Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Inverted Repeat Sequences”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,459 records · Page 81Linked to original sources
PubMed2004

Structural characterization of the dihydroflavonol 4-reductase B (DFR-B) gene in the sweet potato.

A genomic fragment containing the dihydroflavonol 4-reductase B (DFR-B) gene was cloned from the sweet potato (Ipomoea batatas) and its nucleotide sequence was analyzed. The exons and flanking regions were highly homologous to those of previously reported DFR-B genes of the Japanese morning glory, whereas the introns and the intergenic region were less conserved. In addition to the sequences of three miniature inverted-repeat transposable elements (MITEs) and one direct repeat previously reported in the DFR-B gene of Japanese morning glory, two mobile element-like sequences were newly identified in the sweet potato DFR-B gene. At least four allelic sequences were found to exist by amplification of the DFR-B gene from various sweet potato cultivars. One of these allelic sequences had a 2-kb deletion in the intergenic region and was observed in the cultivars with high anthocyanin content in their storage roots.

Alcohol Oxidoreductases↗
PubMed1987

Regulation of in vitro and in vivo transcription of early-region IV of adenovirus type 5 by multiple cis-acting elements.

A series of deletion mutants spanning the promoter of the adenovirus early-region IV (EIV) gene were tested for transcriptional activity, using both in vitro and in vivo assays. Four distinct domains had additive effects on efficient transcription from the EIV promoter in HeLa whole-cell extracts. The first resided 20 to 27 bases upstream of the initiation site and included the TATA box. Deletion of the TATA box drastically reduced the transcriptional activity in vitro but had a lesser effect in vivo. The second region extended from -32 to -177 and contained two 17-base-pair inverted repeats, centered around -40 and -162. Sequences lying between -140 and -173 were important for efficient transcription since deletion of this region reduced the activity fourfold. Deletion of either one of the two inverted repeats or insertion of DNA fragments between them resulted in the synthesis of extra transcripts that initiated at sites upstream from the EIV site. The third region was located between -198 and -250 and contains three guanosine-plus-cytosine-rich sequences, present around -212 (GGGCGG), -233 (GGGCGG), and -251 (CGCGGG). The fourth, most upstream region was located between -260 and -307. Deletion of this region, which contains the NF-1 factor-binding site, slightly reduced transcriptional activity both in vivo and in vitro. The data indicate that multiple cis-acting elements are required for efficient transcription from the EIV promoter in both in vitro and in vivo systems.

Adenoviridae↗
PubMed2006

Development of nuclear gene-derived molecular markers linked to legume genetic maps.

The systematic identification of the orthologous features of related organisms greatly facilitates comparative genomics, including research on genome evolution and comparative genetic mapping. In this study, we selected 274 unique gene sequences for the development of PCR-based genetic markers across fifteen legume genomes, representing six crop or model legume species from the phaseoloid and inverted repeat loss clades (IRLC). DNA sequence analysis demonstrated that 129 of the amplified fragments represented single copy loci across most target diploid genomes. The majority of these markers are intron-spanning (70.5%) and linked to legume genetic maps (85.3%). The markers were grouped into four main categories: (1) intron-spanning relatively conserved, (2) intron-spanning diverged, (3) exon-derived conserved, and (4) exon-derived diverged. The extent of sequence divergence within each category indicates that the corresponding markers may have utility for assessing phylogenetic relationships at different, but overlapping, taxonomic levels. We tested marker performance on genomes that had not been previously sampled, representing 95 different species that span the diversity of the Fabaceae. Phylogenetic analyses support the orthology of amplified sequences, with the notable exception of an ambiguous affiliation of Lotus relative to the IRLC and phaseoloid clades.

Amino Acid Sequence↗
PubMed2005

Hairpin RNA-mediated silencing of Plum pox virus P1 and HC-Pro genes for efficient and predictable resistance to the virus.

