Showing papers on "Genome published in 1986"
TL;DR: Five sequences coding for proteins homologous to components of the respiratory‐chain NADH dehydrogenase from human mitochondria have been found and sequence and expression analyses indicate both prokaryotic and eukaryotic features of the chloroplast genes.
Abstract: The complete nucleotide sequence (155 844 bp) of tobacco (Nicotiana tabacum var. Bright Yellow 4) chloroplast DNA has been determined. It contains two copies of an identical 25 339 bp inverted repeat, which are separated by a 86 684 bp and a 18 482 bp single-copy region. The genes for 4 different rRNAs, 30 different tRNAs, 39 different proteins and 11 other predicted protein coding genes have been located. Among them, 15 genes contain introns. Blot hybridization revealed that all rRNA and tRNA genes and 27 protein genes so far analysed are transcribed in the chloroplast and that primary transcripts of the split genes hitherto examined are spliced. Five sequences coding for proteins homologous to components of the respiratory-chain NADH dehydrogenase from human mitochondria have been found. The 30 tRNAs predicted from their genes are sufficient to read all codons if the ;two out of three' and ;U:N wobble' mechanisms operate in the chloroplast. Two sequences which autonomously replicate in yeast have also been mapped. The sequence and expression analyses indicate both prokaryotic and eukaryotic features of the chloroplast genes.
2,184 citations
TL;DR: Comparisons of the predicted amino acid sequences of VZV proteins with those available for HSV-1 proteins generally suggest evolution from an ancestral genome, and allow the functions of several VzV genes to be deduced, although limited regions where the genomes differ in functional organization were also identified.
Abstract: Summary The entire DNA sequence of varicella-zoster virus (VZV) was determined using the M13-dideoxynucleotide technology. The genome is variable in size, but the sequence which was obtained comprises 124884 bp. Analysis of the sequence indicated that the genome contains 70 genes distributed about equally between the two DNA strands. The genes are organized compactly, but regions of overlap between protein-coding regions are not extensive. Many of the genes are arranged in 3′-coterminal families, and at least one is spliced. The discerned organization of VZV genes and that deduced for herpes simplex virus type 1 (HSV-1) from published transcript mapping data indicate that these two members of the Alphaherpesvirinae are very similar in gene layout. Comparisons of the predicted amino acid sequences of VZV proteins with those available for HSV-1 proteins generally suggest evolution from an ancestral genome, and allow the functions of several VZV genes to be deduced, although limited regions where the genomes differ in functional organization were also identified.
1,451 citations
TL;DR: The complete sequence of the chloroplast DNA from a liverwort, Marchantia polymorpha, is determined and the gene organization is deduced, including coding sequences for four kinds of ribosomal RNAs, 32 species of transfer RNAs and 55 identified open reading frames for proteins, which are separated by short A+T-rich spacers.
Abstract: Chloroplasts contain their own autonomously replicating DNA genome. The majority of proteins present in the chloroplasts are encoded by nuclear DNA, but the rest are encoded by chloroplast DNA and synthesized by the chloroplast transcription–translation machinery1–4. Although the nucleotide sequences of many chloroplast genes from various plant species have been determined, the entire gene organization of the chloroplast genome has not yet been elucidated for any species of plants. To improve our understanding of the chloroplast gene system, we have determined the complete sequence of the chloroplast DNA from a liverwort, Marchantia polymorpha, and deduced the gene organization. As reported here the liverwort chloroplast DNA contains 121,024 base pairs (bp), consisting of a set of large inverted repeats (IRA and IRB, each of 10,058 bp) separated by a small single-copy region (SSC, 19,813 bp) and a large single-copy region (LSC, 81,095 bp). We detected 128 possible genes throughout the liverwort chloroplast genome, including coding sequences for four kinds of ribosomal RNAs, 32 species of transfer RNAs and 55 identified open reading frames (ORFs) for proteins, which are separated by short A+T-rich spacers (Fig. 1). Twenty genes (8 encoding tRNAs, 12 encoding proteins) contain introns in their coding sequences. These introns can be classified as belonging to either group I or group II, as described for mitochondria5. Interestingly, seven of the identified ORFs show high homology to unidentified reading frames (URFs) found in human mitochondria6,7.
