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At least 487 records · Page 27Linked to original sources
PubMed2006

Variations in abundance of 2 repetitive sequences in Leymus and Psathyrostachys species.

The Ns genome of the genus Psathyrostachys is a component of the polyploid genome in the genus Leymus. Using fluorescence in situ hybridization (FISH), the occurrence and abundance of 2 tandem repetitive sequences from Leymus racemosus (Lam.) Tzvelev, pLrTaiI-1 (TaiI family) and pLrPstI-1 (1 class of 350-bp family), were assayed in 4 species of the genera Psathyrostachys and Leymus. The pLrPstI-1 sequence was absent in all 4 Psathyrostachys species. While P. fragilis and P. huashanica did not have the pLrTaiI-1 sequence, 15 accessions of P. juncea and 2 accessions of P. lanuginosa had pLrTaiI-1 sites ranging in number from 7 to 16 and from 2 to 21, respectively. The numbers of pLrTaiI-1 and pLrPstI-1 sites were 1-24 and 0-30, respectively, in L. ramosus; 2-31 and 5-36 in L. racemosus; 0-4 and 0 in L. mollis; 2-9 and 24-27 in L. secalinus. The FISH assay on pLrTaiI-1 was successfully converted to a sequence-tagged-site polymerase chain reaction (STS-PCR) test using a primer pair designed from the sequence of this repetitive DNA. Seventy-three accessions representing 27 Leymus species were assayed for the abundance of pLrTaiI-1 by STS-PCR. With a few exceptions of uniformity in some accessions, nearly all Leymus species observed were heterogeneous for the abundance of pLrTaiI-1 sequence and no Leymus species was totally devoid of this repetitive sequence. These findings may have significance for the understanding of phylogeny, nature of polyploidy, adaptive ranges, and breeding potential of Leymus species.

Blotting, Southern↗
PubMed2004

SUMO conjugation in plants.

Covalent attachment of small proteins to substrates can regulate protein activity in eukaryotes. SUMO, the small ubiquitin-related modifier, can be covalently linked to a broad spectrum of substrates. An understanding of SUMO's role in plant biology is still in its infancy. In this review, we briefly summarize the enzymology of SUMO conjugation (sumoylation), and the current knowledge of SUMO modification in Arabidopsis thaliana (L.) Heynh. and other plants, in comparison to animals and fungi. Furthermore, we assemble a list of potential pathway components in the genome of A. thaliana that have either been functionally defined, or are suggested by similarity to pathway components from other organisms.

Amino Acid Sequence↗
PubMed2026

C-Terminal Truncation and Fusion Partner Determine Oncogenicity of FGFR3.

UNLABELLED: Genomic alterations affecting components of the fibroblast growth factor (FGF) signaling axis can trigger aberrant pathway activation and tumor development. Genomic truncation of the FGF receptor 2 (FGFR2) exon 18 (E18) disrupts the FGFR2 carboxy (C)-terminal tail, acting as a potent driver alteration across multiple tumor types. In this study, we analyzed human oncogenomic datasets to reveal that E18 truncations are similarly prevalent in FGFR3, an FGFR2 paralog. FGFR3 E18 truncations primarily occur due to rearrangements (RE) that involve transforming acidic coiled-coil-containing protein 3 (TACC3), resulting in FGFR3ΔE18-TACC3 gene fusions. In contrast to E18-truncated FGFR2, functional in vitro and in vivo examination of Fgfr3 variants demonstrated that the truncation of Fgfr3 E18 is insufficient to promote oncogenic activity in cell lines or in the lungs and mammary glands of mice. Only the combination of an Fgfr3 E18 truncation with a RE partner gene that encodes a receptor-dimerizing domain resulted in the development of tumors, which were sensitive to FGFR inhibition. Overall, these findings suggest that patients with cancers that are positive for rearranged FGFR3, resulting in E18 truncation and a fusion to dimerizing partners, should be considered for FGFR-targeted therapies. SIGNIFICANCE: FGFR3, unlike its paralog FGFR2, requires both a C-terminal truncation and fusion to a partner gene that retains the expression of a dimerizing domain to effectively drive oncogenic signaling and tumorigenesis.

Receptor, Fibroblast Growth Factor, Type 3↗
PubMed1987

Transition from a heterozygous to a homozygous state of a pair of loci in the inverted repeat sequences of the L component of the herpes simplex virus type 1 genome.

