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PubMed1989

A herpes simplex virus type 2 variant in which a deletion across the L-S junction is replaced by single or multiple reiterations of extraneous DNA.

We have isolated and characterized a novel variant of herpes simplex virus type 2 (HSV-2) strain HG52 which has a deletion of 13.5 kb across the L-S junction of the genome, resulting in all of the IRL region, half of the IRS region and the intervening L-S junction 'a' sequence(s) being removed. The deleted DNA has been replaced by single or multiple (up to 14) reiterations of a DNA sequence approximately 1 kb in length. Individual genomes within the population range in size from approximately 12 kb smaller than unit length to unit length or marginally larger. The L component of the genome is fixed in the prototype orientation while the S component inverts inefficiently. The variant is viable in tissue culture, is not temperature-sensitive, demonstrates impaired single-cycle growth characteristics and, apart from altered mobility of a single species (29.5K), its polypeptide profile in infected cells appears normal. Southern blot analysis has failed to identify the inserted sequences as being derived from HSV-2.

Chromosome Deletion↗
PubMed1995

Molecular cloning of Indian tomato leaf curl virus genome following a simple method of concentrating the supercoiled replicative form of viral DNA.

DNA-A and DNA-B components of the genome of a whitefly transmitted virus causing yellowing and leaf curl in tomato (ITLCV) were cloned following a simple procedure for isolation of the double stranded replicative form of viral DNA from infected tomato plants. The method is based on extraction of total DNA from infected plants followed by concentration of the double stranded replicative form of viral DNA by an alkaline denaturation procedure identical to that used for isolation of plasmid DNA from Escherichia coli. The attempted cloning of DNA showed that 95% of the transformants contained plasmids with an insert of either DNA-A (2.75 kb) or DNA-B (2.55 kb). Cloned DNA-A and DNA-B when used as probes could detect DNA-A/DNA-B in total nucleic acid obtained from fresh diseased tissue. Both DNA-A and DNA-B are needed for infection and they have a common region of 166 bases with about 94% nucleotide sequence homology, a characteristic of all bipartite geminiviruses. Comparison of the amino acid sequence of the putative coat protein product of ITLCV with some other mono- and bipartite geminiviruses revealed a maximum of 86% homology with Indian cassava mosaic virus.

Amino Acid Sequence↗
PubMed2004

Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae.

BACKGROUND: Retrotransposons are an abundant component of eukaryotic genomes. The high quality of the Arabidopsis thaliana genome sequence makes it possible to comprehensively characterize retroelement populations and explore factors that contribute to their genomic distribution. RESULTS: We identified the full complement of A. thaliana long terminal repeat (LTR) retroelements using RetroMap, a software tool that iteratively searches genome sequences for reverse transcriptases and then defines retroelement insertions. Relative ages of full-length elements were estimated by assessing sequence divergence between LTRs: the Pseudoviridae were significantly younger than the Metaviridae. All retroelement insertions were mapped onto the genome sequence and their distribution was distinctly non-uniform. Although both Pseudoviridae and Metaviridae tend to cluster within pericentromeric heterochromatin, this association is significantly more pronounced for all three Metaviridae sublineages (Metavirus, Tat and Athila). Among these, Tat and Athila are strictly associated with pericentromeric heterochromatin. CONCLUSIONS: The non-uniform genomic distribution of the Pseudoviridae and the Metaviridae can be explained by a variety of factors including target-site bias, selection against integration into euchromatin and pericentromeric accumulation of elements as a result of suppression of recombination. However, comparisons based on the age of elements and their chromosomal location indicate that integration-site specificity is likely to be the primary factor determining distribution of the Athila and Tat sublineages of the Metaviridae. We predict that, like retroelements in yeast, the Athila and Tat elements target integration to pericentromeric regions by recognizing a specific feature of pericentromeric heterochromatin.

Arabidopsis↗
PubMed1993

Elucidation of a conserved RNA stem-loop structure in the packaging signal of human immunodeficiency virus type 1.

