| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
The Hebrew University of Jerusalem, Faculty of Agricultural, Food and Environmental Quality Sciences, Rehovot 76100, Israel
Correspondence
Ilan Sela
sela{at}agri.huji.ac.il
 |
ABSTRACT |
|---|
 TOP ABSTRACT INTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
|---|
The GenBank/EMBL/DDBJ accession number of the IAPV sequence reported in this paper is EF219380.
Supplementary material is available with the online version of this paper.
|
INTRODUCTION |
|---|
|
TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
|---|
; Ball & Bailey, 1997; Evans & Hung, 2000; Elus & Munn, 2005). Individual bees often harbour more than one species of virus (Anderson & Gibbs, 1988).
Several bee viruses have been fully sequenced, including KBV (de Miranda et al., 2004), ABPV (Govan et al., 2000), SBV (Ghosh et al., 1999), BQCV (Leat et al., 2000), Kakugo virus (KV; Fujiyuki et al., 2004) and DWV (Lanzi et al., 2006). Based on replicase features, they all belong to the Picornaviridae superfamily (Koonin & Dolja, 1993). Viruses belonging to the subgroup Dicistroviridae (Mayo, 2002) carry two open reading frames (ORFs) for two polyproteins, divided by a short spacer. In dicistroviruses the polyprotein which is processed to the structural proteins is located at the 3'-proximal region of the viral genome (van Munster et al., 2002). Dicistroviral precursor proteins are processed by a virus-encoded protease, homologous to the 3C protease (3C-pro) of picornaviruses. Other insect-infecting picorna-like viruses include Drosophila C virus (DCV; Johnson & Christian, 1998), Triatoma virus (TrV; Czibener et al., 2000), cricket paralysis virus (CrPV; Wilson et al., 2000), aphid lethal paralysis virus (ALPV; van Munster et al., 2002), Homalodisca coagulata virus-1 (HoCV-1; Hunnicutt et al., 2006), himetobi P virus (HiPV; Nakashima et al., 1999), Solenopsis invicta virus 1 (SINV-1; Valles et al., 2004), Plautia stali intestine virus (PSIV; Sasaki et al., 1998), Rhopalosiphum padi virus (RhPV; Moon et al., 1998), and Varroa destructor virus 1 (VDV-1; Ongus et al., 2004).
Recently, severe bee mortality has inflicted heavy losses on Israeli apiculture. Bees exhibited symptoms reminiscent of those inflicted by ABPV, therefore the isolated virus was tentatively named Israeli acute paralysis virus (IAPV).
Recently, Crochu et al. (2004) and Tanne & Sela (2005) reported that DNA versions of non-retro RNA viruses is incorporated into the genome of their hosts. In grapevine, it has been indicated that RNA recombination followed by retrotransposition may have led to this integration. Recently, we reported that a segment of IAPV is also incorporated into some of its bee hosts, and that bees harbouring the viral segment are resistant to subsequent IAPV infection. We also reported that the exchange of genetic information between virus and host is reciprocal, and segments of a host gene were found embedded in a viral defective-interfering (DI)-like RNA (Maori et al., 2007). The presence of subviral RNAs due to recombination has been well documented (e.g. Nagy & Simon, 1997).
In this paper, we characterize IAPV as a new member of the Dicistroviridae family. We sequenced the viral RNA, analysed its two polyproteins and the processed capsid proteins, and report on the presence of recombinant IAPV-related DI-like RNAs within encapsidated virions.
|
METHODS |
|---|
|
TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
|---|
IAPV inoculation.
IAPV was purified as described by Maori et al. (2007). Bees were inoculated by injection into larvae or pupae and by feeding virus-contaminated food to adult workers. Purified virus (1 µl, containing 1 µg of virus) was injected into the abdominal inter-segment space of 20 to 50 individual healthy-looking larvae taken from an apparently non-affected hive. Following a 4 day incubation at 35 °C, the infected, dead larvae were counted. Non-inoculated, as well as buffer-injected larvae served as controls. Larvae injected with tobacco mosaic virus (TMV) served as an additional negative control. Similar injection inoculations were carried out with pupae (Maori et al., 2007). In other experiments, adult worker bees were fed on a ‘cake’ made of 66 % sugar powder, 33 % honey and 1 % starch. Groups of approximately 150 to 200 healthy-looking bees were kept in separate cages at room temperature. Some groups were fed on IAPV-infested cake (approx. 1 µg virus per gram cake). Other groups were fed on virus-free cakes and another control group was fed on TMV-infested cake (1 µg virus per gram cake).
