Bioinformatic analysis of Arabidopsis reverse transcriptases with a zinc-finger domain
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Santiago Valentín Galván-Gordillo
Abstract
Plants, as most eukaryotic organisms, harbor several genes encoding a reverse transcriptase domain. The majority of them are part of transposable elements (TEs) and/or retroviral genomes that have been inserted into their genomes. However, there are some examples of RT domain-containing genes that have been endogenized during plant evolution; these genes appear to display functions other than “selfish” maintenance and replication of TEs, and subjected to host gene regulation. In the present work we have analyzed a subset of genes in Arabidopsis with an RT domain (RVT) containing a zinc finger motif (Znf), termed RVT-Znf domain, with structural characteristics of endogenous genes i.e., contain potential upstream regions as well as 5’UTR, and 3’UTR, and are not flanked by retroelement features. Phylogenetic analysis of these genes, based on the RVT-Znf domain, indicates that there are three clades, the members of which having additional domains. When compared to additional sequences, RVT-Znf formed a cluster that is more closely related to non-LTR retrotransposons and group II introns. Extant data from microarray databases indicate that several Arabidopsis genes are expressed. These data indicate that these RTs may have been endogenized. Possible roles for these genes are discussed.
Acknowledgements
This work was supported by CONACyT-México grants Nos 109885 (to BX-C) and 156162 (to RR-M). SVG-G and ACM-N acknowledge doctoral fellowship support from CONAcyT.
References
Bennetzen J. 2005. Transposable elements, gene creation and genome rearrangement in flowering plants. Curr. Opin. Genet. & Dev. 15: 621-627. 10.1016/j.gde.2005.09.010.Search in Google Scholar PubMed
Bundock P. & Hooykaas P. 2005. An Arabidopsis hAT-like transposase is essential for plant development. Nature 436: 282–284. 10.1038/nature03667Search in Google Scholar PubMed
Creasey K.M., Zhai J., Borges F., Van Ex F., Regulski M., Meyers B.C. & Martienssen R.A. 2014. miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis. Nature 508: 411-415. 10.1038/nature13069.Search in Google Scholar PubMed PubMed Central
Crooks G.E., Hon G., Chandonia J.M. & Brenner S.E. 2004. WebLogo: A sequence logo generator. Genome Res. 14: 1188-1190.10.1101/gr.849004Search in Google Scholar PubMed PubMed Central
Duan K., Ding X., Zhang Q., Zhu H., Pan A. & Huang J. 2008. AtCopeg1, the unique gene originated from AtCopia95 retrotransposon family, is sensitive to external hormones and abiotic stresses. Plant Cell Rep. 27:1065–1073. 10.1007/s00299-008-0520-2.Search in Google Scholar PubMed
Felsenstein J. 1985. Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution 39: 783-791. 10.2307/2408678.Search in Google Scholar
Feschotte C., Jiang N. & Wessler S. 2002. Plant transposable elements: where genetics meets genomics. Nat. Rev. Genet. 3: 329–341. 10.1038/nrg793.Search in Google Scholar PubMed
Feschotte C. 2008. Transposable elements and the evolution of regulatory networks. Nat. Rev. Genet. 9: 397-405. 10.1038/nrg2337.Search in Google Scholar PubMed PubMed Central
Gouy M., Guindon S., Gascuel O. 2010. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 27: 221-224. 10.1093/molbev/msp259.Search in Google Scholar PubMed
Grandbastien M.A. 2015. LTR retrotransposons, handy hitchhikers of plant regulation and stress response. Biochim. Biophys. Acta 1849: 403-416. 10.1016/j.bbagrm.2014.07.017.Search in Google Scholar PubMed
Hruz T., Laule O., Szabo G., Wessendorp F., Bleuler S., Oertle L. et al. 2008. Genevestigator V3, a reference expression database for the meta-analysis of transcriptomes. Adv. Bioinformatics 2008: 420747. 10.1155/2008/420747.Search in Google Scholar PubMed PubMed Central
Huang C.R., Burns K.H., Boeke J.D. 2012. Active transposition in genomes. Annu. Rev. Genet. 46: 651-675. 10.1146/annurev-genet-110711-155616.Search in Google Scholar PubMed PubMed Central