We report the application of the hairpin-mediated RNA silencing technology for obtaining resistance to Plum pox virus (PPV) infection in Nicotiana benthamiana plants. Four sequences, covering the P1 and silencing suppressor HC-Pro genes of an Italian PPV M isolate, were introduced into N. benthamiana plants as two inverted repeats separated by an intron sequence under the transcriptional control of the Cauliflower Mosaic Virus 35S promoter. In a leaf disk infection assay, 38 out of 40 T0 transgenic plants were resistant to PPV infection. Eight lines, 2 for each construct, randomly selected among the 38 resistant plants were further analysed. Two hundred forty eight out of 253 T1 transgenic plants were resistant to local and systemic PPV infection. All transgenic single locus lines were completely resistant. These data indicate that the RNA silencing of PPV P1/HCPro sequences results in an efficient and predictable PPV resistance, which may be utilized in obtaining stone fruit plants resistant to the devastating Sharka disease.

Gene Expression Regulation, Plant↗
PubMed1988

The ethanol regulon in Aspergillus nidulans: characterization and sequence of the positive regulatory gene alcR.

The regulatory gene, alcR, of Aspergillus nidulans, encodes a protein that induces the expression of the alcA and aldA genes. The alcR gene is inducible, autoregulated, and subject to carbon catabolite repression. We report the complete nucleotide sequence of the alcR gene and its 5' and 3' non-coding regions. In the 5' flanking region of the alcR gene, several repeats and inverted repeats were found, and small sequence similarities were also found with the 5' flanking regions of the alcA and aldA genes. One intron of small size interrupts the open reading frame. The start point of transcription was mapped 50 nucleotides upstream from the putative start codon, and a sequence CAATG was found 5' to the polyadenylation site of the transcript that could play a role in selection of the polyadenylation site. The putative alcR-encoded protein was identified in vivo as an inducible polypeptide of 96 kDa in a transformant carrying multiple copies of the alcR gene.

Alcohol Dehydrogenase↗
PubMed1989

Isolation and characterization of the promoter and flanking regions of the gene encoding the human protein-synthesis-initiation factor 2 alpha.

The promoter region of the gene (eIF-2 alpha) for eukaryotic initiation factor 2 alpha (eIF-2 alpha) was isolated from a human genomic library and its structure was determined by restriction mapping and nucleotide (nt) sequence analysis. The promoter region and twelve in vivo transcriptional start points (tsp) have been identified by endonuclease S1 mapping and their location confirmed by primer-extension analysis, using RNA isolated from human cells. The untranslated leader is 102 to 140 nt long depending upon the tsp, and the 5' region of the mRNA has the potential for forming stable stem-loop structures. The nt sequence of the regions upstream and downstream from the tsp contains neither a 'TATA box' nor a 'CAAT box', but does contain several direct and inverted repeats, as well as palindromic sequences near the tsp. In addition, multiple consensus binding sites for a wide variety of regulatory proteins are present throughout upstream and downstream tsp-flanking regions.

Base Sequence↗
PubMed1983

S1 sensitive sites in adenovirus DNA.

S1 nuclease has been used as a probe for regions of DNA secondary structure in supercoiled recombinant plasmids containing adenovirus (Ad) DNA sequences. In the sequences examined two S1 sensitive sites were identified in the left-terminal 16.5% of Ad 12 DNA, one of which aligned approximately with an inverted repeat region in the DNA sequence. In addition an S1 sensitive site was dictated by a potential cruciform structure in the region of the Ad 2 major late promoter. In contrast to the expected cleavage site at the loop of the cruciform, cleavage occurred at the base of the stem in the region of the TATA box. All three S1 sensitive sites identified were more sensitive to S1 than the endogenous sites in the parent plasmids.

Adenoviridae↗
PubMed2003

Molecular evolutionary analysis of the widespread piggyBac transposon family and related "domesticated" sequences.

piggyBac is a short inverted-repeat-type DNA transposable element originally isolated from the genome of the moth Trichoplusia ni. It is currently the gene vector of choice for the transformation of various insect species. A few sequences with similarity to piggyBac have previously been identified from organisms such as humans ( Looper), the pufferfish Takifugu rubripes ( Pigibaku), Xenopus ( Tx), Daphnia ( Pokey), and the Oriental fruit fly Bactrocera dorsalis. We have now identified 50 piggyBac-like sequences from publicly available genome sequences and expressed sequence tags (ESTs). This survey allows the first comparative examination of the distinctive piggyBac transposase, suggesting that it might contain a highly divergent DDD domain, comparable to the widespread DDE domain found in many DNA transposases and retroviral integrases which consists of two absolutely conserved aspartic acids separated by about 70 amino acids with a highly conserved glutamic acid about 35 amino acids further away. Many piggyBac-like sequences were found in the genomes of a phylogenetically diverse range of organisms including fungi, plants, insects, crustaceans, urochordates, amphibians, fishes and mammals. Also, several instances of "domestication" of the piggyBac transposase sequence by the host genome for cellular functions were identified. Novel members of the piggyBac family may be useful in genetic engineering of many organisms.