RNA extraction and electrophoresis.
Purified virions were RNase-treated. Addition of RNasin was following proteinase K digestion. The viral RNA was extracted by phenol or TRI Reagent (Ambion) according to the manufacturer's protocol. RNA was electrophoresed on 1 % agarose gels.
Semiquantitative RT-PCR assays.
The amount of each type of RNA was determined by the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). A mixture containing 90 % RNA from an IAPV preparation and 10 % TMV RNA was submitted to reverse-transcription with a mixture of hexamer primers (Applied Biosystems). The resultant cDNA was amplified with specific primers (Supplementary Table S1, available with the online version of this paper). Samples were drawn every three cycles and electrophoresed. The appearance of the first visible band in each preparation was indicative of the amount of the respective template relative to other templates. Correlation between PCR thresholds and actual amount of RNA was drawn from a calibration curve with TMV-RNA.
Molecular procedures and cloning of full-length viral RNA.
Standard molecular procedures such as Northern and Western blots, PCR and sequencing were carried out according to Sambrook & Russell (2001). The longest RNA from a gel was extracted and served as the template for cDNA cloning. First and second DNA strands were prepared from the viral RNA according to the kit provider protocol (Stratagene). First, the RT step was primed with oligo(dT), and the PCR stage was performed with that primer and random primers. The longest product was 1905 bp in length, and all smaller products were of sequences found within the longer one, confirming that they had all reacted with the same template. At later stages, an IAPV-specific 20-base-long anchor was added to the oligo(dT) primer (Supplementary Table S1). The resultant DNA fragments were cloned into the vector 
Zap Express (Stratagene) and their sequence was determined from the rescued plasmids. The longest fragment thus obtained was 1905 bases long. BLAST analysis indicated that it is homologous (75.4 % identity) to the 3' section of KBV, carrying a segment of an ORF for the viral structural polyprotein and its 3' untranslated region (UTR). Primers for further RT-PCR assays were designed from the innermost section of this sequence, gradually advancing towards the 5' end using the SMART procedure (Clontech). The 5' rapid amplification of cDNA ends (RACE) was repeated several times and always resulted in the same 5' sequence. The sequence was determined by aligning overlapping fragments. The sequence was further confirmed by a series of PCRs with different sets of primers. Primer descriptions and designations are given in Supplementary Table S1.
Protein analyses.
IAPV capsid proteins were analysed following electrophoresis on SDS-polyacrylamide gels. Extraction of bee proteins and Western blot analyses were performed according to Sambrook & Russell (2001). Edman degradation procedure for the determination of N termini was performed by the Biological Services unit of the Weizmann Institute of Science (Rehovot, Israel). IAPV proteins were first resolved on denatured gels, transferred onto a membrane, and each band was analysed for the first 3–6 amino acids at the peptide's N terminus. The resolution of gels performed according to protocols specified for Edman degradation analysis was better than that of gels electrophoresed according to the protocol for Western blot analysis. Serological relationships with other bee viruses were tested by immunodiffusion assay (Mansi, 1958). Instructions and antibodies were provided by Dr Brenda Ball, and the tests were carried out at the Rothamsted Research Laboratory, England.
Isolation and determination of virion-associated DI-like RNAs.
Only a single fragment of IAPV was found integrated into the bee genome. In addition, a DI-like fragment, fused to a segment of the host gene, was isolated from IAPV virions by PCR with primers designed for flanking sequences of the genome-inserted fragment (Maori et al., 2007). We therefore assumed that the ends of these fragments serve as ‘hot spots’ for recombination. DI-like RNAs residing within virions were extracted from RNase-treated, CsCl-purified virions, to eliminate any contamination on the outside of the virions. RT-PCR was carried out with the aforementioned primers (Supplementary Table S1, available with the online version of this paper), and products deviating from the expected size were gel-purified, TA-cloned and sequenced.
Sequence analyses.
