Genome sequences were determined for a novel RNA virus, Leptomonas seymouri Narna-like virus 1 (LepseyNLV1). A 2.9-kb segment encodes an RNA-dependent RNA polymerase (RdRp), while a smaller 1.5-kb segment showed no database search matches. This is the first report of bisegmented Narnaviridae from insect trypanosomatids

Akopyants, Natalia S

Beverley, Stephen M

Dobson, Deborah E

Lye, Lon-Fye

PubMed

ABSTRACT
          
            Genome sequences were determined for a novel RNA virus,
            Leptomonas seymouri
            Narna-like virus 1 (LepseyNLV1). A 2.9-kb segment encodes an RNA-dependent RNA polymerase (RdRp), while a smaller 1.5-kb segment showed no database search matches. This is the first report of bisegmented
            Narnaviridae
            from insect trypanosomatids.
          </jats:p

Lon-Fye Lye

Natalia S. Akopyants

Deborah E. Dobson

Stephen M. Beverley

Crossref

Genome Announcements

A
            <i>Narnavirus</i>
            -Like Element from the Trypanosomatid Protozoan Parasite
            <i>Leptomonas seymouri</i>

Digital Commons@Becker

Washington University School of MedicineDigital Commons@BeckerOpen Access Publications2016A narnavirus-like element from the trypanosomatidprotozoan parasite Leptomonas seymouriLon-Fye LyeWashington University School of Medicine in St. LouisNatalia S. AkopyantsWashington University School of Medicine in St. LouisDeborah E. DobsonWashington University School of Medicine in St. LouisStephen M. BeverleyWashington University School of Medicine in St. LouisFollow this and additional works at: http://digitalcommons.wustl.edu/open_access_pubsThis Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in OpenAccess Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact engeszer@wustl.edu.Recommended CitationLye, Lon-Fye; Akopyants, Natalia S.; Dobson, Deborah E.; and Beverley, Stephen M., ,"A narnavirus-like element from thetrypanosomatid protozoan parasite Leptomonas seymouri." Genome Announcements.4,4. e00713-16. (2016).http://digitalcommons.wustl.edu/open_access_pubs/5284A Narnavirus-Like Element from the Trypanosomatid ProtozoanParasite Leptomonas seymouriLon-Fye Lye, Natalia S. Akopyants, Deborah E. Dobson, Stephen M. BeverleyDepartment of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USAGenome sequences were determined for a novel RNA virus, Leptomonas seymouriNarna-like virus 1 (LepseyNLV1). A 2.9-kbsegment encodes an RNA-dependent RNA polymerase (RdRp), while a smaller 1.5-kb segment showed no database searchmatches. This is the first report of bisegmentedNarnaviridae from insect trypanosomatids.Received 29 May 2016 Accepted 15 June 2016 Published 4 August 2016Citation Lye L-F, Akopyants NS, Dobson DE, Beverley SM. 2016. A Narnavirus-like element from the trypanosomatid protozoan parasite Leptomonas seymouri. GenomeAnnounc 4(4):e00713-16. doi:10.1128/genomeA.00713-16.Copyright © 2016 Lye et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Address correspondence to Stephen M. Beverley, beverley@wusm.wustl.edu.From in silico screens of metatranscriptomic datasets for proto-zoan viruses, we encountered within archives of Leptomonasseymouri (order Kinetoplastida, Excavata eukaryotic supergroup)a hit to members of the Narnaviridae (1–3), which had not beenpreviously identified in trypanosomatid protozoa. From a total of300 million reads, 0.22% were assembled into a contig of 2,914 nu-cleotides (nt), predicting a 932-amino acid (aa) protein