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Protein interaction world – an alternative hypothesis about the origins of life

Peter Andras, PhD1 and Csaba Andras, MSc2

1School of Computing Science,

University of Newcastle,

Newcastle upon Tyne, NE1 7RU, UK

2Department of Chemical Engineering,

Budapest University of Technology and Economics,

Budapest, Hungary

Correspondence:

Peter Andras

School of Computing Science

University of Newcastle

Newcastle upon Tyne

NE1 7RU

United Kingdom

tel: +44-191-2227946

fax: +44-191-2228232

e-mail: peter.andras@ncl.ac.uk

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ABSTRACT

The protein interaction world hypothesis about the origins of life is introduced in this

paper. According to this hypothesis, life emerged as a self reproducing and expanding

system of protein interactions, which is conceptualized as an abstract communication

system. We describe key components of abstract communication systems and how

such systems work, including the role of memories of communications. Protein

interaction systems are made of communications that are the interactions between

proteins. In the context of the protein interaction world hypothesis RNA molecules

serve as memories of protein interactions and DNA molecules are memories of RNA

interactions. The protein interaction world hypothesis is based on plausible prebiotic

processes and offers a systematic view on how life emerged and evolved towards

current cellular life forms. We compare the protein interaction world hypothesis with

the most commonly accepted RNA world hypothesis about the origins of life. We

conclude that the protein interaction world hypothesis is more plausible than the RNA

word hypothesis. We discuss the role of rare nucleic bases in the context of the

protein interaction world, and we show that their role can be explained more

parsimoniously in this context than in the context of the RNA world. We also discuss

the replication in the context of the two theories, and we highlight that while in the

case of the RNA world the replication refers to material replication of some molecules,

in the context of the protein interaction world hypothesis the replication happens at

the level of replication of interactions between proteins.

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1. INTRODUCTION

To a good extent the origins of life constitute still a mystery (1, 2, 3, 4). Since the

1950s there were several experiments aimed to elucidate how life emerged on the

Earth (5). During the past 50 years several meteorite remnants have been analysed to

find traces of life related molecules (6, 7, 8). These works led to the conclusion that

many organic molecules could emerge in abiotic conditions, including amino acids,

lipids, aromatic compounds and possibly simple sugars (5), and even small globular

vesicles may form in such conditions (9). At the same time these experiments

provided no indication of how self-replicating structures like cells, ribonucleic acid

(RNA) and deoxyribonucleic acid (DNA) molecules could emerge.

Currently the most widely accepted hypothesis about the origins of life is based on the

assumption that RNA molecules emerged in abiotic conditions (10, 11, 12, 13).

Theoretical investigations and experimental evidence indicate that the building blocks

of nucleotides (i.e., nucleic bases and sugars) were synthesised in the prebiotic

environment (10, 14, 15, 16, 17, 18, 19). It is supposed that these molecules

constituted nucleotides, which formed heteropolymers in the form of RNA molecules.

Such RNA molecules could catalyze organic chemical reactions and replicate

themselves forming the basis of self-replicating life. Of course there are several

unanswered questions in the context of the RNA world hypothesis, like how did

purine (adenine and guanine) and pyrimidine (cytosine, thymine and uracil) bases

combine with sugars (ribose) to form nucleotides in abiotic conditions (20), or how

did the replication process achieve a high enough precision in order to allow stable

evolutionary selection of some RNAs (21).

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The other major alternative hypothesis is the protein world hypothesis (22). This

supposes that proteins and peptides were the first molecules that started life and RNA

molecules emerged later to support the replication of protein molecules. The

fundamental problem of this hypothesis is that proteins are unable to replicate

themselves, which questions the beginning of the protein world based on self-

replication of proteins. Variants of the protein world hypothesis suggest that the

protein world may have started as a world of thioesters (23), or that proteins could

have co-evolved together with RNA molecules (22).

Systems theory offers powerful analysis methods to untangle complex problems (24,

25). The fundamental assumption of systems theory analysis is that the analysed

phenomenon can be conceptualised as an abstract communication system. The

phenomenon itself consists of communications in this communication system.

Analysing such communication systems allows defining components of the complex

system and functions of these components. The components are characterized by a set

of constraints on communications. Earlier versions of systems theory have been

applied to problems of life sciences (26), but these applications lacked the conceptual

clarity brought by new advances in systems theory of abstract communication systems.