Protein molecular masses were computed from their actual sequence by the ‘compute pI/Mw’ program. Post-translational protein modifications were determined by the following programs: NetOGlyc, NetNGlyc, NetPhos and SUMOplot. 3C-pro cleavage sites were determined by NetPicoRNA. All the aforementioned programs can be found in the ExPASy Proteomic Tool package (www.expasy.org/tools). RNA folding was predicted by the program ‘RNA secondary structure prediction’ (www.genebee.msu.su).
|
RESULTS |
|---|
|
TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
|---|
).
|
.
|
IAPV-injected bees died within 4 days. Bees fed on IAPV-infested cakes gradually developed symptoms and died within 10 days. Early on, the only indication of infection was darkening of the abdomen tip. Between the 3rd and 6th day of infection, the thorax darkened as well, and the bees were unsettled: they were constantly going around in circles, and barely flew or ate. Between the 7th and 10th days, the bees' abdomen and thorax became dark (dark brown to black), and the thorax became hairless. The bees stopped flying, barely moved, underwent periods of spasms, and eventually died.
Viral genome
Nucleic acids were extracted from RNase-treated purified viral preparations and electrophoresed. A band of approximately 9 kb was observed, which was DNase-insensitive and RNase-sensitive. In addition to the full-length band, several strong, but shorter bands appeared under denaturing conditions (Fig. 1a
). These shorter RNA forms were considered to be DI-like RNAs and are described in detail further on.
The viral RNA was cloned and sequenced (GenBank accession no. EF219380). It is 9487 nt long (excluding the poly-A tail) and carries two ORFs, both coding for polyproteins. The 5' proximal ORF, translating to 1900 aa, codes for proteins involved in RNA replication and protein processing. The ORF near the 3' end, translating to 908 aa, codes for a polyprotein which is processed to the various capsid proteins. Since the protein initiation site may not be AUG (Johnson & Christian, 1998; Domier & McCoppin, 2003; Nishiyama et al., 2003), the N termini of both polyproteins may differ (by being slightly shorter) from the ones presented here. The two ORFs are separated by a 184-nucleotide-long intergenic region. A schematic illustration of the IAPV genome is given in Fig. 1(c).
Based on homology and genomic structure, IAPV belongs to the family Dicistroviridae (Mayo, 2002).
The non-structural polyprotein
This polyprotein carries motifs for helicase, protease and RNA-dependent RNA polymerase (RdRp) found in non-structural polyproteins of the picornaviridae (Koonin & Dolja, 1993). The helicase domain carries three signature sequences. Motif A is the nucleotide-binding motif GxxGxGK (512GESGVGK518 in IAPV). This motif, responsible for nucleotide binding and hydrolysis (Walker et al., 1982), has been found in all hitherto sequenced dicistroviruses. Motif B, the catalytic core WDGY (557WDNY560 in IAPV) followed by [E/Q]x5D[D/E] (563QNVVVYDD570 in IAPV), is also present in all dicistroviruses (motif alignments are presented in Fig. 5 of Hunnicutt et al., 2006). The protease domain carries two signature sequences as described by Koonin & Dolja (1993): the classical signature of cysteine proteases, GxCG (1301GDCG1304 in IAPV), and the putative substrate-binding motif GxHxxG (1320GIHVAG1325 in IAPV). The RdRp domain of subgroup 1 of RdRp carries eight conserved regions (Koonin & Dolja, 1993; Fig. 2 in Hunnicutt et al., 2006). IAPV carries the 1564TLKDER1568 of conserved region I, 1579KTRVFS1564 of conserved region II, 1619NVY1621 of conserved region III, DFxxFDG (1643DFSTFDG1649 in IAPV) of conserved region IV, THS[Q/I/L]PSG[N/C/H][P/E/Y] (1699THSQPSGNP1677 in IAPV) of conserved region V, YGDD (a signature sequence of RdRp) of conserved region VI, TDExK (1783TDELK1787 in IAPV) and 1805LKR1807 of conserved region VII and APLx10W (1820APLCMDTILEMPNW1833 in IAPV) of conserved region VIII. In addition to linear motifs, two aspartic acid residues situated five residues apart and an asparagine located 69 residues downstream of the second aspartic acid (D1643, D1648 and N1717, respectively) are required for magnesium-binding and discrimination between ribonucleotides and 2' deoxyribonucleotides (Hansen et al., 1997; Love et al., 2004). The exact same distances for this triad have been reported for HoCV-1 (Hunnicutt et al., 2006). Alignment of the RdRp sequences of several dicistroviruses indicated conservation of the aforedescribed motifs (Fig. 2a). However, as expected from the homology determinations, ABPV, KBV and IAPV were set off as a separate, most closely related group (Fig. 2b).
