Showing papers on "Genome published in 1989"

Hypervariability of simple sequences as a general source for polymorphic DNA markers

Abstract: Short simple sequence stretches occur as highly repetitive elements in all eukaryotic genomes and partially also in prokaryotes and eubacteria. They are thought to arise by slippage like events working on randomly occurring internally repetitive sequence stretches. This predicts that they should be generally hypervariable in length. I have used the polymerase chain reaction (PCR) process to show that several randomly chosen simple sequence loci with different nucleotide composition and from different species show extensive length polymorphisms. These simple sequence length polymorphisms (SSLP) may be usefully exploited for identity testing, population studies, linkage analysis and genome mapping.

Altering the genome by homologous recombination.

Abstract: Homologous recombination between DNA sequences residing in the chromosome and newly introduced, cloned DNA sequences (gene targeting) allows the transfer of any modification of the cloned gene into the genome of a living cell. This article discusses the current status of gene targeting with particular emphasis on germ line modification of the mouse genome, and describes the different methods so far employed to identify those rare embryonic stem cells in which the desired targeting event has occurred.

The complete sequence of the rice (Oryza sativa) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals

Abstract: The entire chloroplast genome of the monocot rice (Oryza sativa) has been sequenced and comprises 134525 bp. Predicted genes have been identified along with open reading frames (ORFs) conserved between rice and the previously sequenced chloroplast genomes, a dicot, tobacco (Nicotiana tabacum), and a liverwort (Marchantia polymorpha). The same complement of 30 tRNA and 4 rRNA genes has been conserved between rice and tobacco. Most ORFs extensively conserved betweenN. tabacum andM. polymorpha are also conserved intact in rice. However, several such ORFs are entirely absent in rice, or present only in severely truncated form. Structural changes are also apparent in the genome relative to tobacco. The inverted repeats, characteristic of chloroplast genome structure, have expanded outward to include several genes present only once per genome in tobacco and liverwort and the large single copy region has undergone a series of inversions which predate the divergence of the cereals. A chimeric tRNA pseudogene overlaps an apparent endpoint of the largest inversion, and a model invoking illegitimate recombination between tRNA genes is proposed which accounts simultaneously for the origin of this pseudogene, the large inversion and the creation of repeated sequences near the inversion endpoints.

P-element-mediated enhancer detection: a versatile method to study development in Drosophila.

Abstract: We generated and characterized greater than 500 Drosophila strains that carry single copies of a novel P-element enhancer detector. In the majority of the strains, the beta-galactosidase reporter gene in the P-transposon responds to nearby transcriptional regulatory sequences in the genome. A remarkable diversity of spatially and temporally regulated staining patterns is observed in embryos carrying different insertions. We selected numerous strains as markers for different embryonic organs, tissues, and cells. Many of these strains should allow the study of complex developmental processes, such as nervous system development, which have not been convenient to analyze previously. Also, we present genetic evidence that some of the detected regulatory elements control nearby Drosophila genes. In light of our results, we discuss the diversity and complexity of cis-acting regulatory elements in the genome and the general applications of the enhancer detector method for the study of Drosophila development.

Mutation rates differ among regions of the mammalian genome

Abstract: In the traditional view of molecular evolution, the rate of point mutation is uniform over the genome of an organism and variation in the rate of nucleotide substitution among DNA regions reflects differential selective constraints1,2. Here we provide evidence for significant variation in mutation rate among regions in the mammalian genome. We show first that substitutions at silent (degenerate) sites in protein-coding genes in mammals seem to be effectively neutral (or nearly so) as they do not occur significantly less frequently than substitutions in pseudogenes. We then show that the rate of silent substitution varies among genes and is correlated with the base composition of genes and their flanking DNA. This implies that the variation in both silent substitution rate and base composition3 can be attributed to systematic differences in the rate and pattern of mutation over regions of the genome. We propose that the differences arise because mutation patterns vary with the timing of replication of different chromosomal regions in the germline. This hypothesis can account for both the origin of isochores in mammalian genomes4 and the observation5 that silent nucleotide substitutions in different mammalian genes do not have the same molecular clock.

