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Results for “repetitive elements”

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At least 883 records · Page 49Linked to original sources
PubMed1996

Allelic variation of human serotonin transporter gene expression.

Mood, emotion, cognition, and motor functions as well as circadian and neuroendocrine rhythms, including food intake, sleep, and reproductive activity, are modulated by the midbrain raphe serotonin (5-HT) system. By directing the magnitude and duration of postsynaptic responses, carrier-facilitated 5-HT transport into and release from the presynaptic neuron are essential for the fine tuning of serotonergic neurotransmission. Interest in the mechanism of environmental factor-, disease-, and therapy-induced modification of 5-HT transporter (5-HTT) function and its impact on early brain development, event-related synaptic plasticity, and neurodegeneration is widespread and intensifying. We have recently characterized the human and murine 5-HTT genes and performed functional analyses of their 5'-flanking regulatory regions. A tandemly repeated sequence associated with the transcriptional apparatus of the human 5-HTT gene displays a complex secondary structure, represses promoter activity in nonserotonergic neuronal cells, and contains positive regulatory components. We now report a novel polymorphism of this repetitive element and provide evidence for allele-dependent differential 5-HTT promoter activity. Allelic variation in 5-HTT-related functions may play a role in the expression and modulation of complex traits and behavior.

Alleles↗
PubMed2006

Bacillus safensis sp. nov., isolated from spacecraft and assembly-facility surfaces.

Thirteen strains of a novel spore-forming, Gram-positive, mesophilic heterotrophic bacterium were isolated from spacecraft surfaces (Mars Odyssey Orbiter) and assembly-facility surfaces at the Jet Propulsion Laboratory in California and the Kennedy Space Center in Florida. Phylogenetic analysis of 16S rRNA gene sequences has placed these novel isolates within the genus Bacillus, the greatest sequence similarity (99.9 %) being found with Bacillus pumilus. However, these isolates share a mere 91.2 % gyrB sequence similarity with Bacillus pumilus, rendering their 16S rRNA gene-derived relatedness suspect. Furthermore, DNA-DNA hybridization showed only 54-66 % DNA relatedness between the novel isolates and strains of B. pumilus. rep-PCR fingerprinting and previously reported matrix-assisted laser desorption/ionization time-of-flight mass spectrometry protein profiling clearly distinguished these isolates from B. pumilus. Phenotypic analyses also showed some differentiation between the two genotypic groups, although the fatty acid compositions were almost identical. The polyphasic taxonomic studies revealed distinct clustering of the tested strains into two distinct species. On the basis of phenotypic characteristics and the results of phylogenetic analyses of 16S rRNA and gyrB gene sequences, repetitive element primer-PCR fingerprinting and DNA-DNA hybridization, the 13 isolates represent a novel species of the genus Bacillus, for which the name Bacillus safensis sp. nov. is proposed. The type strain is FO-36b(T) (=ATCC BAA-1126(T)=NBRC 100820(T)).

Bacillus↗
PubMed1996

Crystal structure of UDP-N-acetylglucosamine enolpyruvyltransferase, the target of the antibiotic fosfomycin.

BACKGROUND: The ever increasing number of antibiotic resistant bacteria has fuelled interest in the development of new antibiotics and other antibacterial agents. The major structural element of the bacterial cell wall is the heteropolymer peptidoglycan and the enzymes of peptidoglycan biosynthesis are potential targets for antibacterial agents. One such enzyme is UDP-N-acetylglucosamine enolpyruvyltransferase (EPT) which catalyzes the first committed step in peptidoglycan biosynthesis: the transfer of the enolpyruvyl moiety of phosphoenolpyruvate (PEP) to the 3-hydroxyl of UDP-N-acetylglucosamine (UDPGlcNAc). EPT is of potential pharmaceutical interest because it is inhibited by the broad spectrum antibiotic fosfomycin. RESULTS: The crystal structure of substrate-free EPT has been determined at 2.0 A resolution. The structure reveals a two-domain protein with an unusual fold (inside out alpha/beta barrel) which is built up from the sixfold repetition of one folding unit. The only repetitive element in the amino acid sequence is a short motif, Leu-X3-Gly(Ala), which is responsible for the formation of hydrogen-bond interactions between the folding units. An enzyme which catalyzes a similar reaction to EPT, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), has a very similar structure despite an amino acid sequence identity of only 25%. To date, only these two enzymes appear to display this characteristic fold. CONCLUSIONS: The present structure reflects the open conformation of the enzyme which is probably stabilized through two residues, a lysine and an arginine, located in the cleft between the domains. Binding of the negatively charged UDPGlcNAc to these residues could neutralize the repulsive force between the two domains, thereby allowing the movement of a catalytically active cysteine residue towards the cleft.