The behavior of herpes simplex virus type 1 heterozygous isolates, in which the two inverted repeats of the L component (RL) were differentiated by a polymorphism marker (the presence [type B] or absence [type A] of a SalI site), was investigated. The progeny viruses derived from the heterozygote (A/B) consisted of heterozygotes (A/B), type A homozygotes (A/A), and type B homozygotes (B/B). The heterology between RL, albeit tolerated, was unstable, as is the case with heterology between the repeats of the S component. The two repeats TRL (terminal) and IRL (internal) were equipotent in generating homozygotes from a heterozygote. Data obtained from an analysis of 426 progeny viruses derived from heterozygous clones supported the hypothesis that the two loci in RL of a herpes simplex virus type 1 genome are determined as a random combination of the corresponding two loci in RL of the parent virus and that the ratio of heterozygotes/type A homozygotes/type B homozygotes in the progeny viruses from a heterozygote is expected to be 2:1:1. An ephemeral dominance of one type of homozygote over the other was observed in subclones from several heterozygous clones.

Animals↗
PubMed1992

DNA-DNA hybridization phylogeny of sand dollars and highly reproducible extent of hybridization values.

A DNA hybridization phylogeny of four sand dollars using a sea biscuit as an outgroup is presented. The study is unusual in that the normalized percent hybridization (NPH) values were all less than 50%, yet the same topology was obtained regardless of which distance metric was used, i.e., whether reciprocal distances were averaged or not, or whether or not a molecular clock was assumed. The tree also appears robust under jackknifing and bootstrapping. The extent of hybridization between homologous hybrids was measured with a five- to sevenfold higher precision than is typical, and by implication NPH was also measured with a higher than normal precision. The ability to measure highly reproducible NPH values offers the possibility of examining the phylogeny of more widely divergent species than typically studied using DNA hybridization techniques, using 1/NPH as a distance metric. The hypothesis of a molecular clock within the sand dollars was rejected, adding sand dollars to the growing list of groups where significant rate variation is known. A small fraction of the sand dollar genomes hybridized with the distantly related regular sea urchin Lytechinus. These slowly evolving sequences probably represent conserved exonic components of the genome.

Animals↗
PubMed1994

Detection of a 45 kD protein derived from the N terminus of the pea seedborne mosaic potyvirus polyprotein in vivo and in vitro.

A 45 kD protein (Pro1) derived from the N terminus of the pea seedborne mosaic potyvirus (PSbMV) polyprotein has been detected in extracts of infected pea plants and among in vitro translation products of PSbMV genomic RNA. The genomic region coding for the first 231 amino acids of the PSbMV polyprotein was cloned and expressed in Escherichia coli as a fusion protein with beta-galactosidase. A rabbit antiserum raised against the fusion protein recognized an approximately 45 kD protein in immunoblots of extracts of PSbMV-infected pea leaves that was not present in extracts of healthy leaves. The highest concentration of the 45 kD protein was found in extracts of young leaves, suggesting the protein may be rapidly degraded in vivo. After in vitro translation of PSbMV genomic RNA in a wheat germ extract, the antiserum immunoprecipitated a 45 kD polypeptide as well as some lower molecular weight translation products. On the other hand, an approximately 90 kD polypeptide was immunoprecipitated from in vitro translation products of genomic RNA in a rabbit reticulocyte lysate, corresponding to the combined molecular weights of Pro1 and the helper component predicted from genomic sequence data.

Binding Sites↗
PubMed1994

Plant transposable elements and the genome.

Transposable elements are ubiquitous in the plant kingdom and share many common features, both structural and mechanistic, with mobile elements from other eukaryotes. Transposition of these elements can influence plant genes and genomes in many ways. It is also becoming clear that transposable element derived sequences can be a major component of plant genomes. These sequences are probably, therefore, very significant factors in plant evolution.

Biological Evolution↗
PubMed2001

Integrons: natural tools for bacterial genome evolution.

Integrons were first identified as the primary mechanism for antibiotic resistance gene capture and dissemination among Gram-negative bacteria. More recently, their role in genome evolution has been extended with the discovery of larger integron structures, the super-integrons, as genuine components of the genomes of many species throughout the gamma-proteobacterial radiation. The functional platforms of these integrons appear to be sedentary, whereas their gene cassette contents are highly variable. Nevertheless, the gene cassettes for which an activity has been experimentally demonstrated encode proteins related to simple adaptive functions and their recruitment is seen as providing the bacterial host with a selective advantage. The widespread occurrence of the integron system among Gram-negative bacteria is discussed, with special focus on the super-integrons. Some of the adaptive functions encoded by these genes are also reviewed, and implications of integron-mediated genome evolution in the emergence of novel bacterial species are highlighted.