Origins and evolutionary relationships of retroviruses.

Abstract: As is the case for some other RNA viruses, the amino acid sequences of retroviral proteins change at an astonishing rate. For example, the proteases of the human immunodeficiency virus (HIV) and the visna lentivirus with which it is often compared are as different as the proteases of fungi and mammals, and those of the human type I leukemia virus are as different from HIV or visna as are the proteins of humans and bacteria. That the sequences of retrovirus proteins can be recognized as sharing common ancestry with non-retroviral proteins implies that the vastly accelerated change has begun only recently or occurs very sporadically. Only a scheme whereby exogenous retroviruses exist as short-lived bursts upon a backdrop of germline-encoded endogenous viruses is consistent with the sequence data. Retroviruses are related to many other reverse transcriptase-bearing entities present in the genomes of eukaryotes. They also have proteins that are homologous with those of some plant and animal DNA viruses, and t...

A direct repeat is a hotspot for large-scale deletion of human mitochondrial DNA

Abstract: Kearns-Sayre syndrome (KSS) and progressive external ophthalmoplegia (PEO) are related neuromuscular disorders characterized by ocular myopathy and ophthalmoplegia. Almost all patients with KSS and about half with PEO harbor large deletions in their mitochondrial genomes. The deletions differ in both size and location, except for one, 5 kilobases long, that is found in more than one-third of all patients examined. This common deletion was found to be flanked by a perfect 13-base pair direct repeat in the normal mitochondrial genome. This result suggests that homologous recombination deleting large regions of intervening mitochondrial DNA, which previously had been observed only in lower eukaryotes and plants, operates in mammalian mitochondrial genomes as well, and is at least one cause of the deletions found in these two related mitochondrial myopathies.

The complete nucleotide sequence of the Rattus norvegicus mitochondrial genome: cryptic signals revealed by comparative analysis between vertebrates.

Abstract: This paper reports the nucleotide sequence of rat mitochondrial DNA, only the fourth mammalian mitochondrial genome to be completely sequenced. Extensive comparative studies performed with similar genomes from other organisms revealed a number of interesting features. 1) Messenger RNA genes: the codon strategy is mainly dictated by the base compositional constraints of the corresponding codogenic DNA strand. The usage of the initiation and termination codons follows well-established rules. In general the canonical initiator, ATG, and terminators, TAA and TAG (in rat, only TAA), are always present when there is gene overlapping or when the mRNAs possess untranslated nucleotides at the 5' or 3' ends. 2) Transfer RNA genes: a number of features suggest the peculiar evolutionary behavior of this class of genes and confirm their role in the duplication and rearrangement processes that took place in the evolution of the animal mitochondrial genome. 3) Ribosomal RNA genes: accurate sequence analysis revealed a number of significant examples of complementarity between ribosomal and messenger RNAs. This suggests that they might play an important role in the regulation of mitochondrial translation and transcription mechanisms. The properties revealed by our work shed new light on the organization and evolution of the vertebrate mitochondrial genome and more importantly open up the way to clearly aimed experimental studies of the regulatory mechanisms in mitochondria.

New World tetraploid cottons contain Old World cytoplasm

Abstract: New World tetraploid cottons (Gossypium spp.) originated through hybridization of ancestral diploid species that presently have allopatric ranges in Asia-Africa (the A genome) and the New World tropics and subtropics (the D genome). Despite intensive study, the identity of the parental diploids and the antiquity of polyploidization remain unresolved. In this study, variation in the maternally inherited chloroplast genome was assessed among species representing both of the parental genomes and the tetraploids. Approximately 560 restriction sites were assayed in each accession, representing sequence information for about 3200 nucleotides. The resulting maternal phylogeny has no convergent restriction site mutations and demonstrates that the cytoplasm donor for all tetraploid species was an A genome diploid with a chloroplast genome that is similar to Gossypium arboreum and Gossypium herbaceum. No mutational differences were detected between these two species, and few mutations distinguish the chloroplast genomes of A genome diploids from those of tetraploid taxa. In contrast to expectations based on extensive taxonomic, geographic, and genetic diversity, a surprisingly low level of sequence divergence has accumulated subsequent to polyploidization. Chloroplast genomes of tetraploid species are distinguished from each other by between one and six apparent point mutations. The data suggest that tetraploid cotton originated relatively recently, perhaps within the last 1-2 million years, with subsequent rapid evolution and diversification throughout the New World tropics.

