Abstract
A ribosomal protein of the L25 family specifically binding to 5S rRNA is an evolutionary feature of bacteria. Structural studies showed that within the ribosome this protein contacts not only 5S rRNA, but also the C-terminal region of protein L16. Earlier we demonstrated that ribosomes from the ΔL25 strain of Escherichia coli have reduced functional activity. In the present work, it is established that the reason for this is a fraction of functionally inactive 50S ribosomal subunits. These subunits have a deficit of protein L16 and associate very weakly with 30S subunits. To study the role of the contact of these two proteins in the formation of the active ribosome, we created a number of E. coli strains containing protein L16 with changes in its C-terminal region. We found that some mutations (K133L or K127L/K133L) in this protein lead to a noticeable slowing of cell growth and decrease in the activity of their translational apparatus. As in the case of the ribosomes from the ΔL25 strain, the fraction of 50S subunits, which are deficient in protein L16, is present in the ribosomes of the mutant strains. All these data indicate that the contact with protein L25 is important for the retention of protein L16 within the E. coli ribosome in vivo. In the light of these findings, the role of the protein of the L25 family in maintaining the active state of the bacterial ribosome is discussed.
Similar content being viewed by others
References
Schuwirth, B. S., Borovinskaya, M. A., Hau, C. W., Zhang, W., Vila-Sanjurjo, A., Holton, J. M., and Cate, J. H. D. (2005) Structures of the bacterial ribosome at 3.5 Å resolution, Science, 310, 827–834.
Selmer, M., Dunham, C. M., Murphy, F. V., IVth, Weixlbaumer, A., Petry, S., Kelley, A. C., Weir, J. R., and Ramakrishnan, V. (2006) Structure of the 70S ribosome complexed with mRNA and tRNA, Science, 313, 19351942.
Korostelev, A., Trakhanov, S., Laurberg, M., and Noller, H. F. (2006) Crystal structure of a 70S ribosome–tRNA complex reveals functional interactions and rearrangements, Cell, 126, 1065–1077.
Yusupova, G., Jenner, L., Rees, B., Moras, D., and Yusupov, M. (2006) Structural basis for messenger RNA movement on the ribosome, Nature, 444, 391–394.
Laurberg, M., Asahara, H., Korostelev, A., Zhu, J., Trakhanov, S., and Noller, H. F. (2008) Structural basis for translation on the 70S ribosome, Nature, 454, 852–857.
Voorhees, R. M., Weixlbaumer, A., Loakes, D., Kelley, A. C., and Ramakrishnan, V. (2009) Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome, Nat. Struct. Mol. Biol., 16, 528–533.
Schmeing, T. M., Voorhees, R. M., Kelley, A. C., Gao, Y. G., Murphy, F. V., IVth, Weir, J. R., and Ramakrishnan, V. (2009) The crystal structure of the ribosome bound to EFTu and aminoacyl-tRNA, Science, 326, 688–694.
Gao, Y. G., Selmer, M., Dunham, C. M., Weixlbaumer, A., Kelley, A. C., and Ramakrishnan, V. (2009) The structure of the ribosome with elongation factor G trapped in the posttranslocation state, Science, 326, 694–699.
Dunkle, J. A., Wang, L., Feldman, M. B., Pulk, A., Chen, V. B., Kapral, G. J., Noeske, J., Richardson, J. S., Blanchard, S. C., and Cate, J. H. D. (2011) Structures of the bacterial ribosome in classical and hybrid states of tRNA binding, Science, 332, 981–984.
Lecompte, O., Ripp, R., Thierry, J. C., Moras, D., and Poch, O. (2002) Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale, Nucleic Acids Res., 30, 5382–5390.
Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Wheeler, D. L. (2008) GenBank, Nucleic Acids Res., 36, 25–30.
