scholarly journals Sequence Analysis of Mus dunni Endogenous Virus Reveals a Hybrid VL30/Gibbon Ape Leukemia Virus-Like Structure and a Distinct Envelope

1998 ◽  
Vol 72 (9) ◽  
pp. 7459-7466 ◽  
Author(s):  
Greg Wolgamot ◽  
Lynn Bonham ◽  
A. Dusty Miller
Keyword(s):  
Leukemia Virus ◽  
Open Reading Frames ◽  
Cell Entry ◽  
Endogenous Virus ◽  
Entire Genome ◽  
Naturally Occurring ◽  
Gibbon Ape Leukemia Virus ◽  
Apparent Similarity ◽  
Packaging Sequence ◽  
Reading Frames

ABSTRACT Mus dunni endogenous virus (MDEV) can be activated fromM. dunni cells by exposing the cells to hydrocortisone or 5-iodo-2′-deoxyuridine. Interference analysis has revealed that MDEV uses a receptor for cell entry that is different from those used by other murine retroviruses. The entire genome has now been sequenced, revealing a long terminal repeat (LTR)-gag-pol-env-LTR structure typical of simple retroviruses of the murine leukemia virus genus, with no additional open reading frames between env and the 3′ LTR. The LTRs and other noncoding regions of MDEV are most closely related to those of VL30 elements, while the majority of the coding sequences are most closely related to those of gibbon ape leukemia virus. MDEV represents the first example of a naturally occurring, replication-competent virus with sequences closely related to VL30 elements. The U3 region of MDEV contains six nearly perfect 80-bp repeats and the beginning of a seventh, and the region expected to contain the packaging sequence contains approximately four imperfect 33-bp repeats. The receptor specificity domains of the envelope are unique among retroviruses and show no apparent similarity to regions of known proteins.

scholarly journals Genome Analysis of an Alphabaculovirus Isolated from the Larch Looper, Erannis ankeraria

Viruses ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 34
Author(s):  
Long Liu ◽  
Zhilin Zhang ◽  
Chenglin Liu ◽  
Liangjian Qu ◽  
Dun Wang
Keyword(s):  
Insect Pests ◽  
Field Trials ◽  
Open Reading Frames ◽  
Parameter Analysis ◽  
Naturally Occurring ◽  
Larch Forests ◽  
Genome Phylogeny ◽  
Occlusion Bodies ◽  
Reading Frames ◽  
Core Genes

The larch looper, Erannis ankeraria Staudinger (Lepidoptera: Geometridae), is one of the major insect pests of larch forests, widely distributed from southeastern Europe to East Asia. A naturally occurring baculovirus, Erannis ankeraria nucleopolyhedrovirus (EranNPV), was isolated from E. ankeraria larvae. This virus was characterized by electron microscopy and by sequencing the whole viral genome. The occlusion bodies (OBs) of EranNPV exhibited irregular polyhedral shapes containing multiple enveloped rod-shaped virions with a single nucleocapsid per virion. The EranNPV genome was 125,247 bp in length with a nucleotide distribution of 34.9% G+C. A total of 131 hypothetical open reading frames (ORFs) were identified, including the 38 baculovirus core genes and five multi-copy genes. Five homologous regions (hrs) were found in the EranNPV genome. Phylogeny and pairwise kimura 2-parameter analysis indicated that EranNPV was a novel group II alphabaculovirus and was most closely related to Apocheima cinerarium NPV (ApciNPV). Field trials showed that EranNPV was effective in controlling E. ankeraria in larch forests. The above results will be relevant to the functional research on EranNPV and promote the use of this virus as a biocontrol agent.

scholarly journals Attenuation of bovine leukemia virus by deletion of R3 and G4 open reading frames.

1994 ◽  
Vol 91 (24) ◽  
pp. 11532-11536 ◽  
Author(s):  
L. Willems ◽  
P. Kerkhofs ◽  
F. Dequiedt ◽  
D. Portetelle ◽  
M. Mammerickx ◽  
...  
Keyword(s):  
Bovine Leukemia Virus ◽  
Leukemia Virus ◽  
Open Reading Frames ◽  
Reading Frames

scholarly journals An O-Phosphotransferase Catalyzes Phosphorylation of Hygromycin A in the Antibiotic-Producing Organism Streptomyces hygroscopicus

2008 ◽  
Vol 52 (10) ◽  
pp. 3580-3588 ◽  
Author(s):  
Vidya Dhote ◽  
Shuchi Gupta ◽  
Kevin A. Reynolds
Keyword(s):  
Ribosomal Subunit ◽  
Biosynthetic Gene Cluster ◽  
Open Reading Frames ◽  
Streptomyces Hygroscopicus ◽  
Gram Negative Bacteria ◽  
E Coli ◽  
Naturally Occurring ◽  
Insertional Inactivation ◽  
Pathway Regulation ◽  
Reading Frames

