Biopolym. Cell. 2013; 29(1):55-63.
http://dx.doi.org/10.7124/bc.000806
Genomics, Transcriptomics and Proteomics
Isoforms of elongation factor eEF1A may be differently regulated at post-transcriptional level in breast cancer progression
1Vislovukh A. A., 1Naumovets M. G., 1Kovalenko M. I., 2Groisman R. S., 2Groisman I. S., 1Negrutskii B. S., 1El'skaya A. V.
  1. State Key Laboratory of Molecular and Cellular Biology
    Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680
  2. CNRS FRE 3377 and Universite Paris-Sud, CEA
    Saclay, F-91191 Gif-sur-Yvette, France

Abstract

Eukaryotic translation elongation factor 1A exists as two 98 % homologous isoforms: eEF1A1 (A1) and eEF1A2 (A2) which are tissue and development specific. Despite high homology in an open reading frame (ORF) region, mRNAs coding for eEF1A1 and eEF1A2 are different in their untranslated regions (UTR), suggesting a possibility of their dissimilar post-transcriptional regulation. Aim. To analyze the existence of cis-acting motifs in the UTRs of EEF1A1/A2 mRNAs, to confirm the possibility of post-transcriptional control of eEF1A1 and eEF1A2 expression. Methods. An ensemble of bioinformatic methods was applied to predict regulatory motifs in the UTRs of EEF1A1/A2 mRNAs. Dual-luciferase reporter assay was employed to detect post-transcriptional regulation of eEF1A1/A2 expression. Results. Numerous regulatory motifs in the UTR of EEF1A1/A2 mRNAs were found bioinformatically. The experimental evidence was obtained for the existence of negative regulation of EEF1A1 and positive regulation of EEF1A2 mRNA in the model of breast cancer development. Conclusions. EEF1A1 and EEF1A2 mRNAs contain distinct motifs in the UTRs and are differently regulated in cancer suggesting the possibility of their control by different cellular signals.
Keywords: EEF1A1, EEF1A2, UTR, miRNA, breast cancer
Full text: (PDF, in English)

References

[1] Negrutskii B. S., El'skaya A. V. 1998 Eukaryotic translation elongation factor 1 alpha: structure, expression, functions, and possible role in aminoacyl-tRNA channeling Prog. Nucleic Acid Res. Mol. Biol 60:47–78.
[2] Lee S., Francoeur A. M., Liu S., Wang E. 1992 Tissue-specific expression in mammalian brain, heart, and muscle of S1, a member of the elongation factor-1 alpha gene family J. Biol. Chem 267, N 33:24064–24068.
[3] Newbery H. J., Loh D. H., O'Donoghue J. E., Tomlinson V. A., Chau Y. Y., Boyd J. A., Bergmann J. H., Brownstein D., Abbott C. M. 2007 Translation elongation factor eEF1A2 is essential for postweaning survival in mice J. Biol. Chem 282, N 39:28951–28959.
[4] Mateyak M. K., Kinzy T. G. 2010 eEF1A: thinking outside the ribosome J. Biol. Chem 285, N 28:21209–21213.
[5] Vislovukh A. A., Shalak V. F., Savytskyi O. V., Kovalenko N. I., Gralievska N. L., Negrutskii B. S., El'skaya A. V. 2012 PTI-1: novel way to oncogenicity Biopolym. Cell 28, N 5:404–410.
[6] Novosylna A. V., Timchenko A. A., Tiktopulo E. I., Serdyuk I. N., Negrutskii B. S., El'skaya A. V. 2007 Characterization of physical properties of two isoforms of translation elongation factor 1A Biopolym. Cell 23, N 5:386–390.
[7] Anand N., Murthy S., Amann G., Wernick M., Porter L. A., Cukier I. H., Collins C., Gray J. W., Diebold J., Demetrick D. J., Lee J. M. 2002 Protein elongation factor EEF1A2 is a putative oncogene in ovarian cancer Nat. Genet 31, N 3:301–305.