Here we will use concepts of systems theory to analyse cells and early life forms, and

to formulate an alternative hypothesis about the origins of life.

We follow the protein world hypothesis and propose that the prebiotic world was

made by a mixture of small organic molecules (e.g., short-chain fatty acids, amino

acids) that produced relatively short peptides (e.g., the products of protenoids (27) and

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thioesters (23), or peptides generate using carbonyl sulphide in aqueous medium (28)).

This prebiotic world led to the emergence of proteins (i.e., polypeptides; more

specifically those peptides which are made of 20 biotic amino acids which are

produced in living cells) by using smaller peptides to catalyse reactions between

further peptides and other molecules. We propose that the emerging life constituted as

a protein interaction world. We see this world as an abstract communication system

constituted by communications in the form of interactions between proteins. The

replication of the system consists of the replication of these interactions. According to

our hypothesis the protein interaction world led to the emergence of encapsulated

reproduction of sequences of protein interactions in form of protocells. Such

protocells turned into advanced protocells by developing memories of protein

interactions in form of RNA molecules. This was followed by evolving into proper

cells having complex intracellular processes and long term memory in the form of

DNA. In this paper we describe how systems theory provides the conceptual

foundations for our hypothesis and we argue that the protein interaction world

hypothesis may be more plausible than the RNA world hypothesis.

Our proposal shows similarities with the earlier proposal of Lacey et al. (22), who

suggested the co-evolution of proteins and RNA molecules, including the suggestion

that RNA molecules may have served as the memories of proteins. Similar ideas can

be found also in the work of Kauffman (29), who suggested that life may have

emerged as a system of biochemical interactions, which reached a critical level of

compound variability and interaction density. To some extent similarly to our ideas,

Segre and Lancet (3) have also suggested that life may have emerged as a system of

molecular interactions that reproduced itself.

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The rest of the paper is structured as follows: Section 2 describes briefly the RNA

world hypothesis; in Section 3 we provide a review of key systems theory concepts; in

Section 4 we describe in detail the protein interaction world hypothesis; Section 5

contains discussion of implications of the protein interaction world hypothesis; the

paper is closed by the conclusions in Section 6.

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2. RNA WORLD

RNA or ribonucleic acid molecules are sequences of nucleotides, containing typically

four types of bases: adenine, guanine, cytosine and uracil. The identity of an RNA

molecule is determined by the sequence of the nucleotides. An RNA molecule may

contain a few tens or even thousands of nucleotides. The role of RNA molecules in

cells is to drive the building process of proteins that takes place at the ribosomes (2,

30). The RNA molecules are built within the cell nucleus by copying segments of the

DNA. The primary RNA molecules go through a maturation process, when parts of

them are cut out or possibly changed.

It is a widely accepted hypothesis that RNA molecules were present in the prebiotic

environment on the Earth (e.g., 11, 20). RNA molecules can act as information

storage molecules due to their specificity in terms of interactions with other molecules

(31), i.e., they store the information about which molecules they should interact with,

for example by building them in the case of mRNAs. The RNA world hypothesis is

built on the assumption that information (i.e., the sequence of nucleotides, which is

different from random) was stored in RNA in the prebiotic environment and this

information was replicated by copying of RNA molecules.

A cornerstone of the RNA world hypothesis is that RNA molecules can catalyze

biosynthesis processes (30). By catalysing interactions between other organic

molecules (e.g., proteins) the RNA molecules can facilitate the molecular interaction

mechanisms needed for the synthesis and replication of the RNA (12). Consequently

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the RNA molecules can organize autocatalytic processes required for self-

reproductive biochemical systems (1, 32).

The replication of RNA molecules can be more efficient if the ingredients of the RNA

catalyzed self-reproductive system are enclosed, which may have led to the

emergence of protocells (9). Such protocells may have contained a mixture of proteins

which were used during the RNA replication process. The DNA may have evolved as

a long term information storage molecule, which being more stable than the RNA,

could maintain the information needed for the RNA replication over periods of

disturbance. The evolution of the replication mechanism of information encoded in

RNA molecules led to the evolution of cells with complex intracellular mechanisms,

involving a large number of proteins and DNA used as the cell’s long term

information storage device.

