Translation initiation factor eIF3 promotes programmed stop codon readthrough.

Programmed stop codon readthrough is a post-transcription regulatory mechanism specifically increasing proteome diversity by creating a pool of C-terminally extended proteins. During this process, the stop codon is decoded as a sense codon by a near-cognate tRNA, which programs the ribosome to continue elongation. The efficiency of competition for the stop codon between release factors (eRFs) and near-cognate tRNAs is largely dependent on its nucleotide context; however, the molecular mechanism underlying this process is unknown. Here, we show that it is the translation initiation (not termination) factor, namely eIF3, which critically promotes programmed readthrough on all three stop codons. In order to do so, eIF3 must associate with pre-termination complexes where it interferes with the eRF1 decoding of the third/wobble position of the stop codon set in the unfavorable termination context, thus allowing incorporation of near-cognate tRNAs with a mismatch at the same position. We clearly demonstrate that efficient readthrough is enabled by near-cognate tRNAs with a mismatch only at the third/wobble position. Importantly, the eIF3 role in programmed readthrough is conserved between yeast and humans

Atomic mutagenesis of stop codon nucleotides reveals the chemical prerequisites for release factor-mediated peptide release.

Termination of protein synthesis is triggered by the recognition of a stop codon at the ribosomal A site and is mediated by class I release factors (RFs). Whereas in bacteria, RF1 and RF2 promote termination at UAA/UAG and UAA/UGA stop codons, respectively, eukaryotes only depend on one RF (eRF1) to initiate peptide release at all three stop codons. Based on several structural as well as biochemical studies, interactions between mRNA, tRNA, and rRNA have been proposed to be required for stop codon recognition. In this study, the influence of these interactions was investigated by using chemically modified stop codons. Single functional groups within stop codon nucleotides were substituted to weaken or completely eliminate specific interactions between the respective mRNA and RFs. Our findings provide detailed insight into the recognition mode of bacterial and eukaryotic RFs, thereby revealing the chemical groups of nucleotides that define the identity of stop codons and provide the means to discriminate against noncognate stop codons or UGG sense codons

How mutations in tRNA distant from the anticodon affect the fidelity of decoding

The ribosome converts genetic information into protein by selecting aminoacyl tRNAs whose anticodons base-pair to an mRNA codon. Mutations in the tRNA body can perturb this process and affect fidelity. The Hirsh suppressor is a well-studied tRNA^(Trp) harboring a G24A mutation that allows readthrough of UGA stop codons. Here we present crystal structures of the 70S ribosome complexed with EF-Tu and aminoacyl tRNA (native tRNA^(Trp), G24A tRNA^(Trp) or the miscoding A9C tRNA^(Trp)) bound to cognate UGG or near-cognate UGA codons, determined at 3.2-Å resolution. The A9C and G24A mutations lead to miscoding by facilitating the distortion of tRNA required for decoding. A9C accomplishes this by increasing tRNA flexibility, whereas G24A allows the formation of an additional hydrogen bond that stabilizes the distortion. Our results also suggest that each native tRNA will adopt a unique conformation when delivered to the ribosome that allows accurate decoding

The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes

Many cases of non-standard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely mechanism for codon reassignment in each case. Reassignment events can be classified according to the gain-loss framework. The gain represents the appearance of a new tRNA for the reassigned codon or the change of an existing tRNA such that it gains the ability to pair with the codon. The loss represents the deletion of a tRNA or the change in a tRNA so that it no longer translates the codon. One possible mechanism is Codon Disappearance, where the codon disappears from the genome prior to the gain and loss events. In the alternative mechanisms the codon does not disappear. In the Unassigned Codon mechanism, the loss occurs first, whereas in the Ambiguous Intermediate mechanism, the gain occurs first. Codon usage analysis gives clear evidence of cases where the codon disappeared at the point of the reassignment and also cases where it did not disappear. Codon disappearance is the probable explanation for stop to sense reassignments and a small number of reassignments of sense codons. However, the majority of sense to sense reassignments cannot be explained by codon disappearance. In the latter cases, by analysis of the presence or absence of tRNAs in the genome and of the changes in tRNA sequences, it is sometimes possible to distinguish between the Unassigned Codon and Ambiguous Intermediate mechanisms. We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully.Comment: 53 pages (45 pages, including 4 figures + 8 pages of supplementary information). To appear in J.Mol.Evo

Entanglement and secret-key-agreement capacities of bipartite quantum interactions and read-only memory devices

