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How life can arise from chemistry
Current Biology
Magazine Feature
How life can arise from chemistry Rapid progress in several research fields relating to the origin of life bring us closer to the point where it may become feasible to recreate coherent and plausible models of early life in the laboratory. Michael Gross reports. Life, in many people’s view, is special and different from all non-living matter to an extent that ancient cultures tended to credit its existence and astounding diversity to an almighty creator. Since then, Darwin and his successors have rationalised the diversity, Wöhler has shown that the molecules of life are chemicals like everything else, and science has abandoned the ancient concept of a vis vitalis or life force that was supposed to set living matter apart. And yet, to this day, some philosophically inclined authors like to emphasize the ‘sense of purpose’ of living beings, a resurgent vis vitalis now known as teleonomy, and argue that Darwin does not reveal how organisms ‘purposefully’ using energy to counter the unifying effects of entropy may have arisen from purely chemical systems simply obeying the laws of thermodynamics. Just how the transition from non-life to life may have happened was indeed a gaping hole in our understanding of evolution in the 20th century, which a few inspired experiments like Stanley Miller’s famous 1952 primordial soup kitchen couldn’t quite bridge. Recently, however, progress in understanding and recreating elements of the RNA world, believed to have been an evolutionary phase preceding and enabling the emergence of DNA and proteins, has advanced to a point where an understanding of how life might arise — on our planet or on one of the many others that are now being discovered — comes within our grasp. RNA world marches on The idea that RNA may have served both as genetic material and as biocatalyst before DNA and proteins evolved emerged soon after the discoveries of ribozymes by Tom Cech and Sidney Altman. Although ideas of ancestral nucleic-acid-only worlds had already been explored in the 1960s, the ability of RNA to stand in for both
DNA and proteins was crucial for the assembly of the RNA world hypothesis as we know it today. A key argument was the important roles that RNA plays in protein biosynthesis. Unlike nucleic acids, proteins can’t serve as templates for their own synthesis, so some elementary version of the current, highly complex protein synthesis apparatus must have been around before proteins could be made, and this apparatus happens to consist mainly of RNA surrounded by some helpful proteins. The hypothesis received a spectacular boost from the first crystal structures of the ribosome, which clearly showed that proteins played supporting roles only. As Tom Cech proclaimed in a commentary in Science magazine: “The ribosome is a ribozyme.” The other side of the hypothesis, stating that RNA was also the primeval genetic material, was comparatively
much more obvious from the start — the subtle differences that set DNA apart from RNA are clearly evolutionary improvements serving long-term stability and copying fidelity. So now that most experts agree that life probably did pass through a phase with RNA genes and ribozymes running the show, the riddle to be solved is reduced to the question of how an evolving RNA system could arise from non-evolving chemical precursors. This could have happened directly, or via some simpler form of evolving molecular system yet to be identified. As Irene Chen from the University of California at Santa Barbara, USA, and colleagues have elaborated in a recent review in this journal (Curr. Biol. (2015) 25, R953–R963), it would be futile to ask how exactly this process happened on our planet. Instead, in the context of our rapidly growing knowledge of many thousands of extrasolar planets (Curr. Biol. (2015) 25, R1151–R1153), the question that is both more universally relevant and more tractable is, how can the transition from non-life to RNAbased life happen? In their review, Chen and colleagues show that a growing number of key steps that could be part of the emergence and early evolution of life
Creative act: Rapid progress in investigations into the origin of life is adding to our understanding of how the emergence of evolving systems from prebiotic chemistry may have happened — without the need for magic. (Photo: Rama, Wikimedia Commons.)
