The 5′ non-translated region of Varroa destructor virus 1 (genus Iflavirus): structure prediction and IRES activity in Lymantria dispar cells

Ongus, Juliette R.; Roode, Els C.; Pleij, C.W.A.; Vlak, Just M.; Oers, Monique M. van

doi:10.1099/vir.0.82122-0

Cited by 57 publications

(55 citation statements)

References 43 publications

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“…Insect expression vectors encoding short hairpin RNA were constructed by annealing previously described DNA oligonucleotides (69) either against Firefly luciferase or enhanced green fluorescent protein (eGFP) and cloning these as KpnI-XbaI fragments in pMT-B (Invitrogen) behind the Drosophila metallothionein gene promoter. For the RNA silencing experiments in U4.4 cells, Firefly and Renilla luciferase constructs were used, which have previously been described (46) and are expressed via the OpIE2 or AcIE1 promoters, respectively.…”

Section: Methodsmentioning

confidence: 99%

Noncoding Flavivirus RNA Displays RNA Interference Suppressor Activity in Insect and Mammalian Cells

Schnettler

Sterken

Leung

et al. 2012

J Virol

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Section: Methodsmentioning

confidence: 99%

Noncoding Flavivirus RNA Displays RNA Interference Suppressor Activity in Insect and Mammalian Cells

Schnettler

Sterken

Leung

et al. 2012

J Virol

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261

277

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“…)] and resembles the hairpin structures found close to the 59 termini of the genomic RNAs of Perina nuda virus (PnV) and Ectropis obliqua picorna-like virus (EoPV) (Ongus et al, 2006;Wang et al, 2004;Wu et al, 2002 )], which do not have much in common with those identified in other iflaviruses (Ongus et al, 2006). High diversity of the 59-NTR secondary structure elements has been reported, for example, in the family Picornaviridae (Witwer et al, 2001).…”

mentioning

confidence: 97%

“…A 59-proximal hairpin structure formed by nt 7-38 contains a 14 nt stem with the 59-AUUU-39 loop [free energy 224. (Ongus et al, 2006). High diversity of the 59-NTR secondary structure elements has been reported, for example, in the family Picornaviridae (Witwer et al, 2001).…”

mentioning

confidence: 99%

“…The BrBV RNA, like other iflaviruses, has a low G+C content (31 mol% A, 35 mol% U, 16 mol% C and 18 mol% G). The extended 59-NTR of BrBV RNA is likely to function in RNA replication and as an internal ribosome entry signal (Ongus et al, 2006). The secondary RNA structure prediction for the BrBV 59 NTR carried out by Mfold algorithm (Zuker, 2003) showed the presence of a number of structural elements.…”

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confidence: 99%

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A novel virus isolated from the aphid Brevicoryne brassicae with similarity to Hymenoptera picorna-like viruses

Ryabov

2007

Journal of General Virology

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A novel virus, Brevicoryne brassicae virus (BrBV), has been identified in the cabbage aphid using a method based on the random amplification of encapsidated RNA. The complete sequence of the RNA genome of BrBV has been determined. The positive-strand genomic RNA is 10 161 nt, excluding the 39 poly(A) tail, and contains a single open reading frame (positions 793-9744) encoding a putative polyprotein of 2983 aa. The N-terminal part of the polyprotein shows similarity with the structural proteins of iflaviruses. The C-terminal part possesses consensus sequences of the helicase, cysteine protease and RNA-dependent RNA polymerase similar to those of iflaviruses and other picorna-like viruses. The highest sequence similarity observed was with iflaviruses from honeybee and an endoparasitic wasp. Replication and transmission of BrBV was not dependent on endoparasitic wasp infestation of the aphids.Aphids are major pests of crops and the regulation of aphid populations by pathogens and parasitoid wasp is poorly understood. The aphid viruses sequenced to date include one DNA virus [Myzus persicae densovirus (van Munster et al., 2003)] and four RNA viruses. The latter include aphid lethal paralysis virus (ALPV) (van Munster et al., 2002) and Rhopalosiphum padi virus (RhPV) (Moon et al., 1998), both members of the family Dicistroviridae, which infect a variety of insect hosts, and the unclassified Acyrthosiphon pisum virus (APV) (van der Wilk et al., 1997) together with the closely related rosy apple aphid virus (our unpublished data). These viruses were isolated from laboratory cultures of aphids from which significant quantities of virus could be obtained. However, the spectrum of viruses in laboratory cultures may not reflect that present in nature and also decreases the possibility of detecting viruses that cause pathology. In addition, it is difficult to use field-collected aphids for this purpose because field colonies often contain very few insects. To overcome this problem we have developed a novel approach to amplify viral nucleic acid from a small number of field-collected aphids, which has been used to identify the first aphid iflavirus, Brevicoryne brassicae virus (BrBV). Here we report the complete nucleotide sequence and describe the genome organization of BrBV and evidence that BrBV replicates in B. brassicae.Amplification of the encapsidated RNA was adapted from the procedure described by Allander et al. (2005). Fifty adult B. brassicae aphids (total weight 15 mg), collected from different locations in Warwickshire, UK, during the summer of 2005 and stored at 280 uC, were homogenized with 15 ml 10 mM sodium phosphate buffer, pH 7.5. The homogenate was then centrifuged at 350 g for 10 min in a bench top Eppendorf centrifuge. The debris-free supernatant was filtered through a 0.80/0.22 mm filter (Millipore) and then centrifuged at 45 000 r.p.m. in a Ti80 rotor (Beckman) at 4 u C for 120 min. In order to remove traces of DNA contamination, 100 units of DNase I (Stratagene) were added and the sample was incubate...