Animals↗
PubMed1991

Vaccinia virus homologues of the Shope fibroma virus inverted terminal repeat proteins and a discontinuous ORF related to the tumor necrosis factor receptor family.

Nucleotide sequencing data from a region extending 35 kb inward from the right inverted terminal repeat (ITR) of the vaccinia virus (VV) genome established the presence of VV homologues of the Shope fibroma virus (SFV) ITR proteins. The nucleotide sequences, comprising a total of 8.6 kb, and the amino acid translations for nine predicted open reading frames (ORFs) (designated SalF4L, SalF 19R, SalF21R, B4R, B8R, B9R, B10R, and B14R) are presented. Eight of the nine VV genes and all the SFV ORFs are transcribed towards their genomic termini. However, the relative positions of the VV genes (genus Orthopoxvirus) are different than those of the corresponding ORFs in SFV (genus Leporipoxvirus), indicating complex rearrangements of DNA in the genome of one or both of these viruses subsequent to their divergence from a common ancestor. Several other features of the VV ORFs were noted. SalF4L, B7R, B8R, and B9R have hydrophobic amino-terminal signal sequences but lack discernible membrane anchor domains suggesting that the proteins may be secreted. VV ORF SalF19R has a single cysteine-rich region homologous to the multiple domains of nerve growth factor receptor (NGFR), CD40, OX40 (a glycoprotein from the surface of activated murine T lymphocytes), and the recently described tumor necrosis factor receptors. Just downstream of the ORF SalF19R and in a different reading frame, there are another two related cysteine-rich domains, indicating that SalF19R was once a larger gene. B4R has homology to the host range gene of cowpox virus and to related genes near the opposite end of the vaccinia virus genome, and contains regions homologous to the repeat domains of erythrocyte ankyrin. In addition, several of the VV ORFs have homology to ORFs from near the opposite end of the VV genome, thus increasing the number of known VV gene families.

Amino Acid Sequence↗
PubMed1994

Molecular cloning and sequence analysis of the cellobiohydrolase I gene from Trichoderma koningii G-39.

The cellobiohydrolase I gene, cbh1, has been cloned from an enhanced cellulase-producing strain, Trichoderma koningii G-39. Sequence comparisons show that T. koningii cbh1 is identical to that of T. reesei with the exception of 6 bp--two causing silent substitutions in the coding region, three differing in one of the introns, and one in 5'-noncoding region. Thus, it should encode an identical CBHI to that of T. reesei despite the differences in morphological characters of the two species. Analysis of approximately 1.4 kb of the 5' flanking region shows a number of surprisingly interesting putative regulatory features. There are no unusual features within about 600 bp upstream of the translation start ATG. However, prior to the 600-bp region, there are seven CAAT sequences, a number of direct and inverted repeats, and two C/T-rich regions. Also, there are five consensus 5'-(G/C)PyGGGG-3' sequences that have been identified to be carbon catabolite repressor binding sites of Aspergillus nidulans CREA and Saccharomyces cerevisiae MIG1 repressors. The structural organization around these consensus sequence regions is similar to those of A. nidulas alcR and alcA promoters. While the production of large amounts of CBHI by T. koningii upon induction apparently correlates with the large number of CAAT boxes in the 5' upstream untranslated region of cbh1, the presence of five CREA/MIG1 repressor-binding consensus sequences in the region suggests the wide-domain carbon catabolite repression regulatory system that controls the A. nidulans ethanol regulon, and yeast GAL genes transcription might also be operative and responsible for regulation of T. koningii cbh1 transcription.

Amino Acid Sequence↗
PubMed1985

Partition of unit-copy miniplasmids to daughter cells. III. The DNA sequence and functional organization of the P1 partition region.

