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Executive Summary

This is a progress report from the University of Illinois NAI Team on the Project “Towards Universal Biology: Constraints from Early and Continuing Evolutionary Dynamics of Life on Earth”, and covers the highlights of our research in the time period from January 1 2015 to Dec 31 2015, since the time of our previous research summary. The specific objectives of our research are the following four Themes which are, in brief: [1] Theoretical understanding of the universal features governing living systems, their operation, evolution and origin; [2] Constraints on the nature of life before the Last Universal Common Ancestor (LUCA), in particular to identify new signatures of the collective state of life (“progenote”) which enabled the evolution of the cell to occur so rapidly; [3] To explore the breakdown of the progenote and the transition to vertical evolution; [4] Explore the interplay between biological and environmental determinants of the rate of evolution.

These Thematic areas are fundamental to astrobiology, because they explore questions that are common properties of all living, evolving, metabolizing and information processing systems. While we can only perform experiments, analyzed or interpreted by theory, on terrestrial life, the interpretation allows us to draw conclusions that should be relevant to life elsewhere in the universe. It is our intention that some of our work can provide clues as to how to recognize simple forms of life, where biosignatures relating to modern DNA-based life would be lacking. Additionally, our work addresses the question of how likely life is to emerge in the first place, through a strong focus on the rate of evolution. Two key factors influence this study in our Team’s work. The first is collective pathways of evolution, primarily through horizontal gene transfer mediated by viruses for example. The second is the role of environmental stress and gradients, that can drive evolutionary adaptations and fixation within (bacterial) populations. These processes can be explored through state-of-the-art experiments on bacteria contained within microfluidic devices, as well as by population level experiments on error-prone polymerases, capable of quantifying the effects of stress-induced mutagenesis.

We have made significant progress in each of these areas, during the previous 12 months, organized along the lines of 11 Projects, which cover the following topics: The origin of homochirality; Cells as Engines; Theory of the Darwinian Transition; Experimental work on the Darwinian Transition; Control of Evolvability; Diversity of Life; Mining Archaeal Genomes; The Eukaryote-Archaeal Common Ancestor; Metapopulation Structure; Codon Usage and Evolution; Culturing Microbial Communities in Microenvironments.

Selected highlights achieved during the past grant period are described below.

Homochirality
A universal aspect of living systems on Earth is their homochirality: Life uses dextrorotary sugars and levorotary amino acids. The reasons for this are hotly debated and not close to being settled. However, the leading idea is that autocatalytic reactions grew exponentially fast at the origin of life, and whatever chiral symmetry breaking was accidentally present became amplified subsequently. For this argument to be viable, it has to be shown that autocatalysis can indeed amplify homochirality. Secondly, one must consider the potentially confounding effects of spatial extension, which could give rise to spatial heterogeneity in the pattern of chiral symmetry breaking. We have succeeded in providing an improved formulation of the famous homochirality model of F.C. Frank, one that removes the unphysical requirement of competition between the chiral enantiomers, and moreover includes the inevitable and important stochasticity arising from chemical reactions. The mathematics shows that homochirality can arise by a previously unnoticed mechanism – the stabilization of homochirality into states that are least affected by noise. This mechanism is different from potential-based mechanisms for bistability, because it is the noise itself that generates the symmetry breaking. We have also succeeded in formulating this stochastic model with spatial extension. Despite the complexity, we were able to solve this model exactly. We then generalized our result to a fully-spatially-extended system and solved that by stochastic simulation. Our results showed convergence to a homochiral state, with the dynamic universality class being compact directed percolation. Our analysis and mathematical mechanism works in the limit that evolution has allowed the self-replication process to become more efficient. The significance of these results is that we are confident that any non-equilibrium processes driving autocatalysis of chiral molecules or systems will experience dynamic symmetry breaking to a homochiral state. The fact that the mechanism does not depend on chemical specifics means that homochirality, along with the optimality and universality of the genetic code, can now be confidently stated to be a feature of universal biology, and its presence is a strong biosignature. Note in particular that this result establishes a 100% homochiral state, rather than a mere enantiomeric excess predicted by other theories not based on autocatalysis. This work has appeared in Physical Review Letters, the premier physics journal, because our contribution is highly technical, and not suitable for a biological journal.

Farshid Jafarpour, Tommaso Biancalani and Nigel Goldenfeld. Noise-induced mechanism for Biological Homochirality of Early Life Self-Replicators. Phys. Rev. Lett. 115, 158101 (5 pages) 2015.

