An endogenous retrovirus presumed to have been endogenized or relocated recently in a marsupial, the red-necked wallaby

An albino infant wallaby was born to a mother with the wild-type body color. PCR and sequencing analyses of TYR (encoding tyrosinase, which is essential for melanin biosynthesis) of this albino wallaby revealed a 7.1-kb-long DNA fragment inserted in the first exon. Because the fragment carried long terminal repeats, we assumed it to be a copy of an endogenous retrovirus, which we named walb. We cloned other walb copies residing in the genomes of this species and another wallaby species. The copies exhibited length variation, and the longest copy (>8.0 kb) contained open reading frames whose deduced amino acid sequences were well aligned with those of gag, pol, and env of retroviruses. It is not known through which of the following likely processes the walb copy was inserted into TYR: endogenization (infection of a germline cell by an exogenous virus), reinfection (infection by a virus produced from a previously endogenized provirus), or retrotransposition (intracellular relocation of a provirus). In any case, the insertion into TYR is considered to have been a recent event on an evolutionary timescale because albino mutant alleles generally do not persist for long because of their deleterious effects in wild circumstances.

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Cloning of two Bombyx homologues of the Drosophila rosy gene and their relationship to larval translucent skin colour mutants

Genetics Research ◽

10.1017/s0016672397003078 ◽

1998 ◽

Vol 71 (1) ◽

pp. 11-19 ◽

Cited By ~ 13

Author(s):

YUJI YASUKOCHI ◽

TOSHIO KANDA ◽

TOSHIKI TAMURA

Keyword(s):

Tissue Specificity ◽

Amino Acid Sequences ◽

Open Reading Frames ◽

Striking Similarity ◽

Wild Type ◽

Rt Pcr ◽

Significant Difference ◽

Phage Dna ◽

Polymerase Chain ◽

Reading Frames

To clone the Bombyx xanthine dehydrogenase (XDH) gene as a dominant marker for silkworm transgenesis, we performed nested reverse transcriptase–polymerase chain reaction (RT-PCR) using embryonic mRNA and primers designed from the conserved region of Drosophila and rat XDH genes. Sequencing of amplified 180 bp fragments showed that two different sequences were present in the fragments. Since both possessed striking similarity to XDH genes of other organisms, we considered these to be portions of silkworm XDH genes and designated them BmXDH1 and BmXDH2. Subsequently we cloned separately the entire region of the two cDNAs by PCR using phage DNA of an embryonic cDNA library and sequenced them. The two cDNAs were around 4 kb in size and possessed complete open reading frames. The deduced amino acid sequences of the two BmXDHs were very similar to each other and to those of other organisms. The expression pattern of wild-type larvae basically followed the tissue specificity of the enzyme and no significant difference was observed between the two XDH genes. The expression of both genes was detected in the XDH-deficient mutants, oq and og, but non-synonymous substitutions were specifically detected in the BmXDH1 of the oq mutant. In addition, a length polymorphism of the second intron of the BmXDH1 co-segregated with the oq translucent phenotype, suggesting that deficiency in BmXDH1 is the cause of the oq translucent phenotype.

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Cloning and Characterization of a New Site-Specific Methyl-Directed ElmI Endonuclease Recognizing and Cleaving C5-methylated DNA Sequence 5’-G(5mC)^NG(5mC)-3’

Acta Naturae ◽

10.32607/20758251-2016-8-1-117-125 ◽

2016 ◽

Vol 8 (1) ◽

pp. 117-125 ◽

Cited By ~ 1

Author(s):

V. A. Chernukhin ◽

D. A. Gonchar ◽

M. A. Abdurashitov ◽

O. A. Belichenko ◽

V. S. Dedkov ◽

...

