Spontaneous changes in the reading frame of translation are rare (frequency of 10−3 – 10−4 per codon)1, but can be induced by specific features in the messenger RNA (mRNA). In the presence of mRNA secondary structures, a heptanucleotide “slippery sequence” usually defined by the motif X XXY YYZ, and (in some prokaryotic cases) mRNA sequences that base pair with the 3′ end of the 16S ribosomal rRNA (internal Shine-Dalgarno (SD) sequences), there is an increased probability that a specific programmed change of frame occurs, wherein the ribosome shifts one nucleotide backwards into an overlapping reading frame (−1 frame) and continues by translating a new sequence of amino acids2,3. Despite extensive biochemical and genetic studies, there is no clear mechanistic description for frameshifting. Here, we apply single-molecule fluorescence to track the compositional and conformational dynamics of the individual ribosomes at each codon during translation of a frameshift-inducing mRNA from the dnaX gene in Escherichia coli. Ribosomes that frameshift into the −1 frame are characterized by a 10-fold longer pause in elongation compared to non-frameshifted ribosomes, which translate through unperturbed. During the pause, interactions of the ribosome with the mRNA stimulatory elements uncouple EF-G catalyzed translocation from normal ribosomal subunit reverse-rotation, leaving the ribosome in a non-canonical intersubunit rotated state with an exposed codon in the aminoacyl-tRNA site (A site). tRNALys sampling and accommodation to the empty A site either lead to the slippage of the tRNAs into the −1 frame or maintain the ribosome into the 0 frame. Our results provide a general mechanistic and conformational framework for −1 frameshifting, highlighting multiple kinetic branchpoints during elongation.

N6-methylation of adenosine (m6A) is the most abundant post-transcriptional modification within the coding region of mRNA, but its role during translation remains unknown. Here, we used bulk kinetic and single-molecule methods to probe the effect of m6A in mRNA decoding. Although m6A base pairs with uridine during decoding as shown by x-ray crystallographic analyses of Thermus thermophilus ribosomal complexes, our measurements employing an Escherichia coli translation system revealed that m6A modification of mRNA can act as a barrier to tRNA accommodation and translation elongation. The interaction between an m6A-modified codon and cognate tRNA echoes the interaction between a near-cognate codon and tRNA, as delay in tRNA accommodation depends on the position and context of m6A within codons and on the accuracy level of translation. Overall, our results demonstrate that chemical modification of mRNA can change translational dynamics.

When the nonfluorescent chromoprotein asFP595 from Anemonia sulcata is subjected to sufficiently intense illumination near the absorbance maximum (lambda(abs)(max) = 568 nm), it undergoes a remarkable transition, termed "kindling", to a long-lived fluorescent state (lambda(em)(max) = 595 nm). In the dark recovery phase, the kindled state relaxes thermally on a time scale of seconds or can instantly be reverted upon illumination at 450 nm. The kindling phenomenon is enhanced by the Ala143 --> Gly point mutation, which slows the dark recovery time constant to 100 s at room temperature and increases the fluorescence quantum yield. To investigate the chemical nature of the chromophore and the possible role of chromophore isomerization in the kindling phenomenon, we determined the crystal structure of the "kindling fluorescent protein" asFP595-A143G (KFP) in the dark-adapted state at 1.38 A resolution and 100 K. The chromophore, derived from the Met63-Tyr64-Gly65 tripeptide, closely resembles that of the nonfluorescent chromoprotein Rtms5 in that the configuration is trans about the methylene bridge and there is substantial distortion from planarity. Unlike in Rtms5, in the native protein the polypeptide backbone is cleaved between Cys62 and Met63. The size and shape of the chromophore pocket suggest that the cis isomer of the chromophore could also be accommodated. Within the pocket, partially disordered His197 displays two conformations, which may constitute a binary switch that stabilizes different chromophore configurations. The energy barrier for thermal relaxation was found by Arrhenius plot analysis to be approximately 71 kJ/mol, somewhat higher than the value of approximately 55 kJ/mol observed for cis-trans isomerization of a model chromophore in solution.

Zero-mode waveguides provide a powerful technology for studying single-molecule real-time dynamics of biological systems at physiological ligand concentrations. We customized a commercial zero-mode waveguide-based DNA sequencer for use as a versatile instrument for single-molecule fluorescence detection and showed that the system provides long fluorophore lifetimes with good signal to noise and low spectral cross-talk. We then used a ribosomal translation assay to show real-time fluidic delivery during data acquisition, showing it is possible to follow the conformation and composition of thousands of single biomolecules simultaneously through four spectral channels. This instrument allows high-throughput multiplexed dynamics of single-molecule biological processes over long timescales. The instrumentation presented here has broad applications to single-molecule studies of biological systems and is easily accessible to the biophysical community.D etermining the molecular details of the time evolution of complex multicomponent biological systems requires analysis at the single-molecule level because of their stochastic and heterogeneous nature. Ideally, such experiments would track simultaneously the composition of a biological system (bound ligands, factors, and cofactors) and the conformation of the individual molecules in real time. Single-molecule fluorescence methods, such as total internal reflection fluorescence (TIRF) microscopy, allow the observations of the compositional dynamics (through arrival of fluorescently labeled ligands, factors, or cofactors) and conformational dynamics (through FRET) of single-molecular species. However, these traditional singlemolecule methods are hindered by limitations in maximal fluorescent component concentrations (up to 50 nM) (1), limited simultaneous detection (two to three colors) (2-6), and low throughput (a few hundred molecules at most per experiment) (7). As such, the full potential of single-molecule fluorescence to investigate a range of biological problems under physiologically relevant conditions has not yet been harnessed.Zero-mode waveguides (ZMWs) are small metallic apertures patterned on glass substrates that overcome the concentration restrictions by optically limiting background excitation (8). Each ZMW consists of an ∼150-nm-diameter metallic aperture that restricts the excitation light to a zeptoliter volume, making possible experiments with near-physiological concentrations (up to 20 μM) of fluorescently labeled ligands (1). Previous advances in nanofabrication (9), surface chemistry (10), and detection instrumentation (11) have led to ZMW-based instrumentation capable of the direct observation of DNA polymerization (12), reverse transcription (13), processive myosin motion (14), and translation by the ribosome (15, 16) with multicolor single-molecule detection. However, this sophisticated technology has not been broadly available to the scientific community. Despite multiple efforts to develop ZMW instrumentation, the combined difficulties in fabrica...

During translation elongation, the compositional factors, elongation factor G (EF-G; encoded by fusA) and transfer RNA (tRNA), alternately bind to the ribosome to direct protein synthesis, in turn regulating the conformation of the ribosome. Here, we use single-molecule fluorescence with zero-mode waveguides to correlate directly ribosome conformations and compositions during multiple rounds of elongation at high factor concentrations in Escherichia coli. Our results show that EF-G-GTP continuously samples both rotational sates of the ribosome, binding with higher affinity to the rotated state. Upon successful accommodation into the rotated ribosome, the EF-G-ribosome complex evolves through several rate-limiting conformational changes and the hydrolysis of GTP, which results in a transition back to the non-rotated state, in turn driving translocation and facilitating both EF-G-GDP and E-site tRNA release. These experiments highlight the power of tracking single-molecule conformation and composition simultaneously in real-time.