Two Problems in the Origin of Life. Chrisantha Fernando

Part 1. The Origin of Metabolism.

Metabolism. Active or passive entrance of material and energy into the system which transforms them (by chemical processes) into its own internal constituents. Waste products are produced. ‘External/Internal’ does not refer to spatial separation, but alludes to whether or not the material is a part of the organization of the living unit.

How could life happen without metabolism? An organism without metabolism would be one that did not synthesize any of its materials from precursors (X), but obtained the materials directly from the environment. Heterotrophic theories (Oparin and Haldane) assume high concentrations of complex organic molecules could have been found and maintained at sufficient concentration in the environment.

Heterotrophic Theories (Replicator First Theories) Lancet’s GARD model and other models of reflexive autocatalytic sets such as Eigen’s hypercycle Farmer’s et al. autocatalytic binary strings, Fox’s microspheres, and more recently Szostak’s protocell all make the same assumption. How much time would it take the biosphere to deplete this alleged free gift of complex molecules?

For non-metabolising ‘life’ to maintain low internal entropy, unless all its energy could be obtained from sources external to its chemical precursors (X), X would have to be used as a chemical energy source, and so degraded to waste products. Also X decays to simpler molecules at a finite rate. This happens independently of any reactions required for the maintenance of the organism. Therefore, long-term persistence of non- metabolising entities assumes the existence of mechanisms in the environment able to replenish X.

No known mechanisms, other than living systems with metabolism, are capable of synthesizing complex organic molecules continuously. Since there is no continued influx of complex organics from outer space, non-metabolising organisms can therefore only exist as transients in a system initialized with abundant complex organic molecules, because eventually these will run out. Alternatively, non-metabolisers can be “parasitic” upon complex organics produced by entities capable of synthesising complex organic molecules from a subset of X. Viruses are an example.

In the long-term, the concentration of these metabolising entities will be the rate-limiting factor for the non-metabolising entities. The biosphere is to a first approximation is a closed thermodynamic system. How can X be recycled effectively and indefinitely by a biosphere? As a prerequisite for the persistence of life, we require entities that are capable of obtaining energy from outside the system in order to re- cycle the chemical system (autotrophs or nonliving ‘autotrophic’ metabolic systems).

All known cellular life possesses an autocatalytic metabolism, even if the cells are heterotrophic.

Autocatalytic Cycles. e.g. The Formose Cycle.

For the autocatalytic nature of the whole metabolic network it is not necessary to be able to identify a smaller autocatalytic core as the reductive citric acid cycle or the Calvin cycle. Imagine the following thought experiment. Take away all metabolites from a cell but leave all the water and the informational macromolecules in place. Can the network be recreated from the food materials only, or not? Let us be generous and provide enough ATP also for the supposed kick-start.

No contemporary cell could resume its activity in this experiment. Consequently, all cells today possess a distributive autocatalytic network then cannot be seeded from outside, because some of its seed components cannot be taken up from medium. All cells today possess endogenous autocatalysis.

Thought Experiment. Imagine an experiment that simulates early earth conditions. Construct multiple “micro- environments” each with different characteristics, e.g. abiotic energy sources, UV light (oscillating as night and day), redox potentials (e.g. surfaces), different temperatures, salinity, pH, local chemical concentrations. Equilibrium positions and chemical reaction rates vary between these micro-environments.

So keep system very far from equilibrium Initialize the system with a subset of atoms and small molecules e.g. C, H, N, O, P, S, and leave it for some time. Under what circumstances will the system settle down into a boring point attractor, e.g. tar, and under what circumstances will it produce life? Under what circumstances would an autocatalytic cycle arise? How would the “platonic space” of all possible chemical reactions be explored?

How many potential autocatalytic cycles will there be in a random bimolecular network of chemical reactions?

G.A.M King modeled a recycling chemical network (i.e, where every molecule type is produced in at least one reaction, and consumed in at least one reaction) of bimolecular reactions (i.e., where two reagent molecules react to produce two product molecules) and showed that the number of “platonic” autocatalytic cycles C is given by Number of reactions that the ith reactant takes part in Number of reactant types, i

Basic Dynamics. Rates of decay of constituents must equal their rate of creation from reagents, at steady state. Rates of decay are increased by “OR-reactions” that tap the cycle, i.e. reactions where a constituent may undergo side-reactions. There will exist a “limiting reagent”. Exponential growth of the autocatalytic cycle will only occur when the limiting reagent (whichever one it is at the time) is present in excess, so for the cycle to persist, this limiting reagent must be generated at sufficient concentration.

How specific must the reactions of an autocatalytic cycle be for it to grow? Imagine a cycle with n constituents, and m other active substances in the medium (which also include the reagents). Considering all possible reactions between the constituents and the other substances, King found that the cycle grows exponentially only if,

How probable is it that a randomly generated autocatalytic cycle of size n will persist? Assuming randomly assigned rate coefficients and concentrations, King defines a “kinetic complexity” to a cycle as Y = n(m-1), where n is the number of constituents and m is the number of the active substances in the medium including reagents, and calculates the probability that a cycle of size n will persist under these conditions.

