Showing papers on "Genome published in 1984"
TL;DR: Many, probably even all possible types of simple sequence are repetitive components of eukaryotic genomes and it is proposed that they arise by common mechanisms namely slippage replication and unequal crossover and that they might have no general function with regards to gene expression.
Abstract: Simple sequences are stretches of DNA which consist of only one, or a few tandemly repeated nucleotides, for example poly (dA) X poly (dT) or poly (dG-dT) X poly (dC-dA). These two types of simple sequence have been shown to be repetitive and interspersed in many eukaryotic genomes. Several other types have been found by sequencing eukaryotic DNA. In this report we have undertaken a systematical survey for simple sequences. We hybridized synthetical simple sequence DNA to genome blots of phylogenetically different organisms. We found that many, probably even all possible types of simple sequence are repetitive components of eukaryotic genomes. We propose therefore that they arise by common mechanisms namely slippage replication and unequal crossover and that they might have no general function with regards to gene expression. This latter inference is supported by the fact that we have detected simple sequences only in the metabolically inactive micronucleus of the protozoan Stylonychia, but not in the metabolically active macronucleus which is derived from the micronucleus by chromosome diminution.
1,382 citations
TL;DR: It is shown that this DNA homology (the homeo box) is due to a conserved protein-coding sequence present in these three pattern-formation genes and is reflected in a structural homology in their gene products.
807 citations
TL;DR: A cis-acting element within 1.8 kbp of the viral genome that allows recombinant plasmids carrying it to be selected at high frequency and maintained as plasmid in cells latently infected by EBV is identified.
Abstract: The Epstein-Barr viral (EBV) genome of approximately equal to 170 kilobase pairs (kbp) is maintained as a plasmid in human B lymphoblasts transformed by the virus. We have identified a cis-acting element within 1.8 kbp of the viral genome that allows recombinant plasmids carrying it to be selected at high frequency and maintained as plasmids in cells latently infected by EBV. This functional element(s) requires a segment of DNA at least 800 bp and at most 1800 bp long, which contains a family of 30-bp tandem repeats at one end. Since this region confers efficient stable replication only to plasmids transfected into cells containing EBV genomes, its function probably requires trans-acting products encoded elsewhere in the viral genome.
703 citations
TL;DR: The extent of homology between JC virus DNA and the genomes of simian virus 40 (69%) and BK virus (75%) confirmed the close evolutionary relationship of these three polyomaviruses.
Abstract: The complete DNA sequence of the human JC virus, which was found to consist of 5,130 nucleotide pairs, is presented. The amino acid sequence of six proteins could be deduced: the early, nonstructural proteins, large T and small t antigens; the late capsid proteins, VP1, VP2, and VP3; and the agnogene product encoded within the late leader sequence, called the agnoprotein in simian virus 40. The extent of homology between JC virus DNA and the genomes of simian virus 40 (69%) and BK virus (75%) confirmed the close evolutionary relationship of these three polyomaviruses. The sequences showing the greatest divergence in these viral DNAs occurred within the tandem repeats located to the late side of the replication origins.
647 citations
TL;DR: While the REP sequences do not appear to modulate differential gene expression within an operon, they can affect the expression of both upstream and downstream genes to a small extent, probably by affecting the rate of mRNA degradation.
577 citations
TL;DR: The complete nucleotide sequences of the genomes of the type 2 ( P712, Ch, 2ab ) and type 3 (Leon 12a1b ) poliovirus vaccine strains were determined and suggested that the serotypes of poliov virus derived from a common prototype.
413 citations
TL;DR: The method described here provides a powerful and generally applicable molecular taxonomic approach towards a global phylogeny encompassing all organisms and organelles.
Abstract: To probe the earliest evolutionary events attending the origin of the five known genome types (archaebacterial, eubacterial, nuclear, mitochondrial and plastid), we have analyzed sequences corresponding to a ubiquitous, highly conserved core of secondary structure in small subunit rRNA. Our results support (i) the existence of three primary lineages (archaebacterial, eubacterial, and nuclear), (ii) a specific eubacterial ancestry for plastids and mitochondria (plant, animal, fungal), and (iii) an endosymbiotic, evolutionary origin of the two types of organelle from within distinct groups of eubacteria (blue-green algae (cyanobacteria) in the case of plastids, nonphotosynthetic aerobic bacteria in the case of mitochondria). In addition, our analysis suggests (iv) a biphyletic origin of mitochondria, with animal and fungal mitochondria branching together but separately from plant mitochondria, and (v) a monophyletic origin of plastids. The method described here provides a powerful and generally applicable molecular taxonomic approach towards a global phylogeny encompassing all organisms and organelles.
