Biopolym. Cell. 2016; 32(2):131-139.
Viruses and Cell
Extreme evolutionary stability of conserved non-protein coding element of baculovirus genome
1Makarenko V. E., 1Kikhno I. M., 1Kashuba V. I.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

Aim. To estimate a level of evolutionary stability of the baculovirus conserved non protein-coding element (CNE) playing an essential role in baculovirus pathogenesis. Methods. NCBI-BLAST was applied to identify the orthologous sequences in genomes of 50 alphabaculoviruses. The orthologous sequences were aligned by using ClustalW software. Alistat tool was applied to obtain the pairwise percent identity ( %ID) matrix data. Results. An average pairwise ID value (73 %) calculated for the 1225-member sample was shown to be comparable with those of coding parts of the most conserved baculovirus genes polh and pif2 as well as with those of the polh and p18 promoter regions which are the most conserved representatives of a small group of the evolutionary stable promoter regions of the alphabaculovirus late genes. Conclusion. CNE is one of the most conserved elements of the alphabaculovirus genome.
Keywords: Baculovirus, conserved non-coding element

References

[1] Elgar G. Pan-vertebrate conserved non-coding sequences associated with developmental regulation. Brief Funct Genomic Proteomic. 2009;8(4):256-65.
[2] Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK, Vavouri T, Smith SF, North P, Callaway H, Kelly K, Walter K, Abnizova I, Gilks W, Edwards YJ, Cooke JE, Elgar G. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 2005;3(1):e7.
[3] Harmston N, Baresic A, Lenhard B. The mystery of extreme non-coding conservation. Philos Trans R Soc Lond B Biol Sci. 2013;368(1632):20130021.
[4] Dubchak I, Brudno M, Loots GG, Pachter L, Mayor C, Rubin EM, Frazer KA. Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res. 2000;10(9):1304-6.
[5] Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. Ultraconserved elements in the human genome. Science. 2004;304(5675):1321-5.
[6] Clarke SL, VanderMeer JE, Wenger AM, Schaar BT, Ahituv N, Bejerano G. Human developmental enhancers conserved between deuterostomes and protostomes. PLoS Genet. 2012;8(8):e1002852.
[7] Kikhno I. Identification of a conserved non-protein-coding genomic element that plays an essential role in Alphabaculovirus pathogenesis. PLoS One. 2014;9(4):e95322.
[8] Chen YR, Zhong S, Fei Z, Hashimoto Y, Xiang JZ, Zhang S, Blissard GW. The transcriptome of the baculovirus Autographa californica multiple nucleopolyhedrovirus in Trichoplusia ni cells. J Virol. 2013;87(11):6391-405.
[9] Krappa R, Behn-Krappa A, Jahnel F, Doerfler W, Knebel-Mörsdorf D. Differential factor binding at the promoter of early baculovirus gene PE38 during viral infection: GATA motif is recognized by an insect protein. J Virol. 1992;66(6):3494-503.
[10] Carson DD, Summers MD, Guarino LA. Molecular analysis of a baculovirus regulatory gene. Virology. 1991;182(1):279-86.
[11] Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22(22):4673-80.
[12] Herniou EA, Jehle JA. Baculovirus phylogeny and evolution. Curr Drug Targets. 2007;8(10):1043-50.
[13] Chen X, Zhang WJ, Wong J, Chun G, Lu A, McCutchen BF, Presnail JK, Herrmann R, Dolan M, Tingey S, Hu ZH, Vlak JM. Comparative analysis of the complete genome sequences of Helicoverpa zea and Helicoverpa armigera single-nucleocapsid nucleopolyhedroviruses. J Gen Virol. 2002;83(Pt 3):673-84.
[14] Tang P, Zhang H, Li Y, Han B, Wang G, Qin Q, Zhang Z. Genomic sequencing and analyses of HearMNPV--a new Multinucleocapsid nucleopolyhedrovirus isolated from Helicoverpa armigera. Virol J. 2012;9:168.
[15] Gomi S, Majima K, Maeda S. Sequence analysis of the genome of Bombyx mori nucleopolyhedrovirus. J Gen Virol. 1999;80 ( Pt 5):1323-37.
