Biopolym. Cell. 2009; 25(6):457-465.
http://dx.doi.org/10.7124/bc.0007F8
Structure and Function of Biopolymers
Interaction of different tRNAs with translation elongation factors 1A from lower and higher eukaryotes
1Futernyk P. V., 1Negrutskii B. S., 1El'skaya A. V.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

The work is aimed at confirmation of earlier assumed mechanism of tRNA channeling. Methods. The methods of band shift assay and Forsters resonance energy transfer were used. Results. The affinities of mammalian tRNAs for two tissue specific isoforms of elongator factor eEF1A1 and eEF1A2 were compared. For the first time we have shown the ability of yeast eEF1A*GDP to form non-canonical ternary complex with deacylated tRNAs. The complexation of eukaryotic eEF1A with initiator tRNA, of both bacterial and mammalian origin, was also demonstrated. Conclusions. The formation of the non-canonical complexes of eEF1A*GDP with deacylated tRNAs is common for higher and lower eukaryotes, which is in favor of universality of eukaryotic tRNA-channeling.
Keywords: elongation factor, tRNA, translation, channeling, elongation
Full text: (PDF, in English)

References

[1] Negrutskii B. S., El'skaya A. V. Eukaryotic translation elongation factor 1 alpha: structure, expression, functions, and possible role in aminoacyl-tRNA channeling. Prog. Nucl. Acid Res. Mol. Biol 1998 60:47–78.
[2] Negrutskii B. S., Deutscher M. P. A sequestered pool of aminoacyltRNA in mammalian cells Proc. Nat. Acad. Sci. USA 1992 89, N 8:3601–3604.
[3] Negrutskii B. S., Stapulionis R., Deutscher M. P. Supramolecular organization of the mammalian translation system Proc. Nat. Acad. Sci. USA 1994 91, N 3:964–968.
[4] Petrushenko Z. M., Negrutskii B. S., Ladokhin A. S., Budkevich T. V., Shalak V. F., El'skaya A. V. Evidence for the formation of an unusual ternary complex of rabbit liver EF-1 with GDP and deacylated tRNA FEBS Lett 1997 407, N 1:13–17.
[5] Petrushenko Z. M., Budkevich T. V., Shalak V. F., Negrutskii B. S., El'skaya A. V. Novel complexes of mammalian translation elongation factor eEF1A. GDP with uncharged tRNA and aminoacyl-tRNA synthetase. Implications for tRNA channeling Eur. J. Biochem 2002 269, N 19:4811–4818.
[6] Futernyk P. V., Negrutskii B. S., El'ska G. V. Noncanonical complexes of mammalian eEF1A with various deacylated tRNAs Biopolym. Cell 2008 24, N 6:453–462.
[7] Berchtold H., Reshetnikova L., Reiser C. O., Schirmer N. K., Spinzl M., Hilgenfeld R. Crystal structure of active elongation factor Tu reveals major domain rearrangements Nature 1993 365, N 6442:126–132.
[8] Abel K., Yoder M. D., Hilgenfeld R., Jurnak F. An alpha to beta conformational switch in EF-Tu Structure 1996 4, N 10:1153–1159.
[9] Polekhina G., Thirup S., Kjeldgaard M., Nissen P., Lippmann C., Nyborg J. Helix unwinding in the effector region of elongation factor EF-Tu-GDP Structure 1996 4, N 10 P. 1141–1151.
[10] LaRiviere F. J., Wolfson A. D., Uhlenbeck O. C. Uniform binding of amynoacyl-tRNAs to elongation factor Tu bynthermodynamic compensation Science 2001 294, N 5540:165–168.
[11] Asahara H., Uhlenbeck O. C. The tRNA specificity of Thermus thermophilus EF-Tu Proc. Nat. Acad. Sci. USA 2002 99, N 6:3499–3504.
[12] Dale T., Sanderson L. E., Uhlenbeck O. C. The affinity of elongation factor Tu for an aminoacyl-tRNA is modulated by the esterified amino acid Biochemistry 2004 43, N 20 P. 6159–6166.
[13] Sanderson L. E., Uhlenbeck O. C. Exploring the specificity of elongation factor Tu for different tRNA bodies Biochemistry 2007 46, N 21:6194–6200.
[14] Nissen P., Kjeldgaard M., Thirup S., Polekhina G., Reshetnikova L., Clark B. F. C., Nyborg J. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog Science 1995 270, N 5241:1464–1472.
[15] Nissen P., Thirup S., Kjeldgaard M., Nyborg J. The crystal structure of Cys-tRNACys–EF-Tu–GDPNP reveals general and specific features in the ternary complex in the tRNA Structure 1999 7, N 2:143–156.
[16] Dreher T. W., Uhlenbeck O. C., Browningi K. S. Quantitative assessment of EF-1a*GTP binding to aminoacyl-tRNAs, aminoacyl-viral RNA, and tRNA shows close correspondence to the RNA binding properties of EF-Tu J. Bol. Chem 1999 274, N 2:666–672.
[17] Allers J., Shamoo Y. Structure-based analysis of proteinRNA interactions using the program ENTANGLE J. Mol. Biol 2001 311, N 1:75–86.
[18] Jones S., Daley D. T., Luscombe N. M., Berman H. M., Thornton J. M. Protein-RNA interactions: A structural analysis Nucl. Acids Res 2001 29, N 4:943–954.