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“…These processes also involve the 59-and 39-UTRs, as well as numerous host factors (Belsham, 2009). Translation is probably initiated by an internal ribosome entry site (IRES) in the 59-UTR (Ongus et al, 2006;Roberts & Groppelli, 2009), thus avoiding the host's cap-dependent translation (Belsham, 2009). The first amino acid is probably methionine (Belsham, 2009), although this is not obligatory for IRES-mediated translation (Jan, 2006).…”

mentioning

confidence: 99%

Genetic characterization of slow bee paralysis virus of the honeybee (Apis mellifera L.)

Miranda

Dainat

Locke

et al. 2010

Journal of General Virology

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Complete genome sequences were determined for two distinct strains of slow bee paralysis virus (SBPV) of honeybees (Apis mellifera). The SBPV genome is approximately 9.5 kb long and contains a single ORF flanked by 59-and 39-UTRs and a naturally polyadenylated 39 tail, with a genome organization typical of members of the family Iflaviridae. The two strains, labelled 'Rothamsted' and 'Harpenden', are 83 % identical at the nucleotide level (94 % identical at the amino acid level), although this variation is distributed unevenly over the genome. The two strains were found to co-exist at different proportions in two independently propagated SBPV preparations. The natural prevalence of SBPV for 847 colonies in 162 apiaries across five European countries was ,2 %, with positive samples found only in England and Switzerland, in colonies with variable degrees of Varroa infestation.Slow bee paralysis virus (SBPV) is one of several honeybee (Apis mellifera) viruses linked to high mortality of colonies infested with the ectoparasitic mite Varroa destructor (Carreck et al., 2010;Martin et al., 1998). SBPV was discovered fortuitously in England in 1974, during propagation experiments involving bee virus X. It induces paralysis of the anterior two pairs of legs about 10 days after injection into the abdomen of adult bees (Bailey & Woods, 1974), with high virus accumulation in the head, the hypopharyngeal, mandibular and salivary glands, the fat body, crop and forelegs, but less in the hindlegs, midgut, rectum and thorax (Denholm, 1999). Like most honeybee viruses, SBPV persists naturally as a covert infection, most likely through oral transmission (Bailey & Ball, 1991). However, SBPV can be transmitted readily among adult bees and to pupae by Varroa mites (Santillán-Galicia et al., 2010), with lethal consequences at the individual bee and colony levels (Carreck et al., 2010). Overt SBPV infection can also be induced in adult bees (but not in pupae) by injection with inert fluids, especially the The GenBank/EMBL/DDBJ accession numbers for the complete genome sequences of SBPV strains Rothamsted and Harpenden are EU035616 and GU938761, respectively.A supplementary table showing primers and performance indicators of several universal and strain-specific RT-qPCR assays is available with the online version of this paper.

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The 5′ non-translated region of Varroa destructor virus 1 (genus Iflavirus): structure prediction and IRES activity in Lymantria dispar cells

Cited by 57 publications

References 43 publications

Noncoding Flavivirus RNA Displays RNA Interference Suppressor Activity in Insect and Mammalian Cells

Noncoding Flavivirus RNA Displays RNA Interference Suppressor Activity in Insect and Mammalian Cells

A novel virus isolated from the aphid Brevicoryne brassicae with similarity to Hymenoptera picorna-like viruses

Genetic characterization of slow bee paralysis virus of the honeybee (Apis mellifera L.)

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