[16] Harrison RL, Bonning BC. Comparative analysis of the genomes of Rachiplusia ou and Autographa californica multiple nucleopolyhedroviruses. J Gen Virol. 2003;84(Pt 7):1827-42.
[17] Lauzon HA, Jamieson PB, Krell PJ, Arif BM. Gene organization and sequencing of the Choristoneura fumiferana defective nucleopolyhedrovirus genome. J Gen Virol. 2005;86(Pt 4):945-61.
[18] Nai YS, Wu CY, Wang TC, Chen YR, Lau WH, Lo CF, Tsai MF, Wang CH. Genomic sequencing and analyses of Lymantria xylina multiple nucleopolyhedrovirus. BMC Genomics. 2010;11:116.
[19] Ahrens CH, Russell RL, Funk CJ, Evans JT, Harwood SH, Rohrmann GF. The sequence of the Orgyia pseudotsugata multinucleocapsid nuclear polyhedrosis virus genome. Virology. 1997;229(2):381-99.
[20] Kuzio J, Pearson MN, Harwood SH, Funk CJ, Evans JT, Slavicek JM, Rohrmann GF. Sequence and analysis of the genome of a baculovirus pathogenic for Lymantria dispar. Virology. 1999;253(1):17-34.
[21] Thumbi DK, Eveleigh RJ, Lucarotti CJ, Lapointe R, Graham RI, Pavlik L, Lauzon HA, Arif BM. Complete sequence, analysis and organization of the Orgyia leucostigma nucleopolyhedrovirus genome. Viruses. 2011;3(11):2301-27.
[22] Chen X, IJkel WF, Tarchini R, Sun X, Sandbrink H, Wang H, Peters S, Zuidema D, Lankhorst RK, Vlak JM, Hu Z. The sequence of the Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus genome. J Gen Virol. 2001;82(Pt 1):241-57.
[23] Rost B. Twilight zone of protein sequence alignments. Protein Eng. 1999;12(2):85-94.
[24] Pearson WR. An introduction to sequence similarity ("homology") searching. Curr Protoc Bioinformatics. 2013;Chapter 3:Unit3.1.
[25] Miele SA, Garavaglia MJ, Belaich MN, Ghiringhelli PD. Baculovirus: molecular insights on their diversity and conservation. Int J Evol Biol. 2011;2011:379424.
[26] Hayakawa T, Rohrmann GF, Hashimoto Y. Patterns of genome organization and content in lepidopteran baculoviruses. Virology. 2000;278(1):1-12.
[27] Singh J, Singh CP, Bhavani A, Nagaraju J. Discovering microRNAs from Bombyx mori nucleopolyhedrosis virus. Virology. 2010;407(1):120-8.
[28] Huang J, Levin DB. Identification and functional analysis of a putative non-hr origin of DNA replication from the Spodoptera littoralis type B multinucleocapsid nucleopolyhedrovirus. J Gen Virol. 1999;80 ( Pt 8):2263-74.
[29] Rodems SM, Friesen PD. Transcriptional enhancer activity of hr5 requires dual-palindrome half sites that mediate binding of a dimeric form of the baculovirus transregulator IE1. J Virol. 1995;69(9):5368-75.
[30] Andreassen R, Worren MM, Høyheim B. Discovery and characterization of miRNA genes in Atlantic salmon (Salmo salar) by use of a deep sequencing approach. BMC Genomics. 2013;14:482.
[31] Morris TD, Miller LK. Mutational analysis of a baculovirus major late promoter. Gene. 1994;140(2):147-53.
[32] Weyer U, Possee RD. Analysis of the promoter of the Autographa californica nuclear polyhedrosis virus p10 gene. J Gen Virol. 1989;70 ( Pt 1):203-8.
[33] Krejmer M, Skrzecz I, Wasag B, Szewczyk B, Rabalski L. The genome of Dasychira pudibunda nucleopolyhedrovirus (DapuNPV) reveals novel genetic connection between baculoviruses infecting moths of the Lymantriidae family. BMC Genomics. 2015;16(1):759.
[34] Brázda V, Laister RC, Jagelská EB, Arrowsmith C. Cruciform structures are a common DNA feature important for regulating biological processes. BMC Mol Biol. 2011;12:33.
[35] Guturu H, Doxey AC, Wenger AM, Bejerano G. Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements. Philos Trans R Soc Lond B Biol Sci. 2013;368(1632):20130029.
[36] Merika M, Thanos D. Enhanceosomes. Curr Opin Genet Dev. 2001;11(2):205-8.
[37] Panne D, Maniatis T, Harrison SC. An atomic model of the interferon-beta enhanceosome. Cell. 2007;129(6):1111-23.