Current Biology 26, R1247–R1271, December 19, 2016 R1247
Current Biology
Magazine
RNA clue: The ribosome, which makes proteins but consists of two-thirds RNA by weight and co-operates with RNA molecules including mRNA and tRNAs, is essentially a ribozyme coated in accessory proteins. This finding is one of the strongest pieces of circumstantial evidence in favour of the RNA world hypothesis. (Image: Courtesy of PDB-101 and the RCSB PDB rcsb.org)
can now be rationalised with plausible and reproducible mechanisms, and that some of the problems that the pioneers of the field had highlighted, including the ‘nightmare’ of highly heterogeneous mixtures of chemicals, may be more manageable than thought. Thus, the authors conclude, the RNA world has emerged as a plausible and practical model enabling scientists to study many aspects of the early evolution of life and the functioning of simple life forms. Since this review, further research along those lines has reinforced this optimistic view and added new pieces to the jigsaw. Just add phosphate A key inorganic component that life must have recruited early on is phosphate. It is ubiquitous in all life forms we know, not only in the backbone of nucleic acids but also in important small molecules carrying energy (ATP), reduction potential (NADPH) or information (GTP). How this ion may have made the transition from inert, mostly insoluble inorganic compounds into RNA and other biomolecules is a crucial point that needs an explanation. R1248
Prebiotic chemistry has long struggled with the recruitment of phosphate. This anion likes to associate with bivalent metal ions such as calcium or magnesium, and the resulting salts would be poorly soluble under conditions compatible with life. Moreover, its transfer from inorganic salts into nucleic acids or other biomolecules involves a condensation reaction, i.e. the removal of a water molecule. When water is the solvent and thus present in huge excess, the opposite direction, namely the hydrolysis of the phosphor ester bond, is favoured. Until recently, phosphorylation of prebiotically relevant organic molecules only succeeded in water-free medium, such as in organic solvents, at high temperatures, and with the use of specialised phosphate reagents whose occurrence on prebiotic Earth would appear unlikely. The teams of César Menor-Salván and Nicholas Hud at Georgia Institute of Technology in Atlanta, USA, have recently suggested a surprisingly simple solution for this riddle, based on a set of conditions that may naturally adjust themselves as a puddle
Current Biology 26, R1247–R1271, December 19, 2016
evaporates (Angew. Chem. Int. Ed. (2016) 55, 13249–13253). Specifically, they used a mixture of urea, ammonium formate and water in the molar ratios 1:2:4. This is the so-called eutectic mix, in which all components are optimally soluble and on cooling will remain dissolved until the mixture solidifies with this composition. Upon slow evaporation, any component in excess will precipitate in larger amounts and thus lead the remaining liquid towards the eutectic condition. Both urea and ammonium formate are readily produced in experimental setups mimicking presumed prebiotic conditions. Urea had already been found to be a useful ingredient in previous studies using non-aqueous solvents. After adding disodium phosphate and adenosine to this mix, and incubating at 65°C for 19 days, the researchers could isolate the biologically relevant 5’-adenosine monophosphate (AMP) at over 20% yield. Further experiments showed that the same route also works for the three other ribonucleosides needed for RNA, laying the foundation for an important connection between plausible prebiotic chemistry and the still hypothetical RNA world. Nucleating nucleosides So prebiotic environments could link phosphate to nucleosides, but where did they get the nucleosides from? We tend to conceptualise these organic molecules as a combination of ribose and a heterocyclic base, which is either a single-ring pyrimidine (cytosine, uracil), or a bicyclic purine (guanosine, adenosine). However, sticking ribose and base together under prebiotic conditions has been a challenge. In 2009, the group of John Sutherland at the University of Manchester, UK, managed to bypass this problem for pyrimidines with an ingenious synthesis that creates the chemical bond between these ring compounds before it completes the actual rings. The synthesis even incorporates phosphate, which serves as catalyst and as reagent, and binds it to ribose (Nature (2009) 459, 239–242). For the more complex purines, the group of Thomas Carell at the University of Munich has now opened
Current Biology
Magazine up new possibilities in describing a synthesis that starts from simple prebiotic molecules and closes the second ring of the purine in the reaction with the sugar (Science (2016) 352, 833–836). The crucial intermediates are formamidopyrimidines, after which the researchers call their approach the FaPy pathway. Unlike historic efforts at linking up ribose and purines, which had a tendency to favour the wrong nitrogen atom, this synthesis leads to the correct product in good yield. Establishing a link to astrobiology, the authors point out that all of their reagents have also been found in comets such as 67P/ Churyumov-Gerasimenko, suggesting that they would also have been part of the chemical repertoire present on prebiotic Earth. RNA at work Meanwhile, other researchers are making progress in finding out how reproduction and metabolism may have worked in organisms without DNA or proteins. In this endeavour, researchers benefit from the vast repertoire of molecular biology tools developed for modern-day life, and also from the established method of in vitro evolution of functional RNA as pioneered by researchers including Jack Szostak at Harvard and Gerald Joyce at the Scripps Research Institute at La Jolla, USA. David Horning and Gerald Joyce have recently used directed evolution to modify a known RNA polymerase ribozyme such that it can now synthetise a wide range of functional RNA molecules including other ribozymes, transfer RNAs and aptamers (Proc. Natl. Acad. Sci. USA (2016) 113, 9786–9791). Such functional RNAs need stable secondary structure elements, which would also influence the structural propensities of any RNA genes coding for their sequences. The new ribozyme has now for the first time acquired the ability to melt such secondary structure for the duration of the RNA copying process — although it still isn’t able to do the same for its own, more complex structure. Moreover, the new ribozyme is able to amplify RNA genes exponentially by repeated copying. Thus, it can mimic a reaction that is widely practised in
Fossil record: Although fossils have told us much about the evolution of plants and animals, their evidence gets sparse and harder to interpret in the earlier phases of evolution. The first replicating and evolving systems are unlikely to have left any such traces. The image shows stromatolites from the Grand Canyon. Formed as layered biofilms involving cyanobacteria, these structures may be as old as 3.7 billion years. (Image: Carl Bowman, Grand Canyon National Park Service, Flickr.)
