Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis

Charest, Nathaniel; Shen, Yuning; Lai, Yei-Chen; Chen, Irene A.; Shea, Joan-Emma

doi:10.1261/rna.079541.122

Cited by 2 publications

(1 citation statement)

References 47 publications

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“…This signaled a potential connection between physical effects of encapsulation and ribozyme evolution. For over a decade, our laboratory has also been engaged in studying the sequence-activity relationship of ribozymes (known as the “fitness landscape”) to understand the emergence and evolution of RNA function. − The fitness landscape is the function of fitness over multidimensional sequence space. For molecules, fitness is often equated with chemical activity, such as rate, meaning that the activity being studied is assumed to be important for the organism or system.…”

Section: Protocells As Evolutionary Accelerantmentioning

confidence: 99%

Protocell Effects on RNA Folding, Function, and Evolution

Saha,

Choi,

Chen

2024

Acc. Chem. Res.

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Metrics & MoreArticle Recommendations CONSPECTUS: Creating a living system from nonliving matter is a great challenge in chemistry and biophysics. The early history of life can provide inspiration from the idea of the prebiotic "RNA World" established by ribozymes, in which all genetic and catalytic activities were executed by RNA. Such a system could be much simpler than the interdependent central dogma characterizing life today. At the same time, cooperative systems require a mechanism such as cellular compartmentalization in order to survive and evolve. Minimal cells might therefore consist of simple vesicles enclosing a prebiotic RNA metabolism.The internal volume of a vesicle is a distinctive environment due to its closed boundary, which alters diffusion and available volume for macromolecules and changes effective molecular concentrations, among other considerations. These physical effects are mechanistically distinct from chemical interactions, such as electrostatic repulsion, that might also occur between the membrane boundary and encapsulated contents. Both indirect and direct interactions between the membrane and RNA can give rise to nonintuitive, "emergent" behaviors in the model protocell system. We have been examining how encapsulation inside membrane vesicles would affect the folding and activity of entrapped RNA.Using biophysical techniques such as FRET, we characterized ribozyme folding and activity inside vesicles. Encapsulation inside model protocells generally promoted RNA folding, consistent with an excluded volume effect, independently of chemical interactions. This energetic stabilization translated into increased ribozyme activity in two different systems that were studied (hairpin ribozyme and self-aminoacylating RNAs). A particularly intriguing finding was that encapsulation could rescue the activity of mutant ribozymes, suggesting that encapsulation could affect not only folding and activity but also evolution. To study this further, we developed a high-throughput sequencing assay to measure the aminoacylation kinetics of many thousands of ribozyme variants in parallel. The results revealed an unexpected tendency for encapsulation to improve the better ribozyme variants more than worse variants. During evolution, this effect would create a tilted playing field, so to speak, that would give additional fitness gains to already-high-activity variants. According to Fisher's Fundamental Theorem of Natural Selection, the increased variance in fitness should manifest as faster evolutionary adaptation. This prediction was borne out experimentally during in vitro evolution, where we observed that the initially diverse ribozyme population converged more quickly to the most active sequences when they were encapsulated inside vesicles. The studies in this Account have expanded our understanding of emergent protocell behavior, by showing how simply entrapping an RNA inside a vesicle, which could occur spontaneously during vesicle formation, might profoundly affect the evolutionary landscape of the RN...

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Section: Protocells As Evolutionary Accelerantmentioning

confidence: 99%

Protocell Effects on RNA Folding, Function, and Evolution

Saha,

Choi,

Chen

2024

Acc. Chem. Res.

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Fitness Landscapes and Evolution of Catalytic RNA

Saha,

Vázquez-Salazar,

Nandy

et al. 2024

Annual Review of Biophysics

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The relationship between genotype and phenotype, or the fitness landscape, is the foundation of genetic engineering and evolution. However, mapping fitness landscapes poses a major technical challenge due to the amount of quantifiable data that is required. Catalytic RNA is a special topic in the study of fitness landscapes due to its relatively small sequence space combined with its importance in synthetic biology. The combination of in vitro selection and high-throughput sequencing has recently provided empirical maps of both complete and local RNA fitness landscapes, but the astronomical size of sequence space limits purely experimental investigations. Next steps are likely to involve data-driven interpolation and extrapolation over sequence space using various machine learning techniques. We discuss recent progress in understanding RNA fitness landscapes, particularly with respect to protocells and machine representations of RNA. The confluence of technical advances may significantly impact synthetic biology in the near future.

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Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis

Cited by 2 publications

References 47 publications

Protocell Effects on RNA Folding, Function, and Evolution

Protocell Effects on RNA Folding, Function, and Evolution

Fitness Landscapes and Evolution of Catalytic RNA

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