A MSc thesis which describes a theoretical model for gene replication on circular RNA under prebiotic conditions / The origin of life is one of the most captivating and difficult questions that science has yet to answer. Several different questions remain, including how genetic replication may have begun. Replication is a fundamental property of life that allows for evolution and the long-term survival of life. Non-enzymatic replication should have been present at the origin of life. The RNA world theory proposes that because it can act as both an enzyme and gene, RNA could have performed the function of a replicator at the origin of life. Abiotic chemistry for RNA nucleotides is known, as well as mechanisms for simple but random RNA sequence synthesis. However non-enzymatic replication of RNA sequences which might hold functions, has only achieved mild success. This is in no small part because of replication infidelity between RNA bases, and product inhibition during template directed replication. The rolling circle mechanism found in viroids and some RNA viruses, is a likely way to avoid these issues in the RNA World. Here we present a summary of key topics to origins of life and the RNA world, a deterministic model for rolling circle replication, followed by an original computational model for gene fixation in rolling circle replication. In these simulations we observe the dynamics of populations of protocells, each containing multiple copies of rolling circle RNAs that can replicate non-enzymatically. Selection for speed of replication tends to reduce circles to a minimum length. However, errors provide a natural doubling mechanism that creates strands multiple times the length of the minimal sequence. We show 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. This provides a route for the evolution of longer circles encoding multiple genes. / Thesis / Master of Science (MSc) / The origin of life is a topic that many people are inherently curious about. However, science is only just making progress towards an answer. The first organisms must have been able to replicate. Modern organisms use proteins, DNA, and RNA to do this, however it is unlikely these three molecules could have co-ordinated at the origin of life. A simpler model for replication uses only RNA, which can be both a gene and a catalyst. Here we propose some computational models which study RNA replication. These models simulates strands undergoing rolling circle replication, a method of replication some viruses use which has been suggested to be sustainable at the origin of life. We show that rolling circle replication can create long strands which can have new helpful sequences of RNA. This mechanism could have helped the first organisms achieve better replication and evolution, which is a key characteristic of life.

The biology of modern life predicts the existence of an ancient RNA world. A phase of evolution in which organisms utilized RNA as a genetic material and a catalyst. However, the existence of an RNA organism necessitates RNA’s ability to self-replicate, which has yet to be proven. In this thesis, we utilize computational modeling to address some of the problems facing RNA replication. In chapter 2, we consider a polymerase ribozyme replicating by the Qβ bacteriophage mechanism. When bound to a surface, limited diffusion allows for survival so long as the termination error rate is below an error threshold. In Chapter 3, we consider the replication of short oligomers through an abiotic mechanism proposed in prebiotic experiments. When limited by substrate availability, competition results in the emergence of uniform RNA polymers from a messy prebiotic soup containing nucleotides of different chirality and sugars. In chapter 4, we consider the possibility of an RNA world lacking cytosine. Without cytosine, the ability of RNA to fold to complex secondary structures is limited. Furthermore, G-U wobble base pairing hinders the transfer of information during replication. Nevertheless, we conclude that an RNA world lacking cytosine may be possible, but more difficult for the initial emergence of life. In chapter 5, we analyze abiotic and viral mechanisms of RNA replication using known kinetic and thermodynamic data. While most mechanisms fail under non-enzymatic conditions, rolling-circle replication appears possible. In chapter 6, we extend our analysis of the rolling-circle mechanism to consider the fidelity of replication. Due to the thermodynamic penalty of incorporating an error, rolling-circle replication appears to undergo error correction. This results in highly accurate replication and circumvents Eigen’s paradox. Rolling-circle replication therefore presents an appealing option for the emergence of RNA replication in an RNA world. / Thesis / Doctor of Philosophy (PhD)

