Life without the double helix: Oparin Revisited

by Doron Lancet iewing a Watson-Crick model of Department of Molecular Genetics and the DNA is an exhilarating experience. It Crown Human Genome Center, The Weizmann Vbecomes crystal-clear how the base- Institute of Science, Rehovot, Israel paired double helix allows information to be stored and copied. Yet, in the post-1953 euphoria, scientists were tempted to believe that having such an explicit chemical entity as a functional core of present-day life implies that life began with it. The RNA-world model conjectures that the first chemical entity capable of self-replication was a base-paired polynucleotide. The present paper highlights reasons why this is unlikely to be right, and delineates an alternative scenario that draws upon Oparin’s early teachings.

From structure to origin A living cell is an utterly complex molecular machine. Origin of life scientists hope that by understanding its intricacies they will stumble upon an explanation for how it emerged. This aspiration is based on experience with simpler systems. For example, by studying moon rocks it is possible to come up with a mechanism of its formation by a cataclysmic planetary collision. However, this may not be true for entities whose complexity is many orders of magnitude higher. In such cases it is necessary to employ divergent thinking, guided by an assessment of which features are fundamental and which are consequential. It is widely agreed that the most crucial property of living entities is a capacity to generate similes. This attribute underlies the process of evolution and natural selection, and must have been present very early in life’s history. An often stated chicken-and-egg conundrum is that life cannot reach even a most rudimentary level of complexity without self-replication, but that only minimally

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126 127 DNA: MOLECULE OF INHERITANCE Life Without the Double Helix