|
The patterns of dicistroviruses' mature capsid proteins differ from one species to the next. In several papers, three major proteins have been demonstrated, along with an additional minor protein (or proteins), and possibly a short peptide (C4, less than 10 kDa), believed to be cleaved off after virion assembly (for example, Sasaki et al., 1998). Four capsid proteins, of approximately 9.5, 24, 33 and 35 kDa, have been identified in ABPV and KBV, the two closest relatives of IAPV. Electrophoretic patterns of denatured IAPV indicated that the major IAPV capsid proteins are approximately 17, 26, 33 and 35 kDa and three additional minor proteins of approximately 19, 30 and 46 kDa were also observed (Fig. 3a). Western blot analysis (of a somewhat lower resolution gel) exhibited the same general pattern (Fig. 3b). The IAPV antibodies did not react with any protein of healthy bees (Maori et al., 2007), thus they are specific to viral proteins only. Edman degradation of gel-extracted bands determined five N-terminal sequences. (i) SVL, corresponding to 126SVL128 of the translated sequence. (ii) SQPKTS, corresponding in five out of its six amino acids to 339SQKSTS344 as determined from the translated IAPV sequence. (iii) SKP, corresponding to 400SKP402 of the translated sequence. In IAPV this latter sequence resides within the 398GWSKP402 motif. This motif, G[F/W]SKP, has been identified as a CP4/CP2 cleavage site, approximately residing between residues 300 and 400 in the structural polyproteins of ALPV, RhPV, DCV, CrPV, BQCV, PSIV, TrV, ABPV and Taura syndrome virus (TSV) (summarized in van Munster et al., 2002) and in KBV. (iv) SVP, corresponding to 427SVP429 of the translated sequence. (v) INIGNK, identical to the translated IAPV sequence (701INIGNK706) and similar to the INLSNK cleavage site in KBV (GenBank accession no. NC_004807). In addition, in silico analysis identified two strong potential 3C-pro cleavage sites: 208YASFQEAYD216 and 270DIVKQGASR278. Analysis of cleavage sites and comparison to the capsid-protein profile indicated that alternate protein processing and sequential processing may have taken place. In this scenario, the polyprotein is first cleaved at the exposed sites, skipping other cleavage sites. The cleaved products then present new accessible sites and are further cleaved at those newly exposed sites (discussed further on). The minor bands probably represent remnants of the primary processed peptides which were then further processed at a later stage.
|
. Analysis of only IAPV, KBV and ABPV, as in Fig. 2(b), reiterated the close relationship among the latter three viruses (data not shown).
|
shows the phylogenetic relationship among dicistroviruses, based on the amino acid sequence of the RdRp domain of the non-structural polyprotein. Similar relationships were obtained with amino acid and nucleotide sequences of other parts of the genomes. While most of the ORFs' sequences are highly homologous to KBV and ABPV, the homology of IAPV UTRs to those of KBV and ABPV is weak (Supplementary Table S2, available with the online version of this paper). However, IAPV could be easily discerned from its closest relatives, KBV and ABPV, by differential PCR assay, even when RNAs of two of these viruses were present in the same RNA preparation (Supplementary Figure S1, available with the online version of this paper). Differential PCR primers distinguished all three viruses (Supplementary Figure S1). Bees can harbour more than one virus, and the ability to distinguish IAPV from the other viruses in mixed infections indicated that IAPV is a unique viral entity. The structural polyprotein of IAPV is most related to KBV and ABPV, yet IAPV did not react with antibodies against KBV, ABPV, DWV, BQCV, slow paralysis virus (SPV), SBV, cloudy wing virus (CWV) or CBPV. In addition, the homology of IAPV UTRs to its closest relatives is very weak (Supplementary Table S2, available with the online version of this paper). Another indication that IAPV varies from other dicistroviruses is its different pattern of capsid proteins, suggesting different cleavage sites in these highly homologous polyproteins.