Initiation of replication of the human hepatitis delta virus genome from cloned DNA: role of delta antigen.

Abstract: Beginning with three partial cDNA clones of the RNA genome of human hepatitis delta virus (HDV), we assembled the complete 1,679-base sequence on a single molecule and then inserted a trimer of this into plasmid pSLV, a simian virus 40-based eucaryotic expression vector. This construct was used to transfect both monkey kidney (COS7) and human hepatocellular carcinoma (HuH7) cell lines. In this way we obtained replication of the HDV RNA genome and the appearance, in the nucleoli, of the delta antigen, the only known virus-coded protein. This proved both that the HDV genome could replicate in nonliver as well as liver cells and that there was no requirement for the presence of hepatitis B virus sequences or proteins. When the pSVL construct was made with a dimer of an HDV sequence with a 2-base-pair deletion in the open reading frame, genome replication was reduced at least 40-fold. However, when we cotransfected with a plasmid that expressed the correct delta antigen, the mutated dimer achieved a level of genome replication comparable to that of the nonmutated sequence. We thus conclude that the delta antigen can act in trans and is essential for replication of the HDV genome.

A new family of mouse homeo box-containing genes: molecular structure, chromosomal location, and developmental expression of Hox-7.1.

Abstract: Two families of homeo box-containing genes have been identified in mammals to date, the Antennapedia- and engrailed-like homeo boxes, based on the sequence similarity to those from Drosophila. Here, we report the isolation of a homeo box-containing gene that belongs to a new family of which there are at least three related genes in the mouse genome. The homeo box of this new gene shows remarkable similarity to the Drosophila Msh homeo box that we designate as the prototype for this family. The gene maps to the proximal end of mouse chromosome 5 and does not cosegregate with any known homeo box-containing gene. We designate this locus Hox-7.1. In situ hybridizations to mouse embryos at different stages show a unique pattern of expression, as compared to other homeo box-containing genes described thus far. Hox-7.1 transcripts are detected in 9.5-day-old embryos in the neural crest, developing limb bud, and visceral arches. Later, this gene is expressed in regions of the face that are derived from neural crest and in the interdigital mesenchymal tissues in both the fore- and hindlimbs.

Regulatory Interactions between Nuclear and Plastid Genomes

Abstract: Article de synthese sur les interactions entre les genomes nucleaires et plastidiques chez les vegetaux comprenant la regulation nucleaire des genes de developpement des plastes et le controle chloroplastique de l'expression des genes nucleaires

The isochore organization of the human genome

Abstract: The investigations reviewed here indicate that the eukaryotic genome is an integrated structural, functional, and evolutionary system. This view arose from a comparative study of vertebrate genomes, centered on the analysis of their compositional patterms, namely of the compositional distributions of large DNA fragments, coding sequences, and introns

Repeat-induced G-C to A-T mutations in Neurospora.

Abstract: In the Neurospora genome duplicate sequences are detected and altered in the sexual phase. Both copies of duplicate genes are inactivated at high frequency, whether or not they are linked. Restriction sites change, and affected sequences typically become heavily methylated. To characterize the alterations of the DNA, duplicated sequences were isolated before and after one or more sexual cycles. DNA sequencing and heteroduplex analyses demonstrated that the process (termed RIP) produces exclusively G-C to A-T mutations. Changes occur principally at sites where adenine is 3' of the changed cytosine. A sequence duplicated at a distant site in the genome lost approximately 10 percent of its G-C pairs in one passage through a cross. A closely linked duplication of the same sequence that was passed twice through a cross lost about half of its G-C pairs. The results suggest a mechanism for the RIP process.