Alkyl and Aryl Transferases↗
PubMed2001

Human intrachromosomal telomeric-like repeats: sequence organization and mechanisms of origin.

The intrachromosomal location of (T2AG3)n telomeric sequences has been reported in several species. It was proposed that interstitial telomeres (ITs) originated through telomeric fusion of ancestral chromosomes. However, the data so far obtained derive mainly from cytogenetic observations. Cloning and database searching of human IT sequences allowed us to identify three classes: (i) short ITs, composed of few, essentially exact T2AG3 units; (ii) subtelomeric ITs, composed of larger arrays (several hundred base pairs) including many degenerate units within subtelomeric domains; (iii) fusion ITs, in which two extended stretches of telomeric repeats are oriented head-to-head. The number of short ITs is over 50 and subtelomeric ITs are probably present at all chromosomal ends. Surprisingly, the telomeric sequence in 2q13 remains the only fusion IT so far characterized, and evidence presented here suggests that another member of this class may be present in 1q41. Different molecular mechanisms generated the three classes. In particular, several short ITs interrupt precisely repetitive elements or are flanked by direct repeats of 10-41 bp, and are conserved in gorilla and chimpanzee. These features strongly suggest that telomeric repeats were inserted at intrachromosomal sites through the repair of double-strand breaks that occurred in the germline during evolution.

Animals↗
PubMed1998

Completing the sequence of the Sulfolobus solfataricus P2 genome.

The Sulfolobus solfataricus P2 genome collaborators are poised to sequence the entire 3-Mbp genome of this crenarchaeote archaeon. About 80% of the genome has been sequenced to date, with the rest of the sequence being assembled fast. In this publication we introduce the genomic sequencing and automated analysis strategy and present intial data derived from the sequence analysis. After an overview of the general sequence features, metabolic pathway studies are explained, using sugar metabolism as an example. The paper closes with an overview of repetitive elements in S. solfataricus.

Base Sequence↗
PubMed1994

The mouse type-III procollagen-encoding gene: genomic cloning and complete DNA sequence.

Overlapping cosmid clones were isolated that covered the entire mouse type-III collagen-encoding gene (mCol3) locus including flanking sequences approximately 40 kb upstream and 20 kb downstream from the gene. This gene was characterized initially by restriction mapping and then followed by sequencing of 43.6 kb, including 5 kb upstream from the transcription start point (tsp) and all exons and introns of the entire gene. The optimal parameters for sequencing a gene of this size were determined by sequencing 5-10-kb fragments at different ratios of random and directed sequencing, and comparing their efficiency. Based on our experience for sequencing mCol3, we have estimated that the most cost-efficient method was to achieve a twofold redundancy in sequencing by using random DNA subclones as templates for sequencing prior to initiating directed DNA sequencing to close the gaps between contiguous regions. mCol3 spans 37.6 kb from the tsp to the single polyadenylation site and contains 51 exons. The overall structure of mCol3 is similar to that of other members of the fibrillar collagen-encoding gene family. Several repetitive elements were located within the gene boundaries. Based on the nucleotide (nt) sequence, the predicted sizes of the mouse type-III collagen (mCOL3) mRNA and polypeptide are 4767 nt and 1464 amino acids (aa), respectively. A comparison of mCOL3 versus the human type-III collagen (hCOL3) showed 91% identity at the aa level.

Amino Acid Sequence↗
PubMed1991

Genomic cloning, complete nucleotide sequence, and structure of the human gene encoding the major intrinsic protein (MIP) of the lens.

