The RNA-peptide world
The RNA-peptide world tries to build a bridge between the replication first, and metabolism first scenarios, advancing the RNA world and combining it with catalytic peptides and primitive metabolism.
Stephen D. Fried (2022): Diverse lines of research in molecular biology, bioinformatics, geochemistry, biophysics, and astrobiology provide clues about the progression and early evolution of proteins, and lend credence to the idea that early peptides served many central prebiotic roles before they were encodable by a polynucleotide template, in a putative ‘peptide-polynucleotide stage’. 23
The presupposition is that a result of chemical prebiotic conditions permitted the emergence of activated ribonucleotides and amino acids. The proposal hypothesizes that RNAs started to interact and get into a relationship with small peptides ( small amino acid strands) right from the beginning, rather than everything starting exclusively with RNAs, that later would transition to mutually beneficial interaction with amino acids. In modern cells, DNA that stores the genetic data using the genetic code is transcribed into messenger RNA (mRNA), subsequently translated in the ribosome apparatus into functional amino acid sequences, which form polypeptides, and in the end, proteins. The core problem is the origin of the codon-amino acid assignment through the genetic code. The RNA-peptide world attempts to address this current state of affairs, starting with an RNA-peptide world, which constitutes the first step to arrive at the end of the current solution, where the sophisticated translation is performed through the ribosome.
Charles W. Carter, Jr. (2015): In the RNA-world scenario, the necessary catalysts were initially entirely RNA-based and did not include genetically encoded proteins. IN the RNA-peptide world, the idea that coded peptides functioned catalytically in the early stages of the origin of life directly contradicts the second central tenet of the “RNA World” scenario. The important distinction between this scenario and the RNA World hypothesis is that the requisite specificity is low in the initial stages of the former but unacceptably high in the latter. Low specificity processes occur with greater frequency and hence are more likely to have occurred first. The unavailability of activated amino acids was the most critical barrier to the emergence of protein synthesis. 16
Dave Speijer (2015): Wery small RNAs (versatile and stable due to base-pairing) and amino acids, as well as dipeptides, coevolved. The “RNA world” hypothesis is seen as one of the main contenders for a viable theory on the origin of life. Relatively small RNAs have catalytic power, RNA is everywhere in present-day life, the ribosome is seen as a ribozyme, and rRNA and tRNA are crucial for modern protein synthesis. However, this view is incomplete at best. The modern protein-RNA ribosome most probably is not a distorted form of a “pure RNA ribosome” evolution started out with. Though the oldest center of the ribosome seems “RNA only”, we cannot conclude from this that it ever functioned in an environment without amino acids and/or peptides. Very small RNAs (versatile and stable due to base-pairing) and amino acids, as well as dipeptides, coevolved. Remember, it is the amino group of aminoacylated tRNA that attacks peptidyl-tRNA, destroying the bond between peptide and tRNA. This activity of the amino acid part of aminoacyl-tRNA illustrates the centrality of amino acids in life. With the rise of the “RNA world” view of early life, the pendulum seems to have swung too much towards the ribozymatic part of early biochemistry. The necessary presence and activity of amino acids and peptides is in need of highlighting. We argue that an RNA world completely independent of amino acids never existed.
Indeed, I agree, that an RNA world never existed. But did an RNA-peptide world?
Speijer: The idea of an independent RNA world without oligopeptides or amino acids stabilizing structures and helping in catalysis does not seem a viable concept. On the other hand, the idea of catalytic protein existing without RNA storing the polypeptide sequences, which have catalytic activity, and organizing the production of these sequences, also does not seem a viable concept. Here we argue for a “coevolutionary” theory in which amino acids and (very small) peptides, as well as small RNAs, existed together and where their separate abilities not only reinforced each other’s survival but allowed life to more quickly climbing the ladder of complexity.
Every naturalistic approach works only from the simple to the complex in a slow, gradual manner. Even if not linear but with ups and downs, the outcome is always that there is more functional complexity at the end. That is as well Speijers proposal: "Starting with small molecules (easily) derived from prebiotic chemistry, we will try to reconstruct a possible history in which every stage of increased complexity arises from the previous more simple stage because specific nucleotide/amino acid (RNA/peptide) interactions allowed it do so." Observe how Speijer introduces teleonomy into the explanation. As if RNAs and amino acids operated or behaved with the "aim" or purpose of keeping a state of affairs, that wasn't even there. RNAs and amino acids on their own are not alive. They are molecules used in biology. But molecules have no innate drive or "urge" to keep a specific state of affairs, that would favor a future outcome, the gradual complexification that would, in the end, result in the existence of self-replicating cells.