1,407 citations
TL;DR: Codon usage in the highly expressed group shows a higher correlation with tRNA abundance, a greater degree of third base pyrimidine bias, and a lesser tendency to the A+T richness which is characteristic of the yeast genome.
Abstract: Codon usage data has been compiled for 110 yeast genes. Cluster analysis on relative synonymous codon usage revealed two distinct groups of genes. One group corresponds to highly expressed genes, and has much more extreme synonymous codon preference. The pattern of codon usage observed is consistent with that expected if a need to match abundant tRNAs, and intermediacy of tRNA-mRNA interaction energies are important selective constraints. Thus codon usage in the highly expressed group shows a higher correlation with tRNA abundance, a greater degree of third base pyrimidine bias, and a lesser tendency to the A+T richness which is characteristic of the yeast genome. The cluster analysis can be used to predict the likely level of gene expression of any gene, and identifies the pattern of codon usage likely to yield optimal gene expression in yeast.
1,051 citations
TL;DR: It is shown here that nearly all possible simple motifs occur 5–10 times more frequently than equivalent random motifs, and a new computer algorithm reveals the widespread occurrence of significantly high levels of a new type of ‘cryptic simplicity’ in both coding and noncoding DNA.
Abstract: DNA regions which are composed of a single or relatively few short sequence motifs usually in tandem (‘pure simple sequences’) have been reported in the genomes of diverse species (for reviews see refs 1–4), and have been implicated in a range of functions including gene regulation (for reviews see refs 5–7), signals for gene conversion and recombination8–10, and the replication of telomeres11They are thought to accumulate by DNA slippage12–16 and mispairing during replication and recombination or extension of single-strand ends2,4,10,11. In order to systematize the range of DNA simplicity and the genetic nature of the regions that are simple, we have undertaken an extensive computer search of the DNA sequence library of the European Molecular Biology Laboratory (EMBL)17. We show here that nearly all possible simple motifs occur 5–10 times more frequently than equivalent random motifs. Furthermore, a new computer algorithm reveals the widespread occurrence of significantly high levels of a new type of ‘cryptic simplicity’ in both coding and noncoding DNA. Cryptically simple regions are biased in nucleotide composition and consist of scrambled arrangements of repetitive motifs which differ within and between species. The universal existence of DNA simplicity from monotonous arrays of single motifs to variable permutations of relatively short-lived motifs suggests that ubiquitous slippage-like mechanisms are a major source of genetic variation in all regions of the genome, not predictable by the classical mutation process.
710 citations
TL;DR: It is determined how the number, the arrangement, and the chromosomal position of the integrated gene, as well as the number of injected molecules influence the gene-targeting frequency.
660 citations
TL;DR: It is shown that derivatives of a biologically competent molecular clone of HTLV-III, in which the tat-Ill gene is deleted or the normal splicing abrogated, failed to produce or expressed unusually low levels of virus, respectively, when transfected into T-cell cultures.
Abstract: Studies of the genomic structure of human T-lymphotropic virus type III (HTLV-III) and related viruses, implicated as the causal agent of acquired immune deficiency syndrome (AIDS), have identified a sixth open reading frame in addition to the five previously known within the genome (gag, pol, sor, env and 3′orf)1–4. This gene, called tat-III, lies between the sorand env genes and is able to mediate activation, in a trans configuration, of the genes linked to HTLV-III long terminal repeat (LTR) sequences5–8. We now present evidence that the product of far-III is an absolute requirement for virus expression. We show that derivatives of a biologically competent molecular clone of HTLV-III9, in which the tat-Ill gene is deleted or the normal splicing abrogated, failed to produce or expressed unusually low levels of virus, respectively, when transfected into T-cell cultures. The capacity of these tat-III-defective genomes was transiently restored by co-transfection of a plasmid clone containing a functional tat-III gene or by introducing the tat-III protein itself. As HTLV-III and related viruses are the presumed causal agents of AIDS and associated conditions10–12, the observation that tat-III is critical for HTLV-III replication has important clinical implications, and suggests that specific inhibition of the activity of tat-III could be a novel and effective therapeutic approach to the treatment of AIDS.
