More than the sum of their parts: on the evolution of proteins from peptides

Despite their seemingly endless diversity, proteins adopt a limited number of structural forms. It has been estimated that 80% of proteins will be found to adopt one of only about 400 folds, most of which are already known. These folds are largely formed by a limited 'vocabulary' of recurring supersecondary structure elements, often by repetition of the same element and, increasingly, elements similar in both structure and sequence are discovered. This suggests that modern proteins evolved by fusion and recombination from a more ancient peptide world and that many of the core folds observed today may contain homologous building blocks. The peptides forming these building blocks would not in themselves have had the ability to fold, but would have emerged as cofactors supporting RNA-based replication and catalysis (the 'RNA world'). Their association into larger structures and eventual fusion into polypeptide chains would have allowed them to become independent of their RNA scaffold, leading to the evolution of a novel type of macromolecule: the folded protein.     

An RNA-amino acid complex and the origin of the genetic code

The group I RNAs, of which the Tetrahymena ribosomal RNA intron is the most investigated example, catalyze their own splicing reactions. Splicing is initiated at a conserved site on the RNA that facilitates attack by exogenous guanosine (or its nucleotides) on the exon-intron junction. The guanosine site in the RNA's catalytic center also binds arginine, and is quite selective for the arginine side chain. This amino acid-RNA interaction is stereoselective, and L-arginine is preferred. Immediately at the site at which arginine binds there is one of only four RNA triplets in 92 group I RNA sequences: AGA/G and CGA/G. Thus the arginine contact site is within any of four different codons for arginine. Mutation of the conserved G in the middle of the triplet decreases affinity for the amino acid, showing that binding is sequence-specific. A pathway for the origin of the genetic code for arginine is suggested, based on the existence and properties of this sequence-specific, amino acid-specific RNA complex. The existence of a proto-ribosome related to the group I RNAs seems the most likely hypothesis. This notion is used to distinguish three periods in the development of the code. Restrained and exuberant hypotheses about the origin of the genetic code are distinguished, and some objections to these hypotheses are considered.     

Active centrum hypothesis: The origin of chiral homogeneity and the RNA-world

I propose a hypothesis on the origin of chiral homogeneity of bio-molecules based on chiral catalysis. The first chiral active centre may have formed on the surface of complexes comprising metal ions, amino acids, other coenzymes and oligomers (short RNAs). The complexes must have been dominated by short RNAs capable of self-reproduction with ligation. Most of the first complexes may have catalysed the production of nucleotides. A basic assumption is that such complexes can be assembled from their components almost freely, in a huge variety of combinations. This assumption implies that “a few” components can constitute “a huge” number of active centre types. Moreover, an experiment is proposed to test the performance of such complexes in vitro.If the complexes were built up freely from their elements, then Darwinian evolution would operate on the assembly mechanism of complexes. For the production of complexes, first their parts had to appear by forming a proper three-dimensional structure. Three possible re-building mechanisms of the proper geometric structure of complexes are proposed. First, the integration of RNA parts of complexes was assisted presumably by a pre-intron. Second, the binding of RNA parts of a complex may give rise to a “polluted” RNA world. Third, the pairing of short RNA parts and their geometric conformation may have been supported by a pre-genetic code.Finally, an evolutionary step-by-step scenario of the origin of homochirality and a “polluted” RNA world is also introduced based on the proposed combinatorial complex chemistry. Homochirality is evolved by Darwinian selection whenever the efficiency of the reflexive autocatalysis of a dynamical combinatorial library increases with the homochirality of the active centres of reactions cascades and the homochirality of the elements of the dynamical combinatorial library. Moreover, the potential importance of phospholipid membrane is also discussed.     

Ribozymes: Flexible molecular devices at work

The discovery of ribozymes, RNAs with catalytic activity, revealed the extraordinary characteristic of this molecule, and corroborated the idea that RNA was the first informative polymer. The “RNA world” hypothesis asserts that the DNA/RNA/PROTEIN world arose from an earlier RNA world in which were present only RNA molecules able to perform both of the two functions performed separately by DNA and proteins in the present-day cells: the ability to transfer genetic information and to carry out catalytic activity.The catalytic properties of ribozymes are exclusively due to the capacity of RNA molecules to assume particular structures. Moreover, the structural versatility of RNA can allow to a single RNA sequence to fold in more than one structure, able to perform more than one function. In the first part of this work we will discuss the RNA plasticity, focusing on “bifunctional” ribozymes isolated by in vitro selection experiments, and on the consequences of this plasticity in the prospective of the emergence of new specific functions.The possibility that one sequence could have more than one structure/function, greatly increase the evolutionary potential of RNA, and the capacity of RNA to switch from a structure/function to another is probably one of the reasons of the evolutionary success also in modern-day cells. Naturally occurring ribozymes discovered in contemporary cells, demonstrate the crucial role that ribozymes still have in the modern protein world. In the second part of this paper we will discuss the capacity of natural ribozymes to modulate gene expression making use of their exclusive catalytic properties. Moreover, we will consider the possibility of their ancient origin.     