that boremotifs typical of narnaviral RNA-dependent RNA polymerase(RdRps) (1–3). As this was absent from previous assemblies (4),we isolated RNA from the L. seymouri strain ATCC 30220 usingTRIzol reagent (Thermo Fisher), followed by digestion withDNase I (Thermo Fisher), purification with RCC-25 kit (ZymoResearch), and digestion by S1 nuclease (Thermo Fisher).Two cytoplasmic double-stranded RNAs (dsRNAs) of ~3 and~1.5 kb were visualized after agarose gel electrophoresis (4, 5),which were eluted and used for generation of cDNA. Reversetranscriptase-PCR (RT-PCR) tests showed that the 3-kb band cor-responded to the 2,914-nt RdRp contig. cDNA for the 1.5-kb bandwas inserted into bacterial vectors and sequenced (6), identifying a1,455-nt contig in the metatranscriptomic assembly, which wasconfirmed by RT-PCR amplification. Blast-based searches did notyield any matches in the sequence databases tested.Provisionally, we term these elements the L. seymouri Narna-like virus 1 (LepseyNLV1) L and S segments; however, their func-tional association remains to be proven. Some data suggest thatboth segments are unstable during culture, as sensitive RT-PCRtests of this strain acquired independently from another labora-tory did not reveal them (the authenticity of this strain was con-firmed by sequence of two nuclear genes, GAPDH and PTR1). Asin other multisegmented RNA viruses, loss of the RdRp would beexpected to result in the loss of the remaining segments.Viruses in the familyNarnaviridae (“naked RNA”) lack capsidsor envelopes and do not form infectious viral particles. They re-side in the cytosol as an RNA-protein complex containing onesingle-stranded RNA segment of about 3 kb, with a single openreading frame (ORF) encoding the RdRp (1–3). Two genera arerecognized; unlike cytosolic narnaviruses, mitoviruses are foundin the mitochondrion of fungi and translated using the mitochon-drial genetic code (2). Phylogenetic comparisons of the L segmentRdRp with otherNarnaviridae place it firmly withinNarnavirus asa new species, since the overall amino acid divergence exceeds80%. Interestingly, the trisegmented Ourmiavirus spp. show acloser relationship toNarnavirus than toMitovirus (2, 7), suggest-ing that the bisegmented LepseyNLV1 exhibits some characteris-tics intermediate between Narnavirus and Ourmiavirus.Leptomonas is a monoxenous kinetoplastid parasite of insects,and related parasites are widespread in insects around the world(8). Interestingly, L. seymouri has been repeatedly isolated frompatients infected by Leishmania donovani (9), although in vitro, itis unable to survive in mammalian macrophages (4, 10). Becauseviruses within the related protozoan Leishmania guyanensis havebeen associated with elevated pathogenicity in animal models(11), LepseyNLV1 potentially contributes to the pathogenicity ofLeptomonas-Leishmania coinfections (9).Nucleotide sequence accession numbers. The genome se-quences of the LepseyNLV1 L and S segments have been depositedin GenBank under accession numbers KU935604 and KU935605.ACKNOWLEDGMENTSWe thank members of our laboratory and Nicolas Fasel for discussions, aswell as colleagues who provided Leptomonas strains that had been cul-tured independently.This work was supported by grants NIH AID R56 AI099364 and RO1-AI29646 to S.M.B.FUNDING INFORMATIONThis work, including the efforts of Lon-Fye Lye, Natalia S.Akopyants, Deborah E. Dobson, and Stephen M. Beverley, wasfunded by HHS | National Institutes