The Path of Messenger RNA through the Ribosome

Using X-ray crystallography, we have directly observed the path of mRNA in the 70S ribosome in Fourier difference maps at 7 A resolution. About 30 nucleotides of the mRNA are wrapped in a groove that encircles the neck of the 30S subunit. The Shine-Dalgarno helix is bound in a large cleft between the head and the back of the platform. At the interface, only about eight nucleotides (-1 to +7), centered on the junction between the A and P codons, are exposed, and bond almost exclusively to 16S rRNA. The mRNA enters the ribosome around position +13 to +15, the location of downstream pseudoknots that stimulate -1 translational frame shifting.

[1]  A. Spirin,et al.  Factor-free ("non-enzymic") and factor-dependent systems of translation of polyuridylic acid by Escherichia coli ribosomes. , 1976, Journal of molecular biology.

[2]  Joachim Frank,et al.  EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome , 1999, Nature Structural Biology.

[3]  J. Shine,et al.  The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[4]  S C Schultz,et al.  Molecular basis of double‐stranded RNA‐protein interactions: structure of a dsRNA‐binding domain complexed with dsRNA , 1998, The EMBO journal.

[5]  S. Ochoa,et al.  1. Polypeptide Chain Initiation , 1974 .

[6]  T. Earnest,et al.  X-ray crystal structures of 70S ribosome functional complexes. , 1999, Science.

[7]  R. Brimacombe,et al.  Site-directed cross-linking of mRNA analogues to 16S ribosomal RNA; a complete scan of cross-links from all positions between '+1' and '+16' on the mRNA, downstream from the decoding site. , 1993, Nucleic acids research.

[8]  H. Noller.  Structure of ribosomal RNA. , 1984, Annual review of biochemistry.

[9]  H. Noller,et al.  Binding of tRNA to the ribosomal A and P sites protects two distinct sets of nucleotides in 16 S rRNA. , 1990, Journal of molecular biology.

[10]  H F Noller,et al.  Identification of bases in 16S rRNA essential for tRNA binding at the 30S ribosomal P site , 1995, Science.

[11]  J. F. Atkins,et al.  Programmed ribosomal frameshifting: much ado about knotting! , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[12]  A. Spirin,et al.  Template‐free ribosomal synthesis of polylysine from lysyl‐tRNA , 1981, FEBS letters.

[13]  M. Bretscher.  Direct Translation of a Circular Messenger DNA , 1968, Nature.

[14]  Harry F. Noller,et al.  Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes , 1986, Cell.

[15]  T. Earnest,et al.  Crystal Structure of the Ribosome at 5.5 Å Resolution , 2001, Science.

[16]  R. Brimacombe,et al.  Contacts between 16S ribosomal RNA and mRNA, within the spacer region separating the AUG initiator codon and the Shine-Dalgarno sequence; a site-directed cross-linking study. , 1994, Nucleic acids research.

[17]  I. Brierley,et al.  Characterization of an efficient coronavirus ribosomal frameshifting signal: Requirement for an RNA pseudoknot , 1989, Cell.

[18]  P. Wollenzien,et al.  The mRNA binding track in the Escherichia coli ribosome for mRNAs of different sequences. , 1992, Biochemistry.

[19]  C. Gualerzi,et al.  Initial rate kinetic analysis of the mechanism of initiation complex formation and the role of initiation factor IF-3. , 1977, Biochemistry.

[20]  V. Ramakrishnan,et al.  Structure of the 30 S ribosomal subunit , 2022 .

[21]  Harry F. Noller,et al.  Interaction of antibiotics with functional sites in 16S ribosomal RNA , 1987, Nature.

[22]  T A Jones,et al.  Electron-density map interpretation. , 1997, Methods in enzymology.

[23]  R. Brimacombe,et al.  The cross-link from the upstream region of mRNA to ribosomal protein S7 is located in the C-terminal peptide: experimental verification of a prediction from modeling studies. , 1999, RNA.

[24]  P. Wollenzien,et al.  Arrangement of messenger RNA on Escherichia coli ribosomes with respect to 10 16S rRNA cross-linking sites. , 1994, Biochemistry.

[25]  H. Noller,et al.  Footprinting mRNA‐ribosome complexes with chemical probes. , 1994, The EMBO journal.

[26]  J Frank,et al.  Three-dimensional reconstruction of the Escherichia coli 30 S ribosomal subunit in ice. , 1996, Journal of molecular biology.

[27]  F. Schluenzen,et al.  Structure of Functionally Activated Small Ribosomal Subunit at 3.3 Å Resolution , 2000, Cell.

[28]  R. Brimacombe,et al.  The path of mRNA through the bacterial ribosome: a site-directed crosslinking study using new photoreactive derivatives of guanosine and uridine. , 1997, RNA.

[29]  A. Bogdanov,et al.  How does the mRNA pass through the ribosome? , 1991, Biochimie.

[30]  J. Frank,et al.  A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome , 1995, Nature.

[31]  R. Brimacombe,et al.  The structure of ribosomal RNA: a three-dimensional jigsaw puzzle. , 1995, European journal of biochemistry.

[32]  C. Vonrhein,et al.  Structure of the 30S ribosomal subunit , 2000, Nature.

[33]  A. Bogdanov,et al.  Transition of the mRNA sequence downstream from the initiation codon into a single-stranded conformation is strongly promoted by binding of the initiator tRNA , 1990, Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression.

[34]  R. Brimacombe,et al.  Three widely separated positions in the 16S RNA lie in or close to the ribosomal decoding region; a site‐directed cross‐linking study with mRNA analogues. , 1992, The EMBO journal.

[35]  V. Ramakrishnan,et al.  Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit , 2001, Science.

[36]  P. Wollenzien,et al.  Distribution of Cross-links between mRNA Analogues and 16 S rRNA in Escherichia coli 70 S Ribosomes Made under Equilibrium Conditions and Their Response to tRNA Binding (*) , 1995, The Journal of Biological Chemistry.

[37]  J. Steitz.  Polypeptide Chain Initiation: Nucleotide Sequences of the Three Ribosomal Binding Sites in Bacteriophage R17 RNA , 1969, Nature.