Origins of Biology: How energy flow structures metabolism and heredity at the origin of life

Lead Research Organisation: University College London
Department Name: Genetics Evolution and Environment

Abstract

The origin of life is one of the most iconic questions in science. Work over decades has seemingly made good progress in synthesizing the basic building blocks of life under purportedly 'prebiotic' conditions. These building blocks include the nucleotides that make up the genetic material in DNA. However, there is a serious disconnect between this prebiotic chemistry and the actual biochemistry of known cells in almost every respect. To close this gap between geochemistry and biochemistry and elucidate the fundamental rules of life, we propose a different approach to the problem, grounded in life itself.

We take as our starting point an important rule of life - energy flow across membranes. This feature of life is as deeply conserved across the tree of life as the genetic code itself. Yet while the importance of energy flow in biology cannot be overstated, the origin and evolutionary implications of the specific mechanism involved - the flow of protons (hydrogen ions) across membranes - has historically been neglected. Recent work on reconstructing the properties of the earliest cells is now opening up new possibilities. Our overarching hypothesis is that the flow of protons across membranes can drive the difficult reaction between carbon dioxide and hydrogen gas to form the carbon 'skeletons' that are used to make all the other building blocks of cells. We propose that analogous processes can be driven in structured prebiotic environments such as hydrothermal vents, giving rise to the familiar metabolism and biochemistry of cells. In particular, we hypothesize that genetic information first arose in this setting. Genetic heredity is strictly another form of growth, in which a genetic template is repeatedly copied (doubled) and passed on. We propose that its mysterious origins (which have resisted interpretation over decades, despite many clues) can best be understood in the context of actively growing protocells, driven by energy flow through a structured environment.

We will explore this fundamental organizing principle: energy flow across barriers drives the synthesis of organic molecules - growth - and the building blocks needed for genetic heredity. Our specific objectives are to: (i) understand the driving force for growth; (ii) use biology as a guide to protometabolism; and (iii) resolve the origins of the genetic code in protocells. We have previously detailed possible mechanisms. In this grant, we will rigorously model the steps going from a strictly inorganic but structured setting (such as geologically sustained proton gradients across inorganic barriers in hydrothermal systems) to the formation of simple protocells with a rudimentary form of heredity, and finally to the emergence of true genetic heredity in protocells. We will test the predictions of this computational modelling experimentally, using a combination of microfluidic reactors and screening of possible prebiotic conditions based on the chemistry of cells. We will feedback the results of experiments into the models to refine our concepts and ultimately deliver a coherent, integrated understanding of the energetic rules of life. Our extensive pilot data gives strong credence to the work proposed here.

We believe these rules will help to elucidate the forces that drive life into existence on a geologically active but sterile planet. We are primarily interested in understanding the rules that govern the emergence of life but our work also has
implications for the search for life elsewhere in the universe, guiding future space exploration. At home, this work has vital implications for understanding the structure of our own metabolism, potentially elucidating both normal and altered patterns of metabolic flux in lifelong health and disease. Finally, fixing carbon dioxide as organic molecules using a biomimetic form of energy flow could facilitate carbon capture to produce synthetic gasoline, giving a net zero-emissions solution to energy security.