Allelic Loss in Colorectal Carcinoma

Abstract: Clinical and pathological associations with molecular genetic alterations were studied in colorectal carcinomas from 83 patients. Fractional allelic loss, a measure of allelic deletions throughout the genome, and allelic deletions of specific chromosomal arms (the short arm of 17 and long arm of 18) each provided independent prognostic information by multivariate analysis when considered individually with Dukes'classification. Distant metastasis was significantly associated with high fractional allelic loss and with deletions of 17p and 18q. Mutations of ras proto-oncogenes and deletions of 5q had no prognostic importance. Statistically significant associations were also found between allelic losses and a family history of cancer, left-sided tumor location, and absence of extracellular tumor mucin. Allelic deletion analysis thus identified subsets of colorectal carcinoma with increased predilection for distant metastasis and cancer-related death. Further studies may define a subset of genetic alterations that can be used clinically to help assess prognosis. (JAMA. 1989;261:3099-3103)

A dominant control region from the human β-globin locus conferring integration site-independent gene expression

Abstract: The regulatory elements that determine the expression pattern of a number of eukaryotic genes expressed specifically in certain tissues have been defined and studied in detail. In general, however, the expression conferred by these elements on genes reintroduced into the genomes of cell lines and transgenic animals has turned out to be at a low level relative to that of endogenous genes, and influenced by the chromosomal site of insertion of the exogenous construct. We have previously shown that if regions flanking the human beta-globin locus are introduced into the mouse genome along with the human beta-globin gene, a level of expression comparable to that of endogenous genes can be achieved that is also independent of integration site. We have now defined a dominant control region with these properties consisting of 6.5 kilobases of DNA encompassing erythroid cell-specific DNase I hypersensitive sites. The identification of such dominant control regions could have important applications in somatic gene therapy.

Host species-specific conservation of a family of repeated DNA sequences in the genome of a fungal plant pathogen

Abstract: We have identified a family of dispersed repetitive DNA sequences in the genome of Magnaporthe grisea, the fungus that causes rice blast disease. We have named this family of DNA sequences "MGR" for M. grisea repeat. Analysis of five MGR clones demonstrates that MGR sequences are highly polymorphic. The segregation of MGR sequences in genetic crosses and hybridization of MGR probes to separated, chromosome-size DNA molecules of M. grisea shows that this family of sequences is distributed among the M. grisea chromosomes. MGR sequences also hybridize to discrete poly(A)+ RNAs. Southern blot analysis using a MGR probe can distinguish rice pathogens from various sources. However, MGR sequences are not highly conserved in the genomes of M. grisea field isolates that do not infect rice. These results suggest that host selection for a specific pathogen genotype has occurred during the breeding and cultivation of rice.

The characterization and comparative analysis of high-molecular-weight glutenin genes from genomes A and B of a hexaploid bread wheat

Abstract: Two high-molecular-weight subunit (HMWS) glutenin genes from the A and B genomes of the hexaploid bread wheat Triticum aestivum L. cv Cheyenne have been isolated and sequenced. Both of these genes are of the high Mr class (x-type) of HMW glutenins, and have not been previously reported. The entire set of six HMW genes from cultivar Cheyenne have now been isolated and characterized. An analysis of the Ax and Bx sequences shows that the Ax sequence is similar to the homoeologous gene from the D genome, while the Bx repeat structure is significantly different. The repetitive region of these proteins can be modelled as a series of interspersed copies of repeat modifs of 6, 9, and 15 amino acid residues. The evolution of these genes includes single-base substitutions over the entire coding region, plus insertion/deletions of single or blocks of repeats in the central repetitive domain.

Genetic and molecular analysis of a Caenorhabditis elegans beta-tubulin that conveys benzimidazole sensitivity.

