Mutational Analysis of S12 Protein and Implications for the Accuracy of Decoding by the Ribosome

Journal of Molecular Biology

Volumn 374, Issue 4, 2007, Pages 1065-1076

  Sharma, Divya ^a   Cukras, Anthony R ^a   Rogers, Elizabeth J ^a   Southworth, Daniel R ^a   Green, Rachel ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

decoding; domain closure; miscoding; paromomycin; S12

Indexed keywords

AMINOACYL TRANSFER RNA; PAROMOMYCIN; RIBOSOME PROTEIN; RIBOSOME PROTEIN S12; RNA 16S; STREPTOMYCIN; UNCLASSIFIED DRUG;

ARTICLE; CONFORMATIONAL TRANSITION; MOLECULAR RECOGNITION; MUTATIONAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN SYNTHESIS REGULATION; RIBOSOME; SPECIES DIFFERENCE; TRANSLATION REGULATION;

EID: 35748984942     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.10.003     Document Type: Article

References (29)

1. Kramer E.B., and Farabaugh P.J. The frequency of translational misreading errors in E. coli is largely determined by tRNA competition. RNA 13 (2007) 87-96
2. Parker J. Errors and alternatives in reading the universal genetic code. Microbiol. Rev. 53 (1989) 273-298
3. Gromadski K.B., and Rodnina M.V. Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Mol. Cell 13 (2004) 191-200
4. Pape T., Wintermeyer W., and Rodnina M. Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosome. EMBO J. 18 (1999) 3800-3807
5. Gromadski K.B., and Rodnina M.V. Streptomycin interferes with conformational coupling between codon recognition and GTPase activation on the ribosome. Nat. Struct. Mol. Biol. 11 (2004) 316-322
6. Pape T., Wintermeyer W., and Rodnina M.V. Conformational switch in the decoding region of 16S rRNA during aminoacyl-tRNA selection on the ribosome. Nat. Struct. Biol. 7 (2000) 104-107
7. Cochella L., and Green R. An active role for tRNA in decoding beyond codon:anticodon pairing. Science 308 (2005) 1178-1180
8. Ogle J.M., Brodersen D.E., Clemons Jr. W.M., Tarry M.J., Carter A.P., and Ramakrishnan V. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292 (2001) 897-902
9. Ogle J.M., Murphy F.V., Tarry M.J., and Ramakrishnan V. Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell 111 (2002) 721-732
10. Cochella L., Brunelle J.L., and Green R. Mutational analysis reveals two independent molecular requirements during transfer RNA selection on the ribosome. Nat. Struct. Mol. Biol. 14 (2007) 30-36
11. Funatsu G., and Wittmann H.G. Ribosomal proteins. 33. Location of amino-acid replacements in protein S12 isolated from Escherichia coli mutants resistant to streptomycin. J. Mol. Biol. 68 (1972) 547-550
12. Gregory S.T., Cate J.H., and Dahlberg A.E. Streptomycin-resistant and streptomycin-dependent mutants of the extreme thermophile Thermus thermophilus. J. Mol. Biol. 309 (2001) 333-338
13. Traub P., and Nomura M. Streptomycin resistance mutation in Escherichia coli: altered ribosomal protein. Science 160 (1968) 198-199
14. Gorini L. The contrasting role of strA and ram gene products in ribosomal functioning. Cold Spring Harbor Symp. Quant. Biol. 34 (1969) 101-109
15. Datsenko K.A., and Wanner B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97 (2000) 6640-6645
16. Moazed D., and Noller H.F. Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes. Cell 47 (1986) 985-994
17. Moazed D., and Noller H.F. Interaction of antibiotics with functional sites in 16S ribosomal RNA. Nature 327 (1987) 389-394
18. Pilch D.S., Kaul M., Barbieri C.M., and Kerrigan J.E. Thermodynamics of aminoglycoside-rRNA recognition. Biopolymers 70 (2003) 58-79
19. Carter A.P., Clemons W.M., Brodersen D.E., Morgan-Warren R.J., Wimberly B.T., and Ramakrishnan V. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407 (2000) 340-348
20. Wirmer J., and Westhof E. Molecular contacts between antibiotics and the 30S ribosomal particle. Methods Enzymol. 415 (2006) 180-202
21. Borovinskaya M.A., Pai R.D., Zhang W., Schuwirth B.S., Holton J.M., Hirokawa G., et al. Structural basis for aminoglycoside inhibition of bacterial ribosome recycling. Nat. Struct. Mol. Biol. 14 (2007) 727-732
22. DeLano W.L. The PyMOL Molecular Graphics System (2002), DeLano Scientific, San Carlos, CA. http://www.pymol.org http://www.pymol.org
23. Carr J.F., Hamburg D.M., Gregory S.T., Limbach P. A., and Dahlberg A.E. Effects of streptomycin resistance mutations on posttranslational modification of ribosomal protein S12. J. Bacteriol. 188 (2006) 2020-2023
24. Kowalak J.A., and Walsh K.A. Beta-methylthio-aspartic acid: identification of a novel posttranslational modification in ribosomal protein S12 from Escherichia coli. Protein Sci. 5 (1996) 1625-1632
25. Carr J.F., Gregory S.T., and Dahlberg A.E. Severity of the streptomycin resistance and streptomycin dependence phenotypes of ribosomal protein S12 of Thermus thermophilus depends on the identity of highly conserved amino acid residues. J. Bacteriol. 187 (2005) 3548-3550
26. Bilgin N., Claesens F., Pahverk H., and Ehrenberg M. Kinetic properties of Escherichia coli ribosomes with altered forms of S12. J. Mol. Biol. 224 (1992) 1011-1027
27. Allen P.N., and Noller H.F. Mutations in ribosomal proteins S4 and S12 influence the higher order structure of 16 S ribosomal RNA. J. Mol. Biol. 208 (1989) 457-468
28. Gromadski K.B., Daviter T., and Rodnina M.V. A uniform response to mismatches in codon-anticodon complexes ensures ribosomal fidelity. Mol. Cell 21 (2006) 369-377
29. Merryman C., and Noller H.F. Footprinting and modification-interference analysis of binding sites on RNA. In: Smith C.W.J. (Ed). RNA: Protein Interactions: A Practical Approach (1998), Oxford University Press, Oxford