IAPV-related RNA fragments resembling DI-RNA
IAPV RNA was extracted from RNase-treated, CsCl-purified virions. All viral preparations were purified from subsequent passages of the original purified IAPV isolate. Electrophoretic analysis indicated that various viral preparations carry shorter than full-length intra-virion RNAs alongside the full-length viral genome (Fig. 1). Northern blots (Fig. 5) and sequence analyses indicated that the encapsidated RNAs carried IAPV sequences, albeit fused to viral and non-viral sequences. It appears that some DI-like RNAs carried signals enabling their encapsidation. This agrees with similar previous findings, and explains the appearance of a multitude of viral-related RNA species in IAPV-infected tissues (Fig. 2 in Maori et al., 2007). Apparently, recombination events take place quite frequently, but only a small proportion of the generated DI-like RNAs are capable of encapsidation. The composition of DI-like RNAs in any given virion depends on what recombination events have taken place in the infected cells prior to virus assembly.
|
). Figs 1 and 5 indicate the presence, within the virions, of RNAs carrying IAPV sequences which are smaller than full-length. Looking for recombinants, we carried out Northern blot analyses with RNA extracted from two different viral preparations. Two membranes, each carrying the same RNAs, were prepared: one was reacted with a probe corresponding to the 5' IAPV sequence and the other with that of the 3' end. Fig. 5 indicates that besides the full-length RNA, shorter bands reacted with one or the other of these probes. Some reacted with both probes, a priori indicating middle-sequence deletions, and some reacted with only one of the probes. The Northern blot patterns of the two viral preparations were similar, but not identical, indicating ongoing recombination during infection.
Only a single IAPV fragment has been found integrated into the bee genome (Maori et al., 2007), and we therefore tentatively assumed that it carries sequences serving as ‘hot spots’ for recombination. We amplified RNA from virions (using primers flanking the ends of the integrated IAPV segment) and sequenced them. In addition, to identify DI-like RNAs in which the middle portion of the IAPV genome had been deleted, RT-PCR was carried out with primers corresponding to the 5' and 3' ends of IAPV RNA. Sequence analysis revealed four types of DI RNAs. (i) Deleted DIs: DI-like RNAs in which part of the middle section of the viral RNA has been deleted. An example of a deleted DI is shown in Fig. 6(c), its sequence is shown in Supplementary Figure S2(a), available with the online version of this paper. Positioning of this deleted DI sequence within the IAPV genome reveals that it is flanked by two inverted repeats, and it is predicted to fold as shown in Fig. 6(b). The middle portion of the IAPV genome has been looped-out, and the possibility of replicase crossing from one proximal IAPV sequence to the opposite proximal sequence is strongly supported by this model. (ii) Inverted repeats of segments of the IAPV genome: a segment of IAPV RNA folds on an (almost) inverted repeat of itself (Fig. 6d, e), the sequence is shown in Supplementary Figure S2(b). (iii) A sequence of IAPV and an inverted sequence which is most highly homologous to KBV, indicating inter-viral recombination. An example of the organization and predicted folding pattern of such a sequence are shown in Fig. 6(f, g), the sequence is shown in Supplementary Figure S2(c). (iv) IAPV-derived DI RNAs carrying non-viral (host?) sequences (an example is shown in Fig. 6f). A case in which a non-viral sequence originates from the host is demonstrated in Maori et al. (2007).
|
For qRT-PCR analysis, a calibration curve was first drawn for TMV RNA. The relative amount of one prominent deleted DI-like RNA (the one depicted in Fig. 6) in this particular viral preparation was determined. RNA isolated from the viral preparation (1008 ng) was mixed with TMV RNA (112 ng), such that TMV RNA constituted 10 % of the total and served as an internal control. Portions of this mixture were taken for qRT-PCR (the equivalent of 123 ng RNA per reaction). IAPV RNA amplification was carried out with primer pairs specific to the 5' end of IAPV, and to the 3' end of the viral RNA, to ensure that the quantitative determination was of the full-length IAPV RNA and not of the DI-like RNA. As shown in Fig. 7, IAPV amplification products were first observed at cycle 18, those of TMV RNA at cycle 21, and those of the DI-like RNA at cycle 24. Calibration against TMV RNA indicated that the relative amount of IAPV RNA in the viral RNA preparation was 88.9 % and that of the tested DI-like RNA, 0.99 %. The remaining 10.11 % probably represents other DI-like RNAs. Indeed, the weak bands of Fig. 7(c) were isolated and sequenced and found to be forms of ‘deleted DIs’ of IAPV demonstrating strong ‘hot spots’ between bases 9100 and 9300 of IAPV.
