derived Sequences.- Crown Gall Specific Gene Products: Octopine and Nopaline Synthase.- Viral Genome Organization and Expression.- Structure of Plant Viral Genomes.- Translation of Plant Virus RNAs.- Expression of the Cauliflower Mosaic Virus Genome in Turnips (Brassica rapa).- Controlling Elements in Maize: Viroids.- A Re-examination of McClintock's "Controlling elements" in Maize in View of Recent Advances in Molecular Biology.- Structure and Function of Viroids.

Integration of Moloney leukaemia virus into the germ line of mice: correlation between site of integration and virus activation.

Abstract: Endogenous avian1–3 and murine4–9 C-type viruses are genetic elements which are transmitted at several distinct chromosomal loci. Different patterns of virus activation have been observed in a variety of different mouse strains10–12. However, because there are multiple copies of closely related endogenous viruses in every mouse strain, the genetic basis of the differential expression of these genes is poorly understood. A new substrain of mice, BALB/Mo, was derived previously13 carrying the exogenous Moloney leukaemia virus (M-MuLV) genome on chromosome 6 (ref. 14). Virus activation occurs in lymphatic tissues of all BALB/Mo mice soon after birth12. We report here the derivation of three new substrains of mice each carrying a single M-MuLV genome on different chromosomal integration sites. Each locus was associated with a distinct phenotype of virus expression. Evidence is presented that apparently identical viral genomes show differences in spontaneous virus activation and that defective viral genomes can be carried in the germ line of mice.

Restriction endonucleases in identification of a genome type of adenovirus 19 associated with keratoconjunctivitis.

Abstract: Adenovirus type 19 (Ad19) was first associated with disease in 1973 when several outbreaks of keratoconjunctivitis were reported from Europe and North America. We have examined Ad19 isolates by deoxyribonucleic acid restriction with BamHI, BglI, and SmaI restriction endonucleases. All keratoconjunctivitis-associated Ad19 isolates were identical but different from the Ad19 prototype. The total number of resolved restriction fragments of the Ad19 prototype genome was 31, only 17 of which migrated as the restriction fragments of keratoconjunctivitis-associated genomes. We conclude that two different genome types of Ad19 exist, one of which has been responsible for the recent outbreaks of keratoconjunctivitis.

Organization and expression of the mitochondrial genome of plants I. The genes for wheat mitochondrial ribosomal and transfer RNA: evidence for an unusual arrangement

Abstract: We show here that mitochondrial-specific ribosomal and transfer RNAs of wheat (Triticum vulgare Vill. [Triticum aestivum L.] var. Thatcher) are encoded by the mitochondrial DNA (mtDNA). Individual wheat mitochondrial rRNA species (26S, 18S, 5S) each hybridized with several mtDNA fragments in a particular restriction digest (Eco RI, Xho I, or Sal I). In each case, the DNA fragments to which 18S and 5S rRNAs hybridized were the same, but different from those to which 26S rRNA hybridized. From these results, we conclude that the structural genes for wheat mitochondrial 18S and 5S rRNAs are closely linked, but are physically distant from the genes for wheat mitochondrial 26S rRNA. This arrangement of rRNA genes is clearly different from that in prokaryotes and chloroplasts, where 23S, 16S and 5S rRNA genes are closely linked, even though wheat mitochondrial 18S rRNA has previously been shown to be prokaryotic in nature. The mixed population of wheat mitochondrial 4S RNAs (tRNAs) hybridized with many large restriction fragments, indicating that the tRNA genes are broadly distributed throughout the mitochondrial genome, with some apparent clustering in regions containing 18S and 5S rRNA genes.

Inheritance of chloroplast DNA in Chlamydomonas reinhardtii.

Abstract: Two symmetrically located deletions of approximately 100 base pairs each have been identified in chloroplast DNA of Chlamydomonas reinhardtii. Although present in a mutant strain that requires acetate for growth, both deletions have been shown to be distinct from the nonphotosynthetic phenotype of this strain. These physical markers in the chloroplast genome and maternally inherited genetic markers showed strict cotransmission in reciprocal crosses. Thus, our results are consistent with the location of the well-characterized maternally inherited genetic markers in chloroplast DNA of C. reinhardtii.

Amplification of rearranged repeated DNA sequences in cereal plants

Abstract: A simple repeating unit of the rye genome, previously known in tandem arrays, has now been shown to occur also in more complex repeating units. One such unit has been cloned and found to contain some sequences unrelated to the simple repeat. It is proposed that tandem arrays of complex repeats are often produced by amplification of DNA segments formed by recombination of different repeats and possibly unique sequences. Some complex variants of repeats are not in high copy number on all rye chromosomes.

Isolation and mapping of a cloned ribosomal protein gene of Drosophila melanogaster

Abstract: Molecular cloning techniques are particularly well suited to the study of gene organization in Drasophila melanogaster because recombinant DNA can easily be localized in the genome by in situ hybridization to salivary gland polytene chromosomes. We report here the isolation and preliminary characterization of a recombinant phage, designated C25, containing a bona fide D. melanogaster ribosomal protein gene. In situ hybridization demonstrates that this sequence maps to region 99D on chromosome 3.

The cyanobacterial genome, its expression, and the control of that expression.

Abstract: Publisher Summary This chapter reviews the cyanobacterial genome, the machineries of its expression, and the ways in which that expression appears to be controlled. It explains that cyanobacteria are of molecular biological interest for a number of independent reasons, each sufficient to justify their more intensive investigation: evolutionary position, autotrophic physiology, differentiation, ecology, and photosynthesis and nitrogen fixation. Cytochemical and ultrastructural studies showed that the frequently centrally located cyanobacterial “nucleoplasm” is not membrane bounded and contains loosely organized DNA fibrils. Attempts to identify structural analogs of eukaryotic chromosomes within it became less frequent with the growing recognition that cyanobacteria are not, after all, merely simple plants. A “histone-like” DNA binding protein is present in cyanobacteria although cytochemically identifiable histones may be absent. This protein is immunologically indistinguishable from the Escherichia coli (E. coli) histone-like protein HUE and very similar to it and a thermoplasrna “histone” in amino acid composition. There is preliminary evidence that the DNA of can be isolated as an RNA- and protein-containing “nucleoid” analogous to that of E. coli.