Ban, N., Beckmann, R., Cate, J. H., Dinman, J. D., Dragon, F., Ellis, S. R., Lafontaine, D. L., Lindahl, L., Liljas, A., Lipton, J. M., McAlear, M. A., Moore, P. B., Noller, H. F., Ortega, J., Panse, V. G., Ramakrishnan, V., Spahn, C. M., Steitz, T. A., Tchorzewski, M., Tollervey, D., Warren, A. J., Williamson, J. R., Wilson, D., Yonath, A., and Yusupov, M. (2014) A new system for naming ribosomal proteins, Curr. Opin. Stuct. Biol., 24, 1–5.
Gongadze, G. M., Korepanov, A. P., Korobeinikova, A. V., and Garber, M. B. (2008) Bacterial 5S rRNA-binding proteins of the CTC family, Biochemistry (Moscow), 73, 14051417.
Hecker, M., and Volker, U. (1990) General stress proteins in Bacillus subtilis, FEMS Microbiol. Ecol., 74, 197–214.
Schmalisch, M., Langbein, I., and Stulke, J. (2002) The general stress protein CTC of Bacillus subtilis is a ribosomal protein, J. Mol. Microbiol. Biotechnol., 4, 495–501.
Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., and Mori, H. (2006) Construction of Escherichia coli K-12 inframe, single-gene knockout mutants: the Keio collection, Mol. Syst. Biol., 2, 1–11.
Korepanov, A. P., Gongadze, G. M., Garber, M. B., Court, D. L., and Bubunenko, M. G. (2007) Importance of the 5S rRNA-binding ribosomal proteins for cell viability and translation in Escherichia coli, J. Mol. Biol., 366, 1199–1208.
Lotti, M., Noah, M., Stoffler-Meilicke, M., and Stoffler, G. (1989) Localization of L4, L5, L20 and L25 on the ribosomal surface by immune-electron microscopy, Mol. Gen. Genet., 216, 245–253.
Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F., and Yonath, A. (2001) High resolution structure of the large ribosomal subunit from a mesophilic eubacterium, Cell, 107, 679–688.
Kazemie, M. (1976) Binding of aminoacyl-tRNA to reconstituted subparticles of Escherichia coli large ribosomal subunits, Eur. J. Biochem., 67, 373–378.
Teraoka, H., and Nierhaus, K. H. (1978) Protein L16 induces a conformational change when incorporated into a L16-deficient core derived from Escherichia coli ribosomes, FEBS Lett., 88, 223–227.
Tate, W. P., Schulze, H., and Nierhaus, K. H. (1983) The importance of the Escherichia coli ribosomal protein L16 for the reconstitution of the peptidyl-tRNA hydrolysis activity of peptide chain termination, J. Biol. Chem., 258, 12810–12815.
Anikaev, A. Y., Korepanov, A. P., Korobeinikova, A. V., Kljashtorny, V. G., Piendl, W., Nikonov, S. V., Garber, M. B., and Gongadze, G. M. (2014) Mutant forms of Escherichia coli protein L25 unable to bind to 5S rRNA are incorporated efficiently into the ribosome in vivo, Biochemistry (Moscow), 79, 826–835.
Miller, J. H. (1972) Experiments in Molecular Genetics, Cold Spring Harbor Laboratory Press, N. Y.
Yu, D., Ellis, H. M., Lee, E. C., Jenkins, N. A., Copeland, N. G., and Court, D. L. (2000) An efficient recombination system for chromosome engineering in Escherichia coli, Proc. Natl. Acad. Sci. USA, 97, 5978–5983.
Thomason, L. C., Bubunenko, M., Costantino, N., Wilson, H., Oppenheim, A., Datta, S., and Court, D. L. (2007) Recombineering: genetic engineering in bacteria using homologous recombination, Curr. Protoc. Mol. Biol., doi: 10.1002/0471142727.mb0116s78.
Erbe, R. W., Nau, M. M., and Leder, P. (1969) Translation and translocation of defined RNA messengers, J. Mol. Biol., 38, 441–460.