ABSTRACT The antibiotic hygromycin A (HA) binds to the 50S ribosomal subunit and inhibits protein synthesis in gram-positive and gram-negative bacteria. The HA biosynthetic gene cluster in Streptomyces hygroscopicus NRRL 2388 contains 29 open reading frames, which have been assigned putative roles in biosynthesis, pathway regulation, and self-resistance. The hyg21 gene encodes an O-phosphotransferase with a proposed role in self-resistance. We observed that insertional inactivation of hyg21 in S. hygroscopicus leads to a greater than 90% decrease in HA production. The wild type and the hyg21 mutant were comparably resistant to HA. Using Escherichia coli as a heterologous host, we expressed and purified Hyg21. Kinetic analyses revealed that the recombinant protein catalyzes phosphorylation of HA (Km = 30 ± 4 μM) at the C-2‴ position of the fucofuranose ring in the presence of ATP (Km = 200 ± 20 μM) or GTP (Km = 350 ± 60 μM) with a k cat of 2.2 ± 0.1 min−1. The phosphorylated HA is inactive against HA-sensitive ΔtolC E. coli and Streptomyces lividans. Hyg21 also phosphorylates methoxyhygromycin A and desmethylenehygromycin A with k cat and Km values similar to those observed with HA. Phosphorylation of the naturally occurring isomers of 5‴-dihydrohygromycin A and 5‴-dihydromethoxyhygromycin A was about 12 times slower than for the corresponding non-natural isomers. These studies demonstrate that Hyg21 is an O-phosphotransferase with broad substrate specificity, tolerating changes in the aminocyclitol moiety more than in the fucofuranose moiety, and that phosphorylation by Hyg21 is one of several possible mechanisms of self-resistance in S. hygroscopicus NRRL 2388.

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 Complete nucleotide sequence of a mouse VL30 retro-element.

1988 ◽  
Vol 8 (8) ◽  
pp. 2989-2998 ◽  
Author(s):  
S E Adams ◽  
P D Rathjen ◽  
C A Stanway ◽  
S M Fulton ◽  
M H Malim ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Leukemia Virus ◽  
Open Reading Frames ◽  
Long Terminal Repeats ◽  
Base Pairs ◽  
Viral Packaging ◽  
Protein Functions ◽  
Active Promoter ◽  
Reading Frames

The complete nucleotide sequence of a mouse retro-element is presented. The cloned element is composed of 4,834 base pairs (bp) with long terminal repeats of 568 bp separated by an internal region of 3,698 bp. The element did not appear to have any open reading frames that would be capable of encoding the functional proteins that are normally produced by retro-elements. However, some regions of the genome showed some homology to retroviral gag and pol open reading frames. There was no region in VL30 corresponding to a retroviral env gene. This implies that VL30 is related to retrotransposons rather than to retroviruses. The sequence also contained regions that were homologous to known reverse transcriptase priming sites and viral packaging sites. These observations, combined with the known transcriptional capacity of the VL30 promoter, suggest that VL30 relies on protein functions of other retro-elements, such as murine leukemia virus, while maintaining highly conserved cis-active promoter, packaging, and priming sites necessary for its replication and cell-to-cell transmission.

scholarly journals Identification of diverse groups of endogenous gammaretroviruses in mega- and microbats

2012 ◽  
Vol 93 (9) ◽  
pp. 2037-2045 ◽  
Author(s):  
Jie Cui ◽  
Gilda Tachedjian ◽  
Mary Tachedjian ◽  
Edward C. Holmes ◽  
Shuyi Zhang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Leukemia Virus ◽  
Large Deletion ◽  
Endogenous Retroviruses ◽  
Myotis Lucifugus ◽  
Phylogenetic Study ◽  
Endogenous Virus ◽  
Pteropus Vampyrus ◽  
Gibbon Ape Leukemia Virus ◽  
Diverse Groups

A previous phylogenetic study suggested that mammalian gammaretroviruses may have originated in bats. Here we report the discovery of RNA transcripts from two putative endogenous gammaretroviruses in frugivorous (Rousettus leschenaultii retrovirus, RlRV) and insectivorous (Megaderma lyra retrovirus, MlRV) bat species. Both genomes possess a large deletion in pol, indicating that they are defective retroviruses. Phylogenetic analysis places RlRV and MlRV within the diversity of mammalian gammaretroviruses, with the former falling closer to porcine endogenous retroviruses and the latter to Mus dunni endogenous virus, koala retrovirus and gibbon ape leukemia virus. Additional genomic mining suggests that both microbat (Myotis lucifugus) and megabat (Pteropus vampyrus) genomes harbour many copies of endogenous retroviral forms related to RlRV and MlRV. Furthermore, phylogenetic analysis reveals the presence of three genetically diverse groups of endogenous gammaretroviruses in bat genomes, with M. lucifugus possessing members of all three groups. Taken together, this study indicates that bats harbour distinct gammaretroviruses and may have played an important role as reservoir hosts during the diversification of mammalian gammaretroviruses.