A region of human immunodeficiency virus type 1 (HIV-1) genomic RNA known to interact with the viral nucleocapsid protein is one of the crucial components for retroviral genomic RNA packaging. We have investigated the secondary structure for this RNA packaging signal of HIV-1 using RNA mapping techniques and extensive computer analyses. Our results suggest that the RNA sequence containing the packaging signal conforms to a stable stem-loop structure and that a portion of this structure is conserved among twenty independent HIV-1 isolates. The heterogeneity of the RNA packaging sequence was not correlated with the amino acid sequence variability of the viral nucleocapsid protein. These findings have critical implication in understanding the viral maturation process.

Amino Acid Sequence↗
PubMed2004

The indigenous Pseudomonas plasmid pQBR103 encodes plant-inducible genes, including three putative helicases.

Plasmid pQBR103 ( approximately 400 kb) is representative of many self-transmissible, mercury resistant plasmids observed in the Pseudomonas community colonising the phytosphere of sugar beet. A promoter trapping strategy (IVET) was employed to identify pQBR103 genes showing elevated levels of expression on plant surfaces. Thirty-seven different plant-inducible gene fusions were isolated that were silent in laboratory media, but active in the plant environment. Three of the fusions were to DNA sequences whose protein products show significant homology to DNA-unwinding helicases. The three helicase-like genes, designated helA, helB and helC, are restricted to a defined group of related Pseudomonas plasmids. They are induced in both the root and shoot environments of sugar beet seedlings. Sequence analysis of the three plasmid-encoded helicase-like genes shows that they are phylogenetically distinct and likely to have independent evolutionary histories. The helA gene is predicted to encode a protein of 1121 amino acids, containing conserved domains found in the ultraviolet (UV) resistance helicase, UvrD. A helA knockout mutant was constructed and no phenotypic changes were found with plasmid-conferred UV resistance or plasmid conjugation. The other 34 fusions are unique with no homologues in the public gene databases, including the Pseudomonas genomes. These data demonstrate the presence of plant responsive genes in plasmid DNA comprising a component of the genomes of plant-associated bacteria.

Adaptation, Physiological↗
PubMed2006

Genetic mapping of a 17q chromosomal region linked to obesity phenotypes in the IRAS family study.

OBJECTIVE: Obesity is widely accepted to be influenced by both environmental and genetic factors. Several recent studies have used the positional cloning approach in an attempt to discover genes contributing to obesity. In the IRAS Family Study a genomewide scan was performed on 1425 individuals of Hispanic descent (90 extended pedigree families) to identify regions of the genome linked to obesity phenotypes. METHODS: Nonparametric QTL linkage analysis was performed using a variance components approach. The genome scan was performed in two phases: an initial genome scan in 45 families and a replication scan in 45 families. Fine mapping and candidate gene analyses were also performed. General estimating equations (GEE1) and quantitative pedigree disequilibrium tests (QPDT) were used for association analysis of single SNP and haplotype data. RESULTS: Evidence for linkage to obesity traits was observed in each scan on the long arm of chromosome 17. When data from both scans was combined, a region on chromosome 17q was identified with evidence of linkage to visceral adipose tissue (VAT; LOD 3.11), waist circumference (WAIST) (LOD 2.5) and body mass index (BMI) (LOD 2.81). Nine additional microsatellite markers were identified and genotyped on all Hispanic individuals, with a mean marker density of approximately 1 marker/3 cM. Evidence of linkage remained significant with LOD 3.05 for VAT, LOD 2.44 for BMI and LOD 1.92 for WAIST. Fine mapping analyses suggest the possibility of two different obesity loci. In addition, the LOD - 1 interval of the major VAT peak decreased from 83-108 to 95-111 cM. Three positional candidate genes under the peak: somatostatin receptor 2 (SSTR2), galanin receptor 2 (GALR2), and growth hormone bound protein receptor 2 (GRB2) were chosen for detailed evaluation. Multiple polymorphisms within each candidate were genotyped and tested for association with the obesity phenotypes. Little evidence of association was detected between polymorphisms and obesity traits. CONCLUSION: In conclusion, replication of linkage and fine mapping suggest that a region on chromosome 17q contains a gene (or genes) that contributes to the genetic etiology of obesity with the strongest evidence for linkage to VAT. Candidate genes in the region do not appear to account for the evidence of linkage. Additional studies are necessary to identify the obesity-related polymorphisms.