One of the greatest scientific mysteries of all time is the Origin of Life on Earth. Life on Earth may have emerged with a unique molecule: Ribonucleic Acids (RNA). The RNA world for the origin of life is a theory that states that life started with RNA before DNA and proteins because RNA molecules can auto-replicate and store genetic information. This thesis aims to expose how such RNA molecules could have been formed on a primitive Earth without the presence of other catalytic biomolecules such as enzymes. The model used in this thesis is the warm little ponds theory for the origin of life. RNA molecules could have been formed in these ponds thanks to wet-cold and warm-dry cycles. We used new experimental and computational technologies to try to answer this dilemma. Using a new machine, the Planet Simulator, which can mimic primitive environments by controlling five physical parameters, we found that extreme heat and low pH would destroy the building blocks of RNA. However, Molecular Dynamics computer simulations showed us that neutral pH could have led to the formation of RNA. Still, the presence of any surfaces and substrates would have decreased the polymerization rate due to the number of interactions between the RNA building blocks and the minerals substrates. We then found a new vision of where life could have come from: in super-saturated water droplets, which could have been formed by geysers or springs on primitive Earth. We tested this theory experimentally using an acoustic levitator to levitate super-saturated droplets and study them in the laboratory. Our preliminary results showed that RNA could have been formed in such droplets on primitive Earth. / Thesis / Master of Science (MSc)

Metabolism is a key attribute of life on Earth at multiple spatial and temporal scales, involved in processes ranging from cellular reproduction to biogeochemical cycles. While metabolic network modeling approaches have enabled significant progress at the cellular-scale, extending these techniques to address questions at both the ecosystem and planetary-scales remains highly unexplored. In this thesis, I integrate various multi-scale metabolic network modeling approaches to address key questions with regard to both the long-term evolution of metabolism in the biosphere and the metabolic processes that take place in complex microbial communities. The first portion of my thesis work, focused on the evolution of ancient metabolic networks, attempts to model the emergence of ecosystem-level metabolism from simple geochemical precursors. By integrating network-based algorithms, physiochemical constraints, and geochemical estimates of ancient Earth, I explored whether a complex metabolic network could have emerged without phosphate, a key molecular component in modern-day living systems, known to be poorly available at the onset of life. We found that phosphate may have not been essential in early living systems, and that thioesters may have been the primitive energy currency in ancient metabolic networks. By generalizing this approach to explore the scope of geochemical scenarios that could have given rise to living systems, I found that other key biomolecules, including fixed nitrogen, may have not been required at the earliest stages in biochemical evolution. The second portion of my thesis deals with a different aspect of ecosystem-level metabolism, namely the role of metabolism in shaping the structure of microbial communities. I studied the relationship between metabolism and microbial community assembly using microbial communities grown in synthetic laboratory environments. We found that a generalized statistical consumer-resource model recapitulates the emergent phenomena observed in these experiments. Future work could seek to better clarify the connection between the fundamental rules that led to life’s emergence over 4 billion years ago and the laws that shape microbial ecosystems today. An ecosystems-level metabolic perspective may aid in our understanding of both the emergence and maintenance of the biosphere.

Earth’s crust and primordial ocean formed more than 4 billion years ago and life is believed to have originated on earth at least 3.6 billion years ago. This suggests that primitive cellular life must have evolved from non-living matter during that period of several hundred million years. To study the transition from chemistry to biology, a simple vesicular system called a protocell is an ideal model that is self-organized and contains informational or metabolic materials. This thesis starts by exploring the replication of a model genetic material under plausible prebiotic conditions. The non-enzymatic copying of RNA was found to be catalyzed by Fe2+, which used to be abundant in aqueous environments on the early anoxic earth. Fe2+ was found to be a better catalyst of non-enzymatic RNA copying and ligation in slightly acidic to neutral pH conditions than Mg2+, the divalent cation used to catalyze these reactions in previous studies. This finding suggests that ferrous iron could have facilitated the replication and evolution of RNA on the prebiotic earth. To gain a better understanding of the properties of protocell membranes, the impact of membrane composition and multi-bilayer structure on non-enzymatic and enzymatic biochemical reactions was studied. A fatty acid/phospholipid hybrid membrane system was proposed as a potential intermediate state in protocellular evolution. This membrane composition was investigated for its stability and permeability, two fundamental features of functional protocells. The system proved stable in the presence of divalent cations and retained permeability to small building block molecule. Vesicles with this composition were shown to host faster non-enzymatic RNA copying, and to enable enzymatic protein synthesis. To study the effects of multi-lamellarity, giant multilamellar vesicles (GMVs) were prepared by an extrusion-dialysis method. Compared with small unilamellar vesicles (SUVs), GMVs show slightly better ability to retain encapsulated RNA, while maintaining good permeability for small charged molecules. The multilamellar structure also promotes non-enzymatic RNA copying, providing preliminary evidence that membranes could also mediate catalytic functions as well as acting as a compartment. / 2020-07-02T00:00:00Z

