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Yokobayashi, Y.

Publications and source records attributed to Yokobayashi, Y..

2 recordsLinked to original sources

RNA condensates as platforms for prebiotic chemistry

The RNA world hypothesis posits the existence of life-like assemblies that consisted mostly of RNA. However, questions remain regarding the emergence of RNA catalysis, stability, reactant availability, and compartmentalization of genetic material. At acidic pH, short RNAs (average {approx} 20 nt) readily phase-separate into a condensed phase en-riched with long RNA. These RNA condensates stably compartmentalize RNA as well as DNA and maintain stable identities even in the absence of membranes. Additionally, the RNA condensates concentrate ions, small molecules, phospholipids, peptides, ri-bozymes, and proteins. Beyond enriching such diverse components, RNA condensates function as microreactors with two catalytic capabilities: they physically enhance reac-tion rates by concentrating reactants within a confined space and simultaneously act as inherent catalysts that directly facilitate chemical transformations. RNA condensates can also support ribozyme and enzymatic activity. Together, these findings suggest that RNA phase separation may have played a crucial role in lifes origins by providing compartmentalization, inherent catalytic activity, and molecular enrichment of long, potentially catalytic biopolymers.

biochemistry↗

Speed fluctuations of bacterial replisomes

Replisomes are multi-protein complexes that replicate genomes with remarkable speed and accuracy. Despite their importance, their dynamics is poorly characterized, especially in vivo. In this paper, we present an approach to infer the replisome dynamics from the DNA abundance distribution measured in a growing bacterial population. Our method is sensitive enough to detect subtle variations of the replisome speed along the genome. As an application, we experimentally measured the DNA abundance distribution in Escherichia coli populations growing at different temperatures using deep sequencing. We find that the average replisome speed increases nearly five-fold between 17{degrees}C and 37{degrees}C. Further, we observe wave-like variations of the replisome speed along the genome. These variations correlate with previously observed variations of the mutation rate. We interpret this correlation as a speed-error trade-off in DNA replication. Our approach has the potential to elucidate replication dynamics in E. coli mutants and in other bacterial species.

biophysics↗