Molecular Genetics and Genomics

, Volume 281, Issue 4, pp 391–405 | Cite as

The application of expression analysis in elucidating the eukaryotic elongation factor one alpha gene family in Arabidopsis thaliana

  • Wendy Danielle Ransom-Hodgkins
Original Paper


Eukaryotic elongation factor one alpha (eEF1A) encoding genes are part of the large GTP binding protein family. The eEF1A family is important for protein synthesis and actin filament and bundle formation. In this study, the expression of four eEF1A genes in Arabidopsis thaliana is reported. Microarray analyses of the gene family showed high expression levels in germinating seeds, embryos, and shoot and root meristems. Quantitative real time RT-PCR was used to determine individual eEF1A gene expression. Unlike animals, in Arabidopsis tissues all four eEF1A genes were expressed in all tissues sampled. However, the abundance of each transcript varied spatially. Knocking out expression of one eEF1A gene produced seedlings with stunted roots and a subsequent change in expression of the other three eEF1A genes. The varying abundance of each gene in different tissues may indicate different concentration requirements for each message product. These results will be very useful for elucidating the role of each gene in growth, development, and stress responses of the plant.


eEF1A Quantitative real time RT-PCR Arabidopsis thaliana Development Microarray Roots 



Eukaryotic elongation factor one alpha


Actin2 and Actin8 genes


Polyubiquitin 10 gene

Q real time RT-PCR

Quantitative real time reverse transcription polymerase chain reaction












Open reading frame


Green fluorescent protein


Coding sequence


Untranslated region


1-N-naphthylphthalamic acid


Abscisic acid








Methyl jasmonate



I would like to thank Dr. Todd Barkman for sequencing the PCR products; and Dr. Charles Ide and Dr. Anna Jelaso for use of the Primer Express Software and assistance in the cDNA microarray analysis. This work was supported by The College of Arts and Sciences, Western Michigan University to W.R.H.

Supplementary material

438_2008_418_MOESM1_ESM.tif (739 kb)
Supplemental Figure 1. Quantitative real time RT-PCR products.The PCR products from reactions using the eEF1A family A1, A2, A3, A4; ACT2,8 or UBQ10primers were analyzed using a DNA500 Lab on a Chip kit in a 2100 Bioanalyzer (AgilentTechnologies). The PCR products are shown. Each PCR product was cloned into pCR4 andsequenced to verify amplification of the correct gene. The sizes of the PCR products are: A1 200bp; A2 186bp; A3 194bp; A4 178bp; UBQ10 74bp; ACT2,8 73bp; and eEF1A Family 75bp(TIFF 739 kb)
438_2008_418_MOESM2_ESM.tif (49.2 mb)
Supplemental Figure 2. Expression of UBQ10 and ACT2,8. Quantitative real time RT-PCR was performed on RNA extracted from developing tissue. Refer to Figure 5B for measurement details. The experiment was repeated twice with triplicate samples for each treatment. The standard deviation is reported.(TIFF 50337 kb)
438_2008_418_MOESM3_ESM.doc (77 kb)
Supplementary Table 1 (DOC 77 kb)
438_2008_418_MOESM4_ESM.doc (30 kb)
Supplementary Table 2 (DOC 30 kb)