Theoretical studies (12) and existing experimental evidence (8, 15) indicate that the

components of RNA molecules, sugars, purines and pyrimidines can be synthesised in

abiotic conditions, although in relatively small quantities (8, 33). There are also

suggestions about how the synthesis of RNA molecules from mono-nucleotides (i.e.,

combinations of purines / pyrimidines and sugars) may have emerged on catalysing

clay surfaces (34, 35). Still, a fundamental problem with the RNA world hypothesis is

that it does not explain how nucleotides, made of purines, pyrimidines and sugars,

formed before the emergence of RNA molecules (20). While synthesis of nucleotides

and of the RNA happens in biotic conditions, robust abiotic counterparts of such

processes are not known (23). This negative result questions the fundament of the

RNA world hypothesis.

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Supposing that RNA molecules and their constituent nucleotides are available in the

prebiotic environment we still face further important problems. RNA molecules are

not very stable and except in relatively cold environment they decompose into their

constituents preventing faithful replication of themselves (36, 37). Theoretical

estimations have shown that the replication of information molecules should be very

precise to allow stable evolution (2, 38) (i.e., otherwise replication noise would turn

back the population of replicating molecules to a random mixture of them).

Considering the instability of RNA molecules and the actual frequency of replication

errors it seems unlikely that simple RNA replication mechanisms could have

reproduced RNA molecules with the required accuracy for stable evolution (2).

Some authors suggested alternative versions of the RNA world hypothesis, including

the start with the DNA world (20) or the initial use of peptide nucleic acids as

information coding molecules (39). These alternatives do not really solve the

fundamental problems of the RNA world; just replace them by comparable problems

associated with the alternative proposal.

Summarizing, the RNA world hypothesis and its alternative versions offer a good

explanation of how life may have emerged supposing the existence of RNA molecules

and sufficiently high fidelity and stable RNA replication mechanisms. The Achilles

heel of the hypothesis is that the existence of prebiotic RNA molecules and high

fidelity RNA replication mechanisms is questionable and so far it was not possible to

be proven.

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3. SYSTEMS THEORY

The origins of systems theory go back to the 1940s, when cybernetics research (40)

programs started to investigate the behaviour of complex engineering systems.

Starting from 1950s the general systems theory was developed following the work of

von Bertalanffy (41). The mathematical theory of complex systems emerged in the

1960s and focuses on systems that can be described by sets of differential equations

and analyses the properties of these equations (e.g., 42). In the period between the

1960s – 1980s Maturana and Varela developed the theory of autopoetic systems (26)

which aims to explain how self-regenerating and self-replicating living systems

emerge and evolve. More recently Luhmann (25) introduced a new approach to

systems theory following to some extent the works of Maturana and Varela.

Luhmann’s work concentrates on abstract communication systems made of

communications, ignoring the communication units that generate these

communications. The theory of abstract communication systems gives a fresh look at

the complex systems, different from the classical approaches of 1940s – 1960s and

also from the approach of mathematical complex systems theory. This new approach

offers powerful analysis tools that allow to identify systems and their components,

and to analyse the function of these components in the context of the system. We

follow the work of Luhmann in this paper.

Communication units produce symbols that are transmitted to other communication

units, which perceive them. Communications are sequences of such symbols. Abstract

communication systems are made of such communications (see Figure 1A for

illustration). By definition, the communication units are not part of the system.

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Communications reference other communications in the sense that the sequence of

symbols contained in a communication is dependent on the contents of other earlier or

simultaneous communications. A dense cluster of inter-referencing communications

surrounded by rare network of communications constitutes a communication system

(see Figure 1B for illustration).

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Figure 1. A) The concept of communication. B) The concept of communication

system. Squares represent communication units, continuous arrows represent

communications, and segmented arrows represent referencing relations between

communications. The communication system is a dense cluster of inter-referencing

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communications (area in the middle), surrounded by a rare network of other

communications. The communication units are not part of the communication system.

A communication system is defined by the regularities that define how referenced

communications determine the content of referencing communication. All

communications that follow the set of rules defining the system are part of the system.

All other communications that do not follow the rules of the system are part of the

system’s environment. Communication systems reproduce themselves by recruiting

new communications between communication units. A communication is recruited to

a system if it follows the referencing rules of the system. How successful is the

recruitment of new communications depends on earlier communications generated by

the system and on the environment of the system. We can view the system as a self-

describing system made of communications. At the same time the system describes its

environment in a complementary sense. Better descriptions of the system’s

environment lead to higher success in recruiting new communications.