Major intrinsic protein (MIP, also called MP26) is the predominant fiber cell membrane protein of the ocular lens. MIP has been suggested to play a role in cell-cell communication in the lens. Its expression is tissue-specific and developmentally regulated. We have isolated and characterized the human gene encoding MIP and report here its genomic structure and entire nucleotide sequence. The gene is 3.6 kb, contains four exons separated by introns ranging in size from 0.4 to 1.6 kb, and is present in single copy per haploid human genome. Primer extension of human lens RNA indicates that transcription of the gene initiates from a single site 26 nt downstream from the TATA box. Three complete Alu repetitive elements are found in tandem in the 5'-flanking region of the gene, and a single complete Alu sequence is present in the third intron. The interspecies comparisons of the MIP gene coding sequence and homologies to other members of a putative transmembrane channel protein superfamily are also discussed.

Amino Acid Sequence↗
PubMed1989

Cosmid-derived map of E. coli strain BHB2600 in comparison to the map of strain W3110.

A physical map for the genome of E. coli K12 strain BHB2600 was constructed by use of 570 cloned DNA elements (CDEs) withdrawn from a cosmid library. Dot blot hybridisation was applied to establish contig interrelations with subsequent fine mapping achieved by analysis of EcoR1 restriction patterns on Southern blots. The derived map covers nearly 95% of the E. coli genome resulting in 12 minor gaps. It may be compared to the almost complete map for strain W3110 of Kohara et al. (1). Except for one tiny gap (lpp,36.5') remaining gaps in BHB2600 do not coincide with those in W3110 so that both maps complement each other establishing an essentially complete clone represented map. Besides numerous minute differences (site and fragment gains and losses) both strains harbour at differing positions extended rearrangements flanked by mutually inverted repetitive elements, in our case insertion elements (IS1 and IS5).

Blotting, Southern↗
PubMed1995

Mobile genetic elements in mycobacteria.

Mobile genetic elements, ranging from plasmids and bacteriophages to insertion sequences and transposons, have come to play key roles in many aspects of basic and applied research in mycobacteriology. Plasmids and bacteriophages have been widely used as cloning vectors, especially for constructing recombinant vaccines based on bacille Calmette-Guérin (BCG); composite transposons have also been used for this purpose. At the same time, insertion sequences have proved invaluable for diagnostic and epidemiological studies, and transposon mutagenesis provides a useful method for inactivating and marking selected mycobacterial genes. Plasmids are commonly found in many mycobacterial species, notably M. avium, although not in M. tuberculosis; the biological significance of these plasmids (if any) is mostly unknown. Insertion sequences, and other repetitive elements, have also been characterized from many mycobacterial species. Special attention is paid to IS6110/IS986, from M. tuberculosis, and the IS900 family from M. avium and related organisms; the latter includes the recently described highly mobile element IS1110. The emphasis of the paper is on the molecular biology and significance of plasmids and insertion sequences/transposons, in mycobacteria and in bacteria of plasmids and insertion sequences/transposons, in mycobacteria and in bacteria in general, and their applications as cloning vectors and in transposon mutagenesis.

BCG Vaccine↗
PubMed1990

Molecular analysis of a phylogenetically conserved carrot gene: developmental and environmental regulation.

Extensive studies of gene expression programs in carrot somatic embryos identified a gene, designated Dc3, that serves as a reliable molecular marker for the acquisition of embryogenic potential by carrot cells in culture. The complete sequence of a carrot genomic region, DcG3, encoding a Dc3-like mRNA, was determined. The DcG3 transcription unit contains a single intron and encodes mRNA that is expressed at high levels in embryonic tissue but is undetectable in somatic tissue of carrot. The predicted protein sequence of DcG3 is 163 amino acids and includes two approximately 50 amino acid direct repeats which in turn include additional repetitive elements with an unusual distribution of charged amino acids. Dc3 and Dc3-like mRNAs are encoded by a small divergent gene family. Furthermore, similarities of the Dc3 gene family with genes from other plant species that are expressed in response to environmental and developmental cues suggest a possible role in seed desiccation and possibly in more general water-stress responses in plants. Analysis of transgenic tobacco containing a beta-glucuronidase (GUS) reporter gene fused to a 1.7 kb 5' upstream element of DcG3 defined a promoter/enhancer complex that confers developmentally and environmentally regulated expression of GUS activity. Thus, DcG3 is phylogenetically conserved together with the trans-acting factors required for its regulated expression in transgenic tobacco.