laboratories, only with proteins copying DNA, namely the polymerase chain reaction (PCR). With the key reactions of gene duplication and genetically guided production of functional molecules in place, it appears conceivable that a working model of RNA-only life could be synthesised soon. The first ribozyme that started polymerising RNA, however, will have had to arise from a nonenzymatic process. Recent results from Jack Szostak’s laboratory show that RNA duplication without a ribozyme is possible in the presence of oligonucleotides activated with a leaving group (eLife (2016) 5, e17756). The initial spark We may never know how the spark was lit that led to some kind of molecular self-propagating, evolving system and onwards to the RNA world and more complex cellular life. Indeed, it is hard to imagine a way in which this initial breakthrough could have left a trace that we might detect. The important part is, however, that it did happen. It may have happened multiple times in different versions, but seeing that the successful ignition meant an onwards progression of exponential proliferation, a single
spark followed by four billion years of evolution would be more than sufficient to explain the entirety of today’s biosphere. Even though we may never find a trace of that spark, synthetic chemical thinking can provide us with realistic models of how it may have happened on our own planet and on many others. “One of the main new aspects of origins research is the growing effort to connect chemistry to geology,” Jack Szostak notes. “Finding reasonable geological settings for the origin of life is a critical aspect of understanding the whole pathway. We’ve moved beyond thinking that life emerged from the oceans or at deep sea hydrothermal vents. New ideas for surface environments that could allow organic materials to accumulate over time, so that prebiotic chemistry could happen in very concentrated solutions, are a big advance.” We can conclude from all of this that the emergence of life in a universe that provides a suitable set of conditions, like ours does, is an entirely natural process and does not require the postulate of a miracle birth. Michael Gross is a science writer based at Oxford. He can be contacted via his web page at www.michaelgross.co.uk
Current Biology 26, R1247–R1271, December 19, 2016 R1249
Magazine Feature
How life can arise from chemistry Rapid progress in several research fields relating to the origin of life bring us closer to the point where it may become feasible to recreate coherent and plausible models of early life in the laboratory. Michael Gross reports. Life, in many people’s view, is special and different from all non-living matter to an extent that ancient cultures tended to credit its existence and astounding diversity to an almighty creator. Since then, Darwin and his successors have rationalised the diversity, Wöhler has shown that the molecules of life are chemicals like everything else, and science has abandoned the ancient concept of a vis vitalis or life force that was supposed to set living matter apart. And yet, to this day, some philosophically inclined authors like to emphasize the ‘sense of purpose’ of living beings, a resurgent vis vitalis now known as teleonomy, and argue that Darwin does not reveal how organisms ‘purposefully’ using energy to counter the unifying effects of entropy may have arisen from purely chemical systems simply obeying the laws of thermodynamics. Just how the transition from non-life to life may have happened was indeed a gaping hole in our understanding of evolution in the 20th century, which a few inspired experiments like Stanley Miller’s famous 1952 primordial soup kitchen couldn’t quite bridge. Recently, however, progress in understanding and recreating elements of the RNA world, believed to have been an evolutionary phase preceding and enabling the emergence of DNA and proteins, has advanced to a point where an understanding of how life might arise — on our planet or on one of the many others that are now being discovered — comes within our grasp. RNA world marches on The idea that RNA may have served both as genetic material and as biocatalyst before DNA and proteins evolved emerged soon after the discoveries of ribozymes by Tom Cech and Sidney Altman. Although ideas of ancestral nucleic-acid-only worlds had already been explored in the 1960s, the ability of RNA to stand in for both
DNA and proteins was crucial for the assembly of the RNA world hypothesis as we know it today. A key argument was the important roles that RNA plays in protein biosynthesis. Unlike nucleic acids, proteins can’t serve as templates for their own synthesis, so some elementary version of the current, highly complex protein synthesis apparatus must have been around before proteins could be made, and this apparatus happens to consist mainly of RNA surrounded by some helpful proteins. The hypothesis received a spectacular boost from the first crystal structures of the ribosome, which clearly showed that proteins played supporting roles only. As Tom Cech proclaimed in a commentary in Science magazine: “The ribosome is a ribozyme.” The other side of the hypothesis, stating that RNA was also the primeval genetic material, was comparatively
much more obvious from the start — the subtle differences that set DNA apart from RNA are clearly evolutionary improvements serving long-term stability and copying fidelity. So now that most experts agree that life probably did pass through a phase with RNA genes and ribozymes running the show, the riddle to be solved is reduced to the question of how an evolving RNA system could arise from non-evolving chemical precursors. This could have happened directly, or via some simpler form of evolving molecular system yet to be identified. As Irene Chen from the University of California at Santa Barbara, USA, and colleagues have elaborated in a recent review in this journal (Curr. Biol. (2015) 25, R953–R963), it would be futile to ask how exactly this process happened on our planet. Instead, in the context of our rapidly growing knowledge of many thousands of extrasolar planets (Curr. Biol. (2015) 25, R1151–R1153), the question that is both more universally relevant and more tractable is, how can the transition from non-life to RNAbased life happen? In their review, Chen and colleagues show that a growing number of key steps that could be part of the emergence and early evolution of life
Creative act: Rapid progress in investigations into the origin of life is adding to our understanding of how the emergence of evolving systems from prebiotic chemistry may have happened — without the need for magic. (Photo: Rama, Wikimedia Commons.)
