scholarly journals Structural analysis of TRAS1, a novel family of telomeric repeat-associated retrotransposons in the silkworm, Bombyx mori.

1995 ◽  
Vol 15 (8) ◽  
pp. 4545-4552 ◽  
Author(s):  
S Okazaki ◽  
H Ishikawa ◽  
H Fujiwara
Keyword(s):  
Bombyx Mori ◽  
Repetitive Sequence ◽  
Repetitive Sequences ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Ltr Retrotransposons ◽  
Reading Frames ◽  
28S Ribosomal Dna ◽  
Silkworm Bombyx Mori

We characterized TRAS1, a retrotransposable element which was inserted into the telomeric repetitive sequence (CCTAA)n of the silkworm, Bombyx mori. The complete sequence of TRAS1, a stretch of 7.8 kb with a poly(A) tract at the 3' end, was determined. No long terminal repeat (LTR) was found at the termini of the element. TRAS1 contains gag- and pol-like open reading frames (ORFs) which are similar to those of non-LTR retrotransposons. The two ORFs overlap but are one nucleotide out of frame (+1 frameshift). Most of the approximately 250 copies of TRAS1 elements in the genome were highly conserved in the structure. Chromosomal in situ hybridization showed that TRAS1 elements are clustered at the telomeres of Bombyx chromosomes. A phylogenetic analysis using the amino acid sequence of the reverse transcriptase domain within the pol-like ORF revealed that TRAS1 falls into one lineage with R1, which is a family of non-LTR retrotransposons inserted into the same site within the 28S ribosomal DNA unit in most insects. TRAS1 may have been derived from R1 and changed the target specificity so that TRAS1 inserts into the telomeric repetitive sequence (CCTAA)n. Southern hybridization and Bal 31 exonuclease analyses showed that TRAS1 elements are clustered proximal to the terminal long tract of (CCTAA)n. TRAS1 is a novel family of non-LTR retrotransposons which are inserted into the telomeric repetitive sequences as target sites.

An Umbra-related Virus Found in Vasconcellea X Heilbornii (Caricaceae)

2021 ◽  
Author(s):  
Juan F Cornejo-Franco ◽  
Francisco Flores ◽  
Dimitre Mollov ◽  
diego fernando quito-avila
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Rna Dependent Rna Polymerase ◽  
Sequence Comparisons ◽  
Genomic Features ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

Abstract The complete sequence of a new viral RNA from babaco (Vasconcellea x heilbornii) was determined. The genome consisted of 4,584 nucleotides organized in two non-overlapping open reading frames (ORFs 1 and 2), a 9-nt-long noncoding region (NCR) at the 5’ terminus and a 1,843 -nt-long NCR at the 3’ terminus. Sequence comparisons of ORF 2 revealed homology to the RNA-dependent-RNA-polymerase (RdRp) of several umbra- and umbra-related viruses. Phylogenetic analysis of the RdRp placed the new virus in a well-supported and cohesive clade that includes umbra-like viruses reported from papaya, citrus, opuntia, maize and sugarcane hosts. This clade shares a most recent ancestor with the umbraviruses but has different genomic features. The creation of a new genus, within the Tombusviridae, is proposed for the classification of these novel viruses.

scholarly journals Sequence of the Genome of the Temperate, Serotype-Converting,Pseudomonas aeruginosa Bacteriophage D3

2000 ◽  
Vol 182 (21) ◽  
pp. 6066-6074 ◽  
Author(s):  
Andrew M. Kropinski
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Sequence Similarity ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Virus Family ◽  
Double Stranded Dna ◽  
High Degree ◽  
Phage Proteins ◽  
Reading Frames

ABSTRACT Temperate bacteriophage D3, a member of the virus familySiphoviridae, is responsible for serotype conversion in its host, Pseudomonas aeruginosa. The complete sequence of the double-stranded DNA genome has been determined. The 56,426 bp contains 90 putative open reading frames (ORFs) and four genes specifying tRNAs. The latter are specific for methionine (AUG), glycine (GGA), asparagine (AAC), and threonine (ACA). The tRNAs may function in the translation of certain highly expressed proteins from this relatively AT-rich genome. D3 proteins which exhibited a high degree of sequence similarity to previously characterized phage proteins included the portal, major head, tail, and tail tape measure proteins, endolysin, integrase, helicase, and NinG. The layout of genes was reminiscent of lambdoid phages, with the exception of the placement of the endolysin gene, which parenthetically also lacked a cognate holin. The greatest sequence similarity was found in the morphogenesis genes to coliphages HK022 and HK97. Among the ORFs was discovered the gene encoding the fucosamine O-acetylase, which is in part responsible for the serotype conversion events.