Amino Acid Sequence↗
PubMed1992

Evolution of a B2 tagged sequence from a long-range repeat family in the genus Mus.

A long-range repeat family of more than 50 kb repeat size is clustered in Chromosomes (Chr) 1 of Mus musculus and M. spretus. In M. musculus this long-range repeat family shows considerable variation of copy-number frequency and contains coding regions for at least two genes. In an intron of a gene, which is part of the repeat, a B2 small interspersed repetitive element (SINE) is inserted at identical positions. The B2 element is present in all copies of the long-range repeat family; it was presumably a component of the ancestral single-copy precursor sequence that gave rise by amplification to the repeat family. Copies of the long-range repeat family vary with respect to the number of TAAA tandem repeats in the A-rich 3' end region of the B2 element. As inferred from polymerase chain reaction (PCR) data, presence and frequency of repeat number variants in the (TAAA)n block are strain and species specific. The B2 element and its flanking regions were sequenced from two copies of the long-range repeat family. Sequence divergence between the two copies (only non-CG base substitutions and deletions/insertions) was determined to be 2.6%. Based on the drift rate in human Alu elements and a correction for the higher drift rates in rodents, an estimate for the divergence time of 1.7 million years was calculated. Since the long-range repeat family is present in M. musculus and M. spretus, it must have evolved by amplification before the separation of the two species about 1-4 million years ago.

Animals↗
PubMed1985

Homeo box gene complex on mouse chromosome 11: molecular cloning, expression in embryogenesis, and homology to a human homeo box locus.

The homeo box is a 180 bp protein-coding domain found within homeotic genes of Drosophila and conserved in a variety of invertebrate and vertebrate species. It has been suggested that the mammalian homeo box sequences may play a role in controlling pattern formation during embryogenesis. We report findings that support this hypothesis. We have cloned three overlapping recombinant phage clones that cover a region of mouse chromosome 11 that contains a cluster of four homeo boxes (the Hox-2 locus). This locus encodes multiple transcripts that are expressed during embryogenesis. Forty kilobases of the Hox-2 region is devoid of repetitive elements and shows extensive homology with the human Hox-2 locus. These results provide direct evidence for genetic expression during embryonic development, a conserved organization in comparison to the cognate human locus, and a complexity of organization and transcript expression similar to that found in Drosophila.

Animals↗
PubMed1990

Analysis of a CR1 (chicken repeat) sequence flanking the 5' end of the gene encoding alpha-skeletal actin.

Genomic Southern blots of chicken DNA, probed with radiolabeled DNA fragments that flank the 5'-end of the asa gene encoding chicken alpha-skeletal actin, indicate the presence of repetitive nucleotide sequences. Sequence analysis of this region reveals a member of the CR1 family of middle-repetitive elements. A 186-bp restriction fragment carrying the 3'-end of this CR1 element binds factor(s) present in nuclear extracts, as assayed by band-shift electrophoresis. However, the CR1 repeat has limited influence on transcription from the alpha-skeletal actin promoter, as assessed by CAT assays of transfected chicken myoblasts and fibroblasts.

Actins↗
PubMed1993

Genomic structure of rat liver aryl sulfotransferase IV-encoding gene.

This report contains the first description of the genomic structure for a sulfotransferase (ST). The gene (ASTIV) encodes rat hepatic aryl ST IV, also known as tyrosine-ester ST (EC 2.8.2.9). A phage genomic clone containing 70% of the 3' AST gene coding sequence was isolated after screening a rat genomic library with an ASTIV cDNA. The remaining 5' sequence was determined from a PCR product obtained from rat genomic DNA and ASTIV cDNA-specific primers. ASTIV spans 3.5 kb and contains eight exons and seven introns. The fourth intron of this gene contains sequences homologous to rodent B1 repetitive elements and an Alu repeat found in rat. An alignment of the primary structures of ten different ST revealed several conserved regions, as well as a putative binding site for the cofactor for enzymatic sulfation reactions, 3'-phosphoadenosine-5'-phosphosulfate.

