Emergence of adaptable systems and evolution of a translation device

Adv. Space Res. V o l . 4 , No.12, p p . 1 5 3 - 1 6 1 ,

1984 Printed in Great Britain. All rights reserved.

0273-1177/84 $0.00 + .50 Copyright © C O S P A R

EMERGENCE OF ADAPTABLE SYSTEMS AND EVOLUTION OF A TRANSLATION DEVICE U. Lehmann and H. Kuhn Max-Planck-lnstitut far Biophysikalische Chemie, (Karl-Friedrich Bonhoeffer-lnstitut), Molekularer Systemaufbau, D 3400 GOningen-Nikolausberg, F.R. G.

ABSTRACT An over-all organizational framework for the origin of life is outlined and attempts for realization are given. Evolution can be described as a process resulting in an increase of "knowledge" where knowledge is the number of carriers of genetic information discarded, on the average, until the evolutionary state under consideration is reached. A model for the evolution of a translation device, a crucial event in the origin of life, is described in detail. Aggregates of short polynucleotide strands in a hairpin conformation play a major role in this model. Experimental evidence for the selectivity of aggregation supports the idea of aggregates as error filters. Chromatographic separation as selection process during chemical evolution supports the model of the early translation device leading to the origin of the genetic code. INTRODUCTION In an attempt to find a scenario of the origin of life it is important to search for an over-all organizational framework before searching for mathematical models and chemically plausible steps of prebiotic evolution. Popular questiomssuch as: Was protein or nucleic acid first? How did chirality come about? What was the first energy source? should not be seen as the basic questions since different answers to these questions can correspond to the same over-all organizational framework. ORGANIZATIONAL FRAMEWORK The essence of the process leading to the living state is the emergence of a system that replicates. The system adapts to its environment by multiplication, variation and selection, repeated again and again. It evolves into increasingly complex forms by populating new regions where conditions require more and more complex machinery to survive and multiply. With the first occurrence of a self-reproducing entity a new quality of matter appears: the quality of knowing how to survive as a species. The knowledge-producing state emerges, all of a sudden, and the process of knowledge production continues without limitation. The knowledge (measured by the number of carriers of genetic information that must on the average be discarded until the evolutionary stage under consideration is reached) increases jumpwise (Fig. I). The process begins at some very particular state in the evolution of a particular planet and continues as long as the favourable conditions are present. Living systems can thus be viewed as open systems that consume free energy and produce knowledge. The basic question in the origin of life is: what drives the process of the emergence of a first knowledge-producing system? The simplest possible replicating system is a machinery of some complexity, and to form a machinery needs "hands", in this case a highly specific structure that may be assumed to be present in some particular location on a primeval planet. o The structure must be oscillatory in time, to drive a continuous change between conditions favourable to multiplication and to selection respectively. o The structure must be porous and compartmented to allow small molecules (acting as building blocks and as enery carriers) to get in and out, and to prevent larger molecules to disappear. Such structure keeps together cooperating parts and keeps off competitors. o The structure must be diversified for driving evolution towards increasing complexity. Assume a simple knowledge-producing system emerges at some particular regions. To populate 153

154

U.

Lehmann and H. Kuhn

a neighbour region with less appropriate conditions needs a somewhat more complex machinery but offers great selectional advantage to systems possessing such machinery. Therefore, increasingly complex systems evolve that populate increasingly unfavourable regions•

non-living state

t

first strand appears that multiplies

knowledge t

a

I

-.-time

t favorable environment

I]

1023bits

t

first strand appears that multiplies

b

Fig. I. Transition from non-living into living state (a) and increase of knowledge (b). The probability to get a replicating strand conszstzng of 10 nucleotides b~ picking • " up 10 monomers at random and binding them together is approximately ( 1 % ) l u = 1 0 - 2 0 / 1 / . Therefore, 1020 strands must be thrown away on the average until a correct sample is obtained. About 10 times as much are necessary for survival of the species /4/. The information content per strand is 67 bits (1020 ~ 267 possible compositions of a strand corresponding to 67 choices between two alternatives). The resulting knowledge is 1 0 2 0 x 10 x 67 ~ 1 0 2 3 bits. In this view the evolution of life proceeds by evolving entities that are incresingly independent of the highly specific conditions first present. This step-by-step liberation is coupled with increasing genetic information, increasing complexity, increasing populated space. The fundamental steps of this emancipation process is seen best by considering a short nucleic acid strand in a particular micro-compartmented region (pores in rock formation) and energy rich monomers, A periodic temperature change produced by the day-and-night-rhythm drives the strand to replicate again and again. The molecular species evolve by multiplication, variation and selection (Fig. 2). At a certain stage the systems become independent of the patti-

highly spec, flc condihons periodic

(day-n*ght) micro - cornper tmented [pates in rock-fornlotion)