The serpentinization hypothesis for the origin of life
This project is primarily a collaboration with Dr. Michael Russell of JPL focused on supporting the development and testing of Russell’s “Alkaline Hydrothermal Vent” (“AHV”) model of abiogenesis. Our particular contribution is aimed at understanding the implications of the far-from-equilibrium thermodynamic mechanisms that form the functional core, and a central tenet, of the model. That tenet has two parts. First, that the most universal, essential, and distinguishing property of the ‘living state of matter’ is its being an organized system of chemical processes and structures maintained in extreme and dynamic states of thermodynamic ‘disequilibrium’. Second, that it could never have been otherwise; that is, the initial, enabling occurrence in the transition from the inanimate to animate state must have been the ‘abiotic’ establishment of a core ‘disequilibrium’ system with a clear ancestral relationship to that of extant systems. Seeing how this could have happened, and what specifically that founding core disequilibrium system was, is the first challenge; experimentally testing the resultant model predictions the second.

We have developed and solved a simple statistical-mechanical model of how such escapement-controlled conversion systems work. This model and its implications are being written up in three manuscripts, one of which is already in review (Escapement Mechanisms and the Conversion of Disequilibria; the engines of creation. E. Branscomb, T. Biancalani , N. Goldenfeld and M. Russell).

The Darwinian Transition
One of the key puzzles of astrobiology concerns the precision, uniqueness and rapidity of early evolution. In order for life to have evolved the main components of the modern cell as early 3.8 billion years ago, with a unique genetic code that is virtually optimal in terms of minimizing translational errors, the mode of evolution would have had to be different from the current vertical transmission of genes. We had shown in 2006 that the collective mechanism of horizontal gene transfer (HGT) is the only one capable of solving the puzzle of early evolution. The HGT means that the evolutionary process before LUCA can be thought of as a network of interactions rather than a tree, as would be the case in vertical gene transfer. The multiple connectivity of the network accelerates the evolution and allows rapid convergence to a unique, near-optimal genetic code. With all these advantages of HGT, why would it ever stop? To address this question, we built a quasi-species model of interacting organisms that includes HGT. We ran the simulation in an environment which exhibited a “Mount Fuji” fitness landscale. We discovered that for early times, the system exhibited a progenote phase, with rampant HGT and no unique species. After some time, a transition occurred and HGT switched off, leading to tree-like vertical evolution. It is important to emphasize that the transition is spontaneous and occurs after the population of organisms have evolved their fitness. HGT is still operative, but the actual effect of it becomes minimal because the population has a whole is now near the fitness peak and the likelihood of an improved gene being transferred becomes correspondingly smaller. In other words, HGT drives itself into a regime where it is ineffective.

In parallel to theoretical work, we have made progress in determining whether translation, transcription, and replication have crossed the Darwinian threshold, defined as a stage at which the molecular machinery involve in each of the three processes fails to accept a component from a different domain. The experimental work focuses mostly on two proteins that are central to the replication of the genome in all three forms of life. These proteins are namely the sliding clamp, a donut shaped protein, and a clamp loader, a five sub-unit protein complex, that opens the sliding clamp and loads it onto the DNA. Once the sliding clamp is loaded onto the DNA, the DNA polymerase (enzyme that copies the genome) binds to the clamp and travels at the rapid speed by which the genome can be duplicated in a rapid manner for transfer to daughter cells (progeny). Our experimental work based on Methanosarcina acetivorans demonstrates that before the Archaea and Eukarya diverged, their common ancestor had already developed an origin recognition protein that is different from the one currently present in the domain Bacteria. This finding together with other biochemical, structural and bioinformatics analyses allow us to conclude that the common ancestor of the Archaea/Eukarya sister domains had already evolved a large genome with a sophisticated machinery to replicate the genome for transfer to progeny.

Culturing microbial communities in controlled stress micro-environments
We have developed two different types of microfluidic gradient chambers or GeoBioCells (GBCs). Each GBC is an experimental test bed in which to quantitatively track, in live-time, microbial physiological and evolutionary stress response to micro-environmental gradients. The first GBC test bed contains in-plane gel barriers positioned between porous media and the boundary channels. This device creates precisely controlled micro-environmental gradients in which the physiological and evolutionary response of Escherichia coli is being measured in response to the antibiotic Ciprofloxacin (Cipro). Cipro inhibits DNA gyrase function by sitting in the active site of the enzyme and thus inhibits cell replication. In this environment, E. coli rapidly adapts and perhaps evolves dynamically to the micro-scale environment. The highest biomass occurred near the center of the porous media instead of zones farthest from the stressor source. These represent the optimal ecological zones for survival and will be the target for measuring genetic mutations and other response changes. The second GBC is polydimethylsiloxane (PDMS)-based test bed in which over 1,000 hexagonal incubation wells with small connecting channels have been micro-fabricated. Living cells of E. coli 307, with green fluorescence proteins (GFP) within their plasmids, are introduced in the center of the GBC. Results indicate that Cipro begins to inhibit cell growth at 50 ng/ml. Yet, within 30 hours, the cells had fully adapted to this stress. These results highlight the role of stress gradients in determining the rate of evolution of populations.