The practice of classification and the theory of evolution,and what the demise of Charles Darwin's tree of life hypothesis means for both of them

Debates over the status of the tree of life (TOL) often proceed without agreement as to what it is supposed to be: a hierarchical classification scheme, a tracing of genomic and organismal history or a hypothesis about evolutionary processes and the patterns they can generate. I will argue that for Darwin it was a hypothesis, which lateral gene transfer in prokaryotes now shows to be false. I will propose a more general and relaxed evolutionary theory and point out why anti-evolutionists should take no comfort from disproof of the TOL hypothesis.     

Testing the generalized neutrality hypothesis

Various tests of the hypothesis of selective neutrality based on gene frequency are now available. These tests take as null hypothesis the concept of “strict neutrality”: all new mutants are required to be selectively identical to each other. For evolutionary questions, however, (as opposed to those of genetic polymorphism), a wider null hypothesis might be of interest. Since deleterious alleles have essentially no evolutionary importance, one might wish to test the null hypothesis that only neutral or deleterious mutations occur. The principal alternative to this hypothesis is that there exists heterotic selection of some form for some alleles tending to maintain a level of genetic polymorphism higher than that under neutrality. In this paper an assessment is made of the usefulness of a test of strict neutrality first proposed by this author (Ewens, 1972) as a test of null hypothesis of “generalized neutrality,” i.e. that only neutral or deleterious alleles occur. At the same time some remarks will be made about estimation of the fundamental parameter θ defining these processes.     

The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells

Most evolutionists agree to consider that our present RNA/DNA/protein world has originated from a simpler world in which RNA played both the role of catalyst and genetic material. Recent findings from structural studies and comparative genomics now allow to get a clearer picture of this transition. These data suggest that evolution occurred in several steps, first from an RNA to an RNA/protein world (defining two ages of the RNA world) and finally to the present world based on DNA. The DNA world itself probably originated in two steps, first the U-DNA world, following the invention of ribonucleotide reductase, and later on the T-DNA world, with the independent invention of at least two thymidylate synthases. Recently, several authors have suggested that evolution from the RNA world up to the Last Universal Cellular Ancestor (LUCA) could have occurred before the invention of cells. On the contrary, I argue here that evolution of the RNA world taken place in a framework of competing cells and viruses (preys, predators and symbionts). I focus on the RNA-to-DNA transition and expand my previous hypothesis that viruses played a critical role in the emergence of DNA. The hypothesis that DNA and associated mechanisms (replication, repair, recombination) first evolved and diversified in a world of DNA viruses infecting RNA cells readily explains the existence of viral-encoded DNA transaction proteins without cellular homologues. It also potentially explains puzzling observations from comparative genomic, such as the existence of two non-homologous DNA replication machineries in the cellular world. I suggest here a specific scenario for the transfer of DNA from viruses to cells and briefly explore the intriguing possibility that several independent transfers of this kind produced the two cell types (prokaryote/eukaryote) and the three cellular domains presently known (Archaea, Bacteria and Eukarya).     

A ribonucleopeptide world at the origin of life

The structural flexibility of RNA and its ability to store genetic information has led scientists to postulate that RNA could be the key molecule for the development of life on Earth, further leading to formulate the RNA world hypothesis that received a lot of success and acceptance after the discoveries of the last thirty‐five years. Despite its highly structural and functional significance, the difficulty in synthesizing the four nucleobases that form the RNA polymer from the same primordial soup, its low stability, and limited catalytic repertoire, make the RNA world hypothesis less convincing even though it remains the best explanation for the origin of life. An increasing number of scientists are becoming more supportive of a more realistic approach explaining the appearance of life. In this review, I propose an enhanced explanation for the appearance of life supported by recent discoveries and theories. Accordingly, amino acids and peptides associated with RNA (e.g., ribonucleopeptides) might have existed at the onset of RNA and might have played an important role in the continuous development of self‐sustaining biological systems. Therefore, in this review, I cover the most recent and relevant scientific investigations that propose a better understanding of the ribonucleopeptide world hypothesis and the appearance of life. Finally, I propose two hypotheses for a primitive translation machinery (PTM) that might have been formed of either a T box ribozyme or a ribopolymerase.     