  1. Aguilar F, Montandon PE, Stutz E (1991) Two genes encoding the soybean translation elongation factor eef-1 alpha are transcribed in seedling leaves. Plant Mol Biol 17(3):351–360PubMedCrossRefGoogle Scholar
  2. Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Cheuk R, Gadrinab C, Heller C, Jeske A, Koesema E, Meyers CC, Parker H, Prednis L, Ansari Y, Choy N, Deen H, Geralt M, Hazari N, Hom E, Karnes M, Mulholland C, Ndubaku R, Schmidt I, Guzman P, Aguilar-Henonin L, Schmid M, Weigel D, Carter DE, Marchand T, Risseeuw E, Brogden D, Zeko A, Crosby WL, Berry CC, Ecker JR (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301(5633):653–657PubMedCrossRefGoogle Scholar
  3. Andersen GR, Nissen P, Nyborg J (2003) Elongation factors in protein biosynthesis. Trends Biochem Sci 28(8):434–441PubMedCrossRefGoogle Scholar
  4. Auriac MC, Timmers AC (2007) Nodulation studies in the model legume Medicago truncatula: advantages of using the constitutive ef1alpha promoter and limitations in detecting fluorescent reporter proteins in nodule tissues. Mol Plant Microbe Interact 20(9):1040–1047PubMedCrossRefGoogle Scholar
  5. Axelos M, Bardet C, Liboz T, Le Van Thai A, Curie C, Lescure B (1989) The gene family encoding the Arabidopsis thaliana translation elongation factor ef-1 alpha: molecular cloning, characterization and expression. Mol Gen Genet 219(1–2):106–112PubMedGoogle Scholar
  6. Berberich T, Sugawara K, Harada M, Kusano T (1995) Molecular cloning, characterization and expression of an elongation factor 1 alpha gene in maize. Plant Mol Biol 29(3):611–615PubMedCrossRefGoogle Scholar
  7. Calikowski TT, Meulia T, Meier I (2003) A proteomic study of the Arabidopsis nuclear matrix. J Cell Biochem 90(2):361–378PubMedCrossRefGoogle Scholar
  8. Carneiro NP, Hughes PA, Larkins BA (1999) The eef1a gene family is differentially expressed in maize endosperm. Plant Mol Biol 41(6):801–813PubMedCrossRefGoogle Scholar
  9. Chang YW, Traugh JA (1998) Insulin stimulation of phosphorylation of elongation factor 1 (eef-1) enhances elongation activity. Eur J Biochem 251(1–2):201–207PubMedCrossRefGoogle Scholar
  10. Clore AM, Dannenhoffer JM, Larkins BA (1996) Ef-1[alpha] is associated with a cytoskeletal network surrounding protein bodies in maize endosperm cells. Plant Cell 8(11):2003–2014PubMedCrossRefGoogle Scholar
  11. Demma M, Warren V, Hock R, Dharmawardhane S, Condeelis J (1990) Isolation of an abundant 50, 000-dalton actin filament bundling protein from dictyostelium amoebae. J Biol Chem 264:20518–20525Google Scholar
  12. Djé MK, Mazabraud A, Viel A, le Maire M, Denis H, Crawford E, Brown DD (1990) Three genes under different developmental control encode elongation factor 1-alpha in Xenopus laevis. Nucleic Acids Res 18(12):3489–3493PubMedCrossRefGoogle Scholar
  13. Dunn MA, Morris A, Jack PL, Hughes MA (1993) A low-temperature-responsive translation elongation factor 1 alpha from barley (Hordeum vulgare l.). Plant Mol Biol 23(1):221–225PubMedCrossRefGoogle Scholar
  14. Ejiri S (2002) Moonlighting functions of polypeptide elongation factor 1: from actin bundling to zinc finger protein r1-associated nuclear localization. Biosci Biotechnol Biochem 66(1):1–21PubMedCrossRefGoogle Scholar
  15. Gangwani L, Mikrut M, Galcheva-Gargova Z, Davis RJ (1998). Interaction of zpr1 with translation elongation factor-1alpha in proliferating cells. doi: 10.1083/jcb.143.6.1471. J Cell Biol 143(6):1471–1484Google Scholar
  16. Gilliland LU, Kandasamy MK, Pawloski LC, Meagher RB (2002) Both vegetative and reproductive actin isovariants complement the stunted root hair phenotype of the Arabidopsis act2-1 mutation. Plant Physiol 130(4):2199–2209PubMedCrossRefGoogle Scholar
  17. Gilliland LU, Pawloski LC, Kandasamy MK, Meagher RB (2003) Arabidopsis actin gene act7 plays an essential role in germination and root growth. Plant J 33(2):319–328PubMedCrossRefGoogle Scholar
  18. Gonen H, Smith CE, Siegel NR, Kahana C, Merrick WC, Chakraburtty K, Schwartz AL, Ciechanover A (1994) Protein synthesis elongation factor ef-1 alpha is essential for ubiquitin-dependent degradation of certain n alpha-acetylated proteins and may be substituted for by the bacterial elongation factor ef-tu. Proc Natl Acad Sci USA 91(16):7648–7652PubMedCrossRefGoogle Scholar