[8] Lee M. H., Surh Y. J. eEF1A2 as a putative oncogene Ann. N. Y. Acad. Sci 2009 1171:87–93.
[9] Ruest L. B., Marcotte R., Wang E. 2002 Peptide elongation factor eEF1A-2/S1 expression in cultured differentiated myotubes and its protective effect against caspase-3-mediated apoptosis J. Biol. Chem 277, N 7:5418–5425.
[10] Ann D. K., Lin H. H., Lee S., Tu Z. J., Wang E. 1992 Characterization of the statin-like S1 and rat elongation factor 1 alpha as two distinctly expressed messages in rat J. Biol. Chem 267, N 2:699–702.
[11] Kuersten S., Goodwin E. B. 2003 The power of the 3' UTR: translational control and development Nat. Rev. Genet 4, N 8:626–637.
[12] Grange J., Belly A., Dupas S., Trembleau A., Sadoul R., Goldberg Y. 2009 Specific interaction between Sam68 and neuronal mRNAs: implication for the activity-dependent biosynthesis of elongation factor eEF1A J. Neurosci. Res 87, N 1:12–25.
[13] Inamura N., Nawa H., Takei N. 2005 Enhancement of translation elongation in neurons by brain-derived neurotrophic factor: implications for mammalian target of rapamycin signaling J. Neurochem 95, N 5:1438–1445.
[14] Tsokas P., Grace E. A., Chan P., Ma T., Sealfon S. C., Iyengar R., Landau E. M., Blitzer R. D. 2005 Local protein synthesis mediates a rapid increase in dendritic elongation factor 1A after induction of late long-term potentiation J. Neurosci 25, N 24:5833–5843.
[15] Tomlinson V. A., Newbery H. J., Bergmann J. H., Boyd J., Scott D., Wray N. R., Sellar G. C., Gabra H., Graham A., Williams A. R., Abbott C. M. 2007 Expression of eEF1A2 is associated with clear cell histology in ovarian carcinomas: overexpression of the gene is not dependent on modifications at the EEF1A2 locus Br. J. Cancer 96, N 10:1613–1620.
[16] Vislovukh A. A., Groisman I. S., El'skaya A. V., Negrutskii B. S., Polesskaya A. N. 2012 Transcriptional and post-transcriptional control of eEF1A2 expression during myoblast diffrerentiation Biopolym. Cell 28, N 6:456–460.
[17] Mignone F., Gissi C., Liuni S., Pesole G. 2002 Untranslated regions of mRNAs Genome Biol 3, N 3:REVIEWS0004.
[18] Kozak M. 2002 Pushing the limits of the scanning mechanism for initiation of translation Gene 299, N 1–2:1–34.
[19] Kozak M. 1990 Downstream secondary structure facilitates recognition of initiator codons by eukaryotic ribosomes Proc. Natl Acad. Sci. USA 87, N 21:8301–8305.
[20] Kochetov A. V., Palyanov A., Titov II, Grigorovich D., Sarai A., Kolchanov N. A. 2007 AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site BMC Bioinformatics 8:318.
[21] Grillo G., Turi A., Licciulli F., Mignone F., Liuni S., Banfi S., Gennarino V. A., Horner D. S., Pavesi G., Picardi E., Pesole G. 2010 UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs Nucleic Acids Res 38 D75–80.
[22] Shibui-Nihei A., Ohmori Y., Yoshida K., Imai J., Oosuga I., Iidaka M., Suzuki Y., Mizushima-Sugano J., Yoshitomo-Nakagawa K., Sugano S. 2003 The 5' terminal oligopyrimidine tract of human elongation factor 1A-1 gene functions as a transcriptional initiator and produces a variable number of Us at the transcriptional level Gene 311:137–145.
[23] Amaldi F., Pierandrei-Amaldi P. 1997 TOP genes: a translationally controlled class of genes including those coding for ribosomal proteins Prog. Mol. Subcell. Biol 18:1–17.