-I

of micro-

compartments

of energy-rich I monomers ]

.

of perlOdic regsme

= wndependence

energy-rich monomers

first short strand tl'~t

formation of on

replicates

permeable to energy - rich

envelope which is monomers

envelope becomes opaque

internQl clock

to energy- rich

monomers

Fig. 2. Liberation from environmental restraints. cular microenvironment. They produce an envelope that is impermeable to polymers and permeable to energy-rich monomers. This is the first fundamental step of emancipation• The second fundamental step leads to independence from energy-rich monomers by the development of an entity that produces such monomers from low-energy molecules• At this stage the envelope must be opaque to energy-rich monomers, but must allow the transport of low energy molecules now

Evolution of a Translation Device

155

used as the building blocks from the outer phase to the interior. The third fundamental step much later leads to independence from the oscillatory regime by developing an internal clock. The fundamental steps in this process of liberation cannot be reached without surmounting a number of distinct logistic difficulties (Fig. 3). The capacity of adaption can be realized by replicating short molecular strands. Longer strands cannot occur spontaneously with reasonable probability. However, longer strands must necessarily evolve from shorter strands in an appropriate diversified porous environment and appropriate periodic temperature changes. In this manner the genetic information increases in the course of evolution, i. e. the complexity increases. The number of copying errors increases with increasing length of strands. This limits the length of strands replicable under given conditions. A filter eliminating erroneous copies is needed to overcome this barrier. Such a filter is realized by favourably folded molecular strands that may aggregate. Correct copies aggregate, erroneous copies do not match and are repelled. The systems then possess considerably more genetic information than their ancestors. This allows to overcome a subsequent logic difficulty: How to obtain a genetic translation apparatus, a device to produce specific enzymes, when no driving force to make specific enzymes is present? The production of a simple envelope is considered as the driving force for an evolutionary process which leads to a translation device as a by-product. An envelopemolecule appears that acts as a replicase, suppressing errors in the replication process, and by the presence of this replicase the information to form the replicase is preserved. The required amount of information could not be preserved before since the copying error rate was too large. With the presence of the replicase the envelope-producing device acts as a translation device. Such a translation device allows to develop further enzymes. A metabolism should now be possible, and should be of great advantage, but the following logic difficulty arises: A metabolism requires a compact envelope to avoid loss of metabolites, but a compact envelope cannot be present as long as energy-rich monomers produced in the environment must enter the envelope. The way out of this dile,mm is to postulate the simultaneous emergence of a compact envelope and a device for producing energy-rich monomers. The systems then get independent of energy-rich monomers by developing a simple photosynthetic apparatus bound to a membrane which is impermeable to energy-rich monomers and allows the transport of simpler compounds. Further logistic difficulties (such as the difficulty to avoid nonsensical translation products which requires separation of machinery for replication and for translation) are discussed elsewhere /I/. ATTEMPTS FOR REALIZATION The question now arises how this organizational framework can be realized by chemically plausible detailed steps. Speculations are necessary in proposing such steps, which have the purpose of illustrating principles and stimulating experiments to substanciate the postulated steps or some alternatives. The development can be assumed to arise when energy rich nucleotides are present at some particular location and short strands obtained by occasional condensation of such monomers. It was postulated /I/,/2/ that a nucleic acid strand obtained by spontaneous polymerization of nucleotides acts as matrix for polymerization if it contains only D-ribonucleotides or only L-ribonucleotides. In this case a double helix should be formed between matrix strand and daughter strand. Recently this assumption has been supported by investigating a matrix strand containing D-ribonucleotides in a solution of D- and L-ribonucleotides. It was demonstrated that D-ribonucleotides are incorporated in the daughter strand selectively /3/. The origin of chirality in biosystems was assumed to be due to the fact that one chiral form of nucleotides is selected in replication right from the beginning. The use of D-ribose in biosystems was considered to be a frozen accident /2/. Estimates of the probability of the occurrence of a replicable strand has been presented elsewhere /I/, /4/. The particular conditions necessary for replication not known at present may include some spontaneously occurring polypeptides acting as a catalyst for nucleotide replication /5/,/6/. It was assumed that strands evolve that form folded structures (Fig. 4a). Of particular interest are structures called hairpins which will occur in such systems sooner or later. The replica of a hairpin is again a hairpin; the legs of the hairpin are twisted into a double helix and hairpins aggregate, since they interlock precisely. It can be seen from molecular models that an aggregate of hairpins bound to an open strand should be particu-