  19. Gross SR, Kinzy TG (2005) Translation elongation factor 1a is essential for regulation of the actin cytoskeleton and cell morphology. Nat Struct Mol Biol 12(9):772–778PubMedCrossRefGoogle Scholar
  20. Gross SR, Kinzy TG (2007) Improper organization of the actin cytoskeleton affects protein synthesis at initiation. Mol Cell Biol 27(5):1974–1989PubMedCrossRefGoogle Scholar
  21. Heazlewood JL, Tonti-Filippini JS, Gout AM, Day DA, Whelan J, Millar AH (2004) Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulatory components, provides assessment of targeting prediction programs, and indicates plant-specific mitochondrial proteins. Plant Cell 16(1):241–256PubMedCrossRefGoogle Scholar
  22. Heazlewood JL, Tonti-Filippini J, Verboom RE, Millar AH (2005) Combining experimental and predicted datasets for determination of the subcellular location of proteins in Arabidopsis. Plant Physiol 139(2):598–609PubMedCrossRefGoogle Scholar
  23. Heazlewood JL, Verboom RE, Tonti-Filippini J, Small I, Millar AH (2007) Suba: the Arabidopsis subcellular database. Nucleic Acids Res 35(Database issue): D213–8Google Scholar
  24. Holmes-Davis R, Tanaka CK, Vensel WH, Hurkman WJ, McCormick S (2005) Proteome mapping of mature pollen of Arabidopsis thaliana. Proteomics 5(18):4864–4884PubMedCrossRefGoogle Scholar
  25. Izawa T, Fukata Y, Kimura T, Iwamatsa A, Dohi K, Kaibuchi K (2000) Elongation factor-1α is a novel substrate of rho associated kinase. Biochim Biophys Res Comm 278:72–78CrossRefGoogle Scholar
  26. Jaquinod M, Villiers F, Kieffer-Jaquinod S, Hugouvieux V, Bruley C, Garin J, Bourguignon J (2007) A proteomics dissection of Arabidopsis thaliana vacuoles isolated from cell culture. Mol Cell Proteomics 6(3):394–412PubMedGoogle Scholar
  27. Kahns S, Lund A, Kristensen P, Knudsen CR, Clark BF, Cavallius J, Merrick WC (1998) The elongation factor 1 a-2 isoform from rabbit: cloning of the cdna and characterization of the protein. Nucleic Acids Res 26(8):1884–1890PubMedCrossRefGoogle Scholar
  28. Kandl KA, Munshi R, Ortiz PA, Andersen GR, Kinzy TG, Adams AE (2002) Identification of a role for actin in translational fidelity in yeast. Mol Genet Genomics 268(1):10–18PubMedCrossRefGoogle Scholar
  29. Kaur KJ, Ruben L (1994) Protein translation elongation factor-1 alpha from Trypanosoma brucei binds calmodulin. J Biol Chem 269(37):23045–23050PubMedGoogle Scholar
  30. Kawahara R, Sunabori S, Fukuda H, Komamine A (1992) A gene expressed preferentially in the globular stage of somatic embryogenesis encodes elongation-factor 1α in carrot. Eur J Biochem 209:157–162PubMedCrossRefGoogle Scholar
  31. Kidou S, Ejiri S (1998) Isolation, characterization and mRNA expression of four cDNAs encoding translation elongation factor 1a from rice (Oryza sativa l.). Plant Mol Biol 36(1):137–148PubMedCrossRefGoogle Scholar
  32. Kleffmann T, Russenberger D, von Zychlinski A, Christopher W, Sjölander K, Gruissem W, Baginsky S (2004) The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions. Curr Biol 14(5):354–362PubMedCrossRefGoogle Scholar
  33. Knudsen SM, Frydenberg J, Clark BFC, Leffers H (1993) Tissue-dependent variation in the expression of elongation facor-1α isoforms: isolation and characterization of a cdna encoding a novel variant of human elongation-factor 1α. Eur J Biochem 215:549–554PubMedCrossRefGoogle Scholar
  34. Lopez-Valenzuela JA, Gibbon BC, Hughes PA, Dreher TW, Larkins BA (2003) Eef1a isoforms change in abundance and actin-binding activity during maize endosperm development. Plant Physiol 133(3):1285–1295PubMedCrossRefGoogle Scholar
  35. Marmagne A, Rouet MA, Ferro M, Rolland N, Alcon C, Joyard J, Garin J, Barbier-Brygoo H, Ephritikhine G (2004) Identification of new intrinsic proteins in Arabidopsis plasma membrane proteome. Mol Cell Proteomics 3(7):675–691PubMedCrossRefGoogle Scholar
  36. Martina Schad MSL, Giavalisco P, Smith RD, Kehr J (2005) Evaluation of two-dimensional electrophoresis and liquid chromatography—tandem mass spectrometry for tissue-specific protein profiling of laser-microdissected plant samples. Electrophoresis 26(14):2729–2738PubMedCrossRefGoogle Scholar
  37. Morelli JK, Shewmaker CK, Vayda ME (1994) Biphasic stimulation of translational activity correlates with induction of translation elongation factor 1 subunit alpha upon wounding in potato tubers. Plant Physiol 106(3):897–903Google Scholar