Reflections on Systematics and Phylogenetic Reconstruction

I attempt to raise questions regarding elements of systematics—primarily in the realm of phylogenetic reconstruction—in order to provoke discussion on the current state of affairs in this discipline, and also evolutionary biology in general: e.g., conceptions of homology and homoplasy, hypothesis testing, the nature of and objections to Hennigian “phylogenetic systematics”, and the schism between (neo)Darwinian descendants of the “modern evolutionary synthesis” and their supposed antagonists, cladists and punctuationalists.     

Informatics challenges in structured RNA

The world of regulatory RNAs is fast expanding into mainstream molecular biology as both a subject of intense mechanistic study and as a tool for functional characterization. The RNA world is one of complex structures that carry out catalysis, sense metabolites and synthesize proteins. The dynamic and structural nature of RNAs presents a whole new set of informatics challenges to the computational community. The ability to relate structure and dynamics to function will be key to understanding this complex world. I review several important classes of structured RNAs that present our community with a series of biologically novel informatics challenges. I also review available informatics tools that have been recently developed in the field.     

Small cofactors may assist protein emergence from RNA world: clues from RNA-protein complexes

It is now widely accepted that at an early stage in the evolution of life an RNA world arose, in which RNAs both served as the genetic material and catalyzed diverse biochemical reactions. Then, proteins have gradually replaced RNAs because of their superior catalytic properties in catalysis over time. Therefore, it is important to investigate how primitive functional proteins emerged from RNA world, which can shed light on the evolutionary pathway of life from RNA world to the modern world. In this work, we proposed that the emergence of most primitive functional proteins are assisted by the early primitive nucleotide cofactors, while only a minority are induced directly by RNAs based on the analysis of RNA-protein complexes. Furthermore, the present findings have significant implication for exploring the composition of primitive RNA, i.e., adenine base as principal building blocks.     

Gene duplication and other evolutionary strategies: from the RNA world to the future

Beginning with a hypothetical RNA world, it is apparent that many evolutionary transitions led to the complexity of extant species. The duplication of genetic material is rooted in the RNA world. One of two major routes of gene amplification, retroposition, originated from mechanisms that facilitated the transition to DNA as hereditary material. Even in modern genomes the process of retroposition leads to genetic novelties including the duplication of protein and RNA coding genes, as well as regulatory elements and their juxtapositon. We examine whether and to what extent known evolutionary principles can be applied to an RNA-based world. We conclude that the major basic Neo-Darwinian principles that include amplification, variation and selection already governed evolution in the RNA and RNP worlds. In this hypothetical RNA world there were few restrictions on the exchange of genetic material and principles that acted as borders at later stages, such as Weismann's Barrier, the Central Dogma of Molecular Biology, or the Darwinian Threshold were absent or rudimentary. RNA was more than a gene: it had a dual role harboring, genotypic and phenotypic capabilities, often in the same molecule. Nuons, any discrete nucleic acid sequences, were selected on an individual basis as well as in groups. The performance and success of an individual nuon was markedly dependent on the type of other nuons in a given cell. In the RNA world the transition may already have begun towards the linkage of nuons to yield a composite linear RNA genome, an arrangement necessitating the origin of RNA processing. A concatenated genome may have curbed unlimited exchange of genetic material; concomitantly, selfish nuons were more difficult to purge. A linked genome may also have constituted the beginning of the phenotype/genotype separation. This division of tasks was expanded when templated protein biosynthesis led to the RNP world, and more so when DNA took over as genetic material. The aforementioned barriers and thresholds increased and the significance and extent of horizontal gene transfer fluctuated over major evolutionary transitions. At the dawn of the most recent transformation, a fast evolutionary transition that we will be witnessing in our life times, a form of Lamarckism is raising its head.     