56

U. L e h m a n n

and H. Kuhn

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Evolution of a Translation Device

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larly stable (Fig. 4b). The three bases at the hairpin loop are bound to complementary bases at the open strand, called collector strand. The terminology (+) strand and (-) strand is used to distinguish between a strand (called (+) strand) and its replication product (called (-) strand). It was shown with models that strands with Z-RNA double helical structure match

i.tst,~l.~l

H Sim~l

Ca|~arsWand 5'

Fig. 4. Emergence of translation apparatus a) Nucleic acid strand conformations b) Aggregation: schematic and space filling model. Hairpins bound to collector strand by complementary base pairing c) Aggregates as error filter: erroneous copy (arrow) does not match. Erroneous copy differs from correct copies by one cytidine exchanged for guanosine (G-C base pair + G,G). d) Amino acids gly and ala bound to 3'-end of (+) and (-) hairpin strand e) Aggregate of hairpins (schematic helices with van der Waals outline). Formation of polypeptide sequence related to base sequence in collector strand. best into aggregates /I/,/7/. The postulated existence of Z-RNA /7/ has been justified recently /8/. Computer modelling /9/ has indicated that both Z- and A-double helices form appropriate aggregates. If an error appears during the replication process and the replicate is no more a correct hairpin, it does not bind tightly to the aggregate, diffuses away and a correct copy is introduced instead: aggregation acts as an error filter (Fig. 4c). Hairpins in the (+) form and the complementary (-) copy are identical except that they have complementary bases at the loop and at the ends of the legs, where no base pairing is necessary for aggregation. In this way an automatic correlation exists between the hairpin loop ("anticodon") and the hairpin end where activated amino acids can be specifically attached. The two different hairpin forms ((+) and (-) strand) allow the use of two different amino acids (Fig. 4d). In the molecular model an activated amino acid can be introduced in such a way that it binds specifically to the 3'-end of the hairpin strand, one amino acid to the (+) strand, another

158

U. Lehmann and H. Kuhn

to the (-) strand. Molecular models of the aggregate show that the amino acids interlock to form the peptide bond, and a short peptide-chain consisting of two kinds of amino acids is then obtained (Fig. 4e). The sequence of amino acids in the aggregate is therefore correlated with the sequence of the bases in the collector strand. A mechanism for translating the base sequence in the collector strand into the sequence of amino acids in the polypeptide is thus obtained as a by-product. It is worth mentioning that this model translation device gives a plausible explanation for many constructional details of the genetic apparatus in biosystems if the hairpins are assumed to be the primordial form of transfer nucleic acids, and the collector strand the primordial form of the messenger nucleic acid. These details are: o o o o e o o o

The information on the messenger is read in the 5'-3'-direction The direction of the strand in the transfer nucleic acid is opposite (3'-5'-direction) The reading of the message occurs in triplets Biosystems are chiral (replication advantage of nucleic acid strands in helical structures); L-amino acids are correlated to D-ribose The amino acids are bound to the 3'-end of the transfer nucleic acids The transfer nucleic acids appear to have a common origin with hairpin conformation The transfer nucleic acids consist of about 80 nucleotides The message on the primeval form of the messenger was given in a purine-N-pyrimidine reading frame.

It is of interest to show experimentally the proposed selection of correct copies by binding tightly interlocking components to a collector. We have demonstrated the effect in the analogous case of aggregating dye molecules (Fig. 5).