|
|
DISCUSSION |
|---|
|
TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
|---|
A pronounced protein of approximately 30 kDa (not detected in the virions) appears among the bee-extracted proteins. It may represent a modified capsid protein that is unable to encapsidate and probably plays some role in virus infection, or virus–host interaction. Indeed, the N-terminal part of the IAPV capsid protein precursor carries two strong SUMO signals (127LKAG130 and 273VKQG276). SUMO proteins affect protein modification, cleavage and folding (for example, Ulrich, 2005; Bossis & Melchior, 2006), and it is conceivable that SUMO-bound proteins cannot encapsidate.
We were previously able to isolate and sequence DI-like RNAs from virions. We also demonstrated that RNAs, shorter than the full-length IAPV, are present in IAPV-infected tissues (Maori et al., 2007). Here we demonstrate the abundant accumulation of shorter-than-full-length RNAs within virions. The shorter RNAs appear to be recognized by the viral replicase and replicate efficiently, and some carry assembly recognition signals as well, and are therefore found encapsidated within virions. Several of the DI-like RNAs carry sequences of the 5' and 3' viral ends, but the middle sequences are deleted. The viral genome carries inverted repeats flanking the joining point of the two segments of the deleted DI-like RNA, causing looping out of the middle sequences and enabling the replicase to cross over from one segment to a distant segment of the same RNA. Several other DI-like RNAs are comprised of a segment of a viral sequence in its sense orientation followed by a short spacer and the almost identical viral sequence in an antisense orientation, suggesting template switching of the replicase from a viral-oriented RNA to a nascent complementary RNA. Viral recombinants are known mostly between segments of the same virus, but recombination among related viruses has been previously recorded (Nagy & Simon, 1997). Here, we demonstrate a similar case of an IAPV–KBV ‘hybrid’, but in opposite orientations. Sense:antisense DI-like RNAs fold into a largely double-stranded RNA structure (Fig. 6).
Although RNA recombination requires certain structural features, by and large, it is a random occurrence. Therefore, the amount and characteristics of encapsidated DI-like RNAs may change from one cycle of infection to the next, and viral populations may differ from each other in this respect. We showed different profiles in different viral preparations (Fig. 5). Therefore, the reported quantitative values apply to that particular viral preparation, and may differ when other preparations are tested.
In many instances, bee viruses are found as non-apparent infections in their host. This may result from competition between the viral RNA and the abundant DI-like RNAs, but also from the abundance of double-stranded RNA structures carrying viral sequences. In the latter case, the balance between host factors silencing viral sequences and the virus-induced silencing suppressors may shift in favour of viral silencing. Another postulated consequence inferred from the various types of DI-like RNAs is the modification of proteins resulting from deletions, engendering deleted or frame-shifted proteins. Thus, RNA recombination may elicit protein divergence with obvious evolutionary impact. Furthermore, a reciprocal exchange between host DNA and viral RNA (or a DNA version of a recombinant viral RNA) has been demonstrated (Tanne & Sela, 2005; Maori et al., 2007). Therefore, RNA recombination may engender divergence in host genes, and the evolution of both virus and host may be interrelated and linked to the very same eliciting process.
|
ACKNOWLEDGEMENTS |
|---|
|
REFERENCES |
|---|
|
TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
|---|
Anderson, D. L. & Gibbs, A. J. (1988). Inapparent virus-infections and their interactions in pupae of the honey bee (Apis mellifera Linnaeus) in Australia. J Gen Virol 69, 1617–1625.
Ball, B. V. & Bailey, L. (1997). Viruses. In: Honey Bee Pests, Predators and Diseases, 3rd edn, pp. 11–31. Edited by R. A. Morse & K. Flottum. Medina, OH: A. I. Root.