XI. Yeast sequencing reports. The complete sequence of an 18,002 bp segment ofSaccharomyces cerevisiae chromosome XI contains theHBS1,MRP-L20 andPRP16 genes, and six new open reading frames

Yeast ◽  
1994 ◽  
Vol 10 (2) ◽  
pp. 231-245 ◽  
Author(s):  
Jesús García-Cantalejo ◽  
Victoriano Baladrón ◽  
Pedro F. Esteban ◽  
M. Angeles Santos ◽  
Germán Bou ◽  
...  
Keyword(s):  
Complete Sequence ◽  
Open Reading Frames ◽  
Reading Frames

scholarly journals Genome Structure and Thymic Expression of an Endogenous Retrovirus in Zebrafish

2004 ◽  
Vol 78 (2) ◽  
pp. 899-911 ◽  
Author(s):  
Ching-Hung Shen ◽  
Lisa A. Steiner
Keyword(s):  
Leukemia Virus ◽  
Genome Structure ◽  
Endogenous Retrovirus ◽  
Northern Blotting ◽  
Open Reading Frames ◽  
Genomic Locus ◽  
Dna Libraries ◽  
Adult Thymus ◽  
Reading Frames

ABSTRACT In a search for previously unknown genes that are required for lymphocyte development in zebrafish, a retroviral sequence was identified in a subtracted thymus cDNA library and in genomic DNA libraries. The provirus is 11.2 kb and contains intact open reading frames for the gag, pol, and env genes, as well as nearly identical flanking long terminal repeat sequences. As determined by in situ hybridization, the thymus appears to be a major tissue for retroviral expression in both larval and adult fish. Several viral transcripts were found by Northern blotting in the adult thymus. The provirus was found at the same genomic locus in sperm from four fish, suggesting that it is an endogenous retrovirus. Phylogenetic analysis indicates that it is closest to, yet distinct from, the cluster of murine leukemia virus-related retroviruses, suggesting that this virus represents a new group of retroviruses.

scholarly journals Identification of a pentanucleotide telomeric sequence, (TTAGG)n, in the silkworm Bombyx mori and in other insects.

1993 ◽  
Vol 13 (3) ◽  
pp. 1424-1432 ◽  
Author(s):  
S Okazaki ◽  
K Tsuchida ◽  
H Maekawa ◽  
H Ishikawa ◽  
H Fujiwara
Keyword(s):  
Repetitive Sequence ◽  
Fluorescent In Situ Hybridization ◽  
Genomic Library ◽  
Telomeric Sequence ◽  
Cross Hybridization ◽  
Telomere Sequence ◽  
Eukaryotic Species ◽  
Genomic Dnas ◽  
Silkworm Bombyx Mori

A pentanucleotide repetitive sequence, (TTAGG)n, has been isolated from a silkworm genomic library, using cross-hybridization with a (TTNGGG)5 sequence, which is conserved among most eukaryotic telomeres. Both fluorescent in situ hybridization and Bal 31 exonuclease experiments revealed major clusters of (TTAGG)n at the telomeres of all Bombyx chromosomes. To determine the evolutionary origin of this sequence, two types of telomeric sequence, (TTAGG)5 and a hexanucleotide repetitive sequence, (TTAGGG)4, which is conserved mainly among vertebrate and several invertebrate telomeres so far examined, were hybridized to DNAs from a wide variety of eukaryotic species under highly stringent hybridization conditions. The (TTAGGG)5 oligonucleotide hybridized to genomic DNAs from vertebrates and several nonvertebrate species, as has been reported so far, but not to any DNAs from insects. On the other hand, the Bombyx type of telomere sequence, (TTAGG)n, hybridized to DNAs from 8 of 11 orders of insect species tested but not to vertebrate DNAs, suggesting that this TTAGG repetitive sequence is conserved widely among insects.

scholarly journals Molecular and Evolutionary Characterization of the cp32/18 Family of Supercoiled Plasmids in Borrelia burgdorferi297

2000 ◽  
Vol 68 (3) ◽  
pp. 1574-1586 ◽  
Author(s):  
Melissa J. Caimano ◽  
Xiaofeng Yang ◽  
Taissia G. Popova ◽  
Michael L. Clawson ◽  
Darrin R. Akins ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Genomic Sequence ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Exogenous Dna ◽  
Variable Regions ◽  
Different Types ◽  
Sequence Relatedness ◽  
Reading Frames