Staehelin, T., Maglott, D. M., and Monro, R. E. (1969) On the catalytic center of peptidyl transfer: a part of the 50S ribosome structure, Cold Spring Harb. Symp. Quant. Biol., 34, 39–48.
Schlessinger, D., Mangiarotti, G., and Apirion, D. (1967) The formation and stabilization of 30S and 50S ribosome couples in Escherichia coli, Proc. Natl. Acad. Sci. USA, 58, 1782–1789.
Kohler, R. A., Ron, E. Z., and Davis, B. D. (1968) Significance of the free 70S ribosomes in Escherichia coli extracts, J. Mol. Biol., 36, 71–82.
Kolb, V. A., Makeyev, E. V., and Spirin, A. S. (2000) Cotranslational folding of an eukaryotic multidomain protein in a prokaryotic translation system, J. Biol. Chem., 275, 16597–16601.
Madjar, J., Michel, S., Cozzone, A., and Reboud, J. (1979) A method to identify individual proteins in four different two-dimensional electrophoresis systems: application to E. coli ribosomal proteins, Anal. Biochem., 92, 174–182.
Algranati, I. D., Gonzalez, N. S., and Bade, E. G. (1969) Physiological role of 70S ribosome in bacteria, Proc. Natl. Acad. Sci. USA, 62, 574–580.
Cannon, M. (1967) The ribosomal binding site for peptidyl-transfer-ribonucleic acid, Biochem. J., 104, 934–946.
Klein, D. J., Moore, P. B., and Steitz, T. A. (2004) The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit, J. Mol. Biol., 340, 141–177.
Ben-Shem, A., Garreau de Loubresse, N., Melnikov, S., Jenner, L., Yusupova, G., and Yusupov, M. (2011) The structure of the eukaryotic ribosome at 3.0 Å resolution, Science, 334, 1524–1529.
Wilson, K. S., Ito, K., Noller, H. F., and Nakamura, Y. (2000) Functional sites of interaction between release factor RF1 and the ribosome, Nat. Struct. Biol., 7, 866–870.
La Teana, A., Gualerzi, C. O., and Dahlberg, A. E. (2001) Initiation factor IF2 binds to the a-sarcin loop and helix 89 of Escherichia coli 23S ribosomal RNA, RNA, 7, 11731179.
Scarlett, D. J., McCaughan, K. K., Wilson, D. N., and Tate, W. P. (2003) Mapping functionally important motifs SPF and GGQ of the decoding release factor RF2 to the Escherichia coli ribosome by hydroxyl radical footprinting, J. Biol. Chem., 278, 15095–15104.
Wilson, K. S., and Nechifor, R. (2004) Interactions of translation factor EF-G with the bacterial ribosome before and after mRNA translocation, J. Mol. Biol., 337, 15–30.
Sergiev, P. V., Bogdanov, A. A., and Dontsova, O. A. (2005) How can elongation factors EF-G and EF-Tu discriminate the functional state of the ribosome using the same binding site? FEBS Lett., 579, 5439–5442.
Kiparisov, S. V., Sergiev, P. V., Bogdanov, A. A., and Dontsova, O. A. (2006) The structural changes in the ribosome during the elongation cycle, Mol. Biol. (Moscow), 40, 755–768.
Author information
Authors and Affiliations
Corresponding author
Additional information
Published in Russian in Biokhimiya, 2016, Vol. 81, No. 1, pp. 68-77.
Originally published in Biochemistry (Moscow) On-Line, Papers in Press, as Manuscript BM15-230, November 1, 2015.
Electronic supplementary material
Rights and permissions
About this article
Cite this article
Anikaev, A.Y., Isaev, A.B., Korobeinikova, A.V. et al. Role of protein L25 and its contact with protein L16 in maintaining the active state of Escherichia coli ribosomes in vivo . Biochemistry Moscow 81, 19–27 (2016). https://doi.org/10.1134/S0006297916010028
Received:
Revised:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S0006297916010028