Bossis, G. & Melchior, F. (2006). SUMO: regulating the regulator. Mol Cell 21, 349–357.[CrossRef][Medline]
Crochu, S., Cook, S., Attoui, H., Charrel, R. N., de Chesse, R., Belhoucet, M., Lemasson, J.-J., de Micco, P. & de Lamballerie, X. (2004). Sequences of flavivirus-related RNA viruses persist in DNA form integrated in the genome of Aedes spp. mosquitoes. J Gen Virol 85, 1971–1980.
Czibener, C., La Torre, J. L., Muscio, O. A., Ugalde, R. A. & Scodeller, E. A. (2000). Nucleotide sequence analysis of Triatoma virus shows that it is a member of a novel group of insect RNA viruses. J Gen Virol 81, 1149–1154.
de Miranda, J. R., Drebot, M., Tyler, S., Shen, M., Cameron, C. E., Stoltz, D. B. & Camazine, S. M. (2004). Complete nucleotide sequence of Kashmir bee virus and comparison with acute bee paralysis virus. J Gen Virol 85, 2263–2270.
Domier, L. L. & McCoppin, N. K. (2003). In vivo activity of Rhopalosiphum padi virus internal ribosome entry sites. J Gen Virol 84, 415–419.
Elus, J. D. & Munn, P. A. (2005). The worldwide health status of honey bees. Bee World 86, 88–101.
Evans, J. D. & Hung, A. C. (2000). Molecular phylogenetics and the classification of honey bee viruses. Arch Virol 145, 2015–2026.[CrossRef][Medline]
Fujiyuki, T., Takeuchi, H., Ono, M., Ohka, S., Sasaki, T., Nomoto, A. & Kubo, T. (2004). Novel insect picorna-like virus identified in the brains of aggressive worker honeybees. J Virol 78, 1093–1100.
Ghosh, R. C., Ball, B. V., Willcocks, M. M. & Carter, M. J. (1999). The nucleotide sequence of sacbrood virus of the honey bee: an insect picorna-like virus. J Gen Virol 80, 1541–1549.[Abstract]
Govan, V. A., Leat, N., Allsopp, M. & Davison, S. (2000). Analysis of the complete genome sequence of acute bee paralysis virus shows that it belongs to the novel group of insect-infecting RNA viruses. Virology 277, 457–463.[CrossRef][Medline]
Hansen, J. L., Long, A. M. & Schultz, S. C. (1997). Structure of the RNA-dependent RNA polymerase of poliovirus. Structure 5, 1109–1122.[Medline]
Hunnicutt, L. E., Hunter, W. B., Cave, R. D., Powell, C. A. & Mozoruk, J. J. (2006). Genome sequence and molecular characterization of Homalodisca coagulata virus-1, a novel virus discovered in the glassy-winged sharpshooter (Hemiptera; Cicadellidae). Virology 350, 67–78.[CrossRef][Medline]
Johnson, K. N. & Christian, P. D. (1998). The novel genome organization of the insect picorna-like virus Drosophila C virus suggests this virus belongs to a previously undescribed virus family. J Gen Virol 79, 191–203.[Abstract]
Koonin, E. V. & Dolja, V. V. (1993). Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit Rev Biochem Mol Biol 28, 375–430.[Medline]
Lanzi, G., de Miranda, J. R., Boniotti, M. B., Cameron, C. E., Lavazza, A., Capucci, L., Camazine, S. M. & Rossi, C. (2006). Molecular and biological characterization of deformed wing virus of honeybees (Apis mellifera L.). J Virol 80, 4998–5009.
Leat, N., Ball, B., Govan, V. & Davison, S. (2000). Analysis of the complete genome sequence of black queen-cell virus, a picorna-like virus of honey bees. J Gen Virol 81, 2111–2119.