DNA Transposable Elements↗
PubMed2006

Resources for genetic variation studies.

The rapid growth of genome-wide diversity databases, as well as ongoing large-scale resequencing projects targeting genes and other functional components of our genome, provide valuable resources of natural variation at the DNA sequence level. In this review, we briefly summarize the wealth of data on DNA polymorphisms in humans, the distribution of this diversity in the genome as well as among individuals, and the consequence of recombination on its organization. These data provide a set of powerful tools that can be used to better understand inherited phenotypic variation in humans. We discuss the implications for the design of studies investigating correlations between genotypes and phenotypes, both at the fundamental level of genome function and regulation, and for the mapping of disease genes.

Biomedical Research↗
PubMed2005

Extensive DNA inversions in the B. fragilis genome control variable gene expression.

The obligately anaerobic bacterium Bacteroides fragilis, an opportunistic pathogen and inhabitant of the normal human colonic microbiota, exhibits considerable within-strain phase and antigenic variation of surface components. The complete genome sequence has revealed an unusual breadth (in number and in effect) of DNA inversion events that potentially control expression of many different components, including surface and secreted components, regulatory molecules, and restriction-modification proteins. Invertible promoters of two different types (12 group 1 and 11 group 2) were identified. One group has inversion crossover (fix) sites similar to the hix sites of Salmonella typhimurium. There are also four independent intergenic shufflons that potentially alter the expression and function of varied genes. The composition of the 10 different polysaccharide biosynthesis gene clusters identified (7 with associated invertible promoters) suggests a mechanism of synthesis similar to the O-antigen capsules of Escherichia coli.

Bacterial Outer Membrane Proteins↗
PubMed1971

Components of adenovirus-simian virus 40 hybrid viruses.

The DNA and protein components of the adenovirus 7-simian virus (SV)40 hybrid virus "E46(+)" have been investigated. The Ad.7-SV40 hybrid DNA genome could be distinguished from nonhybrid Ad. 7 genome on the basis of its molecular weight in an alkaline sucrose gradient. The hybrid genome could also be separated from nonhybrid adenovirus 2 DNA when purified transcapsidant adenovirus 2(+t7) (Ad.7-SV40 DNA within an Ad.2 capsid) was studied. The presence and amount of SV40 DNA in the hybrid virus genome was determined by DNA-RNA hybridization. The results presented suggest: (i) that about 10% of the particles in the E46(+) preparations contained SV40 DNA covalently linked to adenovirus DNA; (ii) that the hybrid virus genome has a molecular weight 10-12% lower than that of nonhybrid virus, consistent with a deletion of adenovirus DNA; and (iii) that the hybrid virus contained only 40-50% of a total SV40 genome. The protein components of the Ad.7-SV40 hybrid virus were examined by acrylamide gel electrophoresis in sodium dodecyl sulfate. No significant quantitative or qualitative differences between the proteins of hybrid and nonhybrid adenovirus were demonstrated.

Adenoviridae↗
PubMed1994

Genome characterization and identification of viral-associated dsDNA component of banana bunchy top virus.

The single-stranded (ss) and double-stranded (ds) viral-associated DNAs (VADs) of banana bunchy top virus (BBTV) were characterized. The ssVADs were shown to be the viral genomic DNA and the dsVADs are the likely replication forms. Both dsVADs and ssVADs contain DNA species that cross-hybridize to each other. Under the electron microscope, both circular and linear DNAs were observed from these VAD species. Libraries were constructed from VADs to further characterize them. Two overlapping VAD clones were isolated and their combined sequence indicated that their corresponding VAD, named as BBTV component 2, is circular with a size of 1095 nt. The largest ORF spans from nucleotides 82 to 390, which is sandwiched by a putative TATA box, 54 nt upstream from the first ATG codon, and a AATAAA motif, 7 nt downstream from the UAA codon. Although the sequence of this VAD is different from the previously reported BBTV component 1 (Harding et al., J. Gen. Virol. 74, 323-328, 1993) and the genome of coconut foliar decay virus (Rohde et al., Virology 176, 648-651, 1990), stretches of highly homologous sequences were found between BBTV component 2 and the other two viral genomes by computer analysis. The sequence of BBTV component 1 is highly homologous to one of the clones, pBTs26, in the VAD library. Nevertheless, our libraries still contain many clones which hybridized with ss viral genomic DNAs but not with pBTs26 and BBTV component 2, indicating that the viral genome consists of more than two components.