by the religious constraints prevailing in An often stated chicken-and-egg conundrum is that Western nations. The standard Oparin- RNA/DNA World Lipid World: the GARD model Haldane theory 12 puts forward the production life cannot reach even a most rudimentary level of of organic molecules on the early Earth followed by chemical reactions that produced complexity without self-replication, but that only increased organic complexity. This process is perceived to have led eventually to organic minimally complex chemical entities can multiply. life capable of reproduction, mutation, and selection. In this form, the theory has no specification of which molecules were first, or how self replication came about. In fact, it predates by two decades the Watson-Crick complex chemical systems can multiply. breakthrough, and is therefore unbiased by The discovery of DNA, simple in design and its implications. seemingly capable of creating its own copies, The origin of organic molecules and has led to a wide belief that nucleic acids the origin of replication are two separate provide a solution for such an incongruity. problems. Actually, the first may be viewed However, an examination of the structure as a prerequisite for the second. The of DNA and RNA reveals chemical intricacy groundbreaking experiments of Miller and Figure 1 that defies the notion that they were the Urey 13, first published in the same year as 5) Development of “organizers” that allowed first replicators. Even in the present-day DNA’s structure, were specifically aimed at controlled reproduction to ensure that The two dichotomous stereotyped “world” scenarios for Life’s setting, polynucleotides only undergo the first question. They asked how, under resultant split-related daughter cells have origin. Both are likely to be over- replication in the context of its cellular milieu. primitive earth conditions, a sufficient the same chemical capabilities. simplifications, since prebiotic In a primordial chemically-heterogeneous supply of organics was generated to warrant mixtures must have included diverse compounds, and not just scenario, the spontaneous emergence Oparin’s “primordial soup”, the milieu in 6) Beginnings of evolutionary developments one class of substances. Therefore, of sufficient quantities of the required which reactions leading to life are assumed so that a group of cells could adapt to the two scenarios should be taken carbohydrate moiety and nitrogen base to have occurred. Criticism has often changes in the environment over time. to represent opposing concepts. On the one hand, the “RNA/DNA components is unlikely. Also, phosphodiester been aimed at both Miller and Oparin for world” view asserts that life began polymerization is thermodynamically conjecturing a particular set of atmospheric This clear-cut hierarchical scenario was with individual molecules that had a unfavorable, and the repeated building of conditions for the generation of an organic considered for decades an acceptable view relatively complex covalent structure, enabling them to store information, 24 a long second nucleic acid strand on its soup, conditions that may have not actually of how life began. In later years Oparin had instruct the synthesis of other first strand template would require intricate prevailed historically. The present paper guessed that the hypothesized “organizers” molecules, and undergo a complex catalysis 1, 2. For these and other reasons it avoids this controversy, positing that organic in step 5 might include nucleic acids, but chain of chemical steps that resulted in their own replication. On the other has been argued by quite a few authors that compounds could have arisen by a wide clearly he was not thinking in terms of a full- hand – the “lipid world”, a scenario an RNA-like polymer may not have been the variety of processes under a broad spectrum fledge transcription and ribosome-mediated that claims that much before the early seed of life 3, 4. of planetary conditions 14-23. We address translation apparatus, as these would have appearance of RNA-like biopolymers, there existed “non-covalent The breakthrough discovery of Watson only the ways by which the double helix’s been too complex for the primitive stages polymers”40, assemblies of relatively and Crick 5, 6 led to the practical extinction of discovery affected scientific views on the invoked. Oparin had the insight to consider small molecules, capable of mutual alternative hypotheses. The beauty of DNA earliest replicators. the possibility of simile generation based association by weak chemical forces, including, but not limited to replication was so compelling that any other According to Oparin’s teachings the on a web of chemical interactions, namely hydrophobic interactions 34. In the “dirtier” pathway suddenly looked untenable. following steps have happened en route to what would be called nowadays a prebiotic realm of this scenario, information Yet, in view of the problems posed above, it early life: metabolism-like network 25-27. Self replication was contained in an assembly’s chemical composition rather than is interesting to ponder the untainted state was thought of as related to the splitting in a molecular covalent sequence of art of origin-of-life research as it existed 1) Random synthesis of simple organic of coacervate droplets, including its entire (Fig. 2), and replication was based prior to 1953. In the process, insight may molecules from atmospheric gases. molecular repertoire, a process conceptually on an assembly’s random fission rather than on orderly templating. In be gained with respect to the dichotomy similar to modern cell division. Oparin the minds of lipid world proponents, between the widely accepted RNA-world 2) Formation of larger, more complex was not influenced by the later realization never was there an early bottleneck model and an emerging, more debatable lipid molecules from the simple organic that within each cell lurks an individual in which one individual molecule Alexander Ivanovich Oparin was responsible single-handedly for (1894-1980), Russian world model for life’s emergence (Fig. 1). molecules. component, DNA, capable of information practically all pivotal life-promoting biochemist. Oparin graduated storage and molecular self-replication. functions. Since it is straightforward from Moscow University in to calculate that uncontrolled organic Oparin revisited 3) Formation of coacervates - unique droplets 7 1917 and became professor chemistry may easily produce 10 of plant biochemistry there The Russian biochemist Aleksandr Ivanovich containing the different organic molecules. The nucleic acid takeover different compounds, and since in 1929. He also helped to Oparin first published his pamphletThe In the post-1953 era, origin of life research the simplest free-living cell has found the Bakh Institute of Origin of Life in 1924 7(reprinted in 8). It was 4) Development of a capacity to take up underwent a revolution, not less significant about 1,000 molecule types, the Biochemistry. As early as 1922 RNA world may be typified by a Oparin was speculating on the only a later expanded version published as a and discharge specific molecules, and than that which affected all of molecular molecular count time-sequence 7 origins of life on Earth and later book 9 that got translated to English shortly maintain a characteristic chemical pattern biology. This revolution hinged on the notion of 10 , 1, 10, 100, 1000 while the published The Origin of Life on 10, 11 lipid world would have a sequence thereafter . In that book, Oparin dealt with or composition. that base-paired nucleic acid polymers 7 6 5 Earth (1936) and The Chemical 10 , 10 , 10 , 10000, 1000. Future Origin of Life (1964). the problem of life’s origin, for the first time, might be capable of generating their own research would determine which from a materialistic perspective not inhibited copies. Thus, the vaguer, but potentially more path is more realistic. Science Photo Library

The Secret of Life

128 129 131 The Secret of Life DNA replication. Coloured Transmission Electron Micrograph (TEM) of human DNA from a HeLa cancer cell, showing a stage of DNA replication. The strand of DNA is coloured It has formed into a yellow. molecule termed Y-shaped a replication fork, where the DNA has unwound into two single strands. Normally, DNA consists of two tightly wound spiral strands. During replication, a “bubble” region forms which enlarges to form a replication fork. It is here that daughter strands form as the parent DNA acts as a template for the construction of a new matching strand. In this way the sequence of bases (or genetic nformation) along the DNA molecule is replicated. Life Without the Double Helix Double the Without Life