Systems that reproduce and expand faster than other systems may drive to extinction

the slower reproducing and expanding systems. The limits of system expansion are

determined by the probabilistic nature of referencing rules. A communication may

reference several earlier communications indirectly through other referenced

communications constituting referencing sequences of communications. The

probabilities of referencing rules determine how long can be such referencing

sequences of communications before the last communications becomes a random

continuation. Longer referencing sequences of communications (i.e., more detailed

descriptions) allow better descriptions of the systems and its environment. The

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optimal size of the system (i.e., the number of simultaneous communications being

part of the system) is also determined by the probabilistic indeterminacies of

referencing rules. Systems that overgrow their optimal size may split into two similar

systems with the same (or possibly similar) set of referencing rules.

Communication systems may develop subsystems that are systems within the system,

i.e., they constitute a denser inter-referencing cluster within the dense communication

cluster of the system. Communications that are part of subsystems follow system rules

with additional constraints that are characteristic of the subsystem. More constrained

referencing rules decrease indeterminacies and allow the system to generate better

complementary descriptions of the environment and expand itself faster than systems

without subsystems. Systems may also change by simplification of the set of their

communication symbols (i.e., reduction of the number of such symbols). This may

lead to reduction of probabilistic indeterminacies in the referencing rules.

Consequently systems with simpler sets of communication symbols may expand

faster than systems with larger sets of communication symbols.

Another way of extending reliable descriptions of the environment (i.e., non-random

sequences of referencing communications) is by retaining records of earlier

communications, i.e., by having memories of earlier communications that can be

referenced by later communications. We can view such memories as the use of

additional communication units that reproduce for a certain period a certain

communication. Having memories reduces the indeterminacies in referencing by

allowing direct referencing of much earlier communications, instead of referencing

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them through a chain of references. Systems with memory can expand faster than

systems without memory.

Systems with memory may develop a memory or information subsystem (i.e., the

memory is information about the past of the system) consisting of communications

between communication units generating memory communications. If such

communications constitute a dense cluster of inter-referencing communications

determined by a set of characteristic referencing rules the information subsystem of

the system emerges. Having an information subsystem allows combination of

memories and by this the generation of descriptions of the environment which are

better than environment descriptions in systems with memory but without information

subsystem.

Systems compete with each other for communications. Systems which have better

complementary descriptions of the environment can generate communications that fit

better their environment and make easier the recruitment of new communications.

Systems with better environment descriptions out compete systems with less good

descriptions of the environment. Systems having subsystems, simple communication

symbol set, memory and information subsystem can generate better descriptions of

their environment than systems which lack any of these features.

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4. PROTEIN INTERACTION WORLD

Experiments simulating prebiotic Earth environment (5) and the analysis of larger

meteorite remains indicate that organic molecules like amino acids, short-chain fatty

acids and others can form without requiring the preceding existence of life. These

molecules may form simple autocatalytic interaction systems (1, 43) and small

vesicles delimited by lipidic or amphiphilic membranes (5).

Experiments have shown that amino acids form tight clusters called proteinoids (22,

27) at high temperatures, which may lead to the formation of simpler peptides (i.e.,

short chains of amino acids or oligopeptides) (44). Another way of forming peptides

is by the transformation of thioesters (23, 45), a chemical pathway that works

efficiently in abiotic conditions and is also used in biological organisms (23).

Experimental simulation of marine hydrothermal vents has shown that amino acids

may form short peptides in such conditions (44). Recently, Leman et al. (28) have

shown that peptides may form with high yield in plausible volcanic marine

environments in the presence of carbonyl sulphide, a common volcanic gas. Most

genetic analysis evidence suggest that early life emerged in high temperature

environment rich in sulphur (46), which implies the plausibility of the above

mentioned ways to the synthesis of early peptides. The interactions between peptides

may catalyse the formation of long chain peptides (proto-proteins), long-chain linear

fatty acids, lipids, and other organic molecules. The analysis of common and

evolutionarily preserved parts of many genomes indicate that the most preserved are

about 60 genes which are involved in the translation of genetic information into

proteins (47). This also suggests that early cells may have developed in protein-rich

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environments, which provided the building blocks for the development and

multiplication of cells.

