Systematic chromosomal deletion of bacterial ribosomal protein genes

Journal of Molecular Biology

Volumn 413, Issue 4, 2011, Pages 751-761

  Shoji, Shinichiro ^a   Dambacher, Corey M ^a   Shajani, Zahra ^a   Williamson, James R ^a   Schultz, Peter G ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

protein engineering; recombineering; ribonucleoprotein complex; ribosome; translation

Indexed keywords

BACTERIAL PROTEIN; RIBOSOME PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BINDING SITE; CHROMOSOME DELETION; CONTROLLED STUDY; ESCHERICHIA COLI; GENE DELETION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; RIBOSOME;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 80054861886     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.09.004     Document Type: Article

References (54)

1. Roberts, E., Sethi, A., Montoya, J., Woese, C. R. & Luthey-Schulten, Z. (2008). Molecular signatures of ribosomal evolution. Proc. Natl Acad. Sci. USA, 105, 13953-13958.
2. Ban, N., Nissen, P., Hansen, J., Moore, P. B. & Steitz, T. A. (2000). The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science, 289, 905-920. (Pubitemid 30659939)
3. Wimberly, B. T., Brodersen, D. E., Clemons, W. M., Jr, Morgan-Warren, R. J., Carter, A. P., Vonrhein, C. et al. (2000). Structure of the 30S ribosomal subunit. Nature, 407, 327-339.
4. Jenner, L., Demeshkina, N., Yusupova, G. & Yusupov, M. (2010). Structural rearrangements of the ribosome at the tRNA proofreading step. Nat. Struct. Mol. Biol. 17, 1072-1078.
5. Hoang, L., Fredrick, K. & Noller, H. F. (2004). Creating ribosomes with an all-RNA 30S subunit. Proc. Natl Acad. Sci. USA, 101, 12439-12443. (Pubitemid 39122042)
6. Takyar, S., Hickerson, R. P. & Noller, H. F. (2005). mRNA helicase activity of the ribosome. Cell, 120, 49-58. (Pubitemid 40094602)
7. Schmeing, T. M., Voorhees, R. M., Kelley, A. C., Gao, Y. G., Murphy, F. V. t., Weir, J. R. & Ramakrishnan, V. (2009). The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA. Science, 326, 688-694.
8. Gao, Y. G., Selmer, M., Dunham, C. M., Weixlbaumer, A., Kelley, A. C. & Ramakrishnan, V. (2009). The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science, 326, 694-699.
9. Ogle, J. M. & Ramakrishnan, V. (2005). Structural insights into translational fidelity. Annu. Rev. Biochem. 74, 129-177. (Pubitemid 40995504)
10. Maguire, B. A., Beniaminov, A. D., Ramu, H., Mankin, A. S. & Zimmermann, R. A. (2005). A protein component at the heart of an RNA machine: the importance of protein L27 for the function of the bacterial ribosome. Mol. Cell, 20, 427-435. (Pubitemid 41572299)
11. Cukras, A. R., Southworth, D. R., Brunelle, J. L., Culver, G. M. & Green, R. (2003). Ribosomal proteins S12 and S13 function as control elements for translocation of the mRNA:tRNA complex. Mol. Cell, 12, 321-328. (Pubitemid 37238919)
12. Diaconu, M., Kothe, U., Schlunzen, F., Fischer, N., Harms, J. M., Tonevitsky, A. G. et al. (2005). Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation. Cell, 121, 991-1004. (Pubitemid 40884392)
13. Fei, J., Kosuri, P., MacDougall, D. D. & Gonzalez, R. L. (2008). Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Mol. Cell, 30, 348-359. (Pubitemid 351615315)
14. Zaher, H. S. & Green, R. (2010). Hyperaccurate and error-prone ribosomes exploit distinct mechanisms during tRNA selection. Mol. Cell, 39, 110-120.