372 citations
TL;DR: The availability of the cloned HTLV-III genome will now allow an unambiguous comparison of this virus with other retroviruses that also have been associated with the pathogenesis of AIDS8–11, and will facilitate the development of diagnostic and therapeutic measures in the treatment of AIDS.
Abstract: We recently reported the isolation and characterization of a novel human T-lymphotropic retrovirus, HTLV-III, in patients with acquired immune deficiency syndrome (AIDS) and in those at risk for the disease. After extensive sero-epidemiological studies, together with numerous virus isolations from these patients, we concluded that HTLV-III is the causative agent of AIDS. Here we report the molecular cloning and characterization of two highly related but distinct forms of the HTLV-III genome. The viral genome is approximately 10 kilobases long and is detected in HTLV-III-infected cells but not in uninfected cells, including normal human tissue, indicating that this virus is exogenous to man. We also demonstrate distant nucleic acid sequence homology between the cloned genome of HTLV-III and those of HTLV-I and HTLV-II. The availability of the cloned HTLV-III genome will now allow an unambiguous comparison of this virus with other retroviruses that also have been associated with the pathogenesis of AIDS, and moreover, with facilitate the development of diagnostic and therapeutic measures in the treatment of AIDS.
335 citations
TL;DR: Certain subsegments of the per region, transduced into the genome of arrhythmic pero flies, restore rhythmicity in circadian locomotor behavior and the male's courtship song.
321 citations
TL;DR: Two regions of the Neisseria gonorrheae genome, pilE1 and pilE2, which are involved in pilus expression, are mapped, which indicate that these two loci carry sequences necessary for pilin production when cells are in the piliated P+ state.
Abstract: We have mapped two regions of the Neisseria gonorrheae genome, pilE1 and pilE2, which are involved in pilus expression. When the cells are in the piliated P+ state, these two loci carry sequences necessary for pilin production. A silent locus, pilS1, also maps near pilE1 and pilE2. pilS1 contains structural gene information but lacks pilus promoter sequences. The pilus gene sequences in pilE1 and pilE2 are identical in strain MS11.
313 citations
TL;DR: It is demonstrated that Arabidopsis has an extraordinarily small haploid genome size and a low level of cytosine methylation for an angiosperm, and appears to have little repetitive DNA in its nuclear DNA, in contrast to other higher plants.
Abstract: Arabidopsis thaliana is a small flowering plant of the mustard family. It has a four to five week generation time, can be self- or cross-pollinated and bears as many as 104 seeds per plant. Many visible and biochemical mutations exist and have been mapped by recombination to one of the five chromosomes that comprise the haploid karyotype. With the experiments reported here we demonstrate that Arabidopsis has an extraordinarily small haploid genome size (approximately 7×107 nucleotide pairs) and a low level of cytosine methylation for an angiosperm. In addition, it appears to have little repetitive DNA in its nuclear DNA, in contrast to other higher plants.
TL;DR: The size of the mitochondrial genome from the fertile cytoplasm of maize has been determined by restriction mapping to be 570 kb.
Abstract: The size of the mitochondrial genome from the fertile cytoplasm of maize has been determined by restriction mapping to be 570 kb. The entire sequence complexity of the genome can be represented on a single circular DNA species (the 'master circle'). The presence of reiterated sequences, active in recombination, results in a complex multipartite organisation.
TL;DR: Mo-10 has been mapped to the proximal portion of mouse chromosome 6, and its position in relationship to genes known to influence mouse morphogenesis is discussed.
TL;DR: Comparison of the nucleotide sequence and the predicted amino acid sequence with those of the polioviruses reveals a surprising degree of homology which may allow recognition of regions of antigenic importance and prediction of the virus polyprotein cleavage sites.
Abstract: The complete nucleotide sequence of the single-stranded RNA genome of human rhinovirus 14, one of the causative agents of the common cold, has been determined from cDNA cloned in E. coli. The genome is typical of the picornaviridae family, comprising a 5' non-coding region of 624 nucleotides, a long open reading frame of 6537 nucleotides (90.8% of the genome) and a 3' non-coding region of 47 nucleotides. Comparison of the nucleotide sequence and the predicted amino acid sequence with those of the polioviruses reveals a surprising degree of homology which may allow recognition of regions of antigenic importance and prediction of the virus polyprotein cleavage sites. The results presented here imply a closer genetic relationship between the rhinovirus and enterovirus genera than previously suspected.
TL;DR: Albinism in plants regenerated from pollen by anther culture may result from the same mechanisms as postulated to be responsible for maternal inheritance of chloroplasts, and Southern blotting was used to show that large regions of the chloroplast genome were deleted in the major ctDNA molecules present in eight albino wheat plants Regenerated from separate pollen calluses.