By adopting a systems view perspective, we can see the interactions between amino

acids, peptides and other molecules as abstract communication systems. In this system

the communication units are the peptides and other molecules, while their interactions

constitute the communications, the communication symbols being the constituent

phases of such interactions. Reproduction of this system means the reproduction of

the interactions between these molecules. The interactions between amino acids,

peptides and other molecules depend on earlier interactions between these molecules

that prepare the right molecules in the right conformation to perform interactions.

Subsets of the possible interactions may form a dense cluster of interdependent

interactions, referencing other interactions on the output of which the actual

interaction depends. The peptides being the catalysts of most interaction, and the

catalytic activity of peptides depending to a good extent on interactions with other

peptides, places peptide interactions at the core of dense interdependent interaction

clusters.

Following considerations from systems theory the peptide interaction systems can

reproduce and expand faster if they are in an enclosed environment, reducing the

diffusion of molecules that needed to participate in the generation of interactions to

maintain and expand the system. This may have led to the emergence of protocells

made of isolating lipid membranes encapsulating interacting peptides and other

molecules (9). As such systems grow they reach their growth limit and split in similar

systems, which continue their growth.

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Contemporary living cells can be viewed as protein interaction systems in which

proteins interact with themselves and with other molecules, change their conformation

to prepare for further interactions, and perform phenomenological cellular functions

(e.g., cell respiration) by specific sequences of molecular interactions (e.g., metabolic

cycles, signalling pathways). In this view cells are self-reproducing and expanding

protein interaction systems, which reproduce the interactions between proteins and

other molecules according to system specific rules determining the referential (or

dependency) sequences of these interactions.

The peptide interaction system of protocells describes itself and in complementary

sense its environment. Systems theory indicates that a system with memory is likely

to out perform systems without memory. In this context memory means long term

storage of information about earlier system communications. In the case of peptide

interaction systems the memory should represent the interactions between peptides

and in complementary sense the environment of protocells. In a very rough

approximation the environment of cells is determined by the amount and availability

of atomic building blocks of proteins, namely the carbon (C), nitrogen (N), oxygen

(O), hydrogen (H) and to some extent sulphur (S), phosphorus (P) and halogen (F, Cl,

Br) atoms.

Our hypothesis is that the candidate molecules that could serve as memories of

peptide interactions and representations of the environment are the sugars,

representing C, O, and H content of the environment and also the presence of P in

their phosphorylated compounds, and purines and pyrimidines, representing C, N, H

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content of the environment and also the presence of S and halogens in their

corresponding compounds (e.g., 4-thiouridine (48), 5-chlorocytosine (49)). This

means that protocells may have used sugars, purines and pyrimidines to store

information about interactions between peptides and also in complementary sense

about their environment. Proteins and peptides can be seen as the product of

interaction between other proteins / peptides containing sub-chains of amino acids

corresponding to parts of the amino acid chain of the product protein or peptide (note

that proteins are also peptides). To keep a memory of such interactions the system

memory of protocells should have been able to record the sequence of amino acids of

participating peptides. This may have led to the emergence of proto-RNA, which

encoded the sequence of amino acids of interacting peptides by using specific

combinations of sugars, purines and pyrimidines to encode amino acids. Theoretical

investigations (22) about interactions between peptides and mono-nucleotides support

our hypothesis. According to these earlier works chains of amino acids can form

double helix chains with mono-nucleotides, such that each amino acid is linked to a

triplet of mono-nucleotides. Such complementary chains of peptides could have

turned into heteropolymers of nucleotides forming the ancient version of RNA

molecules.

The requirement that system memories should work as communication units, allowing

the referencing of their memory and the reproduction of the communication content of

their memory, implies that the memory molecules should be able to interact with

peptides and catalyze interactions between peptides. Considering that all peptides are

produced from other peptides and possibly by adding some amino acids, the above

argument implies that proto-RNA molecules should have existed for all peptides and

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amino acids. These molecules would have catalyzed interactions between the

corresponding peptides and amino acids.

Arguments from systems theory suggest that the simplification of the vocabulary of

interactions leads to faster expanding systems. This could have been the reason for the

elimination of many amino acids from the list of amino acids making peptides

participating in the most successful peptide interaction systems, leading to the

selection of the 20 protein forming biotic amino acids commonly occurring in living

organisms and the corresponding proteins made of these amino acids. Having

simplified, more reliable peptide interaction systems led to the increase in length of

the peptides leading through several evolutionary steps to giant proteins of currently

living cells.

