Podcasts about anticodon

Nels and Vincent discuss how evolution of changes in stop codon assignment might occur, and a novel mechanism for altering the meaning of translation stop codons discovered in a trypanosomatid with the apropos name, Blastocrithidia nonstop. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode •Join the MicrobeTV Discord server •Novel stop codon reassignment mechanisms (Nature) Science Picks Nels – Protein Synthesis: An epic on the cellular level  Vincent – Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes discussed on TWiM 277 Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.19.344408v1?rss=1 Authors: Kazantsev, A., Ignatova, Z. Abstract: G{whitebullet}U(T) mismatch has the highest contribution to the error rate of base pair recognition in replication, as well as in codon-anticodon decoding in translation. Recently, this effect was unambiguously linked to keto-enol tautomerization, which enables the Watson-Crick (WC) geometry of the base pair. Structural studies of the ribosome revealing G{whitebullet}U in the WC geometry in the closed state of the A-site challenge the canonical induced-fit model of decoding and currently lack a physicochemical explanation. Using computational and theoretical methods, we herein address effects of the ribosomal A-site on the wobble{leftrightarrow}WC tautomerization reaction in G{whitebullet}U (wb{leftrightarrow}WC reaction), and the consequent implications for the decoding mechanism in translation. The free energy change of the wb-WC reaction in the middle codon-anticodon position was calculated with quantum-mechanical/molecular-mechanical (QM/MM) umbrella sampling simulations. The wb-WC reaction was endoergic in the open A-site, but exoergic in the closed state. This effect can be explained in part by the decreased polarity of the closed A-site. We developed a model of initial selection in translation that incorporates the wb-WC reaction parameters in the open and closed states of the A-site. In the new model the exoergic wb-WC reaction is kinetically restricted by the decoding rates, which explains the observations of the WC geometry at equilibrium conditions. Moreover, the model reveals constraints imposed by the exoergic wb-WC reaction on the decoding accuracy: its equilibration counteracts the favorable contribution from equilibration of the open-closed transition. The similarity of the base-pair recognition mechanism in DNA polymerases allows extending this model to replication as well. Our model can be a next step towards a general recognition model for flexible substrates. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.01.277525v1?rss=1 Authors: Hoffer, E. D., Hong, S., Maehigashi, T., Gonzalez, R. L., Whitford, P., Dunham, C. M. Abstract: Modifications in the tRNA anticodon, adjacent to the three-nucleotide anticodon, influence translation fidelity by stabilizing the tRNA to allow for accurate reading of the mRNA genetic code. One example is the N1-methylguaonosine modification at guanine nucleotide 37 (m1G37) located in the anticodon loop, immediately adjacent to the anticodon nucleotides 34-36. The absence of m1G37 in tRNAPro causes +1 frameshifting on polynucleotide, slippery codons. Here, we report structures of the bacterial ribosome containing tRNAPro bound to either cognate or slippery codons to determine how the m1G37 modification prevents mRNA frameshifting. The structures reveal that certain codon-anticodon contexts and m1G37 destabilize interactions of tRNAPro with the peptidyl site, causing large conformational changes typically only seen during EF-G mediated translocation of the mRNA-tRNA pairs. These studies provide molecular insights into how m1G37 stabilizes the interactions of tRNAPro with the ribosome and the influence of slippery codons on the mRNA reading frame. Copy rights belong to original authors. Visit the link for more info

The role of transfer RNA in building protein chains from the information in messenger-RNA.

Transcript -- The role of transfer RNA in building protein chains from the information in messenger-RNA.

The role of transfer RNA in building protein chains from the information in messenger-RNA.

Transcript -- The role of transfer RNA in building protein chains from the information in messenger-RNA.

Wed, 1 Jan 1986 12:00:00 +0100 https://epub.ub.uni-muenchen.de/8805/1/phage_and_host_genetic_determinations_of_the_specific_anticodon_loop_8805.pdf Snyder, L.; Green, R.; Amitsur, M.; Paz, A.; Teichmann, A.; Borasio, Gian Domenico; David, M.; Kaufmann, G.

Fri, 1 Jan 1982 12:00:00 +0100 https://epub.ub.uni-muenchen.de/8803/1/bacteriophage_t4-induced_anticodon-loop_nuclease_detected_in_a_host_strain_restrictive_to_rna_ligase_mutants_8803.pdf Kaufmann, G.; Borasio, Gian Domenico; David, M.