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-2dye B 15 I0"7m0[I t}

at a fatty acid monolayer

as model

Dye A in aqueous solution shows the broad absorption band of the pure monomer. A monolayer of arachidic acid is spread at the water surface and the reflection spectrum is measured. The reflection at the surface is a measure of the absorption of the layer at the surface. The narrow and strong band in the reflection spectrum is due to a highly cooperative system of dye molecules bound to the fatty acid monolayers (Fig. 5, left). It can be concluded from a number of measurements and considerations that the molecules are tightly packed and interlock in an aggregate like the bricks in a brickstone-work /10/, as indicated in the cross section of the monolayer. If a very small amount of a dye B is added to the solution (200 times less than dye A) then within 6 hours the characteristic band of the dye A-aggregate has fully disappeared and a new band corresponding to dye B-aggregate shows up in the reflection spectrum (Fig. 5, right). The association of the strongly interlocking dye B and its cooperative binding at the fatty acid layer are so effective that dye B displaces dye A even at this small concentration. The fact that no mixed aggregates are observed demonstrates the high selectivity of aggregation. In the model proposed it is assumed that the amino acidsglycine abundant on primordial earth, were used first. Glycine is bound pin strand, alanine to a (-) hairpin strand. Reasons have been cally activated by GMP (guanosine-5'-monophosphate) and alanine phosphate) /I/.

and alanine, presumably most specifically to a (+) hairgiven why glycine is specifiby CMP (cytidine-5'-mono-

The specific activation requires a selection process that is able to separate e. g. alanine and CMP from glycine and GMP. Recently we found that a mixture of alanine, glycine, GMP and CMP can be separated by adsorption on amorphous silica and elution with aqueous salt so-

Evolution of a Translation Device

159

lutions (Fig. 6) /11/,/12/. Activating agents like c y a n a m i d e , dicyandiamide leonitrile are eluted to the same zone as the nucleotides and amino acids•

and diaminoma-

One may imagine the following scenario: a solution with the main-components gly, ala, CMP, GMP, a magnesium- and an a~monium-salt, a phosphate and an activating agent is dried on a spot in the sun. Elution takes place by the action of rain or dew. During the next period of sunshine activation takes place. Further rain or dew allows then the activated amino acids to diffuse to the pores containing the hairpin aggregates. The selection process we propose here can be disturbed by other amino acids if present in substantial amounts relatively to alanine and glycine. From other proteinous amino acids possibly present on prebiotic earth aspartic acid, glutamic acid or serine would compete with glycine; proline, isoleucine, leucine or valine would not disturb the process (Fig. 7).

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Fig. 6. left) Chromatographic separation of glycine (gly) and guanosine-5'-monophosphate (GMP) from alanine (ala) and cytidine-5'-monophosphate (CMP) on silica with an aqueous solution of MgCI3/(NHA)HpPO A (33 mM, pH = 4.2; pH = 5.6 in a slurry of silica in this solution). Spots-of n~cl~ot~des shaded. Possible prebiotic activating agents, magnesiumand phosphate-ions are eluted to the same zone as the amino acids and nucleotides. right) possible scenario of the chromatographic separation. IRf

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160

U. Lehmann and H. Kuhn

It was postulated that the envelope produced by the evolving entity may consist of agglomerating polymers of amino acids such as glycine and alanine /I/,/2/. Lipids present in the environment may associate to the polymer-agglomerate but only to such an extent that the permeability for energy-rich monomers is not suppressed and this envelope may later evolve to an envelope opaque to energy-rich monomers /13/. The possibilities to obtain a lipid membrane have been elucidated by Or6 et al /14/. A

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To gain independence from outside sources of energy-rich molecules they must be generated inside the envelope, and the envelope must be transparent to low-energy monomers and opaque to energy-rich species. A possible mechanism to achieve this goal is based on an envelope that is laced with dye molecules such as porphyrins. Exposure to sun light could then resuit in a membrane potential by which phosphate ions and energy poor nucleotides might be pulled into the membrane, and made to yield energy-rich species that then pass into and are kept inside the "cell". An experimental realization of such an arrangement would be essential. Attempts have been made to produce photoinduced membrane potentials /15/. Electron transfer reactions across bilayer lipid vesicles have been investigated by several authors /16/. For studying vectorial charge transfer at the molecular level the monolayer assembly technique is particularly useful /17/.