Selection factors that led to the selection of some sugar, purine, pyrimidine

combinations could have been: (a) the ability of these nucleotides to form long chain

heteropolymers, (b) thermal stability of these polymers, and (c) specific enzymatic

abilities of proto-RNA molecules. These factors together with simplification –

expansion pressures are likely to have led to the selection of combinations of ribose

with a few purines and pyrimidines as nucleotide coding units in the proto-RNA, and

ultimately to the emergence of present day RNA molecules.

The above presented view suggests that protocells were vesicles surrounded by a lipid

membrane, reproducing inside series of peptide interactions helped by proto-RNA

molecules, which catalyzed these interactions. The building blocks of proto-RNAs

were produced by chemical reactions catalyzed by proteins. The proto-RNAs served

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as memory molecules in the protocells. The competition between protocell systems

led to systems with simplified symbol sets (peptides containing selected amino acids

and few bases used to build proto-RNA) corresponding to early cells containing

proteins made of biotic amino acids and RNA molecules containing mostly the usual

bases ribose-adenine (A), ribose-cytosine (C), ribose-guanine (G) and ribose-uracil (U)

building blocks. Some RNA molecules contain unusual bases as well, which are

combinations of ribose with rare purines and pyrimidines.

The interactions between RNA molecules led to the emergence of the information

subsystem of the cell, which consists of a dense cluster of interactions between RNA

molecules, which depend on earlier interactions between RNA molecules. Some early

cells may have developed memory for their information subsystem. This memory

would have consisted of molecules that could interact with RNA molecules and would

retain the memory of interactions between RNA molecules. The memory of RNA

interactions should have encoded the RNAs that were present at the same time and

same location participating in interactions between them. Our conjecture is that DNA

molecules are memories of RNA interactions, and in early cells they catalyzed the

interaction and possibly formation of corresponding RNAs. Being memories of

memories the DNA acts in the context of the cell system as long term memory. So,

having DNA makes cells more successful in reproducing and expanding themselves

than cells without DNA.

Early versions of protocells could have contained many versions of combinations of

proto-RNAs catalyzing interactions between peptides. The simplification – expansion

argument leads to the conjecture that this mechanism evolved towards a simplified

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version of it, preserving only interactions between proto-RNAs corresponding to

proteins and proto-RNAs corresponding to amino acids. In this way the proteins can

be built up by condensation of single amino acids with an existing partial chain of the

protein, reducing the unreliability of the catalysis of interactions between larger

peptides.

The emergence and expansion of the RNA communication system implies that there

should be many RNA interactions that do not lead directly to generation of proteins,

but in functional terms regulate the process of protein generation (see recent results on

siRNAs and microRNAs (50, 51)). In a similar way the existence of DNA memories

of RNA interactions may have led to the emergence of a system of DNA interactions

forming a new subsystem of the cell. The emergence of dense interdependent DNA

communications (i.e., interactions between DNA molecules) could have led to the

clustering of DNA molecules and the formation of cell nucleus. This also suggests

that in cells with nucleus there should be many DNA interactions that do not lead to

the production of RNA molecules, but rather regulate this process in functional terms.

Summarizing, our hypothesis is that life originated from peptide interaction systems,

which reproduced and expanded as vesicles surrounded by lipid bi-layer membranes.

Such peptide interaction systems led to the emergence of proto-RNA molecules that

served as memories of peptide interactions, facilitating the reproduction and

expansion of protocells. Simplification driven expansion led to the selection of biotic

amino acids and the reduction of the typical RNA alphabet to the four usual bases (A,

C, G, U). Interactions between RNA molecules led to the emergence of the RNA

interaction subsystem of the cell and to the emergence of memories of RNA

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interactions in the form of DNA molecules. The expansion of DNA molecule

interactions led to the clustering of DNA molecules and formation of cell nucleus.

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5. DISCUSSION

A. Protein interaction world vs. RNA world

Experimental results indicate that the protein interaction world that we described may

have originated in an abiotic environment able to produce amino acids, oligopeptides,

short-chain fatty acids and other relatively simple organic molecules. The RNA world

hypothesis is not supported so far by experimental evidence that would describe ways

of abiotic synthesis of nucleotides, the building blocks of RNAs. Consequently the

origin requirements of the protein interaction world hypothesis are more plausibly

satisfied than the origin requirements of the RNA world.