Dr Gopal Murti / Science Photo Library 7, , and much before , and much before 29, 30 In fact, a purist’s point of view would In fact, a purist’s It is possible to envisage how through how through It is possible to envisage

makes the argument that “slowly but surely, that “slowly but surely, makes the argument would be “…broken down and give rise would be “…broken to new pieces…constructed or organized their therefore just like their parent…and the gel was inherited by them from structure formed”. The essence which they were from is that the most important of this argument is just bequeathing the aspect of replication and function of a molecular overall structure an a capacity to propagate ensemble through plus a simple internal chemical consistency, of physical split. process assert that this is true also for a present the molecular day living cell. Accordingly, set templating of DNA is just one of a large which it is assured of mechanisms through that after a physical split the two cellular halves would be capable of replenishing to the en route their molecular repertoires next split. Parallel mechanisms would be synthesis, the assembly ribosomes, protein copying of the centrioles the protein-mediate a very primitive system in which the prefect the prefect system in which a very primitive evolved, has not yet structure Watson-Crick over a replication- the control and in which is in the hands of a more reaction related Addressing catalysts. unwieldy set of organic in such a of templating the chemical nature leads to the notion that general perspective substances may be, sets of mutually catalytic for primitive forms of in principle, sufficient self replication. and of selection a long, gradual process from helix would emerge evolution the double Another way ancestor. its “bag of catalysts” to view this is to say that a fairly complex day metabolism present network resembling to have been likely therefore basic, is more earlier than a double helix-based genetic paper original apparatus. Indeed, Oparin’s 8 to generation, over many generation from took place an thousands of years, there increasing towards improvement…directed the efficiency of the apparatus for absorption and assimilation of nutrient compounds… (and) the ability to metabolize”. Information storage Primordial first article was written before Oparin’s as a genetic role discovery of DNA’s Avery’s information store the mechanism and Crick uncovered Watson nucleic by which this is made possible. To of description acid supporters, Oparin’s how biological information was stockpiled and transmitted looks rather primitive. He ‘gel’ describes how bits of protoplasm-like , all a templating strand is doing when This alternative the very basic view probes reaction. As seen in definition of a templating Fig. 2 the incorporation of a properly directing second nucleotide into a growing base-paired stand is a special case of rate enhancement. does not conform to While this reaction the strict definition of multiple turn-over it is nevertheless a selective enzyme reaction, catalysis phenomenon. One may envisage from the start, and full-fledged double-helix- the from based mechanisms would arise much later. as a capacity of an Replication could emerge ensemble, so that evolution molecular entire would apply to all by gradual improvement a components in unison, and not solely to information carrier. hypothesized core and catalysts Templates One of the most popular means of portraying of early evolution the chicken and egg nature is asking what came first: nucleic acid- based information storage molecules or to synthesize proteins, needed in order catalysts without which globular protein the DNA/RNA machinery would come to a grinding halt. One way to answer the question is to ask which of the two sets of basic. chemical phenomena appears more answer is that The RNA world protagonists’ capable of both since ribonucleic acids are and catalysis, template-based replication then RNA must have been the primordial basic a view derived from However, mover. answer. chemistry may lead to a different ingredients from a village of wary French a village of wary French from ingredients contained only peasants. The pot initially and of course a stone immersed in water, of it, solely irrespective the soup emerged and because meat, vegetables, salt, spices have been stealthily added. The all the rest early evolution moral is that the “recruitment may be somewhat by nucleic acids” picture simplistic, and that alternative, Oparin-style, In the latter, scenarios need to be explored. the hypothesized early entities would include of components right a diverse repertoire ) that 28 Lipid World: Compositional diversity Lipid World: The polynucleotide-first scenario brings The new scenario was simple and