Modeling chemical environments is an important step to understanding the diversity of prebiotic systems that may have formed on the early earth or potentially can occur on other worlds. By using the modern Earth as a test case, these models predict scenarios with systems more conducive to the formation of the organic molecules that are important to life. Here we use the equilibrium thermodynamic modeling program HSC Chem to investigate prebiotic environments. This program uses the raw material that the user inputs into the system in order to calculate the change in amounts of chemical species forming as a function of temperature and pressure using equilibrium (batch reactor) chemistry. Our results show that that ferrous ion (Fe2+), which may be important in the early formation of organic molecules on Earth, is most abundant in the aqueous phase where the atmosphere contains carbon dioxide as a major constituent. A pure methane atmosphere exhibits the lowest concentrations of this ion, and mixtures tend to end up in between the two extremes. Additionally, we have determined the pH of early oceans, which has implications for biomineralization, chemical reactions, and mineral chemistry. We see that the CO2 atmosphere, and to some extent, the mixtures and CH4 atmospheres, exhibit near neutral pHs. These results allow prediction of processes that might have taken place and could have impacted the development of life on the early earth.

A critical event in the origin of life is thought to have been the emergence of a molecule capable of self-replication and evolution. According to the RNA World hypothesis, this could have been an RNA polymerase ribozyme capable of generating copies of itself from simple nucleotide precursors. In vitro evolution experiments have provided modern examples of such ribozymes, such as the R18 RNA polymerase ribozyme, exhibiting basic levels of this crucial catalytic activity; R18’s activity, however, falls far short of that required of an RNA replicase, leaving unanswered the question of whether RNA can catalyse its self-replication. This thesis describes the development and use of a novel in vitro selection system, Compartmentalised Bead-Tagging (CBT), to isolate variants of the R18 ribozyme with improved sequence generality and extension capabilities. CBT evolution and engineering of polymerase ribozymes, together with RNA template evolution, allowed the synthesis of RNA molecules over 100 nucleotides long, as well as the RNA-catalysed transcription of a catalytic hammerhead ribozyme. This demonstrates the catalytic capabilities of ribozyme polymerases. The R18 ribozyme was also exploited as an analogue of a primordial replicase, to determine replicase behaviour in different reaction environments. Substantial ribozyme polymerisation occurred at −7˚C in the liquid eutectic phase of water-ice; increased ribozyme stability at these low temperatures allowed longer extension products to be generated than at ambient temperatures. The concentration effect of eutectic phase formation could also yield RNA synthesis from dilute solutions of substrates, and provide quasicellular compartmentalisation of ribozymes. These beneficial physicochemical features of ice make it a potential protocellular medium for the emergence of primordial replicases. Ice also could serve as a medium for CBT, allowing the isolation of a polymerase ribozyme adapted to the low temperatures in the ice phase, demonstrating the primordial potential and modern feasibility of ribozyme evolution in ice.

<p> Popular theories about the origin of life can be classified to two classes: metabolism first or genes first. As a metabolism first theory, the lipid world theory, in which non-covalent assemblies of lipids, such as micelles and vesicles store information in the form of a non-random molecular composition, has been proposed to investigate the possibility of inheritance without genes. Our models assume that interaction occurs between nearest neighbour molecules only, and account for spatial segregation of molecules of different types within the assembly. We also draw a distinction between a self-assembly model, in which the composition is determined by mutually favourable interaction energies between the molecules, and a catalytic model, in which the composition is determined by mutually favourable catalysis. We show that compositional inheritance occurs in both models, although the self-assembly case seems more relevant if the molecules are simple lipids. In the case where the assemblies are composed of just two types of molecules, there is a strong analogy with the classic two-allele Moran model from population genetics. This highlights the parallel between compositional inheritance and genetic inheritance. We also investigated the polymerization reactions which may bridge the gap between simple organic molecules and the beginning of the RNA world, which belongs to the class of genes first theories. We found that different from normal chemical systems, catalysts for the polymerization system can shift the equilibrium toward longer polymers. Together with RNA's potential as catalyst, the RNA polymerization system may form a feedback loop which makes the formation of functional RNA molecules easier, and come more close to the beginning of RNA world.</p> / Thesis / Master of Science (MSc)