Adult↗
PubMed2002

Contribution of the Atm protein to maintaining cellular homeostasis evidenced by continuous activation of the AP-1 pathway in Atm-deficient brains.

Maintenance of genome stability is essential for keeping cellular homeostasis. The DNA damage response is a central component in maintaining genome integrity. Among of the most cytotoxic DNA lesions are double strand breaks (DSBs) caused by ionizing radiation or radiomimetic chemicals. ATM is missing or inactivated in patients with ataxia-telangiectasia. Ataxia-telangiectasia patients display a pleiotropic phenotype and suffer primarily from progressive ataxia caused by degeneration of cerebellar Purkinje and granule neurons. Additional features are immunodeficiency, genomic instability, radiation sensitivity, and cancer predisposition. Disruption of the mouse Atm locus creates a murine model of ataxia-telangiectasia that exhibits most of the clinical features of the human disease but very mild neuronal abnormality. The ATM protein is a multifunctional protein kinase, which serves as a master regulator of cellular responses to DSBs. There is growing evidence that ATM may be involved in addition to the DSB response in other processes that maintain processes in cellular homeostasis. For example, mounting evidence points to increased oxidative stress in the absence of ATM. Here we report that the AP-1 pathway is constantly active in the brains of Atm-deficient mice not treated with DNA damaging agents. A canonical activation (increased phosphorylation of mitogen-activated protein kinase kinase-4, c-Jun N-terminal kinase, and c-Jun) of the AP-1 pathway was found in Atm-deficient cerebra, whereas induction of the AP-1 pathway in Atm-deficient cerebella is likely to mediate elevated expression of c-Fos and c-Jun. Although Atm(+/+) mice are capable of responding to ionizing radiation by activating stress responses such as the AP-1 pathway, Atm-deficient mice display higher basal AP-1 activity but gradually lose their ability to activate AP-1 DNA-binding activity in response to ionizing radiation. Our results further demonstrate that inactivation of the ATM gene results in a state of constant stress.

Animals↗
PubMed2005

Automatic detection of subsystem/pathway variants in genome analysis.

MOTIVATION: Proteins work together in pathways and networks, collectively comprising the cellular machinery. A subsystem (a generalization of pathway concept) is a group of related functional roles (such as enzymes) jointly involved in a specific aspect of the cellular machinery. Subsystems provide a natural framework for comparative genome analysis and functional annotation. A subsystem may be implemented in a number of different functional variants in individual species. In order to reliably project functional assignments across multiple genomes, we have to be able to identify the variants implemented in each genome. The analysis of such variants across diverse species is an interesting problem by itself and may provide new evolutionary insights. However, no computational techniques are presently available for an automated detection and analysis of subsystem variants. RESULTS: Here we formulate the subsystem variant detection problem as finding the minimum number of subgraphs of a subsystem, which is represented as a graph, and solve the optimization problem by integer programming approach. The performance of our method was tested on subsystems encoded in the SEED, a genomic integration platform developed by the Fellowship for Interpretation of Genomes as a component of a large-scale effort on comparative analysis and annotation of multiple diverse genomes. Here we illustrate the results obtained for two expert-encoded subsystems of the biosynthesis of Coenzyme A and FMN/FAD cofactors. Applications of variant detection, to support genomic annotations and to assess divergence of species, are briefly discussed in the context of these universally conserved and essential metabolic subsystems. SUPPLEMENTARY INFORMATION: The details of the variant detection results are available at http://ffas.burnham.org/svar/supp.html.

Animals↗
PubMed1998

A Ty1 integrase nuclear localization signal required for retrotransposition.