Amino Acid Sequence↗
PubMed1988

Complete sequence and organization of the murine beta-glucuronidase gene.

The murine beta-glucuronidase structural gene (Gus-s) has been isolated from a BALB/cJ sperm DNA bacteriophage library and its nucleotide sequence established. The gene is organized into 12 exons comprising 17.5% of the 14,009 base pair (bp) region spanning the interval between transcription initiation and the putative site of polyadenylation. A TATA box sequence, embedded within a GC-rich region, is found 28 bp upstream from the transcription initiation site. Eleven members of the B1 family and eight members of the B2 family of murine repetitive elements were identified within Gus-s and 2440 bp of flanking sequence. Other novel sequences found within Gus-s, including a (AC)19 homocopolymer tract within intron 3 and a 23 base pair complex direct repeat within intron 9, are presented and discussed.

Amino Acid Sequence↗
PubMed2004

New PCR-based methods for yeast identification.

AIMS: To characterize reference yeast strains and identify indigenous strains isolated from wine fermentations by PCR methods. METHODS AND RESULTS: We compared several PCR techniques for yeast identification. We used oligonucleotide primers that are complementary to (i) intron splice sites, (ii) REP and (iii) ERIC elements to produce PCR fingerprints that display specific patterns between the different yeast species. These three techniques were used to characterize 41 reference yeast strains belonging to 15 different species and to identify 40 indigenous strains isolated from grape must and wine fermentations. Species-specific banding patterns were obtained with the three PCR-techniques with different degrees of intraspecific differentiation depending on the method. By comparing the PCR fingerprints of unknown isolates with those produced by reference strains, we identified yeast strains isolated from an industrial wine fermentation. CONCLUSIONS: All three PCR techniques are rapid, reliable and simple methods of yeast identification. As far as we know, this is the first time that the primers designed for amplifying repetitive elements in bacteria have been successfully used in yeast. SIGNIFICANCE AND IMPACT OF THE STUDY: Industry needs rapid, reliable and simple methods of yeast identification. The proposed PCR techniques will allow to achieve this objective.

DNA Fingerprinting↗
PubMed1992

Extensive cross-homology between the long and the short arm of chromosome 16 may explain leukemic inversions and translocations.

Specific rearrangements of chromosome 16 are well known in acute nonlymphocytic leukemia with abnormal eosinophils. While mapping cosmids relative to breakpoints in chromosome 16 in leukemic cells with fluorescence in situ hybridization (FISH), we have identified three areas of extensive cross-homology between 16p and 16q. Three cosmids among 99 tested showed two large signals on the short arm and one signal on the long arm of chromosome 16. A fourth cosmid showed mainly two signals on the short arm. With the 16p-specific cosmid we can demonstrate that the breakpoints of a pericentric inversion and a reciprocal (16;16) translocation, both of which are characteristic for acute leukemia, map to the most distal of two blocks on the short arm. We suggest that there may be at least two distinct repetitive elements specific for chromosome 16 interdigitated on 16p. The presence of a similar repeat in the short, as well as the long arm of the chromosome, may play a role in the origin of chromosome 16 rearrangements in acute leukemia.

Acute Disease↗
PubMed1991

Generation of a nested series of interstitial deletions in yeast artificial chromosomes carrying human DNA.

We have generated a nested series of interstitial deletions in a fragment of human X chromosome-derived DNA cloned into a yeast artificial chromosome (YAC) vector. A yeast strain carrying the YAC was transformed with a linear recombination substrate containing at one end a sequence that is uniquely represented on the YAC and at the other end a truncated long interspersed repetitive element (LINE 1, or L1). Homologous recombination between the YAC and the input DNA resulted in a nested series of interstitial deletions, the largest of which was 500 kilobases. In combination with terminal deletions that can be generated through homologous recombination, the interstitial deletions are useful for mapping and studying gene structure-function relationships.

Chromosome Deletion↗