Base Sequence↗
PubMed1986

Generation of an inverting herpes simplex virus 1 mutant lacking the L-S junction a sequences, an origin of DNA synthesis, and several genes including those specifying glycoprotein E and the alpha 47 gene.

The herpes simplex virus genome consists of two components, L and S, that invert relative to each other to yield four isomeric arrangements, prototype (P), inversion of the S component (Is), inversion of the L component (Il), and inversion of both components (Isl). Previous studies have shown that the 500-base-pair a sequences flanking the two components contain a cis-acting site for inversion. In an attempt to insert a third copy of the alpha 4 gene, the major regulatory gene mapping in the repeats flanking the S component, a fragment containing the alpha 4 gene and an origin of DNA synthesis, was recombined into the thymidine kinase gene mapping in the unique sequences of the L component. The resulting recombinants showed massive rearrangements and deletions mapping in the S component and in the junction between the L and S components. One recombinant (R7023) yielded two isomeric DNA arrangements, a major component consisting of Is and a minor component consisting of Isl. In these arrangements, the genome lacked the gene specifying glycoprotein E and all contiguous genes located between it and the alpha 0 gene in the inverted repeats of the L component. Among the deleted sequences were those encoding an origin of viral DNA synthesis, the alpha 47 gene, and the a sequences located at the junction between the L and S-components. The recombinant grew well in rabbit skin, 143TK-, and Vero cell lines. We conclude that the four unique genes deleted in R7023 are not essential for the growth of herpes simplex virus, at least in the cell lines tested, and that the b sequence of the inverted repeats of the L component also contains cis-acting sites for the inversion of herpes simplex virus DNA sequences.

Animals↗
PubMed2004

ARIA, an Arabidopsis arm repeat protein interacting with a transcriptional regulator of abscisic acid-responsive gene expression, is a novel abscisic acid signaling component.

Arabidopsis (Arabidopsis thaliana) genome contains more than 90 armadillo (arm) repeat proteins. However, their functions are largely unknown. Here, we report that an Arabidopsis arm repeat protein is involved in abscisic acid (ABA) response. We carried out two-hybrid screens to identify signaling components that modulate ABA-responsive gene expression. Employing a transcription factor, ABF2, which controls the ABA-dependent gene expression via the G-box type ABA-responsive elements, we isolated an arm repeat protein. The ABF2-interacting protein, designated as ARIA (arm repeat protein interacting with ABF2), has another conserved sequence motif, BTB/POZ (broad complex, tramtrak, and bric-a-brac/poxvirus and zinc finger) domain, in the C-terminal region. The physiological relevance of ABF2-ARIA interaction was supported by their similar expression patterns and similar subcellular localization. Plants overexpressing ARIA are hypersensitive to ABA and high osmolarity during germination and insensitive to salt during subsequent seedling growth. By contrast, an ARIA knockout mutant exhibits ABA and glucose insensitivities. Changes in the expression levels of several ABF2-regulated genes were also observed in ARIA overexpression lines, indicating that ARIA modulates the transcriptional activity of ABF2. Together, our data indicate that ARIA is a positive regulator of ABA response.

Abscisic Acid↗
PubMed2006

Impact of RNA structure on the prediction of donor and acceptor splice sites.

BACKGROUND: gene identification in genomic DNA sequences by computational methods has become an important task in bioinformatics and computational gene prediction tools are now essential components of every genome sequencing project. Prediction of splice sites is a key step of all gene structural prediction algorithms. RESULTS: we sought the role of mRNA secondary structures and their information contents for five vertebrate and plant splice site datasets. We selected 900-nucleotide sequences centered at each (real or decoy) donor and acceptor sites, and predicted their corresponding RNA structures by Vienna software. Then, based on whether the nucleotide is in a stem or not, the conventional four-letter nucleotide alphabet was translated into an eight-letter alphabet. Zero-, first- and second-order Markov models were selected as the signal detection methods. It is shown that applying the eight-letter alphabet compared to the four-letter alphabet considerably increases the accuracy of both donor and acceptor site predictions in case of higher order Markov models. CONCLUSION: Our results imply that RNA structure contains important data and future gene prediction programs can take advantage of such information.

Algorithms↗
PubMed2006

Resting metabolic rate and respiratory quotient: results from a genome-wide scan in the Quebec Family Study.