Abstract: Benzimidazole anti-microtubule drugs, such as benomyl, induce paralysis and slow the growth of the nematode Caenorhabditis elegans. We have identified 28 mutations in C. elegans that confer resistance to benzimidazoles. All resistant mutations map to a single locus, ben-1. Virtually all these mutations are genetically dominant. Molecular cloning and DNA sequence analysis established that ben-1 encodes a beta-tubulin. Some resistant mutants are completely deleted for the ben-1 gene. Since the deletion strains appear to be fully resistant to the drugs, the ben-1 product appears to be the only benzimidazole-sensitive beta-tubulin in C. elegans. Furthermore, since animals lacking ben-1 are viable and coordinated, the ben-1 beta-tubulin appears to be nonessential for growth and movement. The ben-1 function is likely to be redundant in the nematode genome.

Evolution of the major histocompatibility complex: independent origin of nonclassical class I genes in different groups of mammals.

Abstract: The class I major histocompatibility complex genes are composed of classical and nonclassical genes, the latter being largely nonfunctional. To understand the evolutionary relationships of the two groups of class I genes, a phylogenetic analysis of DNA sequences was conducted using 45 genes from six mammalian and one avian species. The results indicate that nonclassical genes in one species are more closely related to classical genes from the same species than to nonclassical genes from a species belonging to a different order or family. This indicates that the differentiation of classical and nonclassical genes occurs rather rapidly in the genome. Classical genes are apparently duplicated with a high frequency in the evolutionary process, and many of the duplicated genes seem to degenerate into nonclassical genes as a result of deleterious mutation. The nonclassical Qa genes in the mouse have sequences homologous to regulatory sequences involved in the universal expression of classical class I genes, but they have accumulated numerous nucleotide substitutions in these sequences. The pattern of nucleotide substitution in nonclassical genes is different from that in classical genes. In nonclassical genes, the rate of nonsynonymous substitution is higher in the antigen recognition site than in other gene regions, as is true of classical genes. However, unlike the case of classical genes, the nonsynonymous rate does not always exceed the synonymous rate in the antigen recognition site. Nonclassical proteins further differ from classical proteins in having amino acid replacements in conserved antigen recognition site positions. These observations are consistent with the hypothesis that nonclassical genes have originated from classical genes but have lost classical class I function because of deleterious mutation.

A Specific and Sensitive Assay for the Lyme Disease Spirochete Borrelia burgdorferi Using the Polymerase Chain Reaction

Abstract: A highly specific and sensitive assay for Borrelia burgdorferi, the causative agent of Lyme disease, was developed using the polymerase chain reaction (PCR). The target DNA sequence was of chromosomal origin and conserved, by hybridization analyses, among all strains of B. burgdorferi tested but was not present in the most closely related member of the genus, B. hermsii. The PCR assay developed from this sequence reacted with 17 of 18 strains of B. burgdorferi but not with any other Borrelia species tested. The assay was sensitive to fewer than five copies of the B. burgdorferi genome, even in the presence of a 10(6)-fold excess of eukaryotic DNA. This assay should greatly facilitate the accurate diagnosis of Lyme disease and provide a means with which to investigate the pathogenesis, transmission, and basic biology of B. burgdorferi.