Current Biology 26, R1247–R1271, December 19, 2016 R1247
Current Biology
Magazine
RNA clue: The ribosome, which makes proteins but consists of two-thirds RNA by weight and co-operates with RNA molecules including mRNA and tRNAs, is essentially a ribozyme coated in accessory proteins. This finding is one of the strongest pieces of circumstantial evidence in favour of the RNA world hypothesis. (Image: Courtesy of PDB-101 and the RCSB PDB rcsb.org)
can now be rationalised with plausible and reproducible mechanisms, and that some of the problems that the pioneers of the field had highlighted, including the ‘nightmare’ of highly heterogeneous mixtures of chemicals, may be more manageable than thought. Thus, the authors conclude, the RNA world has emerged as a plausible and practical model enabling scientists to study many aspects of the early evolution of life and the functioning of simple life forms. Since this review, further research along those lines has reinforced this optimistic view and added new pieces to the jigsaw. Just add phosphate A key inorganic component that life must have recruited early on is phosphate. It is ubiquitous in all life forms we know, not only in the backbone of nucleic acids but also in important small molecules carrying energy (ATP), reduction potential (NADPH) or information (GTP). How this ion may have made the transition from inert, mostly insoluble inorganic compounds into RNA and other biomolecules is a crucial point that needs an explanation. R1248
Prebiotic chemistry has long struggled with the recruitment of phosphate. This anion likes to associate with bivalent metal ions such as calcium or magnesium, and the resulting salts would be poorly soluble under conditions compatible with life. Moreover, its transfer from inorganic salts into nucleic acids or other biomolecules involves a condensation reaction, i.e. the removal of a water molecule. When water is the solvent and thus present in huge excess, the opposite direction, namely the hydrolysis of the phosphor ester bond, is favoured. Until recently, phosphorylation of prebiotically relevant organic molecules only succeeded in water-free medium, such as in organic solvents, at high temperatures, and with the use of specialised phosphate reagents whose occurrence on prebiotic Earth would appear unlikely. The teams of César Menor-Salván and Nicholas Hud at Georgia Institute of Technology in Atlanta, USA, have recently suggested a surprisingly simple solution for this riddle, based on a set of conditions that may naturally adjust themselves as a puddle
Current Biology 26, R1247–R1271, December 19, 2016
evaporates (Angew. Chem. Int. Ed. (2016) 55, 13249–13253). Specifically, they used a mixture of urea, ammonium formate and water in the molar ratios 1:2:4. This is the so-called eutectic mix, in which all components are optimally soluble and on cooling will remain dissolved until the mixture solidifies with this composition. Upon slow evaporation, any component in excess will precipitate in larger amounts and thus lead the remaining liquid towards the eutectic condition. Both urea and ammonium formate are readily produced in experimental setups mimicking presumed prebiotic conditions. Urea had already been found to be a useful ingredient in previous studies using non-aqueous solvents. After adding disodium phosphate and adenosine to this mix, and incubating at 65°C for 19 days, the researchers could isolate the biologically relevant 5’-adenosine monophosphate (AMP) at over 20% yield. Further experiments showed that the same route also works for the three other ribonucleosides needed for RNA, laying the foundation for an important connection between plausible prebiotic chemistry and the still hypothetical RNA world. Nucleating nucleosides So prebiotic environments could link phosphate to nucleosides, but where did they get the nucleosides from? We tend to conceptualise these organic molecules as a combination of ribose and a heterocyclic base, which is either a single-ring pyrimidine (cytosine, uracil), or a bicyclic purine (guanosine, adenosine). However, sticking ribose and base together under prebiotic conditions has been a challenge. In 2009, the group of John Sutherland at the University of Manchester, UK, managed to bypass this problem for pyrimidines with an ingenious synthesis that creates the chemical bond between these ring compounds before it completes the actual rings. The synthesis even incorporates phosphate, which serves as catalyst and as reagent, and binds it to ribose (Nature (2009) 459, 239–242). For the more complex purines, the group of Thomas Carell at the University of Munich has now opened
Current Biology
