Multispecies autocatalytic RNA reaction networks in coacervates

Ameta, Sandeep; Kumar, Manoj; Chakraborty, Nayan; Matsubara, Yoshiya J.; Prashanth, S.; Gandavadi, Dhanush; Thutupalli, Shashi

doi:10.1101/2022.11.01.514660

Cited by 3 publications

(2 citation statements)

References 64 publications

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“…Although ribozyme-catalysed replication of sequences longer than 100 nucleotides has not yet been experimentally observed, a possible alternative approach might involve ribozyme-catalysed replication of different fragments of a complete DNA template encoding the ribozyme. The RNA fragments generated can then self-assemble to form the whole ribozyme [59, 60, 61], perhaps with the help of auto-catalytic networks of the smaller ribozyme fragments [62]. The versatility of the replicase thus created and its role in catalysing several other reactions, especially in the presence of both RNA and DNA nucleotides, can create a self-sustained chemical system inside a protocell.…”

Section: Discussionmentioning

confidence: 99%

The RNA-DNA world and the emergence of DNA-encoded heritable traits

Roy

Sengupta

2023

Preprint

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The RNA world hypothesis confers a central role to RNA molecules in information encoding and catalysis. Even though evidence in support of this hypothesis has accumulated from both experiments and computational modelling, the transition from an RNA world to a world where heritable genetic information is encoded in DNA remains an open question. Recent experiments show that both RNA and DNA templates can extend complementary primers using free RNA/DNA nucleotides, either non-enzymatically or in the presence of a replicase ribozyme. Guided by these experiments, we analyse protocellular evolution with an expanded set of reaction pathways made possible through the presence of DNA nucleotides. We allow for the possibility of auto-catalytic synthesis of replicase ribozymes from DNA templates encoding the replicase, after the chance emergence of a replicase through non-enzymatic reactions. By encapsulating these reactions inside three different types of protocellular compartments, each subject to distinct modes of selection, we show how protocells containing replicase-encoded DNA in low copy numbers and replicases in high copy numbers can dominate the population. Our work suggests a plausible pathway for the transition from an RNA world to a mixed RNA-DNA world characterized by Darwinian evolution, where DNA sequences encode heritable phenotypes.

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Section: Discussionmentioning

confidence: 99%

The RNA-DNA world and the emergence of DNA-encoded heritable traits

Roy

Sengupta

2023

Preprint

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“…Even in such a case, the inheritance of compositional information could be robust for the kind of bistable systems we have studied. [65].…”

Section: Discussionmentioning

confidence: 99%

Robustness of compositional heredity to the growth and division dynamics of prebiotic compartments

Matsubara¹,

Ameta²,

Thutupalli³

et al. 2022

Preprint

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An important transition after the origin of life was the first emergence of a Darwinian population, self-reproducing entities exhibiting differential reproduction, phenotypic variation, and inheritance of phenotypic traits. The simplest system we can imagine to have these properties would consist of a compartmentalized autocatalytic reaction system that exhibits two growth states with different chemical compositions. Identifying the chemical composition as the phenotype, this accounts for two of the properties. However, it is not clear what are the necessary conditions for such a chemical system to exhibit inheritance of the compositional states upon growth and division of the compartment. We show that for a general class of autocatalytic chemical systems subject to serial dilution, the inheritance of compositional information only occurs when the time interval between dilutions is below a critical threshold that depends on the efficiency of the catalytic reactions. Further, we show that these thresholds provide rigorous bounds on the properties required for the inheritance of the chemical compositional state for general growth and division cycles. Our result suggests that a serial dilution experiment, which is much easier to set up in a laboratory, can be used to test whether a given autocatalytic chemical system can exhibit heredity. Lastly, we apply our results to a realistic autocatalytic system based on the Azoarcus ribozyme and suggest a protocol to experimentally test whether this system can exhibit heredity.

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Constrained dynamics of oligonucleotides in the phase-separated droplets

Singh

Thutupalli

Kumar

et al. 2023

Preprint

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Phase-separated droplets are excellent means of compartmentalizing functional molecules and have been shown as excellent models for protocells. Although complex functions based on oligonucleotides have been studied, we still lack an understanding of how the oligonucleotide dynamics are affected by the condensed internal environment of these droplets. Particularly, we lack high-resolution experimental measurements of the dynamical parameters that control oligonucleotide diffusion inside the phase-separated droplets. In addition, there is no clarity on how these dynamical parameters differ in the charged (coacervates) vs non-charged (aqueous two-phase system, ATPS) environment of these droplets. In this study, using fluorescence correlation spectroscopy (FCS), we demonstrate the constrained dynamics of oligonucleotides inside membraneless phase-separated droplets at an unprecedented resolution. We further compare transport properties at different lengths of oligonucleotides as well as salt concentrations. We observe that among all the parameters the oligonucleotide's caging (spatial restriction in the movement) inside the matrix has a considerable impact on the diffusive dynamics. Our study provides a way of unravelling, quantifying and understanding physical parameters governing the polymer transport dynamics inside the phase-separated droplets.

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Multispecies autocatalytic RNA reaction networks in coacervates

Cited by 3 publications

References 64 publications

The RNA-DNA world and the emergence of DNA-encoded heritable traits

The RNA-DNA world and the emergence of DNA-encoded heritable traits

Robustness of compositional heredity to the growth and division dynamics of prebiotic compartments

Constrained dynamics of oligonucleotides in the phase-separated droplets

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