story, based on an old French tale, about based on an old French story, hungry soldiers who manage to cook three up a fine soup by cajoling the necessary and their associated sythetases, ribosomes enzymes would all somehow and protein appear and join the original nucleic acid. how the fact that it is not specified Typically, nucleic acid has already a self-replicating turn the other up aids the appearance of molecular constituents. Also, little is said is if a single molecular replicator about how, all the other components about, it will recruit selection and evolution into the replication, game. popular children Brown’s to mind Marcia form in the soup, life would emerge. This is form in the soup, life would emerge. based on the notion that once self replication be is in place, selection and evolution would jump-started and then gradual improvements a naked nucleic acid to a could lead from This scenario envisions that the protocell. additional paraphernalia for a full- needed such as metabolic fledged cell-like entity, pathways for the synthesis of hundreds of molecular components, membrane passive and active transporters, enclosures, mechanisms and ATP-like energy-harvesting compounds, primitive tRNA’s energy-rich free realistic scenario of a “mixed bag” (“garbage scenario realistic terminology Dyson’s bag” in Freeman has been largely self-reproduction undergoes abandoned. seemingly elegant. If only a single self- nucleic acid could base-paired replicating Where does information reside? Where does information

RNA World: Sequence diversity RNA World:

37, 40. it rests in a “compositional vector” whose elements are the counts of the different molecular types. See refs. 35, information resides in the sequence of chemical units (monomers), while in non- covalent molecular assemblies Figure 2 In covalent biopolymers, DNA: MOLECULE OF INHERITANCE OF MOLECULE DNA: 130 DNA: MOLECULE OF INHERITANCE

and the production of new lipid bilayers for organelles such as mitochondria and the Golgi apparatus. While the words of Oparin describe vividly how structure and function might have been passed down the generations, a more A-C-T-A-G-T-T-C A-C-T-A-G-T-T-C accurate and rigorous description would be � needed to convince a modern molecular T-G-A-T-C-A-A-A T-G-A-T-C-A-A-G biologist that the split of a molecular � � assembly is sufficient to do the information transfer job over many generations. To this A-C-T-A-G-T-T-C end, we have advanced in recent years the Graded Autocatalysis Replication T-G-A-T-C-A-A Domain (GARD) model 31-35. The essence of this model relates to the capacity of a daughter molecular assembly, derived by a � � physical split from its ancestor, to withstand A-C-T-A-G-T-T-C A-C-T-A-G-T-T-C the “trauma” of fission (e.g. the loss of scarce but essential molecular species). � � T-G-A-T-C-A-A-C T-G-A-T-C-A-A-T GARD molecular assemblies are shown to be capable of undergoing a complex replenishment process during growth, thus Figure 3 assuring homeostatic growth and a capacity It is proposed that templating is derived concept, and the more for self replication upon fission36, 37. basic notion is catalysis. The elementary step of adding a base to an extending second strand in a double stranded RNA/DNA type In a modern-day cell, this process biopolymer may be summarized in four competing reactions, one is known to depend crucially on protein which involves legitimate Watson-crick pairing (a), and the other synthesis, based on information inscribed in three (b,c,d) forming illegitimate pairing with decreasing kinetic efficacy. The top strand may be considered to be an “enzyme” that RNA and DNA. Such central dogma pathway catalyses chemical reaction a in favor of the side reaction reactions is, however, so complex that it is unlikely to LEICESTER b, c and d. have been present in very early protocells 25, 38, 39. The RNA world concept asserts the existence of very few, template-replication biopolymers, assisted by an ill-specified set of catalysts, potentially RNA itself, to make proteins. The GARD scenario claims that UNI Ligand Lipid early on, none of the three components of the central dogma may have existed, and that Catalysis of binding Catalysis of entry the only resemblance of early replicating and evolving entities to present day cells was in matters of general design. Specifically, GARD assumes a network of mutually catalytic, relatively simple organic molecules, with amphiphilic characteristics, forming small assemblies. The most rudimentary form of rate enhancement is assumed to have occurred upon amphiphile entry into and exit out of the molecular assemblies (Fig. 3), resulting in a behavior receptor that resembles cellular homeostatic growth 33, 37, 40. More advanced versions of GARD Figure 4 currently being developed, include also Left, Membrane lipid phase as catalyst for peptide-receptor catalyzed covalent bond formation that leads interactions 41. Right, in analogy, neighboring lipids in a micelle or a bilayer may catalyse the entry/exit of another molecule into the to oligomerization and to the emergence of amphiphilic assembly. Such a relatively simple notion serves as a a more realistic connected metabolism. In 33, 40 core of the GARD model as described in the text and elsewhere . this view, simple catalysts (enzyme mimetics) underlie the emergence of primitive catalytic networks, and the eventual appearance of DNA simply subserves the making of better

132 Life Without the Double Helix

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