@article {128092, title = {Multispecies autocatalytic RNA reaction networks in coacervates.}, journal = {Communications Chemistry}, volume = {6}, year = {2023}, month = {2023 May 08}, pages = {91}, abstract = {

Robust localization of self-reproducing autocatalytic chemistries is a key step in the realization of heritable and evolvable chemical systems. While autocatalytic chemical reaction networks already possess attributes such as heritable self-reproduction and evolvability, localizing functional multispecies networks within complex primitive phases, such as coacervates, has remained unexplored. Here, we show the self-reproduction of the Azoarcus ribozyme system within charge-rich coacervates where catalytic ribozymes are produced by the autocatalytic assembly of constituent smaller RNA fragments. We systematically demonstrate the catalytic assembly of active ribozymes within phase-separated coacervates-both in micron-sized droplets as well as in a coalesced macrophase, underscoring the facility of the complex, charge-rich phase to support these reactions in multiple configurations. By constructing multispecies reaction networks, we show that these newly assembled molecules are active, participating both in self- and cross-catalysis within the coacervates. Finally, due to differential molecular transport, these phase-separated compartments endow robustness to the composition of the collectively autocatalytic networks against external perturbations. Altogether, our results establish the formation of multispecies self-reproducing reaction networks in phase-separated compartments which in turn render transient robustness to the network composition.

}, issn = {2399-3669}, doi = {10.1038/s42004-023-00887-5}, author = {Ameta, Sandeep and Kumar, Manoj and Chakraborty, Nayan and Matsubara, Yoshiya J and S, Prashanth and Gandavadi, Dhanush and Thutupalli, Shashi} } @article {95781, title = {RNA diversification by a self-reproducing ribozyme revealed by deep sequencing and kinetic modelling.}, journal = {Chem Commun (Camb)}, year = {2021}, month = {2021 Jul 08}, abstract = {

We demonstrate that a recombinase ribozyme achieves multiple functions in the same reaction network: self-reproduction, iterative elongation and circularization of other RNAs, leading to synthesis of diverse products predicted by a kinetic model. This shows that key mechanisms can be integrated and controlled toward Darwinian evolution in RNA reaction networks.

}, issn = {1364-548X}, doi = {10.1039/d1cc02290c}, author = {Jeancolas, Cyrille and Matsubara, Yoshiya J and Vybornyi, Mykhailo and Lambert, Camille N and Blokhuis, Alex and Alline, Thomas and Griffiths, Andrew D and Ameta, Sandeep and Krishna, Sandeep and Nghe, Philippe} } @article {92883, title = {Self-Reproduction and Darwinian Evolution in Autocatalytic Chemical Reaction Systems.}, journal = {Life (Basel)}, volume = {11}, year = {2021}, month = {2021 Apr 01}, abstract = {

Understanding the emergence of life from (primitive) abiotic components has arguably been one of the deepest and yet one of the most elusive scientific questions. Notwithstanding the lack of a clear definition for a living system, it is widely argued that heredity (involving self-reproduction) along with compartmentalization and metabolism are key features that contrast living systems from their non-living counterparts. A minimal living system may be viewed as "a self-sustaining chemical system capable of Darwinian evolution". It has been proposed that autocatalytic sets of chemical reactions (ACSs) could serve as a mechanism to establish chemical compositional identity, heritable self-reproduction, and evolution in a minimal chemical system. Following years of theoretical work, autocatalytic chemical systems have been constructed experimentally using a wide variety of substrates, and most studies, thus far, have focused on the demonstration of chemical self-reproduction under specific conditions. While several recent experimental studies have raised the possibility of carrying out some aspects of experimental evolution using autocatalytic reaction networks, there remain many open challenges. In this review, we start by evaluating theoretical studies of ACSs specifically with a view to establish the conditions required for such chemical systems to exhibit self-reproduction and Darwinian evolution. Then, we follow with an extensive overview of experimental ACS systems and use the theoretically established conditions to critically evaluate these empirical systems for their potential to exhibit Darwinian evolution. We identify various technical and conceptual challenges limiting experimental progress and, finally, conclude with some remarks about open questions.

}, issn = {2075-1729}, doi = {10.3390/life11040308}, author = {Ameta, Sandeep and Matsubara, Yoshiya J and Chakraborty, Nayan and Krishna, Sandeep and Thutupalli, Shashi} }