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

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.

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A Nymphalid-Infecting Group I Alphabaculovirus Isolated from the Major Passion Fruit Caterpillar Pest Dione juno juno (Lepidoptera: Nymphalidae)

Viruses ◽

10.3390/v11070602 ◽

2019 ◽

Vol 11 (7) ◽

pp. 602 ◽

Cited By ~ 2

Author(s):

Bergmann Morais Ribeiro ◽

Ethiane Rozo dos Santos ◽

Luana Beló Trentin ◽

Leonardo Assis da Silva ◽

Fernando Lucas de Melo ◽

...

Keyword(s):

Genome Sequencing ◽

Complete Genome Sequence ◽

Complete Genome ◽

Insect Pests ◽

Open Reading Frames ◽

Thymidylate Kinase ◽

Orgyia Pseudotsugata ◽

Group I ◽

Reading Frames ◽

Core Genes

Baculoviruses are capable of infecting a wide diversity of insect pests. In the 1990s, the Dione juno nucleopolyhedrovirus (DijuNPV) was isolated from larvae of the major passionfruit defoliator pest Dione juno juno (Nymphalidae) and described at ultrastructural and pathological levels. In this study, the complete genome sequence of DijuNPV was determined and analyzed. The circular genome presents 122,075 bp with a G + C content of 50.9%. DijuNPV is the first alphabaculovirus completely sequenced that was isolated from a nymphalid host and may represent a divergent species. It appeared closely related to Orgyia pseudotsugata multiple nucleopolyhedrovirus (OpMNPV) and other Choristoneura-isolated group I alphabaculoviruses. We annotated 153 open reading frames (ORFs), including a set of 38 core genes, 26 ORFs identified as present in lepidopteran baculoviruses, 17 ORFs unique in baculovirus, and several auxiliary genes (e.g., bro, cathepsin, chitinase, iap-1, iap-2, and thymidylate kinase). The thymidylate kinase (tmk) gene was present fused to a dUTPase (dut) gene in other baculovirus genomes. DijuNPV likely lost the dut portion together with the iap-3 homolog. Overall, the genome sequencing of novel alphabaculoviruses enables a wide understanding of baculovirus evolution.

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

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00157-08 ◽

2008 ◽

Vol 52 (10) ◽

pp. 3580-3588 ◽

Cited By ~ 13

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.

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Genomic Characterization of a Novel Freshwater Cyanophage Reveals a New Lineage of Cyanopodovirus

Frontiers in Microbiology ◽

10.3389/fmicb.2021.768868 ◽

2022 ◽

Vol 12 ◽

Author(s):

Dong Zhang ◽

Yiliang He ◽

Karina Yew-Hoong Gin

Keyword(s):

Open Reading Frames ◽

Metabolic Genes ◽

Genes Encoding ◽

Genomic Characterization ◽

Ecological Importance ◽

Auxiliary Metabolic Genes ◽

Reading Frames ◽

Tropical Freshwater ◽

Core Genes

Cyanobacteria are one of the dominant autotrophs in tropical freshwater communities, yet phages infecting them remain poorly characterized. Here we present the characterization of cyanophage S-SRP02, isolated from a tropical freshwater lake in Singapore, which infects Synechococcus sp. Strain SR-C1 isolated from the same lake. S-SRP02 represents a new evolutionary lineage of cyanophage. Out of 47 open reading frames (ORFs), only 20 ORFs share homology with genes encoding proteins of known function. There is lack of auxiliary metabolic genes which was commonly found as core genes in marine cyanopodoviruses. S-SRP02 also harbors unique structural genes highly divergent from other cultured phages. Phylogenetic analysis and viral proteomic tree further demonstrate the divergence of S-SRP02 from other sequenced phage isolates. Nonetheless, S-SRP02 shares synteny with phage genes of uncultured phages obtained from the Mediterranean Sea deep chlorophyll maximum fosmids, indicating the ecological importance of S-SRP02 and its related viruses. This is further supported by metagenomic mapping of environmental viral metagenomic reads onto the S-SRP02 genome.

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Sequence Analysis of the Genome of the Neodiprion sertifer Nucleopolyhedrovirus

Journal of Virology ◽

10.1128/jvi.78.13.7036-7051.2004 ◽

2004 ◽

Vol 78 (13) ◽

pp. 7036-7051 ◽

Cited By ~ 83

Author(s):

Alejandra Garcia-Maruniak ◽

James E. Maruniak ◽

Paolo M. A. Zanotto ◽

Aissa E. Doumbouya ◽

Jaw-Ching Liu ◽

...

Keyword(s):