15. Dabbs, E. R. (1978). Mutational alterations in 50 proteins of the Escherichia coli ribosome. Mol. Gen. Genet. 165, 73-78.
16. Isono, S. & Isono, K. (1978). Mutations affecting the structural genes and the genes coding for modifying enzymes for ribosomal proteins in Escherichia coli. Mol. Gen. Genet. 165, 15-20. (Pubitemid 9021066)
17. Zengel, J. M., Young, R., Dennis, P. P. & Nomura, M. (1977). Role of ribosomal protein S12 in peptide chain elongation: analysis of pleiotropic, streptomycinresistant mutants of Escherichia coli. J. Bacteriol. 129, 1320-1329. (Pubitemid 8109671)
18. Zaman, S., Fitzpatrick, M., Lindahl, L. & Zengel, J. (2007). Novel mutations in ribosomal proteins L4 and L22 that confer erythromycin resistance in Escherichia coli. Mol. Microbiol. 66, 1039-1050. (Pubitemid 350050427)
19. Gorini, L. & Kataja, E. (1964). Phenotypic repair by streptomycin of defective genotypes in E. coli. Proc. Natl Acad. Sci. USA, 51, 487-493.
20. Ozaki, M., Mizushima, S. & Nomura, M. (1969). Identification and functional characterization of the protein controlled by the streptomycin-resistant locus in E. coli. Nature, 222, 333-339.
21. Birge, E. A. & Kurland, C. G. (1970). Reversion of a streptomycin-dependent strain of Escherichia coli. Mol. Gen. Genet. 109, 356-369.
22. Brownstein, B. L. & Lewandowski, L. J. (1967). A mutation suppressing streptomycin dependence. I. An effect on ribosome function. J. Mol. Biol. 25, 99-109.
23. Siller,E.,DeZwaan,D.C.,Anderson, J. F.,Freeman,B.C. &Barral, J. M. (2010). Slowing bacterial translation speed enhances eukaryotic protein folding efficiency. J Mol. Biol. 396s, 1310-1318.
24. Sharan, S. K., Thomason, L. C., Kuznetsov, S. G. & Court, D. L. (2009). Recombineering: a homologous recombination-based method of genetic engineering. Nat. Protoc. 4, 206-223.
25. Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M. et al. (2006). Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, doi:10.1038/ msb4100050.
26. Datsenko, K. A. & Wanner, B. L. (2000). One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA, 97, 6640-6645. (Pubitemid 30412767)
27. Sharpe Elles, L. M., Sykes, M. T., Williamson, J. R. & Uhlenbeck, O. C. (2009). A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit. Nucleic Acids Res. 37, 6503-6514.
28. Wower, I. K., Wower, J. & Zimmermann, R. A. (1998). Ribosomal protein L27 participates in both 50 S subunit assembly and the peptidyl transferase reaction. J. Biol. Chem. 273, 19847-19852. (Pubitemid 28367049)
29. Stoffler-Meilicke, M., Dabbs, E. R., Albrecht-Ehrlich, R. & Stoffler, G. (1985). A mutant from Escherichia coli which lacks ribosomal proteins S17 and L29 used to localize these two proteins on the ribosomal surface. Eur. J. Biochem. 150, 485-490. (Pubitemid 15024826)
30. Dabbs, E. R. (1979). Selection for Escherichia coli mutants with proteins missing from the ribosome. J. Bacteriol. 140, 734-737.
31. Bubunenko, M., Baker, T. & Court, D. L. (2007). Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli. J. Bacteriol. 189, 2844-2853. (Pubitemid 46556067)
32. Franceschi, F. J. & Nierhaus, K. H. (1988). Ribosomal protein L20 can replace the assembly-initiator protein L24 at low temperatures. Biochemistry, 27, 7056-7059.
33. Cukras, A. R. & Green, R. (2005). Multiple effects of S13 in modulating the strength of intersubunit interactions in the ribosome during translation. J. Mol. Biol. 349, 47-59. (Pubitemid 40616447)