[24] Bernhart S. H., Hofacker I. L., Will S., Gruber A. R., Stadler P. F. RNAalifold: improved consensus structure prediction for RNA alignments BMC Bioinformatics 2008 9:474.
[25] Thompson J. D., Gibson T. J., Higgins D. G. Multiple sequence alignment using ClustalW and ClustalX Curr. Protoc. Bioinformatics 2002 Chapter 2, Unit 2.3. bi0203s00.
[26] Darty K., Denise A., Ponty Y. 2009 VARNA: Interactive drawing and editing of the RNA secondary structure Bioinformatics 25, N 15:1974–1975.
[27] Griffiths-Jones S., Bateman A., Marshall M., Khanna A., Eddy S. R. 2003 Rfam: an RNA family database Nucleic Acids Res 31, N 1:439–441.
[28] Fabian M. R., Sonenberg N., Filipowicz W. 2010 Regulation of mRNA translation and stability by microRNAs Annu. Rev. Biochem 79–P. 351–379.
[29] Chen K., Rajewsky N. 2006 Natural selection on human microRNA binding sites inferred from SNP data Nat. Genet 38, N 12:1452–1456.
[30] Grimson A., Farh K. K., Johnston W. K., Garrett-Engele P., Lim L. P., Bartel D. P. 2007 MicroRNA targeting specificity in mammals: determinants beyond seed pairing Mol. Cell 27, N 1:91–105.
[31] Maragkakis M., Vergoulis T., Alexiou P., Reczko M., Plomaritou K., Gousis M., Kourtis K., Koziris N., Dalamagas T., Hatzigeorgiou A. G. 2011 DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association Nucleic Acids Res 39 (Web Server issue):145–148.
[32] John B., Enright A. J., Aravin A., Tuschl T., Sander C., Marks D. S. 2004 Human MicroRNA targets PLoS Biol 2, N 11 e363.
[33] Kertesz M., Iovino N., Unnerstall U., Gaul U., Segal E. 2007 The role of site accessibility in microRNA target recognition Nat. Genet 39, N 10:1278–1284.
[34] Lai E. C., Tam B., Rubin G. M. 2005 Pervasive regulation of Drosophila Notch target genes by GY-box-, Brd-box-, and K-boxclass microRNAs Genes Dev 19, N 9:1067–1080.
[35] Tsuda N., Kawano K., Efferson C. L., Ioannides C. G. 2005 Synthetic microRNA and double-stranded RNA targeting the 3'-untranslated region of HER-2/neu mRNA inhibit HER-2 protein expression in ovarian cancer cells Int. J. Oncol 27, N 5:1299–1306.
[36] Pruitt K. D., Tatusova T., Brown G. R., Maglott D. R. 2012 NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy Nucleic Acids Res 40 (Database issue) D130–135.
[37] Cheng Y., Miura R. M., Tian B. 2006 Prediction of mRNA polyadenylation sites by support vector machine Bioinformatics 22, N 19:2320–2325.
[38] Karolchik D., Hinrichs A. S.,Kent W. J. The UCSC Genome Browser Curr. Protoc. Bioinformatics 2007 Chapter 1: Unit 1.4..
[39] Richter J. D. 2007 CPEB: a life in translation Trends Biochem. Sci 32, N 6:279–285.
[40] Nairismagi M. L., Vislovukh A., Meng Q., Kratassiouk G., Beldiman C., Petretich M., Groisman R., Fuchtbauer E. M., HarelBellan A., Groisman I. 2012 Translational control of TWIST1 expression in MCF-10A cell lines recapitulating breast cancer progression Oncogene 31, N 47:4960–4966.
[41] Groisman I., Jung M. Y., Sarkissian M., Cao Q., Richter J. D. 2002 Translational control of the embryonic cell cycle Cell 109, N 4:473–483.