  38. Munshi R, Kandl KA, Carr-Schmid A, Whitacre JL, Adams AE, Kinzy TG (2001) Overexpression of translation elongation factor 1a affects the organization and function of the actin cytoskeleton in yeast. Genetics 157(4):1425–1436PubMedGoogle Scholar
  39. Negrutskii BS, El’skaya AV (1998) Eukaryotic translation elongation factor 1 alpha: structure, expression, functions, and possible role in aminoacyl-tRNA channeling. Prog Nucleic Acid Res Mol Biol 60:47–78PubMedCrossRefGoogle Scholar
  40. Nishimura T, Yokota E, Wada T, Shimmen T, Okada K (2003) An Arabidopsis act2 dominant-negative mutation, which disturbs f-actin polymerization, reveals its distinctive function in root development. Plant Cell Physiol 44(11):1110–1131CrossRefGoogle Scholar
  41. Noir S, Bräutigam A, Colby T, Schmidt J, Panstruga R (2005) A reference map of the Arabidopsis thaliana mature pollen proteome. Biochem Biophys Res Comm 337(4):1257–1266PubMedCrossRefGoogle Scholar
  42. Ohta K, Toriyama M, Miyazaki M, Murofushi H, Hosoda S, Endo S, Sakai H (1990) The mitotic apparatus-associated 51-kda protein from sea urchin eggs is a gtp-binding protein and is immunologically related to yeast polypeptide elongation factor 1 alpha. J Biol Chem 265(6):3240–3247PubMedGoogle Scholar
  43. Pennisi E (2000) Sequence. Plants join the genome sequencing bandwagon. Science 290(5499):2054–2055PubMedCrossRefGoogle Scholar
  44. Pokalsky AR, Hiatt WR, Ridge N, Rasmussen R, Houck CM, Shewmaker CK (1989) Structure and expression of elongation factor 1 alpha in tomato. Nucleic Acids Res 17(12):4661–4673PubMedCrossRefGoogle Scholar
  45. Rao D, Momcilovic I, Kobayashi S, Callegari E, Ristic Z (2004) Chaperone activity of recombinant maize chloroplast protein synthesis elongation factor, ef-tu. Eur J Biochem 271(18):3684–3692PubMedCrossRefGoogle Scholar
  46. Reddy VS, Ali GS, Reddy AS (2002) Genes encoding calmodulin-binding proteins in the Arabidopsis genome. J Biol Chem 277(12):9840–9852PubMedCrossRefGoogle Scholar
  47. Sun Y, Carneiro N, Clore AM, Moro GL, Habben JE, Larkins BA (1997) Characterization of maize elongation factor 1a and its relationship to protein quality in the endosperm. Plant Physiol 115(3):1101–1107PubMedCrossRefGoogle Scholar
  48. Toueille M, Saint-Jean B, Castroviejo M, Benedetto JP (2007) The elongation factor 1a: a novel regulator in the DNA replication/repair protein network in wheat cells? Plant Physiol Biochem 45(2):113–118PubMedCrossRefGoogle Scholar
  49. Umikawa M, Tanaka K, Kamei T, Shimizu K, Imamura H, Sasaki T, Takai Y (1998) Interaction of rho1p target bni1p with f-actin-binding elongation factor 1alpha: implication in rho1p-regulated reorganization of the actin cytoskeleton in Saccharomyces cerevisiae. Oncogene 16(15):2011–2016PubMedCrossRefGoogle Scholar
  50. Ursin VM, Irvine JM, Hiatt WR, Shewmaker CK (1991) Developmental analysis of elongation factor-1 alpha expression in transgenic tobacco. Plant Cell 3(6):583–591PubMedCrossRefGoogle Scholar
  51. Vayda ME, Shewmaker CK, Morelli JK (1995) Translational arrest in hypoxic potato tubers is correlated with the aberrant association of elongation factor ef-1 alpha with polysomes. Plant Mol Biol 28(4):751–757PubMedCrossRefGoogle Scholar
  52. Wertman KF, Drubin DG, Botstein D (1992) Systematic mutational analysis of the yeast act1 gene. Genetics 132(2):337–350PubMedGoogle Scholar
  53. Wolfram G, Brenner GAR, Köllmer I, Lukas B, Thomas S (2005) Immediate-early and delayed cytokinin response genes of Arabidopsis thaliana identified by genome-wide expression profiling reveal novel cytokinin-sensitive processes and suggest cytokinin action through transcriptional cascades. Plant J 44(2):314–333CrossRefGoogle Scholar
  54. Yang W, Boss WF (1994) Regulation of phosphatidylinositol 4-kinase by the protein activator pik-a49. Activation requires phosphorylation of pik-a49. J Biol Chem 269(5):3852–3857PubMedGoogle Scholar
  55. Yang W, Burkhart W, Cavallius J, Merrick WC, Boss WF (1993) Purification and characterization of a phosphatidylinositol 4-kinase activator in carrot cells. J Biol Chem 268(1):392–398PubMedGoogle Scholar
  56. Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W (2004) Genevestigator. Arabidopsis microarray database and analysis toolbox. doi: 10.1104/pp.104.046367. Plant Physiol 136(1):2621–2632Google Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  1. 1.Department of Biological SciencesWestern Michigan UniversityKalamazooUSA

Personalised recommendations