624 citations
TL;DR: A technique for digital characterization and comparison of DNA fragments, using restriction enzymes, is described, being applied to fragments from the nematode Caenorhabditis elegans to facilitate cross-indexing of clones emanating from different laboratories and to construct a physical map of the genome.
Abstract: A technique for digital characterization and comparison of DNA fragments, using restriction enzymes, is described. The technique is being applied to fragments from the nematode Caenorhabditis elegans (i) to facilitate cross-indexing of clones emanating from different laboratories and (ii) to construct a physical map of the genome. Eight hundred sixty clusters of clones, from 35 to 350 kilobases long and totaling about 60% of the genome, have been characterized.
616 citations
TL;DR: Biochemical and electron microscopic data indicate that the human hepatitis δ viral agent contains a covalently closed circular and single-stranded RNA genome that has certain similarities with viroid-like agents from plants.
Abstract: Biochemical and electron microscopic data indicate that the human hepatitis δ viral agent contains a covalently closed circular and single-stranded RNA genome that has certain similarities with viroid-like agents from plants. The sequence of the viral genome (1,678 nucleotides) has been determined and an open reading frame within the complementary strand has been shown to encode an antigen that binds specifically to antisera from patients with chronic hepatitis δ viral infections.
605 citations
TL;DR: A 3547 bp DNA fragment from male-sterile maize mitochondria, designated TURF 2H3, selected because of its unique and abundant transcripts appears to be uniquely altered in cms-T plants restored to fertility by the nuclear restorer genes Rf1 and Rf2.
TL;DR: Analysis of the putative polypeptides confirms that B19 is only distantly related to the other parvoviruses but reveals that there is a small region in the gene probably encoding the major nonstructural protein of B19, which is closely conserved between all of theParvovirus genomes for which sequence information is currently available.
Abstract: The nucleotide sequence of an almost-full-length clone of human parvovirus B19 was determined. Whereas the extreme left and right ends of this genomic clone are incomplete, the sequence clearly indicates that the two ends of viral DNA are related by inverted terminal repeats similar to those of the Dependovirus genus. The coding regions are complete in the cloned DNA, and the two large open reading frames which span almost the entire genome are restricted to one strand, as has been found for all other parvoviruses characterized to date. From the DNA sequence we conclude that the organization of the B19 transcription units is similar although not identical to those of other parvoviruses. In particular, we predict that the B19 genome may utilize a fourth promoter to transcribe mRNA encoding the major structural polypeptide, VP2. Analysis of the putative polypeptides confirms that B19 is only distantly related to the other parvoviruses but reveals that there is a small region in the gene probably encoding the major nonstructural protein of B19, which is closely conserved between all of the parvovirus genomes for which sequence information is currently available.
TL;DR: It is indicated that noncoding sequences are associated with biological functions and that natural selection plays a more important role in genome evolution than do random events.
Abstract: Nucleotide sequences of all genomes are subject to compositional constraints that (1) affect, to about the same extent, both coding and noncoding sequences; (2) influence not only the structure and function of the genome, but also those of transcripts and proteins; (3) are the result of environmental pressures; and (4) largely control the fixation of mutations. These findings indicate (1) that noncoding sequences are associated with biological functions; (2) that the organismal phenotype comprises two components, the classical phenotype, corresponding to the “gene products,” and a “genome phenotype,” which is defined by the compositional constraints; and (3) that natural selection plays a more important role in genome evolution than do random events.
TL;DR: DNA sequence analyses have shown that transposable elements may share certain structural features that might be useful for classification, and transposition can now be demonstrated by DNA hybridization techniques that were unknown 20 years ago.
