A Conformational Switch in Escherichia coli 16 S Ribosomal RNA During Decoding of Messenger RNA
Abstract
Direct evidence is presented for a conformational switch in 16 S ribosomal RNA (rRNA) that affects tRNA binding to the ribosome and decoding of messenger RNA (mRNA). These data support the hypothesis that dynamic changes in rRNA structure occur during translation. The switch involves two alternating base-paired arrangements apparently facilitated by ribosomal proteins S5 and S12, and produces significant changes in the rRNA structure. Chemical probing shows reciprocal enhancements or protections at sites in 16 S rRNA that are at or very near sites that were previously crosslinked to mRNA. These data indicate that the switch affects codon-anticodon arrangement and proper selection of tRNA at the ribosomal A site, and that the switch is a fundamental mechanism in all ribosomes.
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H27 and its surroundings have been implicated in conformational changes associated with a transition from an error-prone ram state to a hyperaccurate restrictive state.
“H27 and its surroundings have been implicated in conformational changes associated with a transition from an error-prone ram state to a hyperaccurate restrictive state (Allen and Noller 1989; Lodmell and Dahlberg 1997”
From The Structural Basis for the Action of the Antibiotics Tetracycline, Pactamycin, and Hygromycin B on the 30S Ribosomal Subunit (2000) · cites this paper as Lodmell and Dahlberg 1997
H27 has been proposed to switch between two base-pairing schemes during the ram-to-restrictive transition.
“in particular, H27 has been proposed to switch between two base-pairing schemes during this transition. (Lodmell and Dahlberg 1997”
From The Structural Basis for the Action of the Antibiotics Tetracycline, Pactamycin, and Hygromycin B on the 30S Ribosomal Subunit (2000) · cites this paper as Lodmell and Dahlberg 1997
Transition between the two states affects bases at the very top of H44, at the site of HygB binding.
“This is consistent with the finding that transition between the two states affects bases at the very top of H44, i.e., at the site of HygB binding (Lodmell and Dahlberg 1997”
From The Structural Basis for the Action of the Antibiotics Tetracycline, Pactamycin, and Hygromycin B on the 30S Ribosomal Subunit (2000) · cites this paper as Lodmell and Dahlberg 1997
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Structure of the 30S ribosomal subunit
Wimberly, B. T., Brodersen, D. E., Clemons, W. M., Morgan-Warren, R. J., Carter, A. P., Vonrhein, C., Hartsch, T., & Ramakrishnan, V. (2000) · Nature · doi:10.1038/35030006 · Cited by 2,035 · see citing works
Crystal structure of the ribosome at 5.5 Å resolution
Yusupov, M. M., Yusupova, G. Z., Baucom, A., Lieberman, K., Earnest, T. N., Cate, J. H. D., & Noller, H. F. (2001) · Science · doi:10.1126/science.1060089 · Cited by 1,944 · see citing works
Carter, A. P., Clemons, W. M., Brodersen, D. E., Morgan-Warren, R. J., Wimberly, B. T., & Ramakrishnan, V. (2000) · Nature · doi:10.1038/35030019 · Cited by 1,615 · see citing works
Structure of Functionally Activated Small Ribosomal Subunit at 3.3 Å Resolution
Schluenzen, F., Tocilj, A., Zarivach, R., Harms, J., Gluehmann, M., Janell, D., Bashan, A., Bartels, H., Agmon, I., Franceschi, F., et al. (2000) · Cell · doi:10.1016/s0092-8674(00)00084-2 · Cited by 979 · see citing works
Brodersen, D. E., Clemons, W. M., Carter, A. P., Morgan-Warren, R. J., Wimberly, B. T., & Ramakrishnan, V. (2000) · Cell · doi:10.1016/s0092-8674(00)00216-6 · Cited by 950 · see citing works
“This is consistent with the finding that transition further experiments will be needed to ascertain whether between the two states affects bases at the very top the secondary site is a physiologically relevant site or of H44, i.e., at the site of HygB binding (Lodmell and a nonspecific one.”
BackgroundSelection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form
Ogle, J. M., Murphy, F. V., Tarry, M. J., & Ramakrishnan, V. (2002) · Cell · doi:10.1016/s0092-8674(02)01086-3 · Cited by 663 · see citing works
Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3
Pioletti, M., Schlünzen, F., Harms, J., Zarivach, R., Glühmann, M., Avila, H., Bashan, A., Bartels, H., Auerbach, T., Jacobi, C., et al. (2001) · The EMBO Journal · doi:10.1093/emboj/20.8.1829 · Cited by 527 · see citing works
Ribosomal Protection Proteins and Their Mechanism ofTetracyclineResistance
Connell, S. R., Tracz, D. M., Nierhaus, K. H., & Taylor, D. E. (2003) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.47.12.3675-3681.2003 · Cited by 449 · see citing works
Cameron, D. M., Thompson, J., March, P. E., & Dahlberg, A. E. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00235-8 · Cited by 99 · see citing works
- Authors
- Lodmell, J. S., & Dahlberg, A. E.
- Affiliations
- Brown University (US)
- The authors are in the Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.
- Corresponding author
- Lodmell, J. Stephen
- ORCID
- Lodmell, J. Stephen
- Venue
- Science
- Published
- 1997-08-29
- Volume
- 277
- Issue
- 5330
- Pages
- 1262-1267
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2122199512
- Cited by
- 212
- References
- 0
- Citations by year
- 2025: 1 · 2022: 1 · 2021: 3 · 2020: 1 · 2019: 3 · 2018: 1 · 2017: 3 · 2016: 3 · 2014: 10 · 2013: 2 · 2012: 2
- FWCI
- 7.47
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (GM07601, GM19756, T32GM007601)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- 16S rRNA, conformational switching, mRNA decoding, codon-anticodon pairing, tRNA binding, ribosomal A site, ribosomal protein S5, ribosomal protein S12, translation (biology), chemical probing, crosslinking
- MeSH terms
- Anticodon, Base Composition, Codon, Escherichia coli, Mutation, Nucleic Acid Conformation, Ribosomal Proteins, Ribosomes, RNA, Bacterial, RNA, Messenger, RNA, Ribosomal, 16S, RNA, Transfer, Protein Biosynthesis
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