Ring Finger ◽

Open Reading Frames ◽

Neodiprion Sertifer ◽

Pine Sawfly ◽

Culex Nigripalpus ◽

Conserved Genes ◽

European Pine Sawfly ◽

Conserved Core ◽

Reading Frames ◽

Core Genes

ABSTRACT The genome of the Neodiprion sertifer nucleopolyhedrovirus (NeseNPV), which infects the European pine sawfly, N. sertifer (Hymenoptera: Diprionidae), was sequenced and analyzed. The genome was 86,462 bp in size. The C+G content of 34% was lower than that of the majority of baculoviruses. A total of 90 methionine-initiated open reading frames (ORFs) with more than 50 amino acids and minimal overlapping were found. From those, 43 ORFs were homologous to other baculovirus ORFs, and 29 of these were from the 30 conserved core genes among all baculoviruses. A NeseNPV homolog to the ld130 gene, which is present in all other baculovirus genomes sequenced to date, could not be identified. Six NeseNPV ORFs were similar to non-baculovirus-related genes, one of which was a trypsin-like gene. Only one iap gene, containing a single BIR motif and a RING finger, was found in NeseNPV. Two NeseNPV ORFs (nese18 and nese19) were duplicates transcribed in opposite orientations from each other. NeseNPV did not have an AcMNPV ORF 2 homolog characterized as the baculovirus repeat ORF (bro). Six homologous regions (hrs) were located within the NeseNPV genome, each containing small palindromes embedded within direct repeats. A phylogenetic analysis was done to root the tree based upon the sequences of DNA polymerase genes of NeseNPV, 23 other baculoviruses, and other phyla. Baculovirus phylogeny was then constructed with 29 conserved genes from 24 baculovirus genomes. Culex nigripalpus nucleopolyhedrovirus (CuniNPV) was the most distantly related baculovirus, branching to the hymenopteran NeseNPV and the lepidopteran nucleopolyhedroviruses and granuloviruses.

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Nudivirus Sequences Identified from the Southern and Western Corn Rootworms (Coleoptera: Chrysomelidae)

Viruses ◽

10.3390/v13020269 ◽

2021 ◽

Vol 13 (2) ◽

pp. 269

Author(s):

Sijun Liu ◽

Thomas W. Sappington ◽

Brad S. Coates ◽

Bryony C. Bonning

Keyword(s):

Genome Sequence ◽

Insect Pests ◽

Sequence Data ◽

Diabrotica Virgifera Virgifera ◽

Open Reading Frames ◽

Corn Rootworm ◽

Geographically Dispersed ◽

Diabrotica Undecimpunctata Howardi ◽

Short Read Sequence ◽

Core Genes

Analysis of pooled genomic short read sequence data revealed the presence of nudivirus-derived sequences from U.S. populations of both southern corn rootworm (SCR, Diabrotica undecimpunctata howardi Barber) and western corn rootworm (WCR, Diabrotica virgifera virgifera LeConte). A near complete nudivirus genome sequence was assembled from sequence data for an SCR population with relatively high viral titers. A total of 147,179 bp was assembled from five contigs that collectively encode 109 putative open reading frames (ORFs) including 20 nudivirus core genes. In contrast, genome sequence recovery was incomplete for a second nudivirus from WCR, although sequences derived from this virus were present in three geographically dispersed populations. Only 48,989 bp were assembled with 48 putative ORFs including 13 core genes, representing about 20% of a typical nudivirus genome. Phylogenetic analysis indicated that both corn rootworm nudiviruses grouped with the third known nudivirus of beetles, Oryctes rhinoceros nudivirus in the genus Alphanudivirus. On the basis of phylogenetic and additional analyses, we propose further taxonomic separation of nudiviruses within Alphanudivirus and Betanudivirus into two subfamilies and five genera. Identification of nudivirus-derived sequences from two species of corn rootworm highlights the diversity of viruses associated with these agricultural insect pests.

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

Journal of Virology ◽

10.1128/jvi.72.9.7459-7466.1998 ◽

1998 ◽

Vol 72 (9) ◽

pp. 7459-7466 ◽

Cited By ~ 29

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.

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A Novel Alphabaculovirus from the Soybean Looper, Chrysodeixis includens, that Produces Tetrahedral Occlusion Bodies and Encodes Two Copies of he65

Viruses ◽

10.3390/v11070579 ◽

2019 ◽

Vol 11 (7) ◽

pp. 579 ◽

Cited By ~ 2

Author(s):

Robert L. Harrison ◽

Daniel L. Rowley ◽

Holly J. R. Popham

Keyword(s):

Trichoplusia Ni ◽

Unique Feature ◽

Open Reading Frames ◽

Occlusion Bodies ◽

Noctuid Species ◽

Chrysodeixis Chalcites ◽

Soybean Looper ◽

Reading Frames ◽

Chrysodeixis Includens

Isolates of the alphabaculovirus species, Chrysodeixis includens nucleopolyhedrovirus, have been identified that produce polyhedral occlusion bodies and infect larvae of the soybean looper, Chrysodeixis includens. In this study, we report the discovery and characterization of a novel C. includens-infecting alphabaculovirus, Chrysodeixis includens nucleopolyhedrovirus #1 (ChinNPV#1), that produces tetrahedral occlusion bodies. In bioassays against C. includens larvae, ChinNPV #1 exhibited a degree of pathogenicity that was similar to that of other ChinNPV isolates, but killed larvae more slowly. The host range of ChinNPV#1 was found to be very narrow, with no indication of infection occurring in larvae of Trichoplusia ni and six other noctuid species. The ChinNPV#1 genome sequence was determined to be 130,540 bp, with 126 open reading frames (ORFs) annotated but containing no homologous repeat (hr) regions. Phylogenetic analysis placed ChinNPV#1 in a clade with other Group II alphabaculoviruses from hosts of lepidopteran subfamily Plusiinae, including Chrysodeixis chalcites nucleopolyhedrovirus and Trichoplusia ni single nucleopolyhedrovirus. A unique feature of the ChinNPV#1 genome was the presence of two full-length copies of the he65 ORF. The results indicate that ChinNPV#1 is related to, but distinct from, other ChinNPV isolates.

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