BACKGROUND: Genes influencing resting metabolic rate (RMR) and respiratory quotient (RQ) represent candidate genes for obesity, type 2 diabetes, and the metabolic syndrome because of the involvement of these traits in energy balance and substrate oxidation. OBJECTIVE: We conducted a genome-wide scan for quantitative trait loci (QTL) contributing to the variability in RMR and RQ. DESIGN: Regression-based and variance components-based genome-wide autosomal scans on RMR and RQ phenotypes, obtained from indirect calorimetry, were performed in 169 families ascertained via an obese proband or from the general population. RESULTS: We found evidence for linkage to RMR on chromosomes 3q26.1 (lod = 2.74), 1q21.2 (2.44), and 22q12.3 (1.33). QTL influencing RQ were found on chromosomes 12q13 (1.65) and 14q22 (1.83) when the analyses were performed in all families. Considerable locus heterogeneity within this population was suggested because most of the families were unlinked to any one quantitative trait locus. Significant associations between traits and linked microsatellites were detected within the linked, informative subsets. CONCLUSIONS: We found several new QTL for energy metabolism, but the QTL on 1q may be a replication of the one reported in Pima Indians. All 3 RMR linkages overlapped regions previously linked to the metabolic syndrome or its components, and the significant association between RMR and the metabolic syndrome in the present cohort reinforces this relation. We conclude that considerable locus heterogeneity exists even within populations, which should be taken into account when considering candidate gene studies of energy metabolism phenotypes and other complex traits.

Basal Metabolism↗
PubMed1986

Conversion of a fraction of the unique sequence to part of the inverted repeats in the S component of the herpes simplex virus type 1 genome.

A novel genome variant of herpes simplex virus type 1 (HSV-1) was isolated, in the S component of which a fraction of the unique sequence (map units 0.865 to 0.880) was converted to part of the diploid inverted repeats and another fraction of the unique sequence (map units 0.937 to 0.955) had been deleted. The S component of the variant consisted of a shortened unique sequence (map units 0.880 to 0.937) and a pair of elongated inverted repeats (map units 0.820 to 0.880, and 0.937 to 1.000). The conversion occurred as a result of a recombination event between two points (map units 0.880 and 0.937) having a 5 base pair stretch (5'-CCCCG-3') of homology, in an inverted direction in the unique sequence. An involvement of the mechanism causing L-S inversion was inferred to account for the generation of the variant, as there are multiple copies of the 5'-CCCCG-3' stretch in the 'a' sequences. The occurrence of the variant indicates that the products of HSV-1 genes US9, US10, US11 and US12 are unnecessary for an HSV-1 productive infection in tissue culture cells, and also suggests the presence of a mechanism whereby expansion of the inverted repeats could occur.

Base Sequence↗
PubMed1991

The ability of pseudorabies virus to grow in different hosts is affected by the duplication and translocation of sequences from the left end of the genome to the UL-US junction.

Pseudorabies virus is a herpesvirus which has a class 2 genome. However, under certain growth conditions it acquires a genome with class 3-like characteristics. In these variants, the leftmost sequences of the long (L) component of the viral genome have been duplicated and translocated to the right of the L component next to the short (S) component, resulting in an L component that is bracketed by inverted repeats. Consequently, the L component can invert and is found in two orientations relative to the S component. The translocation is accompanied invariably by a deletion of sequences that are normally present in the wild-type genome at the right end of the L component. The virion variants with an invertible L component have a growth advantage over wild-type virus in chicken embryo fibroblasts and chickens; they also have a growth disadvantage in mice or rabbit kidney cells. The changed growth characteristics of the variants reside entirely in the changed structure of the junction between the S and L components. Replacement of that region of the DNA with wild-type sequences restores the wild-type phenotype. To determine whether the modified growth characteristics of the variants are related to the translocation or to the deletion, mutants that have a deletion or that have a deletion as well as a translocation similar to those observed in the variants were constructed, and the growth characteristics of these mutants were determined. We show that the modified growth characteristics of the mutants with an invertible L component can be attributed to the translocation of the leftmost terminal sequences of the genome next to the inverted repeat; they are not related to the deletion of the sequences normally present at the right end of the L component. The translocation of the leftmost 325 bp of the genome is sufficient to confer upon the virus the modified cell-type-specific growth characteristics. Furthermore, the modified growth characteristics are contingent upon the presence of 68 bp spanning the internal junction between the L and S components.

Animals↗