Chloroplast Gene Expression: How Plants Turn Their Plastids On Review

Abstract: Wilhelm Gruissem Department of Botany University of California Berkeley, California 94720 Plant and animal cells are fundamentally very similar. Be- sides the organelles found in both cell types, however, plant cells contain a unique class of organelles, the plastids. Since the early discovery by Correns (1909) and Baur (1909) that mutations affecting plastid phenotypes in higher plants frequently exhibit non-Mendelian inheri- tance, research on the DNA of this organelle has now yielded the complete sequence of the plastid genomes from tobacco (Shinozaki et al., 1986) and liverwort (Oh- yama et al., 1986). Plastids exist in a number of different forms with different functions, but the green chloroplast was the first to be discovered, and is the best studied of all plastids. The diversity of plastid types is controlled by the developmental program of the plant, which indicates that there must be a significant flow of information be- tween two separate genetic compartments in the cell. The use of chloroplasts to study photosynthesis and the in- tricacy of photosynthetic complexes has yielded new infor- mation on controls of organelle gene expression and the communication of different genomes in eukaryotic cells. In developing plants, chloroplasts are derived from small proplastids, which are the undifferentiated plastids present in meristematic cells. During the development of chloroplasts in photosynthetic tissues, photosynthetic electron-transfer components are assembled into pho- tosystems I and II, cytochrome bsf, and ATP synthase complexes, each of which consists of up to 20 polypep- tides. Proplastids and chloroplasts can also differentiate into specialized plastid types that assume other functions in nonphotosynthetic plant organs of higher plants, such as amyloplasts in roots and tubers or chromoplasts in many flowers and fruits. Photosynthesis, together with other plastid functions, requires the products of several hundred genes, of which only about 120 are present in the approximately 150 kb chloroplast genome. All other plas- tid proteins are expressed from nuclear genes. The devel- opment and differentiation of photosynthetically compe- tent chloroplasts and other plastid types thus present a challenging opportunity: to decipher how plastid gene ex- pression is controlled temporally and spatially in different plant organs, and also in coordination with the expression of nuclear genes for chloroplast proteins. Initial efforts to analyze the controls of plastid gene expression have con- centrated on the transcription of genes for photosynthetic proteins and tRNAs. Recent progress appears to support a model that places a major emphasis on posttranscrip- tional and translational regulatory mechanisms. In con- trast, known nuclear genes for photosynthetic proteins ap- pear to be regulated primarily at the level of transcription. The purpose of this review is to discuss some of the cen- tral problems and ideas in the field of chloroplast gene ex- pression, not to provide a comprehensive review on all that is known. (For further information on chloroplast ge- nome structures, genes, and transcriptional and transla- tional components, readers should consult Whitfeld and Bottomley, 1983; Ellis, 1984; Sugiura, 1987; Umesono and Ozeki, 1987; Gruissem, 1989; Mullet, 1988; Bonham- Smith and Bourque, 1988.) Linkage of Genes in Many Chloroplast Transcription Units Is Conserved Compared with the small number of genes in animal, fun- gal and plant mitochondria, the chloroplast genome con- tains a substantially larger number of genes, encoding both genetic and photosynthetic functions. The genes identified thus far include a complete set of 30 tRNAs, four ribosomal RNAs (23S, 16S, 5S, and 4.5s) and 20 ribo- somal proteins. Twenty-two genes encode proteins for thylakoid membrane complexes (photosystem I, photosys- tern II, cytochrome bsf complex, and ATP synthase), and the sequences of six other open reading frames share similarities with the mitochondrial genes for the subunits of the human respiratory chain NADH dehydrogenase. Several of the remaining unidentified reading frames are conserved between diverse species, which suggests that they may also encode functional plastid polypeptides. Most plastid genes are organized into polycistronic tran- scription units reminiscent of bacterial operons. The se- quence analysis of the entire tobacco and liverwort chlo- roplast genomes (Shinozaki et al., 1986; Ohyama et al., 1986) together with the partial sequence and mapping data from other plant chloroplast genomes, has revealed that the arrangement of genes within these transcription units is highly conserved, although transcription are extensively rearranged in some plant species (reviewed by Palmer, 1985). Detailed mapping of chloroplast DNAs from pea and geranium, for example, has found that such rearrangements involve primarily inversions of large clus- ters of genes. Most, but not all, the genes linked in these clusters are cotranscribed. It has been possible, at least some cases, to trace the linkage of chloroplast gene sets to the cyanobacterial genome (Cozens et al., 1986) which is the putative ancestral genome of chloroplast genome. However, the conserved arrangement of genes in plant chloroplast genomes is not found algae, for which Chlamydomonas and Euglena are the best studied examples, possibly indicating different endosymbiotic events. Chloroplast RNA Polymerases and Promoter Regions The possibility that transcriptional regulation chlo- roplast genes could be a key control during chloroplast development in plants spurred early investigations into the transcriptional components of this organelle. Applica- tion of different schemes for preparing DNA-dependent RNA polymerase from chloroplasts led to the intriguing idea that chloroplasts of algae and plants may contain at least two different RNA polymerase activities distinguish-