King assumes an exponential distribution of specificities of reaction, with most reactions having low specificity. Probability of persistence is very low for anything but the smallest cycle. Selection on rate coefficients and concentrations of reagents are needed This makes the spont. metabolism required for the RNA incredible!

Selection on Autocatalytic Cycles. Szathmáry classified autocatalytic cycles as replicators of the “holistic” type, and predicted that their heredity would be limited to a small number of alternative forms (basins of attraction in the chemical space of constituents), which showed only infrequent macromutations. To what extent can autocatalytic cycles evolve as “holistic replicators” in chemical space?

King suggests selection would be largely confined to the specificity of the reaction for uptake of the limiting reagent. This can be achieved by selection on the “autocatalytic particle”. Also achieved by loss of those materials that disrupted the recycling of the limiting reagent, or by exclusion of the m other species from the medium, e.g. using protocell compartments.

Autocatalytic cycles can compete for the same reactant, with competition in the growth phase being dependent on rate of limiting reactant usage, and competition in the decay phase being dependent on the comparative decay rates. Since growth is exponential, there is “survival of the fittest” during the growth phase, and co-existence is not possible, assuming a well-mixed reactor. In a well-mixed reactor, co-existence can only occur if autocatalytic cycles are not competing for the same limiting reagent.

Co-operative interactions between autocatalytic cycles occur when their reactions are consecutive (i.e., the product of one is the reactant of the other) or where the constituent of one autocatalyst is the reagent for another autocatalyst. ACCs can undertake symbioses by some sort of physical coupling between cycle constituents to form a combined “particle” would have been necessary in order for symbiosis to occur. Low limiting reagent concentrations may promote symbiosis of autocatalytic cycles.

How to maintain limiting reagents for autocatalytic cycles? A recycling system of chemical reactions must use external energy e.g. electrical discharges, redox potentials, UV light, concentration by drying in intertidal zones, mineral surface films, or gradients across vesicles. Work has to be done on the system. Selection can act on the persistance of recycling chemical systems as well as on autocatalytic cycles. The problem of the origin of life is the problem of how metabolite channeling can be achieved. This is a mystery but the problem is now defined.

Part 2 The Origin of Long Template Replication?

Why is long template replication important? Unlimited heredity: Number of possible sequences exceeds the number of sequences that can be produced. The quantity of heritable information is then limited only by replication accuracy and population size.

Template Making covalent (P) bound Monomers Product Separation is the rate-limiting step. Longer templates are stuck together by h-bonds. H-bonds

Is there a mechanism of non-enzymatic replication of long templates? Maybe long template replication arose in replicating vesicles that possessed an autocatalytic metabolism capable of synthesizing activated building blocks. i.e. in a member of the chemoton quasi-species.

A Stochastic Model of Template Dynamics!

Stochastic discrete model with explicit p-bonds and h-bonds represented on a 2D grid (Very simplified secondary structure). Intra-polymer reactions. Inter-polymer reactions. One explicit polymer represents 3000 – real polymers. Only one type of building block.

RUN SIMULATION NOW!

Polymer Reactions

Hydrogen Bond Breakage. –Local neighborhood dependent. –Temperature dependent.

Configuration Dependent Hydrogen Bond Formation.

Zipper Mechanism: H-bond formation between p-bonds. H-bonds can form between opposite monomers along a double strand.

Configuration Dependent Phosphodiester Bond Formation. Temperature dependent. Rates scaled up for sake of simulation speed.

Novel Monomer Attachment. 100 x if stacked. Concentration dependent monomer binding.

Polymer Association. Association is tested between each possible ordered polymer pair. Association rate as for monomers but scaled by number of binding sites per polymer.

P-bond Degradation. Temperature dependent p-bond degradation. Scaled up by same amount as p-bond formation rate.

Control Experiments.

Melting Temperature v. Length 1/T m = A + B/N.

T m v. [Polymer]. 1/T m = A’ – B’lnC. C = [Polymer].

Simulated Flow Reactor Two types of replication mechanism were observed with [monomer] fixed.

Type I mechanism. High [Monomer] Low [Polymer] Low Temp. Produces oligomers from monomers which can later be incorporated into long strands. Type II mechanism High [Polymer] Low [monomer] High Temp. Produces long strands by staggered oligomer (& monomer) incorporation. INDEPENDENTLY DISCOVERED “SLIDOMER” Von Kiedrowski type Mechanism !!!!!!!!!!!

1.Competition by successfully unzipping short replicators. 2.No unzipping of long double strands. 3.Premature detachment of incomplete copies from longer strands. The main factors preventing long template persistence are… Therefore for long template persistence, oligomers must be incorporated into polymers by the type II mechanism, faster than they can be produced.