[19] Treger M., Westhof E. Statistical analysis of atomic contacts at RNA-protein interfaces J. Mol. Recognit 2001 14, N 4:199–214.
[20] Cheng A. C., Chen W. W., Fuhrmann C. N., Frankel A. D. Recognition of nucleic acid bases and base pairs by hydrogen bonding to amino acid side chains J. Mol. Biol 2003 327, N 4:781–796.
[21] Gromadski K. B., Schummer T., Stromgaard A., Knudsen C. R., Kinzy T. G., Rodnina M. V. Kinetics of the interactions between yeast elongation factors 1A and 1Ba, Guanine nucleotides, and aminocyl-tRNA J. Biol. Chem 2007 282, N 49:35629–35637.
[22] Sternbach H., von der Haar F., Schlimme E., Gaertner E., Cramer F. Isolation and properties of tRNA nucleotidyl transferase from yeast Eur. J. Biochem 1971 22, N 2 P. 166–172.
[23] Muench K. H., Berg P. Purification of crude aminoacyltRNA synthetases from Escherichia coli. Meth. Enzymol. 1968; 12:357.
[24] Keller E., Zamechnic P. The effect of guanosine diphosphate and triphosphate on the incorporation of labeled amino acids into proteins. J. Biol. Chem. 1956; 222:45–50.
[25] Shalak V. F., Budkevich T. V., Nergutskii B. S., El'skaya A. V. A fast and effective method for purification of elongation factor 1a from rabbit liver. Ukr Biokhim Zh. 1997; 69(2):104–109.
[26] Maniatis T., Fritsch E. F., Sambrook J. Molecular cloning: a laboratory manual New York: Cold Spring Harbor Lab. press, 1989 342 p.
[27] Ott G., Faulhammer H. G., Spinzl M. Interaction of elongation factor Tu from Escherichia coli with aminoacyl-tRNA carrying a fluorescent reporter group on the 3' terminus Eur. J. Biochem 1989 184, N 2:345–352.
[28] Hudson E. N., Weber G. Synthesis and characterization of two fluorescent sulfhydryl reagents Biochemistry 1973 12, N 21:4154–4161.
[29] Silberclang M., Gillum A. M., RajBhandary U. L. Use of in vitro 32P labeling in the sequence analysis of nonradioactive tRNAs Meth. Enzymol 1979 59:58–109.
[30] Carvalho J. F., Carvalho M. D., Merrick W. C. Purification of various forms of elongation factor 1 from rabbit reticulocytes Arch. Biochem. and Biophys 1984 234, N 2:591–602.
[31] Cavallius J., Merrick W. C. Site directed mutagenesis of yeast eEF1A. Variable mutants with altered nucleotide specificity J. Biol. Chem 1998 273, N 44:28752–28758.
[32] Li G., Levitus M., Bustamante C., Widom J. Rapid spontaneous accessibility of nucleosomal DNA Nat. Struct. Mol. Biol 2005 12, N 1:46–53.
[33] Wu P., Brand L. Conformational flexibility in a staphylococcal nuclease mutant K45C from time-resolved resonance energy transfer measurements Biochemistry 1994 33, N 34:10457–10462.
[34] Matsumoto S., Hammes G. G. Fluorescence energy transfer between ligand binding sites on aspartate transcarbamylase Biochemistry 1975 14, N 2:214–224. 464
[35] Simsek M., RajBhandary U. L., Boisnard M., Petrissant G. Nucleotide sequence of rabbit liver and sheep mammary gland cytoplasmic initiatory transfer RNAs Nature 1974 247, N 442:518–520.
[36] Piper P. W., Clark B. F. Primary structure of a mouse mieloma cell initiator transfer RNA Nature 1974 247, N 442 P. 516–518.
[37] Forster C., Chakraburtty K., Sprinzl M. Discrimination between initiation and elongation of protein biosynthesis in yeast: Identity assured by a nucleotide modification in the initiator tRNA Nucl. Acids Res 1993 21, N 24:5679– 5683.
[38] Kiesewetter S., Ott G., Sprinzl M. The role of modified purine 64 in initiator/elongator discrimination of tRNAi Met from yeast and wheat germ Nucl. Acids Res 1990 18, N 16 P. 4677–4682.
[39] Astrom S. U., Bystrom A. S. Rit 1, a tRNA backbone modifying enzyme that mediates initiator and elongator tRNA discrimination Cell 1994 79, N 3:535–546.
[40] Andersen G. R., Pedersen L., Valente L., Chatterjee I., Kinzy T. G., Kjeldgaard M., Nyborg J. Structural basis for nucleotide exchange and competition with tRNA in the yeast elongation factor complex Eef1A:Eef1Ba Mol Cell. 2000;6(5):1261-6.
[41] Andersen G. R., Valente L., Pedersen L., Kinzy T. G., Nyborg J. Crystal structures of nucleotide exchange intermediates in the Eef1A-Eef1Balpha complex Nat. Struct. Biol 2001 8, N 6:531–534.
[42] Kanibolotsky D. S., Novosyl'na O. V., Abbott C. M., Negrutskii B. S., El'skaya A. V. Multiple molecular dynamics simulation of the isoforms of human translation elongation factor 1A reveals reversible fluctuations between «open» and «closed» conformations and suggests specific for eEF1A1 affinity for Ca2+-calmodulin BMC Struct. Biol 2008 8:4.
[43] Sanderson L. E., Uhlenbeck O. C. The 51–63 base pair of tRNA confers specificity for binding by EF-Tu RNA 2007 13, N 6:835–840.