Abstract: Publisher Summary In plants, variegation is most easily recognized as irregularities in pigment patterns on leaves, flowers, and seeds, although other characteristics such as leaf form, flower form, or starch content (in maize kernels) may also be subject to variegation This chapter focuses on variegation in plants due to genetic alterations implemented by transposable elements The distinguishing feature of this kind of variegation, as opposed to other examples discussed, is that the two or more different kinds of tissue in the variegated plant differ genotypically, that is, with respect to the DNA of their nuclear genomes In the simplest case, one kind of tissue contains a transposable element at a given locus and the other does not The term “transposable element” rather than “controlling element” is used to avoid confusion with the terminology of other fields of genetic research First, data from molecular research that have provided new criteria beyond those obtained by classical genetic methods are discussed Thus, DNA sequence analyses have shown that transposable elements may share certain structural features that might be useful for classification Furthermore, transposition can now be demonstrated by DNA hybridization techniques that were unknown 20 years ago In general, a transposable element is characterized by its ability to integrate into the DNA at some position in the genome and thereby alter the expression of the gene(s) in and around itself
TL;DR: This chapter describes a filter hybridization approach for mapping chloroplast DNA (cpDNA) restriction sites along with several strategies for generating restriction fragments for use as hybridization probes.
Abstract: Publisher Summary This chapter describes a filter hybridization approach for mapping chloroplast DNA (cpDNA) restriction sites along with several strategies for generating restriction fragments for use as hybridization probes. Approaches for visualizing and mapping cpDNAs that are difficult or impossible to isolate in very pure form are also discussed. The chloroplast genome is densely packed with genes and many of them have been isolated and sequenced. Chloroplast gene products identified thus far function either in photosynthesis or as components of the chloroplast protein synthesizing system. The basic strategy for mapping by overlap hybridization is to hybridize each one of a set of restriction fragments that together cover an entire chloroplast genome to replica membranes containing various single and double digests of total cpDNA. Three classes of individually purified cpDNA restriction fragments that can be used as hybridization probes are homologous, uncloned fragments; homologous, cloned fragments; and heterologous, cloned fragments. Procedures to obtain each class of probe fragments and the relative merits of each class are discussed.
TL;DR: A comparison of the deduced amino acid sequences encoded by the pol region showed HERV-K to be closely related to types A and D retroviruses and even more so to type B retrovirus.
Abstract: We determined the complete nucleotide sequence of the human endogenous retrovirus genome HERV-K10 isolated as the sequence homologous to the Syrian hamster intracisternal A-particle (type A retrovirus) genome. HERV-K10 is 9,179 base pairs long with long terminal repeats of 968 base pairs at both ends; a sequence 290 base pairs long, however, was found to be deleted. It was concluded that a composite genome having the 290-base-pair fragment is the prototype HERV-K provirus gag (666 codons), protease (334 codons), pol (937 codons), and env (618 codons) genes. The size of the protease gene product of HERV-K is essentially the same as that of A- and D-type oncoviruses but nearly twice that of other retroviruses. A comparison of the deduced amino acid sequences encoded by the pol region showed HERV-K to be closely related to types A and D retroviruses and even more so to type B retrovirus. It was noted that the env gene product of HERV-K structurally resembles the mouse mammary tumor virus (type B retrovirus) env protein, and the possible expression of the HERV-K env gene in human breast cancer cells is discussed.
TL;DR: It is demonstrated that transfer of paternal or maternal nuclei from early haploid preimplantation embryos back to fertilized eggs from which one pron nucleus was removed resulted in development to term, but only if the remaining pronucleus was of the parental type opposite to the donor nucleus.
TL;DR: Comparison of mitochondrial and nuclear DNA divergences among echinoid and vertebrate taxa of similar ages indicates that the rapid rate of vertebrate mitochondrial DNA evolution is, in part, an artifact of a widely divergent rate of nuclear DNA evolution.
Abstract: The discovery that the rate of evolution of vertebrate mitochondrial DNA is rapid, compared to the rate for vertebrate nuclear DNA, has resulted in its widespread use in evolutionary studies. Comparison of mitochondrial and nuclear DNA divergences among echinoid and vertebrate taxa of similar ages indicates that the rapid rate of vertebrate mitochondrial DNA evolution is, in part, an artifact of a widely divergent rate of nuclear DNA evolution. This disparity in relative rates of mitochondrial and nuclear DNA divergence suggests that the controls and constraints under which the mitochondrial and nuclear genomes operate are evolving independently, and provides evidence that is independent of fossil dating for a robust rejection of a generalized molecular clock hypothesis of DNA evolution.
TL;DR: The unstable white-peach (wpch) allele exhibits a spectrum of germ-line and somatic mutability more similar to insertion mutations in maize and in the nematode Caenorhabditis elegans than has been reported for insertion mutation mutations in Drosophila.