A bipartite quantum interaction corresponds to the most general quantum interaction that can occur between two quantum systems in the presence of a bath. In this work, we determine bounds on the capacities of bipartite interactions for entanglement generation and secret key agreement between two quantum systems. Our upper bound on the entanglement generation capacity of a bipartite quantum interaction is given by a quantity called the bidirectional max-Rains information. Our upper bound on the secret-key-agreement capacity of a bipartite quantum interaction is given by a related quantity called the bidirectional max-relative entropy of entanglement. We also derive tighter upper bounds on the capacities of bipartite interactions obeying certain symmetries. Observing that reading of a memory device is a particular kind of bipartite quantum interaction, we leverage our bounds from the bidirectional setting to deliver bounds on the capacity of a task that we introduce, called private reading of a wiretap memory cell. Given a set of point-to-point quantum wiretap channels, the goal of private reading is for an encoder to form codewords from these channels, in order to establish secret key with a party who controls one input and one output of the channels, while a passive eavesdropper has access to one output of the channels. We derive both lower and upper bounds on the private reading capacities of a wiretap memory cell. We then extend these results to determine achievable rates for the generation of entanglement between two distant parties who have coherent access to a controlled point-to-point channel, which is a particular kind of bipartite interaction.Comment: v3: 34 pages, 3 figures, accepted for publication in Physical Review

Entanglement-Assisted Capacity of Quantum Multiple-Access Channels

We find a regularized formula for the entanglement-assisted (EA) capacity region for quantum multiple access channels (QMAC). We illustrate the capacity region calculation with the example of the collective phase-flip channel which admits a single-letter characterization. On the way, we provide a first-principles proof of the EA coding theorem based on a packing argument. We observe that the Holevo-Schumacher-Westmoreland theorem may be obtained from a modification of our EA protocol. We remark on the existence of a family hierarchy of protocols for multiparty scenarios with a single receiver, in analogy to the two-party case. In this way, we relate several previous results regarding QMACs.Comment: Published version. 13 pages, 3 figure

Translational recoding as a feedback controller : systems approaches reveal polyamine-specific effects on the antizyme ribosomal frameshift

Peer reviewedPublisher PD

Selenocysteine, pyrrolysine and the unique energy metabolism of methanogenic archaea

Methanogenic archaea are a group of strictly anaerobic microorganisms characterized by their strict dependence on the process of methanogenesis for energy conservation. Among the archaea, they are also the only known group synthesizing proteins containing selenocysteine or pyrrolysine. All but one of the known archaeal pyrrolysine-containing and all but two of the confirmed archaeal selenocysteine-containing protein are involved in methanogenesis. Synthesis of these proteins proceeds through suppression of translational stop codons but otherwise the two systems are fundamentally different. This paper highlights these differences and summarizes the recent developments in selenocysteine- and pyrrolysine-related research on archaea and aims to put this knowledge into the context of their unique energy metabolism

Mutations in the intersubunit bridge regions of 16S rRNA affect decoding and subunit–subunit interactions on the 70S ribosome

The small and large subunits of the ribosome are held together by a series of bridges, involving RNA-RNA, RNA-protein and protein-protein interactions. Some 12 bridges have been described for the Escherichia coli 70S ribosome. In this work, we have targeted for mutagenesis, some of the 16S rRNA residues involved in the formation of intersubunit bridges B3, B5, B6, B7b and B8. In addition to effects on subunit association, the mutant ribosomes also affect the fidelity of translation; bridges B5, B6 and B8 increase decoding errors during elongation, while disruption of bridges B3 and B7b alters the stringency of start codon selection. Moreover, mutations in the bridge B5, B6 and B8 regions of 16S rRNA also correct the growth and decoding defects associated with alterations in ribosomal protein S12. These results link bridges B5, B6 and B8 with the decoding process and are consistent with the recently described location of translation factor EF-Tu on the ribosome and the proposed involvement of h14 in activating Guanosine-5'-triphosphate (GTP) hydrolysis by aminoacyl-tRNA center dot EF-Tu center dot GTP. These observations are consistent with a model in which bridges B5, B6 and B8 contribute to the fidelity of translation by modulating GTP hydrolysis by aminoacyl-tRNA center dot EF-Tu center dot GTP teRNAry complexes during the elongation phase of protein synthesis

Quantum reading capacity: General definition and bounds

Quantum reading refers to the task of reading out classical information stored in a read-only memory device. In any such protocol, the transmitter and receiver are in the same physical location, and the goal of such a protocol is to use these devices (modeled by independent quantum channels), coupled with a quantum strategy, to read out as much information as possible from a memory device, such as a CD or DVD. As a consequence of the physical setup of quantum reading, the most natural and general definition for quantum reading capacity should allow for an adaptive operation after each call to the channel, and this is how we define quantum reading capacity in this paper. We also establish several bounds on quantum reading capacity, and we introduce an environment-parametrized memory cell with associated environment states, delivering second-order and strong converse bounds for its quantum reading capacity. We calculate the quantum reading capacities for some exemplary memory cells, including a thermal memory cell, a qudit erasure memory cell, and a qudit depolarizing memory cell. We finally provide an explicit example to illustrate the advantage of using an adaptive strategy in the context of zero-error quantum reading capacity.Comment: v3: 17 pages, 2 figures, final version published in IEEE Transactions on Information Theor