The reproduction of protocells and cells in the context of protein interaction world

hypothesis is relatively simple, requiring the reproduction of interactions between

peptides / proteins, which can occur in autocatalytic systems of peptide / protein

interactions. The reproduction of cells in the context of RNA world requires

complicated high precision molecular interaction machinery, which makes

questionable the sufficiently high fidelity reproducibility of early RNA world life that

would be required for evolution towards modern cellular forms. This shows that early

life and evolution according to the protein interaction world hypothesis is simpler to

maintain and reproduce than in the context of the RNA world hypothesis.

The protein interaction world hypothesis offers a well integrated scenario for the

emergence, role and evolution of all macromolecular components of living cells (i.e.,

DNA, RNA, proteins and other molecules), conceptualizing them in the context of the

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cell’s internal communication system as communication units and memories, and

their interactions as communications. The RNA world hypothesis provides an

integrative description of cells, but with several ad-hoc elements (e.g., proteins are

side products that turn to be useful as catalysts of RNA replication) and without

providing a clear conceptual framework that would explain the evolutionary steps

leading to contemporary living cells. This indicates that the protein interaction world

hypothesis may have more explanatory and predictive power than the RNA world

hypothesis with respect to the interpretation of functional processes characterising

living cells and the evolution of cellular life.

B. Rare nucleic bases

Since the 1960s, researchers found several unusual nucleic bases in RNAs of various

micro-organisms. RNA bases like inosine, 1-methyl-guanin, pseudouridin, 4-thio-

uridine, wybutosine, 5-fluoro-uracil and others are found typically in tRNAs

(transport RNA: amino acid specific RNA responsible for the transportation of amino

acids to the protein assembly sites) of bacteria and archaea. In many cases the routes

of biosynthesis of these unusual RNA bases is already known. The RNA world

hypothesis does not provide an easy answer, why such unusual nucleic bases exist and

how did they emerge as RNA bases.

In the context of the protein interaction world hypothesis we can find a relatively

straightforward explanation of the existence and role of unusual nucleic bases. By

considering that RNA memories of protein interactions should represent in a crude

sense the atomic composition of the environment it follows immediately that micro-

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organisms living in environments characterised by high sulphur or halogen content

should represent these in their RNA memories. This implies that such organisms

should have included in their RNA bases that contain sulphur or halogen representing

high bio-impact atomic content (i.e., atoms that relatively easily participate in a large

number of organic chemical compounds) of the environment. Considering that most

RNAs representing proteins went through a long evolutionary selection process driven

partly by simplification – expansion forces, we expect that sulphur and halogen

containing bases should be present in the older, more preserved tRNAs representing

the amino acids that are added to forming proteins during protein synthesis.

Experimental evidence shows that sulphur containing bases occur commonly in

tRNAs of thermophilic archaea (e.g., Thermus thermophilus) (52, 53, 54)). These

organisms typically live in high sulphur concentration, high temperature, deep marine

environments. In accordance with our theory they should have nucleic bases in their

tRNA which represent sulphur, which is confirmed by experimental analysis. In the

case of Escherichia coli growing in presence of iron, which is associated in natural

conditions with the presence of sulphur (55), tRNA molecules include sulphur

containing 2-methylthio-N6-(∆2-isopentenyl)-adenosine bases. If iron is bound by

iron-binding molecules, inducing low iron content and implying low sulphur content,

the same tRNAs will loose the sulphur containing bases, which are replaced by N6-

(∆2-isopentenyl)-adenosine bases (56). This supports our theory, which implies that in

low sulphur environment bacterial tRNA should include less sulphur containing bases

than in high sulphur environments.