34. Kang, Y., Durfee, T., Glasner, J. D., Qiu, Y., Frisch, D., Winterberg, K. M. & Blattner, F. R. (2004). Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186, 4921-4930. (Pubitemid 38970819)
35. Korostelev, A., Trakhanov, S., Laurberg, M. & Noller, H. F. (2006). Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell, 126, 1065-1077. (Pubitemid 44380300)
36. Selmer,M., Dunham, C. M.,Murphy, F. V.,Weixlbaumer, A., Petry, S., Kelley, A. C. et al. (2006). Structure of the 70S ribosome complexed with mRNA and tRNA. Science, 313, 1935-1942. (Pubitemid 44497996)
37. Rhodin, M. H. & Dinman, J. D. (2010). A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding. Nucleic Acids Res. 38, 8377-8389.
38. Schmeing, T. M. & Ramakrishnan, V. (2009). What recent ribosome structures have revealed about the mechanism of translation. Nature, 461, 1234-1242.
39. Kaczanowska, M. & Ryden-Aulin, M. (2007). Ribosome biogenesis and the translation process in Escherichia coli. Microbiol. Mol. Biol. Rev. 71, 477-494. (Pubitemid 47429282)
40. Cech, T. R. (2009). Crawling out of the RNA world. Cell, 136, 599-602.
41. Sykes, M. T. & Williamson, J. R. (2009). A complex assembly landscape for the 30S ribosomal subunit. Annu. Rev. Biophys. 38, 197-215.
42. Herold, M. & Nierhaus, K. H. (1987). Incorporation of six additional proteins to complete the assembly map of the 50 S subunit from Escherichia coli ribosomes. J. Biol. Chem. 262, 8826-8833.
43. Sykes, M. T., Shajani, Z., Sperling, E., Beck, A. H. & Williamson, J. R. (2010). Quantitative proteomic analysis of ribosome assembly and turnover in vivo. J. Mol. Biol. 403, 331-345.
44. Nissen, P., Hansen, J., Ban, N., Moore, P. B. & Steitz, T. A. (2000). The structural basis of ribosome activity in peptide bond synthesis. Science, 289, 920-930. (Pubitemid 30659940)
45. Noller, H. F. (2010). Evolution of protein synthesis from an RNA world. Cold Spring Harbor Perspect. Biol. doi:10.1101/cshperspect.a003681.
46. Rodnina, M. V., Beringer, M. & Wintermeyer, W. (2007). How ribosomes make peptide bonds. Trends Biochem. Sci. 32, 20-26. (Pubitemid 46038738)
47. Liu, C. C. & Schultz, P. G. (2010). Adding new chemistries to the genetic code. Annu. Rev. Biochem. 79, 413-444.
48. Wang, L., Brock, A., Herberich, B. & Schultz, P. G. (2001). Expanding the genetic code of Escherichia coli. Science, 292, 498-500. (Pubitemid 32335951)
49. Anderson, J. C., Wu, N., Santoro, S. W., Lakshman, V., King, D. S. & Schultz, P. G. (2004). An expanded genetic code with a functional quadruplet codon. Proc. Natl Acad. Sci. USA, 101, 7566-7571. (Pubitemid 38658069)
50. Wang, K., Neumann, H., Peak-Chew, S. Y. & Chin, J. W. (2007). Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion. Nat. Biotechnol. 25, 770-777. (Pubitemid 47052187)
51. Neumann, H., Wang, K., Davis, L., Garcia-Alai, M. & Chin, J. W. (2010). Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome. Nature, 464, 441-444.
52. Bokov, K. & Steinberg, S. V. (2009). A hierarchical model for evolution of 23S ribosomal RNA. Nature, 457, 977-980.
53. Young, T. S., Ahmad, I., Yin, J. A. & Schultz, P. G. (2010). An enhanced system for unnatural amino acid mutagenesis in E. coli. J. Mol. Biol. 395, 361-374.
54. Sperling, E., Bunner, A. E., Sykes, M. T. & Williamson, J. R. (2008). Quantitative analysis of isotope distributions in proteomic mass spectrometry using leastsquares Fourier transform convolution. Anal. Chem. 80, 4906-4917. (Pubitemid 351956298)