Keyword(s):

Dna Sequence ◽

Amino Acid Sequences ◽

Open Reading Frames ◽

Site Specific ◽

Pcr Screening ◽

Methylated Dna ◽

Chromatographic Techniques ◽

Dna Fragment ◽

Reading Frames

Putative open reading frames of MD-endonucleases have been identified in Enterobacteria genomes as a result of the search for amino acid sequences homologous to MD-endonuclease BisI. A highly conserved DNA primary structure of these open reading frames in different genera of Enterobacteria (Escherichia, Klebsiella and Cronobacter) has allowed researchers to create primers for PCR screening, which was carried out on Enterobacteria DNA collected from natural sources. The DNA fragment, about 440 bp in length, was amplified by use of the genomic DNA of a wild E.coli LM N17 strain as a template and was inserted into the pMTL22 vector. Endonuclease activity was detected in an E.coli ER 2267 strain transformed with the obtained construction. A new enzyme named ElmI was purified by chromatographic techniques from the recombinant strain biomass. It was discovered that similarly to BisI this enzyme specifically cleaves the methylated DNA sequence 5-GCNGC- 3 before the central nucleotide N if this sequence contains two 5-methylcytosines. However, unlike BisI, ElmI more efficiently cleaves this sequence if more than two cytosine residues are methylated.

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Similarities between the antABC-Encoded Anthranilate Dioxygenase and the benABC-Encoded Benzoate Dioxygenase of Acinetobacter sp. Strain ADP1

Journal of Bacteriology ◽

10.1128/jb.180.17.4466-4474.1998 ◽

1998 ◽

Vol 180 (17) ◽

pp. 4466-4474 ◽

Cited By ~ 56

Author(s):

Becky M. Bundy ◽

Alan L. Campbell ◽

Ellen L. Neidle

Keyword(s):

Carbon Source ◽

Sole Carbon Source ◽

Gene Clusters ◽

Open Reading Frames ◽

Wild Type ◽

Aromatic Compound Degradation ◽

Genes Encoding ◽

Dna Fragment ◽

Benzoate Dioxygenase ◽

Reading Frames

ABSTRACT Acinetobacter sp. strain ADP1 can use benzoate or anthranilate as a sole carbon source. These structurally similar compounds are independently converted to catechol, allowing further degradation to proceed via the β-ketoadipate pathway. In this study, the first step in anthranilate catabolism was characterized. A mutant unable to grow on anthranilate, ACN26, was selected. The sequence of a wild-type DNA fragment that restored growth revealed theantABC genes, encoding 54-, 19-, and 39-kDa proteins, respectively. The deduced AntABC sequences were homologous to those of class IB multicomponent aromatic ring-dihydroxylating enzymes, including the dioxygenase that initiates benzoate catabolism. Expression of antABC in Escherichia coli, a bacterium that normally does not degrade anthranilate, enabled the conversion of anthranilate to catechol. Unlike benzoate dioxygenase (BenABC), anthranilate dioxygenase (AntABC) catalyzed catechol formation without requiring a dehydrogenase. In Acinetobacter mutants,benC substituted for antC during growth on anthranilate, suggesting relatively broad substrate specificity of the BenC reductase, which transfers electrons from NADH to the terminal oxygenase. In contrast, the benAB genes did not substitute for antAB. An antA point mutation in ACN26 prevented anthranilate degradation, and this mutation was independent of a mucK mutation in the same strain that prevented exogenous muconate degradation. Anthranilate induced expression of antA, although no associated transcriptional regulators were identified. Disruption of three open reading frames in the immediate vicinity ofantABC did not prevent the use of anthranilate as a sole carbon source. TheantABC genes were mapped on the ADP1 chromosome and were not linked to the two known supraoperonic gene clusters involved in aromatic compound degradation.

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Woot, an Active Gypsy-Class Retrotransposon in the Flour Beetle, Tribolium castaneum, is Associated With a Recent Mutation

Genetics ◽

10.1093/genetics/143.1.417 ◽

1996 ◽

Vol 143 (1) ◽

pp. 417-426

Author(s):

Richard W Beeman ◽

M Scott Thomson ◽

John M Clark ◽

Marco A DeCamillis ◽

Susan J Brown ◽

...