Magazine up new possibilities in describing a synthesis that starts from simple prebiotic molecules and closes the second ring of the purine in the reaction with the sugar (Science (2016) 352, 833–836). The crucial intermediates are formamidopyrimidines, after which the researchers call their approach the FaPy pathway. Unlike historic efforts at linking up ribose and purines, which had a tendency to favour the wrong nitrogen atom, this synthesis leads to the correct product in good yield. Establishing a link to astrobiology, the authors point out that all of their reagents have also been found in comets such as 67P/ Churyumov-Gerasimenko, suggesting that they would also have been part of the chemical repertoire present on prebiotic Earth. RNA at work Meanwhile, other researchers are making progress in finding out how reproduction and metabolism may have worked in organisms without DNA or proteins. In this endeavour, researchers benefit from the vast repertoire of molecular biology tools developed for modern-day life, and also from the established method of in vitro evolution of functional RNA as pioneered by researchers including Jack Szostak at Harvard and Gerald Joyce at the Scripps Research Institute at La Jolla, USA. David Horning and Gerald Joyce have recently used directed evolution to modify a known RNA polymerase ribozyme such that it can now synthetise a wide range of functional RNA molecules including other ribozymes, transfer RNAs and aptamers (Proc. Natl. Acad. Sci. USA (2016) 113, 9786–9791). Such functional RNAs need stable secondary structure elements, which would also influence the structural propensities of any RNA genes coding for their sequences. The new ribozyme has now for the first time acquired the ability to melt such secondary structure for the duration of the RNA copying process — although it still isn’t able to do the same for its own, more complex structure. Moreover, the new ribozyme is able to amplify RNA genes exponentially by repeated copying. Thus, it can mimic a reaction that is widely practised in
Fossil record: Although fossils have told us much about the evolution of plants and animals, their evidence gets sparse and harder to interpret in the earlier phases of evolution. The first replicating and evolving systems are unlikely to have left any such traces. The image shows stromatolites from the Grand Canyon. Formed as layered biofilms involving cyanobacteria, these structures may be as old as 3.7 billion years. (Image: Carl Bowman, Grand Canyon National Park Service, Flickr.)
laboratories, only with proteins copying DNA, namely the polymerase chain reaction (PCR). With the key reactions of gene duplication and genetically guided production of functional molecules in place, it appears conceivable that a working model of RNA-only life could be synthesised soon. The first ribozyme that started polymerising RNA, however, will have had to arise from a nonenzymatic process. Recent results from Jack Szostak’s laboratory show that RNA duplication without a ribozyme is possible in the presence of oligonucleotides activated with a leaving group (eLife (2016) 5, e17756). The initial spark We may never know how the spark was lit that led to some kind of molecular self-propagating, evolving system and onwards to the RNA world and more complex cellular life. Indeed, it is hard to imagine a way in which this initial breakthrough could have left a trace that we might detect. The important part is, however, that it did happen. It may have happened multiple times in different versions, but seeing that the successful ignition meant an onwards progression of exponential proliferation, a single
spark followed by four billion years of evolution would be more than sufficient to explain the entirety of today’s biosphere. Even though we may never find a trace of that spark, synthetic chemical thinking can provide us with realistic models of how it may have happened on our own planet and on many others. “One of the main new aspects of origins research is the growing effort to connect chemistry to geology,” Jack Szostak notes. “Finding reasonable geological settings for the origin of life is a critical aspect of understanding the whole pathway. We’ve moved beyond thinking that life emerged from the oceans or at deep sea hydrothermal vents. New ideas for surface environments that could allow organic materials to accumulate over time, so that prebiotic chemistry could happen in very concentrated solutions, are a big advance.” We can conclude from all of this that the emergence of life in a universe that provides a suitable set of conditions, like ours does, is an entirely natural process and does not require the postulate of a miracle birth. Michael Gross is a science writer based at Oxford. He can be contacted via his web page at www.michaelgross.co.uk
Current Biology 26, R1247–R1271, December 19, 2016 R1249