In hypothesized RNA-World scenarios, replication of RNA strands is catalyzed by error-prone polymerase ribozymes. Incorrect replication leads to the creation of non-functional, parasitic strands which can invade systems of replicators and lead to their death. Studies have shown two solutions to this problem: spatial clustering of polymerases in models featuring elements to limit diffusion, and group selection in models featuring protocells. Making a quantitative comparison of the methods using results from the literature has proven difficult due to differences in model design. Here we develop computational models of replication of a system of polymerases, polymerase complements and parasites in both spatial models and protocell models with near identical dynamics to make meaningful comparison viable. We compare the models in terms of the maximum mutation rate survivable by the system (the error threshold) as well as the minimum replication rate constant required. We find that protocell models are capable of sustaining much higher maximum mutation rates, and survive under much lower minimum replication rates than equivalent surface models. We then consider cases where parasites are favoured in replication, and show that the advantage of protocell models is increased. Given that a system of RNA strands undergoing catalytic replication by a polymerase is fairly survivable in protocell models, we attempt to determine whether isolated strands can develop into genomes. We extend our protocell model to include additional functional strands varying in length (and thus replication rate) and allow for the linkage of strands to form proto-chromosomes. We determine that linkage is possible over a broad range of lengths, and is stable when considering the joining of short functional strands to the polymerase (and the same for the complementary sequences). Moreover, linkage of short functional strands to the polymerase assures more cells remain viable post division by ensuing a good quantity of polymerase equivalents are present in the parent cell prior to splitting. / Thesis / Master of Science (MSc) / Collections of RNA polymers are good candidates for the origin of life. RNA is able to store genetic information and act as polymerase ribozymes allowing RNA to replicate RNA. Polymerases have been experimentally developed in labs, however none are sufficiently general to work well in an origins of life setting. These polymerases are vulnerable to mistakes during copying, making survival of RNA systems difficult. Such systems have been studied by computer simulations, showing that the strands need to be kept together for survival, either on surfaces or in primitive cells. Differences in the details of the models has made comparing the surfaces to cells difficult. This work creates a unified model base allowing for comparison of these two environments. We find that the existence of primitive cells is very beneficial to systems of RNA polymers and thus it is likely such cells existed at the origin of life.

Esta pesquisa apresenta os resultados de um levantamento empírico de livros didáticos de Biologia e Química aprovados no PNLEM 2007, no sentido de investigar as demandas de conceitos químicos no estudo de uma temática própria da disciplina de Biologia: a origem da vida. Adicionalmente, esta dissertação coteja essas demandas conceituais com os correspondentes saberes químicos sequenciados nos capítulos das coleções de Química e discute a potencial interlocução entre os conjuntos de saberes das duas disciplinas, visto que fazem parte da mesma área do conhecimento escolar. Considerando-se todas as obras divididas em três volumes um para cada ano do Ensino Médio e excetuando-se os volumes únicos, foram analisados os capítulos que tratam da origem da vida em quatro coleções de Biologia e todo o conteúdo programático de duas obras de Química. Reconhecendo a relevância do livro didático no cenário educacional brasileiro, o caráter notadamente disciplinar do currículo e as especificidades do ensino de Ciências, este trabalho reúne argumentos teóricos que fundamentam a necessidade de um olhar abrangente sobre a realidade, sempre complexa e multifacetada. / This research presents the results of an empirical survey from textbooks of Biology and Chemistry approved in PNLEM 2007, to investigate the demands of chemical concepts in the study of one the subjects in Biology: the origin of life. In addition to that, this dissertation collates these conceptual demands with the corresponding chemical knowledge sequenced in chapters of the chemical collections and discusses the potential dialogue between the sets of knowledge of those two disciplines, as part of the same area of school knowledge. Considering the works divided into three volumes one for each year of high school and except for the single volumes, were analyzed the chapters dealing with the origin of life in four collections of Biology and whole academic program in two works of Chemistry. Recognizing the relevance of the textbook in Brazilian educational scenario, the notably disciplinary character of the curriculum and the specificities of Natural Sciences who originated the school disciplines of Biology and Chemistry, this work gathers theoretical arguments that justify the need for a comprehensive look at the reality, always complex and multifaceted.