Abstract: A transposable element has been isolated from an unstable white mutation in Drosophila mauritiana, a sibling species of Drosophila melanogaster. The unstable white-peach (wpch) allele exhibits a spectrum of germ-line and somatic mutability more similar to insertion mutations in maize and in the nematode Caenorhabditis elegans than has been reported for insertion mutations in Drosophila. The inserted element mariner is 1286 nucleotides long and has terminal inverted repeats. The element contains a single open reading frame encoding 346 amino acids. A duplication of 2 base pairs of white sequence is present at the insertion site. Mariner is present in approximately 20 copies in the D. mauritiana genome, is present from 0 to 7 copies in other members of the sibling species group, and is apparently absent from the genome of D. melanogaster.
TL;DR: To characterize the DNA sequence organization of this plant, 50 recombinant lambda clones containing inserts containing inserts with an average length of 12,800 base-pairs are randomly selected and their content of repetitive and unique DNA is analyzed by various genome blot, restriction digestion and RNA blot procedures.
TL;DR: The streptococcal plasmid pMV158 and its derivative pLS1 are able to replicate and confer tetracycline resistance in both Gram-positive and Gram-negative bacteria and were highly homologous to tet genes in two other plasmids of Gram- positive origin but different in both sequence and mode of regulation.
TL;DR: A WNV mutant, which replicates progeny genome RNA more efficiently than parental WNV, was found to have a 3'-genomic sequence identical to that of its parent virus, indicating that this structure is important for the survival of the virus.
TL;DR: In this paper, DNAs from Mycobacterium tuberculosis, M. phlei and M. smegmatis were digested by restriction enzymes and hybridized with three probes consisting of the 5' (16S rRNA), the middle (16 s and 23S rRNB), and the 3' (23S and 5S r RNB) portions of the Escherichia coli rrnB operon.
01 Jan 1986
TL;DR: In a number of cases, the single base changes responsible for the temperature-sensitive phenotype of certain mutants have been determined and may lead to a more directed approach to vaccine production than the empirical strategies used heretofore.
Abstract: In the last few years, our knowledge of the molecular biology of viruses has been greatly expanded by the technology of nucleic acid sequencing. Determination of the complete sequence of virus genomes coupled with mapping of the virus-encoded proteins on those genomes has resulted in a wealth of information about the structure of the genome, the nature of the encoded proteins, the translation strategy used by the virus, and the nature of proteolytic processing or other modification events involved in maturation of viral proteins. Comparison of the nucleic acid and deduced amino acid sequences of related viruses can reveal conserved domains, suggesting that these regions play key roles in either virus replication or morphology. Recombinant DNA technology makes it possible to design experiments to test the function of such domains directly; in particular, manipulation of viral genomes may lead to a more directed approach to vaccine production than the empirical strategies used heretofore. In a number of cases, the single base changes (and resulting amino acid substitutions) responsible for the temperature-sensitive phenotype of certain mutants have been determined. Nucleic acid sequencing is also being used to locate immunological epitopes as well as protein domains involved in virulence and specific tissue tropisms.
TL;DR: Two genes encoding distinct histidine-rich proteins in a Plasmodium falciparum clone exhibit high levels of homology, suggesting they have originated by duplication and divergence from a common ancestral sequence.
Abstract: Two genes encoding distinct histidine-rich proteins in a Plasmodium falciparum clone exhibit high levels of homology, suggesting they have originated by duplication and divergence from a common ancestral sequence. Both genes have a similar interrupted structure and an exon that encodes closely related tandem repeats of very high histidine and alanine content. The most common repeat encoded by one gene, the hexapeptide Ala-His-His-Ala-Ala-Asp, differs in the sixth position from the most common repeat encoded by the other gene, the hexapeptide Ala-His-His-Ala-Ala-Asn. The divergence of the repeat domains is greater than that of the flanking regions, which exhibit 85-90% homology, including untranslated sequences. This suggests the tandem repeats are relatively labile elements within the genome that may provide the parasite with a means of rapid evolutionary change.
TL;DR: Analysis of G +C content distribution along DNA sequences using a DNA Sequence Data Bank supported the view that the vertebrate genome is a mosaic of regions with clear differences in their G + C content.
