A cryo-electron microscopic study of ribosome-bound termination factor RF2

Protein synthesis takes place on the ribosome, where genetic information carried by messenger RNA is translated into a sequence of amino acids. This process is terminated when a stop codon moves into the ribosomal decoding centre (DC) and is recognized by a class-1 release factor (RF). RFs have a conserved GGQ amino-acid motif, which is crucial for peptide release and is believed to interact directly with the peptidyl-transferase centre (PTC) of the 50S ribosomal subunit. Another conserved motif of RFs (SPF in RF2) has been proposed to interact directly with stop codons in the DC of the 30S subunit. The distance between the DC and PTC is approximately 73 A. However, in the X-ray structure of RF2, SPF and GGQ are only 23 A apart, indicating that they cannot be at DC and PTC simultaneously. Here we show that RF2 is in an open conformation when bound to the ribosome, allowing GGQ to reach the PTC while still allowing SPF-stop-codon interaction. The results indicate new interpretations of accuracy in termination, and have implications for how the presence of a stop codon in the DC is signalled to PTC.     

Structure of the Escherichia coli ribosomal termination complex with release factor 2

Termination of protein synthesis occurs when the messenger RNA presents a stop codon in the ribosomal aminoacyl (A) site. Class I release factor proteins (RF1 or RF2) are believed to recognize stop codons via tripeptide motifs, leading to release of the completed polypeptide chain from its covalent attachment to transfer RNA in the ribosomal peptidyl (P) site. Class I RFs possess a conserved GGQ amino-acid motif that is thought to be involved directly in protein-transfer-RNA bond hydrolysis. Crystal structures of bacterial and eukaryotic class I RFs have been determined, but the mechanism of stop codon recognition and peptidyl-tRNA hydrolysis remains unclear. Here we present the structure of the Escherichia coli ribosome in a post-termination complex with RF2, obtained by single-particle cryo-electron microscopy (cryo-EM). Fitting the known 70S and RF2 structures into the electron density map reveals that RF2 adopts a different conformation on the ribosome when compared with the crystal structure of the isolated protein. The amino-terminal helical domain of RF2 contacts the factor-binding site of the ribosome, the 'SPF' loop of the protein is situated close to the mRNA, and the GGQ-containing domain of RF2 interacts with the peptidyl-transferase centre (PTC). By connecting the ribosomal decoding centre with the PTC, RF2 functionally mimics a tRNA molecule in the A site. Translational termination in eukaryotes is likely to be based on a similar mechanism.     

Virology: independent virus development outside a host

Viruses are thought to be functionally inactive once they are outside and independent of their host cell. Here we describe an exceptional property of a newly discovered virus that infects a hyperthermophilic archaeon growing in acidic hot springs: the lemon-shaped viral particle develops a very long tail at each of its pointed ends after being released from its host cell. The process occurs only at the temperature of the host's habitat (75-90 degrees C) and it does not require the presence of the host cell, an exogenous energy source or any cofactors. This host-independent morphological development may be a strategy for viral survival in an environment that is unusually harsh and has limited host availability.     

Coherent control of optical information with matter wave dynamics

In recent years, significant progress has been achieved in manipulating matter with light, and light with matter. Resonant laser fields interacting with cold, dense atom clouds provide a particularly rich system. Such light fields interact strongly with the internal electrons of the atoms, and couple directly to external atomic motion through recoil momenta imparted when photons are absorbed and emitted. Ultraslow light propagation in Bose-Einstein condensates represents an extreme example of resonant light manipulation using cold atoms. Here we demonstrate that a slow light pulse can be stopped and stored in one Bose-Einstein condensate and subsequently revived from a totally different condensate, 160 mum away; information is transferred through conversion of the optical pulse into a travelling matter wave. In the presence of an optical coupling field, a probe laser pulse is first injected into one of the condensates where it is spatially compressed to a length much shorter than the coherent extent of the condensate. The coupling field is then turned off, leaving the atoms in the first condensate in quantum superposition states that comprise a stationary component and a recoiling component in a different internal state. The amplitude and phase of the spatially localized light pulse are imprinted on the recoiling part of the wavefunction, which moves towards the second condensate. When this 'messenger' atom pulse is embedded in the second condensate, the system is re-illuminated with the coupling laser. The probe light is driven back on and the messenger pulse is coherently added to the matter field of the second condensate by way of slow-light-mediated atomic matter-wave amplification. The revived light pulse records the relative amplitude and phase between the recoiling atomic imprint and the revival condensate. Our results provide a dramatic demonstration of coherent optical information processing with matter wave dynamics. Such quantum control may find application in quantum information processing and wavefunction sculpting.