frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation

• Published in: Proceedings of the National Academy of Sciences - PNAS 2014-04, Vol.111 (15), p.5538-5543
• Main Authors: Kim, Hee-Kyung, Liu, Fei, Fei, Jingyi, Bustamante, Carlos, Gonzalez, Ruben L., Tinoco, Ignacio
• Format: Article
• Language: English
• Subjects: Amino acids; Bacterial Proteins - genetics; Binding sites; Biological Sciences; Codons; DNA Polymerase III - genetics; E coli; Escherichia coli; Escherichia coli - genetics; Escherichia coli - physiology; Fluorescence; Fluorescence Resonance Energy Transfer; Frameshifting, Ribosomal - physiology; Histograms; Hybridity; Messenger RNA; Models, Genetic; Models, Molecular; Molecular Conformation; Peptide elongation factors; Proteins; Ribosomes; Ribosomes - metabolism; Ribosomes - physiology; RNA; RNA, Messenger - metabolism; Transfer RNA
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1403457111

Ribosomal frameshifting occurs when a ribosome slips a few nucleotides on an mRNA and generates a new sequence of amino acids. Programmed −1 ribosomal frameshifting (−1PRF) is used in various systems to express two or more proteins from a single mRNA at precisely regulated levels. We used single-molecule fluorescence resonance energy transfer (smFRET) to study the dynamics of −1PRF in the Escherichia coli dnaX gene. The frameshifting mRNA (FSmRNA) contained the frameshifting signals: a Shine–Dalgarno sequence, a slippery sequence, and a downstream stem loop. The dynamics of ribosomal complexes translating through the slippery sequence were characterized using smFRET between the Cy3-labeled L1 stalk of the large ribosomal subunit and a Cy5-labeled tRNA ᴸʸˢ in the ribosomal peptidyl-tRNA–binding (P) site. We observed significantly slower elongation factor G (EF-G)–catalyzed translocation through the slippery sequence of FSmRNA in comparison with an mRNA lacking the stem loop, ΔSL. Furthermore, the P-site tRNA/L1 stalk of FSmRNA-programmed pretranslocation (PRE) ribosomal complexes exhibited multiple fluctuations between the classical/open and hybrid/closed states, respectively, in the presence of EF-G before translocation, in contrast with ΔSL-programmed PRE complexes, which sampled the hybrid/closed state approximately once before undergoing translocation. Quantitative analysis showed that the stimulatory stem loop destabilizes the hybrid state and elevates the energy barriers corresponding to subsequent substeps of translocation. The shift of the FSmRNA-programmed PRE complex equilibrium toward the classical/open state and toward states that favor EF-G dissociation apparently allows the PRE complex to explore alternative translocation pathways such as −1PRF.