Abstract: Correlation was positive between the G + C content at the codon third position in genes of vertebrates and the G + C content of the genome portion surrounding each gene. Exons of genes with a high G + C% at the codon 3rd position are surrounded by G + C-rich introns and G + C-rich flanking sequences, and those with a low G + C% at the position by A + T-rich introns and flanking sequences. Analysis of G + C content distribution along DNA sequences using a DNA Sequence Data Bank supported the view that the vertebrate genome is a mosaic of regions with clear differences in their G + C content. The biological significance of the variation in G + C content throughout the vertebrate genome is discussed in connection with chromosomal banding.
TL;DR: Three repeated sequence clones, pAS1), pAS2 and pAS12, contain repeated sequences which were distributed throughout the genome and will allow assessment of genome plasticity in Aegilops squarrosa.
Abstract: Three repeated sequence clones, pAS1(1.0 Kb), pAS2(1.8 Kb) and pAS12(2.5 Kb), were isolated fromAegilops squarrosa (Triticum tauschii). The inserts of the three clones did not hybridize to each other. Two of the clones, pAS2 and pAS12, contain repeated sequences which were distributed throughout the genome. The clone pAS1 sequence was more restricted and was located in specific areas on telomeres and certain interstitial sites along the chromosome length. This cloned sequence was also found to be restricted to the D genome at the level ofin situ hybridization. The pAS1 sequence will be useful in chromosomal identification and phylogenetic analysis. All three clones will allow assessment of genome plasticity inAegilops squarrosa.
TL;DR: A new member of this multigene family, actin 15, is identified and its complete nucleotide sequence and transcription initiation sites are reported, and it is reported that gene fusion RNAs transcribed from the actin15 and actin 6 vectors were regulated like endogenous actin genes during D. discoideum development.
Abstract: The Dictyostelium discoideum genome contains an estimated 17 to 20 actin genes. We report the identification of a new member of this multigene family, actin 15, and its complete nucleotide sequence and transcription initiation sites. We constructed transformation vectors carrying either the actin 15 promoter fused to the neomycin phosphotransferase gene from transposon Tn903 or the actin 6 promoter fused to the neomycin phosphotransferase gene from Tn5. Cells transformed with the actin 15 vector carried less than five copies of vector DNA, while cells transformed with the actin 6 vector carried more than 200 copies. In both cases, the vector appeared to be integrated into the chromosome as a tandem array. Gene fusion RNAs transcribed from the actin 15 and actin 6 vectors were regulated like endogenous actin genes during D. discoideum development. DNA sequences required for temporal and cell type-specific regulation of these genes were contained within 2.8 kilobases of 5' noncoding DNA for actin 15 and 0.7 kilobases of 5' noncoding DNA for actin 6.
TL;DR: BamHI and PstI cleavage maps were constructed by analysis of the cloned fragments of the chloroplast DNA, and the 11 ribosomal protein genes and other major sequenced genes have been marked on the map.
TL;DR: Six Buschke-Löwenstein tumors, i.e., highly differentiated squamous cell tumors of the genital region, were shown to contain human papillomavirus 6 or HPV 11 genomes, and a tandem duplication of 459 base pairs within the noncoding region of the genome was found in the new subtype HPV 6d.
Abstract: Six Buschke-Lowenstein tumors, i.e., highly differentiated squamous cell tumors of the genital region, were shown to contain human papillomavirus 6 (HPV 6) or HPV 11 genomes. The viral DNA was found in an episomal state, including a very small fraction of circular oligomers. HPV 6a and HPV 6d genomes were cloned from two of the tumors. Comparison with HPV 6b, cloned from a benign genital wart (E. -M. de Villiers, L. Gissmann, and H. zur Hausen, J. Virol. 40:932-935, 1981) by restriction mapping and partial sequence analysis, revealed a very high degree of homology with the different HPV 6 subtypes. A tandem duplication of 459 base pairs within the noncoding region of the genome was found in the new subtype HPV 6d. This structural rearrangement in a region containing the putative control elements for early gene transcription might influence the biological potential of that virus. No evidence for rearrangement of this region was found in the HPV DNA from the five other tumors.