TL;DR: It is reported here that two discontinuous regions within the viral genome can independently support extrachromosomal replication of the Tn5 neomycinr gene in cells that provide viral factors in trans.
TL;DR: Results demonstrate that individual clones used to probe genomic digests of DNA from a pair of Chinese hamster cell lines with or without mouse chromosome 17 have been derived from the t-complex or regions closely linked to it.
TL;DR: The nucleotide sequences of the infectious cloned DNA components of tomato golden mosaic virus (TGMV) have been determined and a model for bidirectional transcription of the two genome components is presented.
Abstract: The nucleotide sequences of the infectious cloned DNA components of tomato golden mosaic virus (TGMV) have been determined. DNA A (2588 nucleotides) and DNA B (2508 nucleotides) have little sequence homology except for a region of ˜200 bases which is almost identical in the two molecules. Analysis of open reading frames revealed six potential coding regions for proteins of mol. wt. >10 000, four in DNA A and two in DNA B. Possible regulatory signals are identified and a model for bidirectional transcription of the two genome components is presented. Comparison of the nucleotide sequences of the DNAs of TGMV and cassava latent virus (CLV) revealed a fairly close relationship between TGMV DNA A and CLV DNA 1 and a comparatively distant relationship between TGMV DNA B and CLV DNA 2. All the potential coding regions in the TGMV DNAs had counterparts in the CLV DNAs suggesting an overall similarity in genome organisation, but six potential coding regions in the CLV DNAs had no counterparts in the TGMV DNAs. The 200-base region common to the two DNAs of each virus had little sequence homology, except for a highly conserved 33-base sequence potentially capable of forming a stable hairpin structure.
TL;DR: At least one of the viral proteins and enzymatic activities required in the reaction has been identified and analysis of this apparently efficient and highly specific site‐directed recombination event in eukaryotic cells promises to provide insights of both fundamental and practical interest.
Abstract: The synthesis and integration of DNA into the genome of its host cell is a normal step in the replication of the retroviruses. Previous studies have provided details concerning the structure of viral DNA and viral and host integration sites. More recent genetic and biochemical results have expanded our understanding considerably: it should soon be possible to describe the exact viral DNA sequence recognized during the integration reaction for several viruses. In addition, at least one of the viral proteins and enzymatic activities required in the reaction has been identified. Analysis of this apparently efficient and highly specific site-directed recombination event in eukaryotic cells promises to provide insights of both fundamental and practical interest.
TL;DR: The nucleotide sequences of brome mosaic virus RNAs 1 and 2 have been determined, completing the primary structure of the 8200 base tripartite BMV genome and suggesting that the 3' ends of the BMV RNAs are the major regulatory regions of the genome.
TL;DR: The complete nucleotide sequence of the genome of 17.6 is determined, which shows that it contains three long open reading frames comparable with gag, pol and env genes in retrovirus, and includes a coding sequence similar to that for reverse transcriptase, suggesting a role for this enzyme in the life cycle of some Drosophila copia-like elements, analogous to the situation in Retrovirus.
Abstract: The largest group of transposable elements in Drosophila melanogaster, copia-like elements1,2, share some important structural features with and are intimately related in evolution to vertebrate retroviruses2–12. To further clarify the relationship between retroviruses and copia-like transposable elements, we set out to determine the complete nucleotide sequence of the genome of 17.6, which has long terminal repeats homologous in nucleotide sequence to those of avian leukaemia–sarcoma virus12. We report here that 17.6 contains three long open reading frames comparable with gag, pol and env genes in retrovirus. At the level of amino acid sequence, the longest open reading frame of 17.6 includes a coding sequence similar to that for reverse transcriptase, suggesting a role for this enzyme in the life cycle of some Drosophila copia-like elements, analogous to the situation in retrovirus.
TL;DR: The genome of the small human virus serologically associated with erythrocyte aplasia and erythema infectiosum (fifth disease) is shown to be a linear, nonpermuted, single-stranded DNA molecule with self-priming hairpin termini, properties which are characteristic of the genomes of the family Parvoviridae.
Abstract: The genome of the small human virus serologically associated with erythrocyte aplasia and erythema infectiosum (fifth disease) is shown to be a linear, nonpermuted, single-stranded DNA molecule with self-priming hairpin termini, properties which are characteristic of the genomes of the family Parvoviridae. This human parvovirus chromosome was molecularly cloned into bacterial plasmid vectors and the cloned DNA was used to explore its relatedness to other mammalian parvovirus serotypes by DNA:DNA hybridization. It is not related to the human adeno-associated viruses but does show a distant evolutionary relationship to genomes of the helper-independent parvoviruses of rodents. This strongly suggests that it is an autonomous parvovirus, and as such is the first example of a member of this group of common animal pathogens to cause disease in man.