Ty1 retrotransposition in Saccharomyces cerevisiae requires integrase (IN)-mediated insertion of Ty1 cDNA into the host genome. The transposition components are assembled in the cytoplasm and must cross the nuclear envelope to reach the genomic target, since, unlike animal cell nuclear membranes, the yeast cell nuclear membrane remains intact throughout the cell cycle. We have identified a bipartite nuclear localization signal (NLS) in IN required for Ty1 transposition (Ty1 IN) that directs IN to the nucleus. Mutations in the NLS that specifically abolish nuclear localization inactivate transpositional integration but do not affect reverse transcription, protein processing, or catalytic activity in vitro. No additional Ty1-encoded proteins are required for IN nuclear localization. Intragenic complementation experiments suggest that Ty1 IN functions as a multimer and contains two distinct domains, one required for integration and the other for nuclear localization. Nuclear targeting of the preintegration complex by an IN NLS may prove to be a general strategy used by retrotransposons and retroviruses that infect nondividing cells.

Amino Acid Sequence↗
PubMed1993

The number of copies of an a-like region in the serotype-3 Marek's disease virus DNA genome is variable.

A 1.2-kilobase-pair DNA region (a-like) in the serotype-3 Marek's disease virus was directly repeated at the ends of the long (L) and short (S) components of the genome and repeated in the opposite orientation at the junction between the L and S components. Four variants from plaque-purified virus that varied in the number of copies of the a-like region were identified. The predominant variant contained one copy at both ends of the genome and at the L-S junction. Two other variants contained either one or two copies at the L end and one to three copies at the L-S junction. The fourth variant lacked the a-like region at the L end and the L-S junction. The fourth variant became the predominate species as the virus was serially passaged in cell culture.

Animals↗
PubMed1999

Retrotransposon BARE-1: expression of encoded proteins and formation of virus-like particles in barley cells

Retrotransposons are ubiquitous and major components of plant genomes, and are characteristically retroviral-like in their genomic structure and in the major proteins encoded. Nevertheless, few have been directly demonstrated to be transcribed or reverse transcribed. The BARE-1 retrotransposon family of barley (Hordeum vulgare) is highly prevalent, actively transcribed, and contains well conserved functional regions. Insertion sites for BARE-1 are highly polymorphic in the barley genome. Here we show that BARE-1 is translated and the capsid protein (GAG) and integrase (IN) components of the predicted polyprotein are processed into polypeptides of expected size. Some of the GAG sediments as virus-like particles together with IN and with BARE-1 cDNA. Reverse transcriptase activity is also present in gradient fractions containing BARE-1 translation products. Virus-like particles have also been visualized in fractions containing BARE-1 components. Thus BARE-1 components necessary for carrying out the life cycle of an active retrotransposon appear to be present in vivo, and to assemble. This would suggest that post-translational mechanisms may be at work to prevent rapid genome inflation through unrestricted integration.

Journal Article↗
PubMed2004

Dense genome-wide linkage analysis of rheumatoid arthritis, including covariates.

OBJECTIVE: Rheumatoid arthritis (RA) is a heterogeneous disease that exhibits a complex genetic component. Previous RA genome scans confirmed the involvement of the HLA region and generated data on suggestive signals at non-HLA regions, albeit with few overlaps in findings between studies. The present study was undertaken to detect potential RA gene regions and to estimate the number of true RA gene regions, taking into account the heterogeneity of RA, through performance of a dense genome scan. METHODS: In a study of 88 French Caucasian families (105 RA sibpairs), 1,088 microsatellite markers were genotyped (3.3-cM genome scan), and a multipoint model-free linkage analysis was performed. The statistical assessment of the results relied on 10,000 computer simulations. A covariate-based multipoint model-free linkage analysis was performed on the locations of regions with suggestive evidence for linkage. RESULTS: Involvement of the HLA region was strongly confirmed (P = 6 x 10(-5)), and 19 non-HLA regions showed suggestive evidence for linkage (P < 0.05); 9 of these overlapped with regions suggested in other published RA genome scans. A routine 12-cM genome scan with the same families would have detected only 7 of the 19 regions, including only 4 of the 9 overlapping regions. From the 10,000 computer simulations, we estimated that 8 +/- 4 regions (mean +/- SD) were true-positives. RA covariate-based analysis provided additional linkage evidence for 3 regions, with age at disease onset, erosions, and HLA-DRB1 shared epitope as covariates. CONCLUSION: The results of this study provide evidence of 19 non-HLA RA gene regions, with an estimate of 8 +/- 4 as true-positives, and provide additional evidence for 3 regions from covariate-based analysis.