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Halogen containing RNA bases are reported in the literature as cancer treatment

agents (e.g., 5-fluoro-uracil) (e.g., 57, 58), which prevent normal development of

some proteins participating in thymine synthesis and indirectly block the replication

of DNA. Others report that halogenated bases are formed in bacteria attacked by

immune cells, and these bases contribute to the killing of bacteria (49). According to

our hypothesis it should be possible to find such nucleic bases in some primitive life

forms living in halogen-rich environment. Considering that the incorporation of

halogen containing bases may prevent the formation of thymine we consider it

unlikely to find DNA containing micro-organisms having halogen containing bases in

their tRNA. At the same time it might be possible to find RNA viruses of halobacteria,

which may contain halogenated RNA bases. Alternatively it may be also possible to

find primitive unicellular organisms living in halogen-rich environment which

replicate without using thymine containing DNA. Such organisms could live only in

isolated ecological niches, where competition with DNA containing life forms would

not have rendered them to become extinct.

C. Replication

A fundamental concept of evolution theory is the replication (31), which means the

identical or almost identical replication of life forms (e.g., cells, whole multi-cellular

organisms). In the context of the RNA world hypothesis the replication happens at the

level of RNA and DNA, which are replicated by a complex molecular interaction

machinery involving RNA, DNA molecules, proteins and other molecules. High

precision replication being required for stable evolution the supposition of such RNA

replication is a cornerstone of the RNA world hypothesis. At the same time this is also

28

the weakest point of this theory, as such high precision replication machinery without

pre-existing large RNA and DNA molecules regulating the replication process is not

known (2).

The protein interaction world hypothesis considers that replication of early life

happens in terms of replication of peptide/protein interactions, organized in sequences

of interdependent interactions. The replication of such interactions requires the

presence of the same molecules to reproduce the interaction. The replication of

conditional sequences of interactions requires the execution of conditioning

interactions that produce the peptides/proteins in the right conformation to perform

the conditional interaction. The replication of longer sequences of conditional

interactions is limited by the diffusion of required molecules. The diffusion of

molecules can be reduced by encapsulating them in vesicles made of lipid membranes.

Such vesicles could have formed in prebiotic conditions according to results of

experiments trying to replicate prebiotic Earth environment (5). This suggests that the

replication required for the protein interaction world hypothesis can be based on

plausible processes.

The emergence of memories of peptide/protein interactions in form of RNAs and of

RNA interactions in form of DNA molecules allows high precision replication of

interactions between large proteins resulting from many interactions between other

proteins, amino acids and other molecules. The protein interaction world hypothesis

provides a well integrated role for RNA and DNA molecules in the process of

replication of life, including the replication of these molecules.

29

A key difference between the replication concept of the protein interaction world and

RNA world hypotheses is that while the RNA world builds on replication of

molecules, the protein world hypothesis builds on the replication of interactions

between molecules. In the context of the protein interaction world the replication of

molecules is a side effect of replication of interactions between molecules.

According to the protein interaction world hypothesis the concept of replication is

extended into the concept of replication and expansion. Protein interaction systems

replicate and expand by producing protein interactions that follow their conditional

rules and in this they way they reproduce and expand themselves. The growth limits

of interaction systems lead to the splitting of systems and to system scale replication

and expansion.

30

6. CONCLUSIONS

The above described protein interaction world hypothesis formulates an alternative to

the most commonly accepted RNA world hypothesis about the origins of life. The

protein interaction world hypothesis is fundamentally different from the RNA world

hypothesis in the sense that while the RNA world hypothesis is build on the concept

of replication of RNA and DNA molecules, the protein world hypothesis is built on

the assumption of replication and expansion of protein interaction systems perceived

as abstract communication systems.

The protein interaction world hypothesis is based on experimentally validated,

plausible assumptions about the emergence of early peptide/protein interaction

systems in the prebiotic Earth environment. The protein interaction world hypothesis

provides a systematic integrated view of how life emerged and developed, providing

well-defined places for RNA molecules that are seen as memories of protein

interactions, and DNA molecules considered as memories of RNA interactions.

Predictions based on the protein interaction world hypothesis about the sulphur

containing unusual RNA bases fit with experimental findings about these bases

providing additional support for this hypothesis. Further predictions about halogen

containing bases are not yet validated by experimental evidence, but they point very

specifically for directions in which potential experimental evidence might be possible

to be found.

31

The perception of living systems as abstract communication systems opens up new

avenues for research about the role of various organic molecules, the evolution of

their role in the context of living systems, and for the analysis of the boundary

between living and non-living systems. We believe that the protein interaction world

hypothesis can provide more parsimonious explanations of how living systems work

and organize themselves than other hypotheses about the origins of life like the RNA

world hypothesis.

32

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