ABSTRACT In this study, we characterized seven members of the cp32/18 family of supercoiled plasmids in Borrelia burgdorferi297. Complete sequence analysis of a 21-kb plasmid (cp18-2) confirmed that the strain 297 plasmids are similar in overall content and organization to their B31 counterparts. Of the 31 open reading frames (ORFs) in cp18-2, only three showed sequence relatedness to proteins with known functions, and only one, a ParA/SopA ortholog, was related to nonborrelial polypeptides. Besides the lipoproteins, none of the ORFs appeared likely to encode a surface-exposed protein. Comparison with the B31 genomic sequence indicated that paralogs for most of the ORFs in cp18-2 can be identified on other genetic elements. cp18-2 was found to lack a 9- to 10-kb fragment present in the 32-kb homologs which, by extrapolation from the B31 cp32 sequences, contains at least 15 genes presumed to be unnecessary for plasmid maintenance. Sequence analysis of the lipoprotein-encoding variable loci provided evidence that recombinatorial processes within these regions may result in the acquisition of exogenous DNA. Pairwise analysis with random shuffling revealed that the multiple lipoproteins (Mlp; formerly designated 2.9 LPs) fall into two distinct homology groups which appear to have arisen by gene fusion events similar to those recently proposed to have generated the three OspE, OspF, and Elp lipoprotein families (D. R. Akins, M. J. Caimano, X. Yang, F. Cerna, M. V. Norgard, and J. D. Radolf, Infect. Immun. 67:1526–1532, 1999). Comparative analysis of the variable regions also indicated that recombination within the loci of each plasmid may occur independently. Last, comparison of variable loci revealed that the cp32/18 plasmid complements of the B31 and 297 isolates differ substantially, indicating that the two strains have been subject to divergent adaptive pressures. In addition to providing evidence for two different types of recombinatorial events involving cp32/18 plasmids, these findings underscore the need for genetic analysis of diverse borrelial isolates in order to elucidate the Lyme disease spirochete's complex parasitic strategies.

scholarly journals Comparison of novel GH 68 levansucrases of levan-overproducing Gluconobacter species

2012 ◽  
Vol 1 (1) ◽  
pp. 2 ◽  
Author(s):  
Frank Jakob ◽  
Daniel Meißner ◽  
Rudi F. Vogel
Keyword(s):  
Open Reading Frames ◽  
Ex Situ ◽  
Inverse Pcr ◽  
E Coli ◽  
Food Biotechnology ◽  
Food Applications ◽  
Pcr Techniques ◽  
Single Primer ◽  
Reading Frames

<em>Gluconobacter</em> species are capable of incomplete oxidations which are exploited in food biotechnology. Levans isolated from exopolysaccharide (EPS)-overproducing <em>Gluconobacter</em> species are promising functional compounds for food applications. Fructan production strongly depends on the corresponding fructosyltransferases (Ftfs), which catalyze the formation of these polymers from sucrose. Therefore, we characterized novel Ftfs from three EPS-overproducing food-grade strains, i.e. <em>Gluconobacter</em> sp. TMW 2.767 and <em>Gluconobacter</em> sp. TMW 2.1191 isolated from water kefir, and <em>Gluconobacter cerinus</em> DSM 9533T isolated from cherries. Several PCR techniques, including degenerate gradient temperature PCR, modified and standard inverse PCR, modified site-finding PCR and modified single primer PCR, were used to finally detect complete open reading frames coding for Ftfs. The prospective ftf-gene sequences were heterologously expressed in <em>Escherichia coli</em> Top 10. <em>E. coli</em> transformants harboring one of the three different ftf-genes produced polysaccharides from sucrose in contrast to the <em>E. coli</em> wildtype. Each of the heterologously expressed proteins encoded a levansucrase, catalyzing the formation of b-(2&rarr;6)-linked fructose polymers, which corresponded to our previous analyses about the chemical nature of the isolated polymers formed by these <em>Gluconobacter</em> strains. Structurally, these enzymes belong to the glycoside hydrolase 68 family (GH 68), sharing the typical modular topology of levansucrases from gram-negative bacteria. In conclusion, we could identify novel active levansucrases, which can be used for <em>ex situ</em> (enzymatic catalyses) or <em>in situ</em> (fermentation) production of functional fructan polymers by <em>Gluconobacter</em> strains in food and other applications.

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