In vitro selection of halo-thermophilic RNA reveals two families of resistant RNA

The "RNA world" hypothesis proposes that early in the evolution of life, RNA was responsible both for the storage and transfer of genetic information and for the catalysis of biochemical reactions. One of the problems of the hypothesis is that RNA is known to be temperature sensitive. Nevertheless, different types of sequences with a thermostable phenotype may exist. In order to test this possibility, we applied an in vitro evolution method (SELEX) to isolate RNA molecules that are resistant at high temperatures (80 degrees C for 65 h) and high salt concentrations (2 M NaCl). The sequences of the resulting cloned halo-thermophilic RNAs can be grouped in two families (I and II) possessing very different thermal and chemical stabilities and very different secondary structures. The selected RNA molecules illustrate two different possibilities leading to thermal resistance which may be related to primitive conditions. We propose that members of family I constitute a good means of storing sequence information while members of family II are less efficient but replicate faster in early steps of the SELEX. These selected RNA behaviors may be related to primitive conditions and could allow to define limits for survival, and demonstrate that what is at stake for RNA molecules, as for living organisms, is survival and reproduction.     

On the RNA World: Evidence in Favor of an Early Ribonucleopeptide World

A highly complex RNA world, as is sometimes presented in view of the widespread and diversified use of RNA enzymes, would have encountered many difficulties in passing to a world with catalysis mediated by proteins. These difficulties can be overcome by postulating a very early relationship between the nucleotide and the amino acid components. In particular, after asserting that some characteristics expressed by (nucleotide) coenzymes in catalysis are easier to understand if a close and early relationship between these coenzymes and amino acids is hypothesized, a model is presented for the origin of the enzyme–coenzyme complex. This model is essentially based on an intermediate formed by a tRNA-like molecule covalently linked to a polypeptide. The model attributes the majority of the catalytic role in the ribonucleoprotein world to the latter complex and thus it takes into account the birth of the key intermediate in the origin of protein synthesis—namely, peptidyl-tRNA, which would have otherwise been extremely difficult to select. The predictions of the model are discussed along with its robustness, using the data derived from the study of intermediary metabolism and those from molecular biology. Finally, the appearance of the genetic code in the late phase of the ribonucleopeptide world is discussed. Received: 13 January 1997 / Accepted: 25 July 1997     

Evolutionary psychiatry and the schizophrenia paradox: a critique

Evolutionary psychiatrists invariably consider schizophrenia to be a paradox: how come natural selection has not yet eliminated the infamous ‘genes for schizophrenia’ if the disorder simply crushes the reproductive success of its carriers, if it has been around for thousands of years already, and if it has a uniform prevalence throughout the world? Usually, the answer is that the schizophrenic genotype is subject to some kind of balancing selection: the benefits it confers would then outbalance the obvious damage it does. In this paper, however, I will show that the assumptions underlying such evolutionary accounts of schizophrenia are at least implausible, and sometimes even erroneous. First of all, I will examine some factual assumptions, in particular about schizophrenia’s impact on reproductive success, its genetics, its history, and its epidemiology. Secondly, I will take a critical look at a major philosophical assumption in evolutionary psychiatric explanations of schizophrenia. Indeed, evolutionary psychiatrists take it for granted that schizophrenia is a natural kind, i.e. a bounded and objectively real entity with discrete biological causes. My refutation of this natural kind view suggests that schizophrenia is in fact a reified umbrella concept, covering a heterogeneous group of disorders. Therefore, schizophrenia, as we now know it, simply doesn’t have an evolutionary history.     

Question 5: Does the RNA-World Still Retain its Appeal After 40 Years of Research?

Forty years after its formulation, the hypothesis of the RNA-World remains rather controversial even though studies of RNA catalysis in cellular processes (for example, in the ubiquitous ribosomal peptide-bond formation) have clearly lent increased plausibility to the idea that an RNA-World existed at some point in the evolution leading to the emergence of cellular life. Indeed, several issues remain that weaken the concept: the synthesis of the RNA monomers under prebiotic conditions, their subsequent, efficient polymerization to yield ribozymes that specifically catalyze their own replication. This communication summarizes existing studies of the RNA polymerization from monomers. In our opinion, the recent developments show that given time plausible answers to some of the issues facing the RNA-World hypothesis will be found. Presented at: International School of Complexity – 4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.     

An evolutionary account of science: A response to Rosenberg's critical notice

In his critical notice, Rosenberg (1991) raises three objections to my evolutionary account of science: whether it is more than a week metaphor, the compatibility of my past objections to reduction and my current advocacy of viewing selection in terms of replication and interaction, and finally, the feasibility of identifying appropriate replicators and interactors in biological evolution, let alone conceptual evolution. I discuss each of these objections in turn.