Processive RNA polymerization and promoter recognition in an RNA World

  title={Processive RNA polymerization and promoter recognition in an RNA World},
  author={Razvan Cojocaru and Peter J. Unrau},
  pages={1225 - 1232}
A processive RNA replicator The RNA World Hypothesis suggests that, before modern life, there were RNA molecules that were capable of carrying genetic information and driving chemical reactions, a task gradually replaced by DNA and enzymes in modern biology. Central to this theory is an RNA replicase capable of mediating general replication of RNA. Using laboratory evolution, Cojocaru et al. isolated a promoter-based RNA polymerase ribozyme that, analogous to modern-day protein polymerases… 

Rolling circle RNA synthesis catalyzed by RNA

All steps of a viroid-like RNA replication pathway can be catalyzed by RNA alone and rolling circle synthesis (RCS) is explored as a potential solution to this strand separation problem.

Rolling Circle RNA Synthesis Catalysed by RNA

All steps of a viroid-like RNA replication pathway can be catalysed by RNA alone, including RCS of a circular Hammerhead ribozyme capable of self-cleavage and re-circularisation.

Cryo-EM structure and functional landscape of an RNA polymerase ribozyme

The combined structural and functional data suggest a model for templated RNA synthesis by the TPR holoenzyme and provide a foundation for a better understanding of RNA’s potential for self-replication.

Pyrophosphate-Mediated Repair of Damaged and Mismatched RNA by a Polymerase Ribozyme

Under conditions of high pyrophosphate concentrations, it is shown that a polymerase ribozyme can repair RNA sequences terminated in a 2′ −3′ cyclic phosphate, a mismatch, or both, to allow further polymerization along a template.

Rolling Circles as a Means of Encoding Genes in the RNA World

Simulation of populations of protocells, each containing multiple copies of rolling circle RNAs that can replicate non-enzymatically, shows that if a beneficial gene appears in this new space, the longer sequence with the beneficial function can be selected, even though it replicates more slowly.

Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets

  • F. Broecker
  • Biology
    International journal of molecular sciences
  • 2021
It is hypothesized that the first iteration of the protogenome was a multi-ribozyme RNA that evolved, likely within liposomes forming in dry-wet cycling environments, through the random fusion of ribozymes by a ligase and was amplified by a polymerase.

Computer simulations of Template-Directed RNA Synthesis driven by temperature cycling in diverse sequence mixtures

It is shown that virtual circles do not emerge naturally in simulations of non-enzymatic template-directed RNA synthesis, and that a system initiated with a virtual circle can only maintain itself if there are no mutational errors and there is no input of new sequences formed by random polymerization.

Witnessing the structural evolution of an RNA enzyme

Despite prior speculation that the catalytic core of the ribozyme had become trapped in a narrow local fitness optimum, the evolving population has broken through to a new fitness locale, suggesting that further improvement of polymerase activity may be achievable.

From RNA World to SARS-CoV-2: The Edited Story of RNA Viral Evolution

The current knowledge of key mechanisms and causes of RNA genome instability covering areas from the RNA world theory to the SARS-CoV-2 pandemic is summarized and the key questions that remain as it pertains to RNA genome stability, mutations accumulation, and experimental strategies for addressing these questions are highlighted.

Self-cleaving ribozymes: substrate specificity and synthetic biology applications

An overview of 10 classes of self-cleaving ribozymes is given and what is understood about their substrate specificity and synthetic applications is captured.