Keyword(s):

Sequence Analysis ◽

Tribolium Castaneum ◽

Frameshift Mutation ◽

Open Reading Frames ◽

Red Flour Beetle ◽

Intron Sequence ◽

Coding Region ◽

Long Terminal Repeats ◽

Flour Beetle ◽

Reading Frames

Abstract A recently isolated, lethal mutation of the homeotic Abdominal gene of the red flour beetle Tribolium castaneum is associated with an insertion of a novel retrotransposon into an intron. Sequence analysis indicates that this retrotransposon, named Woot, is a member of the gypsy family of mobile elements. Most strains of T. castaneum appear to harbor ~25-35 copies of Woot per genome. Woot is composed of long terminal repeats of unprecedented length (3.6 kb each), flanking an internal coding region 5.0 kb in length. For most copies of Woot, the internal region includes two open reading frames (ORFs) that correspond to the gag and pol genes of previously described retrotransposons and retroviruses. The copy of Woot inserted into Abdominal bears an apparent single frameshift mutation that separates the normal second ORF into two. Woot does not appear to generate infectious virions by the criterion that no envelop gene is discernible. The association of Woot with a recent mutation suggests that this retroelement is currently transpositionally active in at least some strains.

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Genetic Investigation of the Catabolic Pathway for Degradation of Abietane Diterpenoids by Pseudomonas abietaniphilaBKME-9

Journal of Bacteriology ◽

10.1128/jb.182.13.3784-3793.2000 ◽

2000 ◽

Vol 182 (13) ◽

pp. 3784-3793 ◽

Cited By ~ 39

Author(s):

Vincent J. J. Martin ◽

William W. Mohn

Keyword(s):

Gene Cluster ◽

Sequence Similarity ◽

Open Reading Frames ◽

Ring Cleavage ◽

Catabolic Pathway ◽

Transcriptional Fusion ◽

Abietane Diterpenoids ◽

Genes Encoding ◽

Dna Fragment ◽

Reading Frames

ABSTRACT We have cloned and sequenced the dit gene cluster encoding enzymes of the catabolic pathway for abietane diterpenoid degradation by Pseudomonas abietaniphila BKME-9. Thedit gene cluster is located on a 16.7-kb DNA fragment containing 13 complete open reading frames (ORFs) and 1 partial ORF. The genes ditA1A2A3 encode the α and β subunits and the ferredoxin of the dioxygenase which hydroxylates 7-oxodehydroabietic acid to 7-oxo-11,12-dihydroxy-8,13-abietadien acid. The dioxygenase mutant strain BKME-941 (ditA1::Tn5) did not grow on nonaromatic abietanes, and transformed palustric and abietic acids to 7-oxodehydroabietic acid in cell suspension assays. Thus, nonaromatic abietanes are aromatized prior to further degradation. Catechol 2,3-dioxygenase activity of xylEtranscriptional fusion strains showed induction of ditA1and ditA3 by abietic, dehydroabietic, and 7-oxodehydroabietic acids, which support the growth of strain BKME-9, as well as by isopimaric and 12,14-dichlorodehydroabietic acids, which are diterpenoids that do not support the growth of strain BKME-9. In addition to the aromatic-ring-hydroxylating dioxygenase genes, thedit cluster includes ditC, encoding an extradiol ring cleavage dioxygenase, and ditR, encoding an IclR-type transcriptional regulator. Although ditR is not strictly required for the growth of strain BKME-9 on abietanes, aditR::Kmr mutation in aditA3::xylE reporter strain demonstrated that it encodes an inducer-dependent transcriptional activator of ditA3. An ORF with sequence similarity to genes encoding permeases (ditE) is linked with genes involved in abietane degradation.

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Adding toYersinia enterocoliticaGene Pool Diversity: Two Cryptic Plasmids from a Biotype 1A Isolate

Journal of Biomedicine and Biotechnology ◽

10.1155/2009/398434 ◽

2009 ◽

Vol 2009 ◽

pp. 1-10 ◽

Cited By ~ 5

Author(s):

Daniela Lepka ◽

Tobias Kerrinnes ◽

Evelyn Skiebe ◽

Birgitt Hahn ◽

Angelika Fruth ◽

...

