Mutational Pressure in Zika Virus: Local ADAR-Editing Areas Associated with Pauses in Translation and Replication

Overview

Journal Front Cell Infect Microbiol

Specialties Cell Biology
Infectious Diseases
Microbiology

Date 2017 Mar 10

PMID 28275585

Citations 22

Authors

Vladislav V Khrustalev

Tatyana A Khrustaleva

Nitin Sharma

Rajanish Giri

Affiliations

Soon will be listed here.

Abstract

Zika virus (ZIKV) spread led to the recent medical health emergency of international concern. Understanding the variations in virus system is of utmost need. Using available complete sequences of ZIKV we estimated directions of mutational pressure along the length of consensus sequences of three lineages of the virus. Results showed that guanine usage is growing in ZIKV RNA plus strand due to adenine to guanine transitions, while adenine usage is growing due to cytosine to adenine transversions. Especially high levels of guanine have been found in two-fold degenerated sites of certain areas of RNA plus strand with high amount of secondary structure. The usage of cytosine in two-fold degenerated sites shows direct dependence on the amount of secondary structure in 52% (consensus sequence of East African ZIKV lineage)-32% (consensus sequence of epidemic strains) of the length of RNA minus strand. These facts are the evidences of ADAR-editing of both strands of ZIKV genome during pauses in replication. RNA plus strand can also be edited by ADAR during pauses in translation caused by the appearance of groups of rare codons. According to our results, RNA minus strand of epidemic ZIKV strain has lower number of points in which polymerase can be stalled (allowing ADAR-editing) compared to other strains. The data on preferable directions of mutational pressure in epidemic ZIKV strain is useful for future vaccine development and understanding the evolution of new strains.

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References

Thurner C, Witwer C, Hofacker I, Stadler P . Conserved RNA secondary structures in Flaviviridae genomes. J Gen Virol. 2004; 85(Pt 5):1113-1124. DOI: 10.1099/vir.0.19462-0. View

Cao-Lormeau V, Blake A, Mons S, Lastere S, Roche C, Vanhomwegen J . Guillain-Barré Syndrome outbreak associated with Zika virus infection in French Polynesia: a case-control study. Lancet. 2016; 387(10027):1531-1539. PMC: 5444521. DOI: 10.1016/S0140-6736(16)00562-6. View

Sueoka N . Directional mutation pressure, mutator mutations, and dynamics of molecular evolution. J Mol Evol. 1993; 37(2):137-53. DOI: 10.1007/BF02407349. View

Nakamura Y, Gojobori T, Ikemura T . Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res. 1999; 28(1):292. PMC: 102460. DOI: 10.1093/nar/28.1.292. View

van Hemert F, Berkhout B . Nucleotide composition of the Zika virus RNA genome and its codon usage. Virol J. 2016; 13:95. PMC: 4898363. DOI: 10.1186/s12985-016-0551-1. View

Lehmann K, Bass B . Double-stranded RNA adenosine deaminases ADAR1 and ADAR2 have overlapping specificities. Biochemistry. 2000; 39(42):12875-84. DOI: 10.1021/bi001383g. View

Kikin O, DAntonio L, Bagga P . QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Res. 2006; 34(Web Server issue):W676-82. PMC: 1538864. DOI: 10.1093/nar/gkl253. View

Cuevas J, Combe M, Torres-Puente M, Garijo R, Guix S, Buesa J . Human norovirus hyper-mutation revealed by ultra-deep sequencing. Infect Genet Evol. 2016; 41:233-239. PMC: 7172324. DOI: 10.1016/j.meegid.2016.04.017. View

Umareddy I, Tang K, Vasudevan S, Devi S, Hibberd M, Gu F . Dengue virus regulates type I interferon signalling in a strain-dependent manner in human cell lines. J Gen Virol. 2008; 89(Pt 12):3052-3062. DOI: 10.1099/vir.0.2008/001594-0. View

10.

Heymann D, Hodgson A, Sall A, Freedman D, Staples J, Althabe F . Zika virus and microcephaly: why is this situation a PHEIC?. Lancet. 2016; 387(10020):719-21. PMC: 7134564. DOI: 10.1016/S0140-6736(16)00320-2. View

11.

Wikan N, Smith D . Zika virus: history of a newly emerging arbovirus. Lancet Infect Dis. 2016; 16(7):e119-e126. DOI: 10.1016/S1473-3099(16)30010-X. View

12.

Cristina J, Fajardo A, Sonora M, Moratorio G, Musto H . A detailed comparative analysis of codon usage bias in Zika virus. Virus Res. 2016; 223:147-52. DOI: 10.1016/j.virusres.2016.06.022. View

13.

Giri R, Kumar D, Sharma N, Uversky V . Intrinsically Disordered Side of the Zika Virus Proteome. Front Cell Infect Microbiol. 2016; 6:144. PMC: 5095677. DOI: 10.3389/fcimb.2016.00144. View

14.

Guo F, Yuan J . Codon usages of genes on chromosome, and surprisingly, genes in plasmid are primarily affected by strand-specific mutational biases in Lawsonia intracellularis. DNA Res. 2009; 16(2):91-104. PMC: 2671203. DOI: 10.1093/dnares/dsp001. View

15.

Angeletti S, Lo Presti A, Giovanetti M, Grifoni A, Amicosante M, Ciotti M . Phylogenesys and homology modeling in Zika virus epidemic: food for thought. Pathog Glob Health. 2016; 110(7-8):269-274. PMC: 5189860. DOI: 10.1080/20477724.2016.1235337. View

16.

Marintchev A . Roles of helicases in translation initiation: a mechanistic view. Biochim Biophys Acta. 2013; 1829(8):799-809. PMC: 3640703. DOI: 10.1016/j.bbagrm.2013.01.005. View

17.

Tomaselli S, Galeano F, Locatelli F, Gallo A . ADARs and the Balance Game between Virus Infection and Innate Immune Cell Response. Curr Issues Mol Biol. 2014; 17:37-51. View

18.

Khrustalev V, Barkovsky E, Khrustaleva T, Lelevich S . Intragenic isochores (intrachores) in the platelet phosphofructokinase gene of Passeriform birds. Gene. 2014; 546(1):16-24. DOI: 10.1016/j.gene.2014.05.045. View

19.

Jaramillo M, Dever T, Merrick W, Sonenberg N . RNA unwinding in translation: assembly of helicase complex intermediates comprising eukaryotic initiation factors eIF-4F and eIF-4B. Mol Cell Biol. 1991; 11(12):5992-7. PMC: 361763. DOI: 10.1128/mcb.11.12.5992-5997.1991. View

20.

Jenkins G, Pagel M, Gould E, Zanotto P, Holmes E . Evolution of base composition and codon usage bias in the genus Flavivirus. J Mol Evol. 2001; 52(4):383-90. DOI: 10.1007/s002390010168. View