Arthritis, Rheumatoid↗
PubMed2007

Functional genomics in Trypanosoma brucei identifies evolutionarily conserved components of motile flagella.

Cilia and flagella are highly conserved, complex organelles involved in a variety of important functions. Flagella are required for motility of several human pathogens and ciliary defects lead to a variety of fatal and debilitating human diseases. Many of the major structural components of cilia and flagella are known, but little is known about regulation of flagellar beat. Trypanosoma brucei, the causative agent of African sleeping sickness, provides an excellent model for studying flagellar motility. We have used comparative genomics to identify a core group of 50 genes unique to organisms with motile flagella. These genes, referred to as T. brucei components of motile flagella (TbCMF) include 30 novel genes, and human homologues of many of the TbCMF genes map to loci associated with human ciliary diseases. To characterize TbCMF protein function we used RNA interference to target 41 TbCMF genes. Sedimentation assays and direct observation demonstrated clear motility defects in a majority of these knockdown mutants. Epitope tagging, fluorescence localization and biochemical fractionation demonstrated flagellar localization for several TbCMF proteins. Finally, ultrastructural analysis identified a family of novel TbCMF proteins that function to maintain connections between outer doublet microtubules, suggesting that they are the first identified components of nexin links. Overall, our results provide insights into the workings of the eukaryotic flagellum, identify several novel human disease gene candidates, reveal unique aspects of the trypanosome flagellum and underscore the value of T. brucei as an experimental system for studying flagellar biology.

Amino Acid Sequence↗
PubMedDate not supplied

A review of genetic differences between limited and extensively passaged human cytomegalovirus strains.

The complete genetic content of human cytomegalovirus (HCMV) has been difficult to determine, since most strains studied in the laboratory have been extensively passaged in human fibroblast cultures which can change the genetic content as well as the biological properties of the virus. Approximately 13 kb of novel DNA sequences located near the right edge of the unique long (UL) component of the genome has been discovered in Toledo, clinical isolates and certain stocks of Towne. This region of novel sequence, designated the UL/b' region, encodes several interesting proteins including vCXC-1, a potent IL-8 homologue, and UL144, a member of the TNF receptor family. This region is missing from the prototypic laboratory variants of Towne and AD169. In contrast to Toledo and other low passage isolates which have relatively small repeats bracketing the UL component, the Towne and AD169 laboratory variants contain large (>10 kb) b/b' repeats. The large size of these repeats in AD169 and Towne appear to have arisen as compensation for the loss of sequences from the UL/b' region that existed in less passaged variants of these strains. Consequently, many of the haploid genes at the left edge of the prototypic wild-type (wt) UL component are diploid in AD169 and Towne. We hypothesise that this plasticity of the genome at the right edge of the UL component results from extensive passage and adaptation to replication in fibroblasts in vitro. Further work will be required to understand the complete genetic content of wt HCMV.

Amino Acid Sequence↗
PubMed2002

Efficient recovery of centric heterochromatin P-element insertions in Drosophila melanogaster.

Approximately one-third of the human and Drosophila melanogaster genomes are heterochromatic, yet we know very little about the structure and function of this enigmatic component of eukaryotic genomes. To facilitate molecular and cytological analysis of heterochromatin we introduced a yellow(+) (y(+))-marked P element into centric heterochromatin by screening for variegated phenotypes, that is, mosaic gene inactivation. We recovered >110 P insertions with variegated yellow expression from approximately 3500 total mobilization events. FISH analysis of 71 of these insertions showed that 69 (97%) were in the centric heterochromatin, rather than telomeres or euchromatin. High-resolution banding analysis showed a wide but nonuniform distribution of insertions within centric heterochromatin; variegated insertions were predominantly recovered near regions of satellite DNA. We successfully used inverse PCR to clone and sequence the flanking DNA for approximately 63% of the insertions. BLAST analysis of the flanks demonstrated that either most of the variegated insertions could not be placed on the genomic scaffold, and thus may be inserted within novel DNA sequence, or that the flanking DNA hit multiple sites on the scaffold, due to insertions within different transposons. Taken together these data suggest that screening for yellow variegation is a very efficient method for recovering centric insertions and that a large-scale screen for variegated yellow P insertions will provide important tools for detailed analysis of centric heterochromatin structure and function.