Keyword(s):

Hypothetical Protein ◽

Replication Initiation ◽

Amino Acid Sequences ◽

Open Reading Frames ◽

Eukaryotic Cells ◽

Base Pairs ◽

Significant Similarity ◽

Replication Initiation Protein ◽

Cryptic Plasmids ◽

Reading Frames

We report the nucleotide sequence of two novel cryptic plasmids (4357 and 14 662 base pairs) carried by aYersinia enterocoliticabiotype 1A strain isolated from pork. As distinguished from most biotype 1A strains, this isolate, designated 07-04449, exhibited adherence to eukaryotic cells. The smaller plasmid pYe4449-1 carries five attributable open reading frames (ORFs) encoding the first CcdA/CcdB-like antitoxin/toxin system described for aYersiniaplasmid, a RepA-like replication initiation protein, and mobilizing factors MobA and MobC. The deduced amino acid sequences showed highest similarity to proteins described inSalmonella(CcdA/B),Klebsiella(RepA), andPlesiomonas(MobA/C) indicating genomic fluidity among members of theEnterobacteriaceae. One additional ORF with unknown function, termed ORF5, was identified with an ancestry distinct from the rest of the plasmid. While the C+G content of ORF5 is 38.3%, the rest of pYe4449-1 shows a C+G content of 55.7%. The C+G content of the larger plasmid pYe4449-2 (54.9%) was similar to that of pYe4449-1 (53.7%) and differed from that of theY. enterocoliticagenome (47.3%). Of the 14 ORFs identified on pYe4449-2, only six ORFs showed significant similarity to database entries. For three of these ORFs likely functions could be ascribed: a TnpR-like resolvase and a phage replication protein, localized each on a low C+G island, and DNA primase TraC. Two ORFs of pYe4449-2, ORF3 and ORF7, seem to encode secretable proteins. Epitope-tagging of ORF3 revealed protein expression at4°Cbut not at or above27°Csuggesting adaptation to a habitat outside swine. The hypothetical protein encoded by ORF7 is the member of a novel repeat protein family sharing theDxxGN(x)nDxxGNmotif. Our findings illustrate the exceptional gene pool diversity within the speciesY. enterocoliticadriven by horizontal gene transfer events.

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Nucleotide Sequence and Genetic Structure of a Novel Carbaryl Hydrolase Gene (cehA) from Rhizobium sp. Strain AC100

Applied and Environmental Microbiology ◽

10.1128/aem.68.3.1220-1227.2002 ◽

2002 ◽

Vol 68 (3) ◽

pp. 1220-1227 ◽

Cited By ~ 50

Author(s):

Masayuki Hashimoto ◽

Mitsuru Fukui ◽

Kouichi Hayano ◽

Masahito Hayatsu

Keyword(s):

Nucleotide Sequence ◽

Insertion Sequence ◽

Amino Acid Sequences ◽

Open Reading Frames ◽

Homology Search ◽

Sequencing Analysis ◽

Terminal Sequence ◽

Homologous Sequences ◽

Naphthyl Acetate ◽

Reading Frames

ABSTRACT Rhizobium sp. strain AC100, which is capable of degrading carbaryl (1-naphthyl-N-methylcarbamate), was isolated from soil treated with carbaryl. This bacterium hydrolyzed carbaryl to 1-naphthol and methylamine. Carbaryl hydrolase from the strain was purified to homogeneity, and its N-terminal sequence, molecular mass (82 kDa), and enzymatic properties were determined. The purified enzyme hydrolyzed 1-naphthyl acetate and 4-nitrophenyl acetate indicating that the enzyme is an esterase. We then cloned the carbaryl hydrolase gene (cehA) from the plasmid DNA of the strain and determined the nucleotide sequence of the 10-kb region containing cehA. No homologous sequences were found by a database homology search using the nucleotide and deduced amino acid sequences of the cehA gene. Six open reading frames including the cehA gene were found in the 10-kb region, and sequencing analysis shows that the cehA gene is flanked by two copies of insertion sequence-like sequence, suggesting that it makes part of a composite transposon.