REFERENCES I.

H. Kuhn and J. Waser, Molecular self-organization and the origin of life, Angew. Chem. 93, 495-515 (1981); Angew. Chem., Int. Ed. Engl. 20, 500 (1981).

2.

H. Kuhn, Self-organization of molecular systems and evolution of the genetic apparatus, Ansew. Chem. 84, 838-862 (1972); Ansew. Chem., Int. Ed. En$1. 11, 798 (1972).

3.

G. M. Visser, J. van Westrenen, C. A. A. van Boeckel and J. H. van Boom, Synthesis of the mirror image of 8-D-riboguanosine-5'-phosphate; a substrate to study chiral selection in non-enzymatic RNA synthesis, Recl. Trav. Chim. Pays Bas 103, 141 (1984).

4.

H. Kuhn and J. Waser, Self-organization of matter and early evolution of life, in: Biophysics, 2nd, eds. W. Hoppe, W. Lohmamm, H. Markl and H. Ziegler, Springer, Berlin, Heidelberg, New York, Tokyo 1983, p. 830.

5.

S. W. Fox, Metabolic microspheres - origins and evolution, Naturwissenschaften 67, 378 (1980).

6.

A. Brack, Prebiotic synthesis and organization of biopolymer-like macromolecules, Origins Life 14, 229 (1984); A. Brack and B. Barbier, Synthesis and organization of prebiotic macromolecules, 25th Plenary Meeting Committee on Space Research (COSPAR), Graz, Austria, June 25 - July 7, 1984, Abstracts p. 302.

Evolution of a Translation Device

161

7.

H. Kuhn, Physikalisch-chemische Modelle alS Denkans~tze zur Frage der Entstehung lebender Systeme, Abh. BraunschW. Wiss. Ges. 31, I0~ (1980).

8.

K. Hall, P. Cruz, I. Tinoco, jr., T. M. Jovin and J. van de Sande, Double-stranded RNA can adopt a Z-form conformation, submitted to Nature.

9.

E. yon Kitzing, Molecular Mechanics Symposium, June 23-24, 1983, Purdue University, Indianapolis and unpublished results.

10.

V. Czikkely, H. D. F~rsterling and H. Kuhn, Light absorption and structure of aggregates of dye molecules, Chem. Phys. Left. 6, 11 (1970); H. BHcher and H. Kuhn, Scheibe aggregate formation of cyanine dyes in monolayers, Chem. Phys. Left. 6, 183 (1970).

11.

U. Lehmann and H. Kuhn, Model approach of the breakthrough of a translation machine and the origin of the genetic code, Origins Life 14, 497 (1984).

12.

U, Lehmann, Chromatographic separation as selection process for prebiotic evolution and the origin of the genetic code, submitted to BioS~stems.

13.

H. Kuhn, Model consideration for the origin of life, Naturwissenschaften 63, 68 (1976).

14.

J. Or6, G. Holzer, M. Rao and T. G. Tornabene, Membrane lipids and the origin of life, in: Origin of Life, ed. Y. Wolman, Dordrecht, Boston, London 1981, p. 313.

15.

H.-M. Ullrich and H. Kuhn, Photoelectric effects in bimolecular lipid-dye membranes, Biochim. Biophys. Acta 266, 584 (1972).

16.

E. E. Yablonskaya and V. Ya. Shafirovich, Electron transfer chains in chemical models of photosynthesis. Quantum yield improvement of photosensitized electron transfer across bilayer lipid vesicles, Nouv. J. Chim. 8, 117 (1984) and references cited there in.

17.

H. Kuhn, Synthetic molecular organisates, J. Photochem. 10, 111 (1979); D. M~bius, Dye sensitized charge separation, in: Li~ht-lnduced Charge Separation in Biology and Chemistry, eds. H. Gerischer and J. J. Katz, Berlin: Dahlem Konferenzen

1979, 171; K.-P. Seefeld, D. MSbius and H. Kuhn, Electron transfer in monolayer assemblies with incorporated ruthenium (II) complexes, Helv. Chim. Acta 60, 2608 (1977) i

D. MSbius, Designed monolayer assemblies, Ber. Bunsen~es. 82, 848 (1978).