Hua-Van A., Le Rouzic A., Maisonhaute C., Capy P. 2005. Abundance, distribution and dynamics of retrotransposable elements and transposons: similarities and differences. Cytogenet. Genome Res. 110: 426-440. 10.1159/000084975.Search in Google Scholar PubMed
Hudson M., Lisch D. & Quail P. 2003. The FHY3 and FAR1 genes encode transposase related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway. Plant J.34: 453–471. 10.1046/j.1365-313X.2003.01741.x.Search in Google Scholar PubMed
Keren I., Bezawork-Geleta A., Kolton M. Maayan I., Belausov E., Levy M., Mett A., Gidoni D., Shaya F., & Ostersetzer-Biran O. 2009. AtnMat2, a nuclear-encoded maturase required for splicing of group-II introns in Arabidopsis mitochondria. RNA 15: 2299-2311. 10.1261/rna.1776409.Search in Google Scholar PubMed PubMed Central
Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J. & Higgins D.G. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 2321: 2947–2948.10.1093/bioinformatics/btm404Search in Google Scholar PubMed
Lisch D. 2013. How important are transposons for plant evolution? Nat. Rev. Genet. 141:49-61. 10.1038/nrg3374.Search in Google Scholar PubMed
Lucas W.J., Groover A., Lichtenberger R., Furuta K., Yadav S.-R., Helariutta Y., He X.Q., Fukuda H., Kang J., Brady S.M., Patrick J.W., Sperry J., Yoshida A., López-Millán A.F., Grusak M.A. & Kachroo P. 2013. The Plant Vascular System: Evolution, Development and Functions. J. Integr. Plant Biol. 55: 294–388. 10.1111/jipb.12041.Search in Google Scholar PubMed
Nakamura T. & Cech T. 1998. Reversing Time: Origin of Telomerase. Cell 92: 587–590. 10.1016/S0092-86740081123-X.Search in Google Scholar
Oliver K. & Greene W. 2008. Transposable elements: powerful facilitators of evolution. BioEssays 31:703–714. 10.1002/bies.200800219.Search in Google Scholar PubMed
Oliver K., McComb J. & Greene W. 2013. Transposable Elements: Powerful Contributors to Angiosperm Evolution and Diversity. Genome Biol. Evol. 5: 1886–1901. 10.1093/gbe/evt141.Search in Google Scholar
Ruiz-Medrano R., Xoconostle-Cázares B., Ham B., Li G. & Lucas W.J. 2011. Vascular expression in Arabidopsis is predicted by the frequency of CT/GA rich repeats in gene promoters. Plant J. 67: 130–144. 10.1111/j.1365-313X.2011.04581.x.Search in Google Scholar
Tamura K., Stecher G., Peterson D., Filipski A. & Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 30: 2725-2729.10.1093/molbev/mst197Search in Google Scholar
Vicient C.M., Jääskeläinen M.J., Kalendar R. & Schulman A.H. 2001. Active retrotransposons are a common feature of grass genomes. Plant Physiol. 125: 1283-1292.10.1104/pp.125.3.1283Search in Google Scholar
Volff J.N. 2006. Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes.BioEssays 28: 913-922.10.1002/bies.20452Search in Google Scholar
Wang W., Zheng H., Fan C., Li J., Shi J., Cai Z., Zhang G., Liu D., Zhang J., Vang S., Lu Z., Wong G.K., Long M. & Wang J. 2006. High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 18: 1791–1802. 10.1105/tpc. 106.041905.Search in Google Scholar
Wessler S. 1996. Plant retrotransposons: Turned on by stress. Curr. Biol. 6: 8:959–961.10.1016/S0960-9822(02)00638-3Search in Google Scholar
Xiong Y. & Eickbush T.H. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9: 3353-3362.10.1002/j.1460-2075.1990.tb07536.xSearch in Google Scholar PubMed PubMed Central
Yamasaki K., Kigawa T., Inoue M., Watanabe S., Tateno M., Seki M., Shinozaki K. & Yokoyama S. 2008. Structures and evolutionary origins of plant-specific transcription factor DNA-binding domains. Plant Physiol. Biochem. 46: 394–401. 10.1016/j.plaphy.2007.12.015.Search in Google Scholar PubMed
Zhao M. & Ma J. 2013. Co-evolution of plant LTR-retrotransposons and their host genomes. Protein Cell 47: 493-501. 10.1007/s13238-013-3037-6.Search in Google Scholar PubMed PubMed Central
Zimmermann P., Hirsch-Hoffmann M., Hennig L. & Gruissem W. 2004. GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox. Plant Physiol. 136: 2621–2632. 10.1104/pp.104.046367.Search in Google Scholar PubMed PubMed Central
© 2016 Institute of Botany, Slovak Academy of Sciences
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