[42] Groisman I., Huang Y. S., Mendez R., Cao Q., Theurkauf W., Richter J. D. 2000 CPEB, maskin, and cyclin B1 mRNA at the mitotic apparatus: implications for local translational control of cell division Cell 103, N 3:435–447.
[43] Stebbins-Boaz B., Hake L. E., Richter J. D. 1996 CPEB controls the cytoplasmic polyadenylation of cyclin, Cdk2 and c-mos mRNAs and is necessary for oocyte maturation in Xenopus EMBO J 15, N 10:2582–2592.
[44] Wu X., Brewer G. 2012 The regulation of mRNA stability in mammalian cells: 2.0 Gene 500, N 1:10–21.
[45] Lopez de Silanes I., Zhan M., Lal A., Yang X., Gorospe M. 2004 Identification of a target RNA motif for RNA-binding protein HuR Proc. Natl Acad. Sci. USA 101, N 9:2987–2992.
[46] Gruber A. R., Fallmann J., Kratochvill F., Kovarik P., Hofacker I. L. 2011 AREsite: a database for the comprehensive investigation of AU-rich elements Nucleic Acids Res 39 D66–69.
[47] Duchler M. 2012 G-quadruplexes: targets and tools in anticancer drug design J. Drug Target 20, N 5:389–400.
[48] Millevoi S., Moine H., Vagner S. 2012 G-quadruplexes in RNA biology Wiley Interdiscip. Rev. RNA 3, N 4:495–507.
[49] Shahid R., Bugaut A., Balasubramanian S. 2010 The BCL-2 5' untranslated region contains an RNA G-quadruplex-forming motif that modulates protein expression Biochemistry 49, N 38:8300–8306.
[50] Decorsiere A., Cayrel A., Vagner S., Millevoi S. 2011 Essential role for the interaction between hnRNP H/F and a G quadruplex in maintaining p53 pre-mRNA 3'-end processing and function during DNA damage Genes Dev 25, N 3:220–225.
[51] Kikin O., Zappala Z., D'Antonio L., Bagga P. S. 2008 GRSDB2 and GRS_UTRdb: databases of quadruplex forming G-rich sequences in pre-mRNAs and mRNAs Nucleic Acids Res 36 (Database issue) D141–148.
[52] Li Z., Qi C. F., Shin D. M., Zingone A., Newbery H. J., Kovalchuk A. L., Abbott C. M., Morse H. C. 3rd 2010 Eef1a2 promotes cell growth, inhibits apoptosis and activates JAK/STAT and AKT signaling in mouse plasmacytomas PloS One 5, N 5 e10755.
[53] Soule H. D., Maloney T. M., Wolman S. R., Peterson W. D. Jr., Brenz R., McGrath C. M., Russo J., Pauley R. J., Jones R. F., Brooks S. C. 1990 Isolation and characterization of a spontaneously immortalized human breast epithelial cell line, MCF-10 Cancer Res 50, N 18:6075–6086.
[54] Basolo F., Elliott J., Tait L., Chen X. Q., Maloney T., Russo I. H., Pauley R., Momiki S., Caamano J., Klein-Szanto A. J., Koszalka M., Russo J. 1991 Transformation of human breast epithelial cells by c-Ha-ras oncogene Mol. Carcinog 4, N 1:25–35.
[55] Miller F. R., Soule H. D., Tait L., Pauley R. J., Wolman S. R., Dawson P. J., Heppner G. H. 1993 Xenograft model of progressive human proliferative breast disease J. Natl Cancer Inst 85, N 21:1725–1732.
[56] Evdokimova V., Tognon C., Ng T., Ruzanov P., Melnyk N., Fink D., Sorokin A., Ovchinnikov L. P., Davicioni E., Triche T. J., Sorensen P. H. 2009 Translational activation of snail1 and other developmentally regulated transcription factors by YB-1 promotes an epithelial-mesenchymal transition Cancer Cell 15, N 5:402–415.