The boundaries of the P1 par (plasmid partition) region of the unit-copy plasmid P1 were defined to within 2.7 X 10(3) base-pairs of DNA. The DNA sequence of the region revealed two large open reading frames that could encode proteins of Mr 44,000 and Mr 38,000. Both would be read in the same direction. The first open reading frame corresponds to the par A gene, the Mr 44,000 protein product of which was shown to be trans acting and essential for partition. The second open reading frame (parB) follows closely and may be cotranscribed with par A. The codon usage frequency for parB is consistent with its producing a protein product. The ParB protein was identified in cell extracts as a product with an apparent Mr of 45,000, suggesting that it behaves anomolously on gel electrophoresis. Following parB is the incB region, an incompatibility determinant thought to be the cis acting site that constitutes the putative attachment point on the DNA for the cellular partition apparatus. Subcloning of this site showed it to consist of a maximum of 174 base-pairs. The incB sequence is highly A + T-rich and contains a 20 base-pair inverted repeat. Another A + T-rich inverted repeat of similar size but different sequence is found between the putative parA promoter and the ribosome initiation sequence at the start of the parA open reading frame and may be involved in the autoregulation of ParA synthesis. The par region appears to contain a functional analog of the centromere of eukaryotic chromosomes. It is responsible for ensuring that newly replicated plasmids are properly distributed to daughter cells during cell division of its Escherichia coli host.

Bacterial Proteins↗
PubMed1985

Nucleotide sequence of bean golden mosaic virus and a model for gene regulation in geminiviruses.

We have sequenced the genome of bean golden mosaic virus, which comprises two circular single-stranded DNA molecules (2646 and 2587 nucleotides long) of mostly unique sequence. Comparison of the sequences of bean golden mosaic virus and of cassava latent virus, which share serological relationship but are very different in host range and geographical origin, shows that each virus has a unique 200-nucleotide sequence (common region) on each 2.6-kilobase molecule of its genome. The common regions of the two viruses have no sequence homology except for a short inverted repeat near the 3' end. Six open reading frames were identified that possess considerable sequence homology between the two viruses and, in bean golden mosaic virus, may encode proteins of 15.6, 19.6, 27.7, 29.7, 33.1, and 40.2 kDa. Conserved open reading frames are found in both the viral strand and the complementary strand, are approximately the same size, and are in the same orientation with respect to the common region in both viruses. We propose that temporal regulation in geminiviruses depends on the polarity of transcription and that the common region represents a replication origin and contains elements that serve to modulate gene expression.

Journal Article↗
PubMed1994

One-ended insertion of IS911.

An apparently nonreplicative integration reaction mediated by the insertion sequence IS911 has been analyzed. It is shown to involve the right-end inverted repeat (IRR) of the element and sequences in the flanking vector DNA. The flanking sequences appear to behave as a surrogate IS911 end, since integration is greatly reduced when limited similarities with IRR are eliminated by site-directed mutagenesis. Data are presented which suggest that the activity of the IRR junction results from the proximity of the transposase gene and may therefore reflect preferential transposase recognition of IRR in cis.

Bacteriophage lambda↗
PubMed1995

Identification of the gonococcal glmU gene encoding the enzyme N-acetylglucosamine 1-phosphate uridyltransferase involved in the synthesis of UDP-GlcNAc.

In searching for the gonococcal sialyltransferase gene(s), we cloned a 3.8-kb DNA fragment from gonococcus strain MS11 that hybridized with the oligonucleotide JU07, which was derived from the conserved C terminus of the sialyl motif present in mammalian sialyltransferases. Sequencing of the fragment revealed four putative open reading frames (ORFs), one of which (ORF-1) contained a partial sialyl motif including the amino acid sequence VGSKT, which is highly conserved among sialyltransferases. The gene was flanked by two inverted repeats containing the neisserial DNA uptake sequence and was preceded by a putative sigma 54 promoter. Database searches, however, revealed a high degree of homology between ORF-1 and the N-acetylglucosamine 1-phosphate uridyltransferase (GlmU) of Escherichia coli and Bacillus subtilis and not with any known sialyltransferase. This homology was further established by the successful complementation of an orf-1 mutation by the E. coli glmU gene. Enzyme assays demonstrated that ORF-1 did not possess sialyltransferase activity but mimicked GlmU function catalyzing the conversion of N-acetylglucosamine 1-phosphate into UDP-N-acetylglucosamine, which is a key metabolite in the syntheses of lipopolysaccharide, peptidoglycan, and sialic acids.

