Origin of Life: Insights from Computational Models

Roy, Suvam (2023) Origin of Life: Insights from Computational Models. PhD thesis, Indian Institute of Science Education and Research Kolkata.

Text (PhD thesis of Suvam Roy (18RS011)) 18RS011.pdf - Submitted Version Restricted to Repository staff only Download (6MB)

Abstract

The RNA world hypothesis of Origin of Life proposes that primordial life made up of RNA molecules only might have existed during an epoch that emerged from the prebiotic chemical world and preceded the modern DNA-protein based life. The key characteristic of this hypothetical RNA world is the presence of protocellular populations, whose internal metabolism was driven by RNA enzymes and RNA replicators only. However, the pathways that lead to the emergence of such an RNA-based life, and how that RNA world subsequently evolved to the DNA-protein based world of today, remains an open question. In this thesis, we tried to address this question by developing theoretical models and carrying out in silico evolution experiments. We divided the evolutionary trajectory into three stages. In the first stage, we considered non-templated and templated RNA polymerization reactions. Starting with free RNA nucleotides only, we showed how segregation of these reactions into distinct day-night induced environmental phases might have played a crucial role in the emergence of RNA enzyme-like complex polymers. Subsequently, we showed that encapsulation of RNA polymers inside spontaneously formed lipid vesicles and erroneous replication of those polymers, could have driven the vesicle population to undergo growth-division cycles. Competition between the vesicles during such growth-division cycles could have led to the emergence and dominance of vesicles containing multiple types of RNA enzymes, that synergistically enhance each others’ creation. Increasing functional diversity of RNA molecules inside the vesicles provides a pathway to increasing protocellular complexity and marks the emergence of a primitive RNA-based protocellular life. We further showed that the regions around primordial hot springs might have been a suitable location for the emergence of such functional diversity inside protocells and may have facilitated the spatial expansion of the protocellular populations. In the final stage, we considered the transition from an RNA world to the RNA-DNA world. We proposed a plausible reaction network for RNA-templated DNA creation and showed that protocells containing genome-like DNA strands can emerge and dominate the population as a result of competition between different protocells. More interestingly, an auto-catalytic reaction that can create RNA enzymes from the DNA genomes encoding them turns out to be one of the dominant reactions inside those protocells. This thesis therefore provides a plausible step-by-step pathway for the transition from the prebiotic chemistry to a primitive DNA-RNA-based protocellular life that may have preceded current life that is based on DNA and proteins.

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