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Identification and Sequencing of β-Myrcene Catabolism Genes from Pseudomonas sp. Strain M1

Applied and Environmental Microbiology ◽

10.1128/aem.65.7.2871-2876.1999 ◽

1999 ◽

Vol 65 (7) ◽

pp. 2871-2876 ◽

Cited By ~ 26

Author(s):

Sandra Iurescia ◽

Andrea M. Marconi ◽

Daniela Tofani ◽

Augusto Gambacorta ◽

Annalisa Paternò ◽

...

Keyword(s):

Genomic Library ◽

Enrichment Culture ◽

Open Reading Frames ◽

Gas Chromatography Mass Spectrometry ◽

Complete Agreement ◽

Wild Type ◽

Genomic Insert ◽

The One ◽

Acyl Coenzyme A ◽

Reading Frames

ABSTRACT The M1 strain, able to grow on β-myrcene as the sole carbon and energy source, was isolated by an enrichment culture and identified as a Pseudomonas sp. One β-myrcene-negative mutant, called N22, obtained by transposon mutagenesis, accumulated (E)-2-methyl-6-methylen-2,7-octadien-1-ol (or myrcen-8-ol) as a unique β-myrcene biotransformation product. This compound was identified by gas chromatography-mass spectrometry. We cloned and sequenced the DNA regions flanking the transposon and used these fragments to identify the M1 genomic library clones containing the wild-type copy of the interrupted gene. One of the selected cosmids, containing a 22-kb genomic insert, was able to complement the N22 mutant for growth on β-myrcene. A 5,370-bp-long sequence spanning the region interrupted by the transposon in the mutant was determined. We identified four open reading frames, named myrA,myrB, myrC, and myrD, which can potentially code for an aldehyde dehydrogenase, an alcohol dehydrogenase, an acyl-coenzyme A (CoA) synthetase, and an enoyl-CoA hydratase, respectively. myrA, myrB, andmyrC are likely organized in an operon, since they are separated by only 19 and 36 nucleotides (nt), respectively, and no promoter-like sequences have been found in these regions. ThemyrD gene starts 224 nt upstream of myrA and is divergently transcribed. The myrB sequence was found to be completely identical to the one flanking the transposon in the mutant. Therefore, we could ascertain that the transposon had been inserted inside the myrB gene, in complete agreement with the accumulation of (E)-2-methyl-6-methylen-2,7-octadien-1-ol by the mutant. Based on sequence and biotransformation data, we propose a pathway for β-myrcene catabolism in Pseudomonas sp. strain M1.

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Characterization of Endogenous Retroviruses in Sheep

Journal of Virology ◽

10.1128/jvi.77.20.11268-11273.2003 ◽

2003 ◽

Vol 77 (20) ◽

pp. 11268-11273 ◽

Cited By ~ 14

Author(s):

Nikolai Klymiuk ◽

Mathias Müller ◽

Gottfried Brem ◽

Bernhard Aigner

Keyword(s):

Endogenous Retrovirus ◽

Ovis Aries ◽

Endogenous Retroviruses ◽

Open Reading Frames ◽

In Vivo Experiments ◽

Pregnant Sheep ◽

Reading Frames

ABSTRACT Endogenous retrovirus (ERV) sequences have been found in all mammals. In vitro and in vivo experiments revealed ERV activation and cross-species infection in several species. Sheep (Ovis aries) are used for various biotechnological purposes; however, they have not yet been comprehensively screened for ERV sequences. Therefore, the aim of the study was to classify the ERV sequences in the ovine genome (OERV) by analyzing the retroviral pro-pol sequences. Three OERV β families and nine OERV γ families were revealed. Novel open reading frames (ORF) in the amplified proviral fragment were found in one OERV β family and two OERV γ families. Hybrid OERV produced by putative recombination events were not detected. Quantitative analysis of the OERV sequences in the ovine genome revealed no relevant variations in the endogenous retroviral loads of different breeds. Expression analysis of different tissues from fetal and pregnant sheep detected mRNA from both gammaretrovirus families, showing ORF fragments. Thus, the release of retroviruses from sheep cells cannot be excluded.

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