Amino Acid Sequence↗
PubMed1995

Nucleotide sequence of infectious laryngotracheitis virus (gallid herpesvirus 1) ICP4 gene.

The infectious laryngotracheitis virus (ILTV) gene encoding a homologue to the ICP4 protein of herpes simplex virus (HSV) has been mapped to the inverted repeat region. The complete nucleotide sequence of ILTV ICP4 has been determined. The ILTV ORF encoding ICP4 is 4386 nucleotides long, calculated from the first of four ATG codons, and has an overall G+C content of 59%. The ILTV ICP4 contains two domains of high homology which have been reported in other studies to be conserved in the ICP4 homologues of alphaherpesviruses, and to be functionally important. Several regulatory features were identified including a serine-rich domain in region one. A more extensive serine-rich domain was located in region five which is also found in varicella-zoster virus (VZV) and bovine herpesvirus 1. A 5.4 kb immediate early transcript was identified in infected primary kidney cells.

Amino Acid Sequence↗
PubMed1993

Identification of an insertion sequence-like element in a subspecies of Mycobacterium kansasii.

Analysis of a genomic DNA clone library of a strain from the genetic subspecies of Mycobacterium kansasii determined the existence of a repetitive insertion sequence-like element. The element is 947 bp long and is present in a minimum of 1 to 11 copies per genome. Similar to insertion sequences, it contains a 3-bp (TAG) direct repeat at its extremities and a transcription promoter-like sequence. In addition, for one of the clones sequenced, a potential cointegrate formation, a characteristic frequently observed with insertion sequences, was revealed. This insertion sequence does not contain short inverted repeats near the ends or a large open reading frame to code for a transposase enzyme. Its host range is restricted to a previously described genetic subspecies of M. kansasii and is not present in typical M. kansasii or other mycobacterial species. When used as a probe for Southern blot hybridization, significant heterogeneity between different isolates of the M. kansasii subspecies was observed. This repeated element will be useful in further studies on the characterization, diagnosis, and epidemiology of M. kansasii.

Base Sequence↗
PubMed1996

The 2 micron plasmid of laboratory yeast strains is a type-1/type-2 hybrid.

Industrial yeast strains carry one of two homeologous 2 microns plasmids designated as type-1 or type-2. The 2 microns plasmid, Scp1, found in common laboratory strains of Saccharomyces cerevisiae is considered a type-2 plasmid, since the ori, STB, RAF and REP1 loci and intergenic sequences of the right-unique region of Scp1 are homologous to the corresponding loci in industrial strain type-2 plasmids. However, within both its 599 bp inverted repeats Scp1 has 142-bp sequences homologous to the bakers' yeast type-1 plasmid. DNA sequence analyses and oligonucleotide hybridizations indicate that the 142-bp insertion in Scp1 was probably due to homeologous recombination between type-1 and type-2 plasmids. These results suggest that some of the plasmid and chromosomal sequence polymorphisms seen in laboratory yeast strains result from homeologous recombination in their ancestral breeding stock.

Base Sequence↗
PubMed1999

GEM, a cluster of repetitive sequences in the Drosophila subobscura genome.

GEM is a new family of repetitive sequences detected in the D. subobscura genome. Two of the four described GEM elements encompass a heterogeneous central module, with no detectable ORF, flanked by two long inverted repeats. These elements are composed of a set of repetitive modules, which are inverted repeat (IR), direct repeat (DR), palindromic sequence (PS), long sequence (LS) and short sequence (SS). These five modules can be found either clustered or dispersed as single modules in the D. subobscura genome, in euchromatic and heterochromatic regions. In addition to the 3' region of Adh retrosequences, single IR and LS blocks were found associated with the promoter region of different genes, in particular, LS-like blocks have also been found associated with functional genes in D. melanogaster and D. virilis. Conversely, the DR block is highly similar to satellite DNAs from some other species of the obscura group. In addition, GEM elements share some structural features with IS elements described in different Drosophila species. It is likely that both GEM and IS sequences would be vestiges of an ancestral transposable element.

Alcohol Dehydrogenase↗