Animals↗
PubMed2004

Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea.

Transposable elements (TEs) are the major component of plant genomes where they contribute significantly to the >1,000-fold genome size variation. To understand the dynamics of TE-mediated genome expansion, we have undertaken a comparative analysis of the TEs in two related organisms: the weed Arabidopsis thaliana (125 megabases) and Brassica oleracea ( approximately 600 megabases), a species with many crop plants. Comparison of the whole genome sequence of A. thaliana with a partial draft of B. oleracea has permitted an estimation of the patterns of TE amplification, diversification, and loss that has occurred in related species since their divergence from a common ancestor. Although we find that nearly all TE lineages are shared, the number of elements in each lineage is almost always greater in B. oleracea. Class 1 (retro) elements are the most abundant TE class in both species with LTR and non-LTR elements comprising the largest fraction of each genome. However, several families of class 2 (DNA) elements have amplified to very high copy number in B. oleracea where they have contributed significantly to genome expansion. Taken together, the results of this analysis indicate that amplification of both class 1 and class 2 TEs is responsible, in part, for B. oleracea genome expansion since divergence from a common ancestor with A. thaliana. In addition, the observation that B. oleracea and A. thaliana share virtually all TE lineages makes it unlikely that wholesale removal of TEs is responsible for the compact genome of A. thaliana.

Arabidopsis↗
PubMed2001

Redox signalling in chloroplasts and mitochondria: genomic and biochemical evidence for two-component regulatory systems in bioenergetic organelles.

Redox chemistry is central to the primary functions of chloroplasts and mitochondria, that is, to energy conversion in photosynthesis and respiration. However, these bioenergetic organelles always contain very small, specialized genetic systems, relics of their bacterial origin. At huge cost, organellar genomes contain, typically, a mere 0.1% of the genetic information in a eukaryotic cell. There is evidence that chloroplast and mitochondrial genomes encode proteins whose function and biogenesis are particularly tightly governed by electron transfer. We have identified nuclear genes for 'bacterial' histidine sensor kinases and aspartate response regulators that seem to be targeted to chloroplast and mitochondrial membranes. Sequence similarities to cyanobacterial redox signalling components indicate homology and suggest conserved sensory and signalling functions. Two-component redox signalling pathways might be ancient, conserved mechanisms that permit endogenous control over the biogenesis, in situ, of bioenergetic complexes of chloroplasts and mitochondria.

Amino Acid Sequence↗
PubMed1990

Single-copy DNA distance between two congeneric sea urchin species exhibiting radically different modes of development.

We have investigated the differences between nuclear genomes of two purportedly congeneric species of sea urchin that differ radically in early development. Heliocidaris tuberculata develops by means of a typical pluteus larva, whereas H. erythrogramma develops directly from an egg that is 100-fold the volume of the H. tuberculata egg. Reassociation kinetic analysis shows that the kinetic components of the genomic DNA from the two species are essentially the same. No single repeat component explains the 30% difference between the H. erythrogramma and H. tuberculata genomes. Reciprocal hybridization of tracer-labeled single-copy DNA fractions between these species indicates that approximately 50% of the single-copy DNA is sufficiently similar to form hybrids at standard hybridization criterion. Thermal denaturation profiles of the hybridized single-copy DNA sequence yields median (T50H) values of 13.8 degrees-16.5 degrees C. This result suggests a divergence time of 10-13 Mya, which is comparable to divergence times between congeneric sea urchin species in other genera that do not differ significantly in development. Radical differences in early developmental processes can evolve rapidly between closely related forms.

Animals↗