scholarly journals Complete Genome Sequence of Feline Leukemia Virus Kawakami-Theilen Strain KT-FeLV-UCD-1

2020 ◽  
Vol 9 (20) ◽  
Author(s):  
Pei-Ju Chin ◽  
Fabio La Neve ◽  
Valeria Zanda ◽  
Arifa S. Khan
Keyword(s):  
Genome Sequence ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Genomic Organization ◽  
Leukemia Virus ◽  
Open Reading Frames ◽  
Feline Leukemia Virus ◽  
Long Terminal Repeats ◽  
Full Length Genome ◽  
Reading Frames

This full-length genome sequence of a feline leukemia virus Kawakami-Theilen strain (designated KT-FeLV-UCD-1), produced from the chronically infected FL74-UCD-1 cell line, was obtained using high-throughput sequencing. It consisted of 8,464 bp and had a genomic organization similar to that of other gammaretroviruses, containing long terminal repeats and open reading frames for Gag, Pol, and Env.

scholarly journals The Nucleotide Sequence of Koala (Phascolarctos cinereus) Retrovirus: a Novel Type C Endogenous Virus Related to Gibbon Ape Leukemia Virus

2000 ◽  
Vol 74 (9) ◽  
pp. 4264-4272 ◽  
Author(s):  
Jon J. Hanger ◽  
Lindell D. Bromham ◽  
Jeff J. McKee ◽  
Tracy M. O'Brien ◽  
Wayne F. Robinson
Keyword(s):  
Reverse Transcriptase ◽  
Genomic Dna ◽  
Leukemia Virus ◽  
Endogenous Retrovirus ◽  
Reverse Transcriptase Activity ◽  
Endogenous Virus ◽  
Peripheral Blood Mononuclear ◽  
Phascolarctos Cinereus ◽  
Clinically Normal ◽  
Gibbon Ape Leukemia Virus

ABSTRACT A novel retrovirus, morphologically consistent with mammalian C-type retroviruses, was detected by electron microscopy in mitogen-stimulated peripheral blood mononuclear cell cultures from 163 koalas and in lymphoma tissue from 3 koalas. PCR amplified provirus from the blood and tissues of 17 wild and captive koalas, and reverse transcriptase-PCR demonstrated viral mRNA, viral genomic RNA, and reverse transcriptase activity in koala serum and cell culture supernatants. Comparison of viral sequences derived from genomic DNA and mRNA showed identity indicative of a single retroviral species—here designated koala retrovirus (KoRV). Southern blot analysis of koala tissue genomic DNA using labelled KoRV probes demonstrated banding consistent with an endogenous retrovirus. Complete and apparently truncated proviruses were detected in DNA of both clinically normal koalas and those with hematopoietic disease. KoRV-related viruses were not detected in other marsupials, and phylogenetic analysis showed that KoRV paradoxically clusters with gibbon ape leukemia virus (GALV). The strong similarity between GALV and KoRV suggests that these viruses are closely related and that recent cross-host transmission has occurred. The complete proviral DNA sequence of KoRV is reported.

scholarly journals Temporal Global Changes in Gene Expression during Temperature Transition in Yersinia pestis

2004 ◽  
Vol 186 (18) ◽  
pp. 6298-6305 ◽  
Author(s):  
Vladimir L. Motin ◽  
Anca M. Georgescu ◽  
Joseph P. Fitch ◽  
Pauline P. Gu ◽  
David O. Nelson ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Dna Microarrays ◽  
Open Reading Frames ◽  
Mammalian Host ◽  
Global Changes ◽  
Temperature Transition ◽  
Entire Genome ◽  
Regulatory Changes ◽  
Chromosomal Genes ◽  
Reading Frames

ABSTRACT DNA microarrays encompassing the entire genome of Yersinia pestis were used to characterize global regulatory changes during steady-state vegetative growth occurring after shift from 26 to 37°C in the presence and absence of Ca2+. Transcriptional profiles revealed that 51, 4, and 13 respective genes and open reading frames (ORFs) on pCD, pPCP, and pMT were thermoinduced and that the majority of these genes carried by pCD were downregulated by Ca2+. In contrast, Ca2+ had little effect on chromosomal genes and ORFs, of which 235 were thermally upregulated and 274 were thermally downregulated. The primary consequence of these regulatory events is profligate catabolism of numerous metabolites available in the mammalian host.

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