of Health (NIH) (R56 AI099364and R01 AI 29646).REFERENCES1. Wickner RB, Fujimura T, Esteban R. 2013. Viruses and prions of Sac-charomyces cerevisiae. Adv Virus Res 86:1–36. http://dx.doi.org/10.1016/B978-0-12-394315-6.00001-5.2. Hillman BI, Cai G. 2013. The family Narnaviridae: simplest of RNAviruses. Adv Virus Res 86:149 –176. http://dx.doi.org/10.1016/B978-0-12-394315-6.00006-4.crossmarkGenome AnnouncementsJuly/August 2016 Volume 4 Issue 4 e00713-16 genomea.asm.org 1 on September 21, 2016 by Washington University in St. Louishttp://genomea.asm.org/Downloaded from 3. Hillman B, Esteban R. 2012. Family Narnaviridae, p 1055–1060. In KingA, Adams M, Carstens E, Lefkowitz E (ed), In virus taxonomy: classifica-tion and nomenclature of viruses, 9th ed. Elsevier, San Diego, CA.4. Kraeva N, Butenko A, Hlaváová J, Kostygov A, Myškova J, GrybchukD, Leštinová T, Votýpka J, Volf P, Opperdoes F, Flegontov P, Lukeš J,Yurchenko V. 2015. Leptomonas seymouri: adaptations to the dixenouslife cycle analyzed by genome sequencing, transcriptome profiling andco-infection with Leishmania donovani. PLoS Pathog 11:e1005127. http://dx.doi.org/10.1371/journal.ppat.1005127.5. Beiting DP, Peixoto L, Akopyants NS, Beverley SM, Wherry EJ,Christian DA, Hunter CA, Brodsky IE, Roos DS. 2014. Differentialinduction of TLR3-dependent innate immune signaling by closely relatedparasite species. PLoS One 9:e88398. http://dx.doi.org/10.1371/journal.pone.0088398.6. Fazeli CF, Habili N, Rezaian MA. 1998. Efficient cloning of cDNA fromgrapevine leafroll-associated virus 4 and demonstration of probe specific-ity by the viral antibody. J Virol Methods 70:201–211. http://dx.doi.org/10.1016/S0166-0934(97)00193-6.7. Rastgou M, Habibi MK, Izadpanah K, Masenga V, Milne RG, Wolf YI,Koonin EV, Turina M. 2009. Molecular characterization of the plantvirus genus Ourmiavirus and evidence of inter-kingdom reassortment ofviral genome segments as its possible route of origin. J Gen Virol 90:2525–2535. http://dx.doi.org/10.1099/vir.0.013086-0.8. Simpson AG, Stevens JR, Lukes J. 2006. The evolution and diversity ofkinetoplastid flagellates. Trends Parasitol 22:168 –174. http://dx.doi.org/10.1016/j.pt.2006.02.006.9. Ghosh S, Banerjee P, Sarkar A, Datta S, Chatterjee M. 2012. Coin-fection of Leptomonas seymouri and Leishmania donovani in Indianleishmaniasis. J Clin Microbiol 50:2774 –2778. http://dx.doi.org/10.1128/JCM.00966-12.10. Ahuja K, Arora G, Khare P, Selvapandiyan A. 2015. Selective eliminationof Leptomonas from the in vitro co-culture with Leishmania. Parasitol Int64:1–5. http://dx.doi.org/10.1016/j.parint.2015.01.003.11. Ives A, Ronet C, Prevel F, Ruzzante G, Fuertes-Marraco S, Schutz F,Zangger H, Revaz-Breton M, Lye LF, Hickerson SM, Beverley SM,Acha-Orbea H, Launois P, Fasel N, Masina S. 2011. Leishmania RNAvirus controls the severity of mucocutaneous leishmaniasis. Science 331:775–778. http://dx.doi.org/10.1126/science.1199326.Lye et al.Genome Announcements2 genomea.asm.org July/August 2016 Volume 4 Issue 4 e00713-16 on September 21, 2016 by Washington University in St. Louishttp://genomea.asm.org/Downloaded from 

A narnavirus-like element from the trypanosomatid protozoan parasite Leptomonas seymouri

http://digitalcommons.wustl.edu/cgi/viewcontent.cgi?article=6288&context=open_access_pubs

A narnavirus-like element from the trypanosomatid protozoan parasite Leptomonas seymouri

Abstract

Similar works

Full text

Available Versions

Crossref

Digital Commons@Becker