TL;DR: It is argued that a strong determinant of the distinct disease specificities of Fr-muLV and Mo-MuLV lies in this 3' end 0.62-kilobase fragment which contains the putative virus enhancers.
Abstract: Nondefective Friend helper murine leukemia virus (Fr-MuLV) induces primarily erythroleukemias in NFS mice, whereas Moloney murine leukemia virus (Mo-MuLV) induces T cell lymphomas. Using molecular clones of these two viruses, we constructed a recombinant in which a 0.62-kilobase fragment encompassing the U3 region at the 3' end of the Fr-MuLV genome replaced the corresponding region of Mo-MuLV. The recombinant virus obtained by transfection of this clone, whose genome is derived primarily from Mo-MuLV, induces almost exclusively erythroleukemias in NFS mice. This and the previous result of Chatis et al. (Proc. Natl. Acad. Sci. U.S.A. 80:4408-4411), showing that the reciprocal recombinant whose genome is primarily derived from Fr-MuLV induces almost exclusively lymphomas, argue that a strong determinant of the distinct disease specificities of Fr-MuLV and Mo-MuLV lies in this 3' end 0.62-kilobase fragment which contains the putative virus enhancers. To more precisely define this determinant, we have begun to construct recombinants in which smaller 3' end fragments of the Fr-MuLV and Mo-MuLV genomes are exchanged. Analysis of the first such recombinant showed that Fr-MuLV can be converted to a lymphoma-inducing virus in NFS mice by substitution of a 0.38-kilobase fragment encompassing the virus enhancers in U3 with the corresponding region of the Mo-MuLV genome.
TL;DR: The sequence of about 4,500 nucleotides of the internal part of tobacco mosaic virus (TMV)-tomato strain (L) RNA has been newly determined using cloned cDNAs and a new method for cDNA cloning was developed by which the cDNA of the 5'-terminus of viral RNA can be cloned efficiently.
Abstract: The sequence of about 4,500 nucleotides of the internal part of tobacco mosaic virus (TMV)-tomato strain (L) RNA has been newly determined using cloned cDNAs. Together with the previously determined partial sequences at both ends, the entire sequence of the 6,384 nucleotide genome has been completed. The 130K (1,115 amino acids), 180K (1,615 amino acids), 30K (263 amino acids) and coat protein (158 amino acids) cistrons are located at residues 72-3442, 72-4922, 4906-5700, and 5703-6182 on the genome, respectively. Sequence polymorphism was not observed except for heterogeneity in the length of the A cluster near the 3' end. The homology of the nucleotide sequences of TMV-L and TMV-vulgare, a common strain, is about 80% on average. Remarkable differences between them were found in a part of the N-terminal portion of the 130K/180K protein and the C-terminal portion of the 30K protein. A new method for cDNA cloning was developed by which the cDNA of the 5'-terminus of viral RNA can be cloned efficiently.
TL;DR: Recombinant viral genomes carrying a selectable drug resistance marker have been constructed by insertion of a hybrid gene for neomycin resistance into the helper-independent adenovirus vector, delta E1/X, demonstrating that early region 1 is not essential for integration of the viral genome.
Abstract: Recombinant viral genomes carrying a selectable drug resistance marker have been constructed by insertion of a hybrid gene for neomycin resistance into the helper-independent adenovirus vector, delta E1/X. The hybrid gene consists of sequences coding for the aminoglycoside 3'-phosphotransferase II from Tn5, under the control of the simian virus 40 early promoter, and renders mammalian cells resistant to the neomycin analog, G-418. Most of adenovirus early region 1 is deleted from delta E1/X (nucleotides 455 to 3330), and recombinant viral genomes carry the hybrid gene in its place. The large and small XbaI fragments of delta E1/X were ligated to the hybrid gene, and the mixture was transfected into 293 cells. Single plaques were isolated and subsequently passaged in 293 cells to produce virus stocks. The recombinant viruses efficiently rendered cultured rat (Rat2) and simian (CV1) cells resistant to G-418. Cloned cell lines selected for resistance to G-418 contained viral DNA integrated into the host cell genome, demonstrating that early region 1 is not essential for integration of the viral genome. Southern transfer experiments revealed that (i) the sites of integration in the host genome were not unique; (ii) in general, transformed CV1 cell lines contained single-copy, full-length viral genomes, colinear with the infecting virus; (iii) transformed Rat2 cell lines generally contained one to several copies of full-length viral genomes integrated colinearly with the infecting viral DNA; and (iv) three of these five lines of transformed Rat2 cell lines contained tandemly repeated viral DNA sequences in which the right and left ends of the viral genome were joined to each other.