Results from Flow Reactor. [Polymer] = 0.1M – 0.05M Temperature = 350K. Type II mechanism predominates. [Polymer] = 0.01M M Temperature = 300K. Type I mechanism predominates. With current p-bond formation rate & [Monomer] maintained at 0.02M.

Short strands out-compete long strands by the type I mechanism. –Although long polymers can occasionally be replicated by the type I mechanism, production of incomplete strands, and the inherently shorter replication period of short strands, means that short strands out-compete long strands for the monomer resource. –Since chemoton replication occurs after a fixed number of monomers have been incorporated, this results in loss of long templates by segregation instability.

The following modifications to the type I mechanism failed to sustain long strands. –Instantaneous p-bond formation failed. –Increased monomer stacking rate failed. –Altering breathing rate failed because rate is the same for parent and incomplete novel strands. –A simulated enzyme that preferentially stabilized hydrogen bonds on incomplete strands failed. –A simulated enzyme that preferentially stabilized h-bonds on only the incomplete strands on parent strands only greater than 7 nt failed.

Conditions for Template Elongation.

Temperature Oscillation

More realistic p-bond formation rate means that dimers and trimers are produced faster than they can be incorporated. Recent results show that with realistic p-bond formation rates, low temperatures (< T m ) and high [oligomer] are necessary for elongation.

Conclusions. For persistence of long templates, oligomer incorporation into polymers (and other losses) must exceed oligomer production. Incorporation of oligomers is promoted by high p-bond formation rates and/or high [oligomer] at low temperatures, i.e. increasing ligation rate.

Self-Replication versus Self-Elongation Or: How to make long oligonucleotides without enzymes, primers, templates, surfaces, or stepwise feeding? Oliver Thoennessen, Mathias Scheffler & G. von Kiedrowski, Ruhr- University Bochum 3rd COST D27 workshop, Heraklion, Crete, Sept. 30-Oct. 3, 2004

The "standard" picture Who agrees? 1. Self-Replication 2. Metabolism 3. Mutability 4. Some way of keeping 1- 3 connected, viz. compartimentation

Chemical self-replication

Open systems, possible non-catalyzed pathways

Open systems: possible template-directed pathways

Dimer building blocks for an open system:nYRp

Dimer synthesis

Ligation versus Cyclisation C n XY p -EDU Cyclisierung B: -EDU O O O N H P P O O O O O O A/G C/T +H + +H 2 O EDC EDU -H + A + B Oligomerisierung 12-Ring CA-Cyclus c( XY ) = 1-10 mM Cyclisierung c( XY ) > 20 mM Oligomerisierung n p B: A: Reaktionsbedingungen: 0.2 M EDC in 0.1 M HEPES-Puffer, 2° - 30°C

Oligomerisation of nCGp-dimers

Reactivity of nYRp building blocks Di mer Tetramer

The current "Guiness" of prebiotic polymerisation

No template effects in reactions using single-sided building blocks

Earlier results from Zielinski & Orgel: Nature 1987: Experiments on a self-replicating tetraribonucleotide analogue confirmed our "square-root law". EDC as the source of energy, efficient replication in: GCn + pGC --> GCnpGC J. Mol. Evolution, a few years later: No self-replication at all in a slightly different system: CGn + pCG --> CGnpCG Speculations about the involvement of "slidomers".

Efficient oligomerisation via sliding, concatenation, and concatomer ligation? free oligomers straight duplexes slidomer duplexes concatomer duplexation sliding aggregation

How a concatomer might look

Better base stacking via slidomer concatenation CG dimerGC dimerCGCG slided duplex

Thermodynamic data support slided concatomers

Two possible modes of ligation

Reaction model

RMS as the function of a common slidomer equilibrium factor

"Template" addition even inhibits polymerisation

Summary and possible significance Summary and possible significance  The current picture to make long prebiotic oligomers is by primer- extension on a solid support (clay) via feeding with nucleotide- phosphorimidazolides (Ferris & Orgel, "crepes scanario"). Traces of 50- mers can be detected after several weeks and daily replenishment of the imidazolides.  "Self-elongation" as an alternative picture: In the presence of the dehydration reagent EDC, the dimer nCGp yields high molecular weight oligomers (quantitatively for n >> 40) after 3 days.  "Self-elongation" and "self-replication" may be different sides of the same coin. Exactly the same reason that caused poor self-replication in a comparable system causes efficient polymerisation in our system.  Eigen, Hartman, and others have speculated that the earliest "genes" were rich in C and G, or even CG-repeats. Our experiments indicate that one may neither need templates nor surfaces to arrive at such structures.  Outlook: Co-oligomerization experiments with nYRp are expected to result in materials still rich in CG but "being doped" with other bases. Such materials may have the capacity to fold into discrete secondary structures.