Love, R. A., Maegley, K. A., Yu, X., Ferre, R. A., Lingardo, L. K., Diehl, W., Parge, H. E., Dragovich, P. S. & Fuhrman, S. A. (2004). The crystal structure of the RNA-dependent RNA polymerase from human rhinovirus: a dual function target for common cold antiviral therapy. Structure 12, 1533–1544.[Medline]
Mansi, W. (1958). Slide gel diffusion precipitation test. Nature 181, 1289[Medline]
Maori, E., Tanne, E. & Sela, I. (2007). Reciprocal sequence exchange between non-retro viruses and hosts leading to the appearance of new host phenotypes. Virology 362, 342–349.[CrossRef][Medline]
Mayo, M. A. (2002). A summary of taxonomic changes recently approved by ICTV. Arch Virol 147, 1655–1656.[CrossRef][Medline]
Moon, J. S., Domier, L. L., McCoppin, N. K., D'Arcy, C. J. & Jin, H. (1998). Nucleotide sequence analysis shows that Rhopalosiphum padi virus is a member of a novel group of insect-infecting RNA viruses. Virology 243, 54–65.[CrossRef][Medline]
Nagy, P. D. & Simon, A. E. (1997). New insights into the mechanisms of RNA recombination. Virology 235, 1–9.[CrossRef][Medline]
Nakashima, N., Sasaki, J. & Toriyama, S. (1999). Determining the nucleotide sequence and capsid-coding region of Himetobi P virus: a member of a novel group of RNA viruses that infect insects. Arch Virol 144, 2051–2058.[CrossRef][Medline]
Nishiyama, T., Yamamoto, H., Shibuya, N., Hatakeyama, Y., Hachimori, A., Uchiumi, T. & Nakashima, N. (2003). Structural elements in the internal ribosome entry site of Plautia stali intestine virus responsible for binding with ribosomes. Nucleic Acids Res 31, 2434–2442.
Ongus, J. R., Peters, D., Bonmatin, J.-M., Bengsch, E., Viak, J. M. & van Oers, M. M. (2004). Complete sequence of a picorna-like virus of the genus Iflavirus replicating in the mite Varroa destructor. J Gen Virol 85, 3747–3755.
Sambrook, J. & Russell, D. W. (2001). Molecular Cloning, a Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
Sasaki, J., Nakashima, N., Saito, H. & Noda, H. (1998). An insect picorna-like virus, Plautia stali intestine virus, has genes of capsid proteins in the 3' part of the genome. Virology 244, 50–58.[CrossRef][Medline]
Tanne, E. & Sela, I. (2005). Occurrence of a DNA sequence of anon-retro RNA virus in the host plant genome and its expression: evidence for recombination between viral and host RNAs. Virology 332, 614–622.[CrossRef][Medline]
Ulrich, H. D. (2005). Mutual interactions between the SUMO and ubiquitin systems: a plea of no contest. Trends Cell Biol 15, 525–532.[CrossRef][Medline]
Valles, S. M., Strong, C. A., Dang, P. M., Hunter, W. B., Pereira, R. M., Oi, D. H., Shapiro, A. M. & Williams, D. F. (2004). A picorna-like virus from the red imported fire ant, Solenopsis invicta: initial discovery, genome sequence, and characterization. Virology 328, 151–157.[CrossRef][Medline]
van Munster, M., Dullemans, A. M., Verbeek, M., van den Heuvel, J. F. J. M., Clerivet, A. & van der Wilk, F. (2002). Sequence analysis and genomic organization of aphid lethal paralysis virus: a new member of the family Dicistroviridae. J Gen Virol 83, 3131–3138.
Walker, J. E., Saraste, M., Runswick, M. J. & Gay, N. J. (1982). Distantly related sequences in the 
-subunits and 
-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 1, 945–951.[Medline]
Wilson, J. E., Powel, M. J., Hoover, S. E. & Sarnow, P. (2000). Naturally occurring dicistronic cricket paralysis virus RNA is regulated by two internal ribosome entry sites. Mol Cell Biol 20, 4990–4999.
Received 4 July 2007;
accepted 24 July 2007.
This article has been cited by other articles:
|
|
 |
|
  R. M. Johnson, J. D. Evans, G. E. Robinson, and M. R. Berenbaum Changes in transcript abundance relating to colony collapse disorder in honey bees (Apis mellifera) PNAS, September 1, 2009; 106(35): 14790 - 14795. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Palacios, J. Hui, P. L. Quan, A. Kalkstein, K. S. Honkavuori, A. V. Bussetti, S. Conlan, J. Evans, Y. P. Chen, D. vanEngelsdorp, et al. Genetic Analysis of Israel Acute Paralysis Virus: Distinct Clusters Are Circulating in the United States J. Virol., July 1, 2008; 82(13): 6209 - 6217. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| INT J SYST EVOL MICROBIOL | MICROBIOLOGY | J GEN VIROL |
| J MED MICROBIOL | ALL SGM JOURNALS | |