TL;DR: The entire Epstein-Barr virus genome is integrated into Burkitt tumor cell DNA at the terminal direct repeat sequence of the virus.
Abstract: The entire Epstein-Barr virus genome is integrated into Burkitt tumor cell DNA at the terminal direct repeat sequence of the virus. There is no homology between the GC-rich (G, guanine; C, cytosine) terminal repeat and the AT-rich (A, adenine; T, thymine) cell sequences with which it has recombined. More than 15 kilobases of cell DNA have been deleted and 236 base pairs are duplicated at one virus-cell junction site.
TL;DR: Poly(dC-dA) (TG-element), a potential Z-DNA sequence, in eucaryotic genomes suggests the abundant presence of poly(dT-dG), and studies on the conformation of a genomic TG-element in a supercoiled plasmid indicate several distinct properties.
Abstract: Hybridization studies suggest the abundant presence of poly(dT-dG).poly(dC-dA) (TG-element), a potential Z-DNA sequence, in eucaryotic genomes. We have isolated and characterized TG-elements from different locations in the human genome: from randomly isolated clones, associated with the actin gene family, and linked to another repeated element. The results indicate that the following features are typical of these TG-elements: the elements consist of 20 to 60 base pairs of (dT-dG)n.(dC-dA)n, the sequences characterized in our study were not flanked by direct or inverted repeats, the sequences are interspersed rather than in satellite blocks, the elements are not usually associated with other repeated elements, and some of the elements are found near coding sequences or in introns. Studies on the conformation of a genomic TG-element in a supercoiled plasmid indicate several distinct properties of the TG-element: it is in the Z-form only at low ionic strength, S1 nuclease recognizes its Z-form with a marked preference for one of the B-Z junctions, and the sensitive region extends for 20 base pairs near the B-Z junction. In contrast to the result with the supercoiled plasmid, S1 nuclease failed to recognize the TG-element in minichromosomes.
TL;DR: Comparisons of nucleotide sequence divergence among chloroplast genes reveals marked similarity across the plant kingdom and beyond to the cyanobacteria (blue-green algae).
Abstract: Comparative data on the evolution of chloroplast genes are reviewed. The chloroplast genome has maintained a similar structural organization over most plant taxa so far examined. Comparisons of nucleotide sequence divergence among chloroplast genes reveals marked similarity across the plant kingdom and beyond to the cyanobacteria (blue-green algae). Estimates of rates of nucleotide substitution indicate a synonymous rate of 1.1 x 10(-9) substitutions per site per year. Noncoding regions also appear to be constrained in their evolution, although addition/deletion events are common. There have also been evolutionary changes in the distribution of introns in chloroplast encoded genes. Relative to mammalian mitochondrial DNA, the chloroplast genome evolves at a conservative rate.
TL;DR: The mitochondrial DNA is not differentially methylated during spermatogenesis, and no methylation differences were detected in mitochondrial DNA from sperm and oocytes following digestion with seven methylation-sensitive restriction enzymes.
TL;DR: The reduced level of chromosome pairing that is often observed in intercultivar hybrids of wheat may be due to heterochromatic differentiation, genic and structural heterozygosity, or hybrid dysgenesis.
Abstract: Heterochromatin distribution and structural differentiation of somatic chromosomes of five common wheat cultivars — Chinese Spring, Wichita, Cheyenne, Timstein, and Hope — were studied by an acetocarmine/N-banding technique. Detailed morphological observations on acetocarmine stained somatic chromosomes of Chinese Spring were made on all A genome chromosomes (except 1A), all B genome chromosomes, and chromosomes 1D, 2D, and 7D. N-banding patterns of chromosomes 2A, 3A, 5A, 6A, 1D, 2D, and 7D were described for the first time. Substitution lines of 21 individual chromosomes each of Cheyenne, Timstein, and Hope in Chinese Spring were analyzed by N-banding. A high frequency of N-band polymorphism was observed, especially for most of the B genome chromosomes. Chromosomes 3A, 5A, 2D, and 7D showed a constant banding pattern. Three cases of doubtful substitutions, Hope 2A, 2B, and Timstein 7A, and several cases of incomplete and chromosomally modified substitutions were observed. The reduced level of chromosome pairing that is often observed in intercultivar hybrids of wheat may be due to heterochromatic differentiation, genic and structural heterozygosity, or hybrid dysgenesis.