Technical Summary

The origin of life frames the 'rules of life', which still underpin biology today. While prebiotic chemists have successfully synthesised the precursors of DNA, RNA and proteins under abiotic conditions, these syntheses are strikingly dissimilar to biochemistry in substrates, reaction pathways, catalysts and energy transduction, giving little insight into the rules of life. We view CO2 fixation and growth as fundamentally structuring metabolism. Critically, carbon and energy metabolism are universally driven by membrane bioenergetics. Here we propose an ambitious programme that links energy flow and growth at the origin of life to the emergence of genetic information. Our objectives are to: (i) understand the driving force for growth; (ii) use biology as a guide to protometabolism; and (iii) resolve the origins of the genetic code in protocells. We will use an iterative combination of computational modelling with experimental testing of predictions. We have developed the modelling approaches, microfluidic reactors, analytical methods and screening procedures needed for the programme. These will be used to elucidate how prebiotic energy flow could drive the reduction of CO2 by H2 to form carboxylic acids, amino acids and fatty acids, giving rise to replicating protocells with rudimentary membrane heredity. We will use intermediary biochemistry as a guide to the origins of metabolism, energy transduction and growth in protocells, including synthesis of nucleotides from amino acids and sugar phosphates. Finally, we will consider the origins of the genetic code based on the links between metabolism, oligonucleotides and peptides in replicating protocells. Our strong pilot data gives credence to the work proposed here, which can potentially deliver a coherent, integrated understanding of the energetic rules of life. These rules have wide-ranging implications, from astrobiology, systems biology and synthetic biology to carbon capture and health across the life-course.

Planned Impact

For any potentially transformative research endeavour, as pioneered by BBSRC Frontier Bioscience in this sLoLa call, the primary benefactor is likely to be society itself. It is notoriously difficult to foresee the long-term potential applications of fundamental research. Yet there is no greater human question than the origin of life, and the appetite for answers to such questions can be seen in the large numbers of people who read books, watch TV programmes and films, or explore online to discover more about our own origins. PI Lane has an established track record of public engagement at the highest level globally and he will continue to address these questions and encourage those involved in this project to do so too. UCL is particularly good at fostering public engagement, with regular winners of the Royal Society Michael Faraday Prize and the Science Book Prize (including Lane in both cases) as well as numerous appearances on TV, radio, film and online media from staff. We will ensure that our findings in this exciting field are transmitted to the public as effectively and engagingly as possible.

The public appetite for insight into the biggest questions in science, including the origin of life, has spread in recent years to the search for life elsewhere in the universe. A new commercial space race is beginning, with concerted efforts to seek life within the solar system and on exoplanets. NASA and ESA have been engaged in publicising and raising funds for missions to Mars, Enceladus and Europa, with all three but especially the icy moons showing signs of the kind of hydrothermal activity discussed in this grant. Private organizations such as the Breakthrough Initiative are funding missions to the icy moons. Those tasked with identifying potential diagnostic features of life that could be detected for example in the plumes of Enceladus will benefit from the fundamental approach to the Rules of Life developed in this proposal. More broadly, the long-term societal benefits feeding back from advanced space technology is likely to be immense.

Despite the fundamental nature of the research proposed, we can also foresee potential benefits to other groups. By elucidating the origins and structure of metabolism, notably the reverse (reductive) Krebs cycles as central to metabolism, we should provide a coherent basis for interpreting extensive new data emerging from metabolomics in relation to lifelong health, and the patterns of metabolic dysregulation in cancer, diabetes and neurodegenerative conditions. The discovery that sections of the Krebs cycle frequently run in reverse in these conditions came as a revelation but makes sense from the perspective developed here. A coherent understanding of the structure of metabolism will benefit all those involved in biomedical research, and especially the rising generation of researchers who are becoming involved in understanding metabolism and health. This could have major implications for personalised medicine and health across the lifecourse with impact on nutraceutical development.

Other groups who are likely to benefit from the research proposed here are synthetic biologists, biochemical engineers and the bioenergy community. By uniting energy flow and structure from a thermodynamic perspective, we aim to generate simple tools that drive protocell growth directly from gases in continuous-flow reactors. These could have numerous applications, from providing new tools for synthetic biologists (as minimal cells) to developing vehicles for sustainable synthesis of plastics, drugs and other chemicals, and ultimately even to facilitating economic carbon capture (powered by pH gradients across barriers) which could have a major impact on lowering atmospheric CO2 levels or synthesising hydrocarbons for the chemical industry or bioenergy industry with net-zero emissions. If economic, this would hold major implications for energy security and sustainable bioenergy production

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