Speijer: We now come at a crucial and, we have to admit, somewhat theoretical juncture: coevolution is illustrated by the presumption that RNAs could not persist without peptide protection, that very short (very early) peptides were made more abundant by RNA-producing them, and that they co-evolve forming longer RNAs and peptides. This would constitute an RNA/peptide world of ribozymes and short oligopeptides. These oligopeptides had RNA protection functions (DADVDGD being the obvious ancestor sequence of the universal RNA polymerase active site sequence NADFDGD) This motif (Asn-Ala-Asp-Phe-Asp-Gly-Asp) is a specific stretch of amino acids that is central in all cellular life. RNA polymerases catalyze the transcription from DNA to mRNA. Dennis R. Salahub (2008): Most known RNA polymerases (RNAPs) share a universal heptapeptide, called the NADFDGD motif. The crystal structures of RNAPs indicate that in all cases this motif forms a loop with an embedded triad of aspartic acid residues. This conserved loop is the key part of the active site. 17
The odds to get this sequence randomly is one in 20^7 or one in 10^10, that is taking a pool of 20 selected amino acids used in life would have to be shuffled 10 billion times to get this specified functional sequence. Not forgetting, that it is incorporated in a much longer polymer sequence that also has to be functional, and embedded and working in a joint venture with other polymer subunit strands of RNA polymerase. A far fetch.
Kunnev (2018): The hypothesis assumes that ribonucleotides would polymerize leading to very short RNAs from 2 to about 40 bases. The polymerization would incorporate random sequences and random 3D structures. The process would preserve mostly stable ones. Wet-Dry cycles could facilitate the process of RNA polymerization. Compartmentalization is another important factor since most of the described events are unlikely to occur in very low concentrations. Some level of environmental separation would be expected, for example, micro-chambers out of porous surface of rocks or lipid vesicles or both. Surface adsorption might have facilitated RNA-RNA interactions, RNA-lipids interactions and some beneficial chemical reactions. Thus, clay surfaces have been shown to promote encapsulation of RNA into vesicles and grow by incorporating fatty acid supplied as micelles and can divide without dilution of their contents. At temperatures between 1°C and to denaturation (about 55°C) temperature, short random RNA oligos would get stabilized via intra and intermolecular hybridization based on Watson-Crick base pairing, forming complexes of various 3D shape and size. Larger hybridized regions would confer greater stability and would be selected for. Highly self-complementary RNAs would be unlikely to exist, forcing intermolecular hybridization of short sequences and the emergence of complexes of several RNA oligos. The formation of RNA complexes also assumes a thermal cycle that would drive the process by sequential denaturation (~55–100°C) and re-annealing (<55°C) phases. Frequent repetition of the thermal cycle and stability selection would favor accumulation of complexes with higher degree of complementarity and higher GC content. Non-enzymatic aminoacylation between 2′ or 3′ positions of ribose and activated amino acids could occur. In addition, ribozymes capable of amino acid transfer from one RNA to another have been selected under laboratory conditions and similar molecules could have participated in aminoacylation of RNAs. Aminoacylated RNAs would be involved in complex formation, bringing some of the aminoacylated RNA 3′-ends in close proximity. This would promote peptide bond formation between two adjacent amino acids, most likely with the assistance of wet/dry natural cycles. All amino acids would have statistically equal probability to aminoacylate RNA. At that stage, any RNA molecule could be aminoacylated and could serve as a template. 18
That means, any available amino acid nearby could be involved in the reaction - inclusive amino acids not used in life, and they could be attached anywhere to the RNA molecule. There is also no restriction in regards of possible RNA configurations with any sort of nucleobases. There is no mechanism that would prevent other than the nucleobases used in life to be involved in the reactions. It would result simply in a disordered random accumulation of RNA-peptides.
Kunnev: We presume that following this initial stage all components of the translation system would co-evolve in a stepwise way. Specialization of ribosomal Large Subunit—LSU will start with evolution of peptidyl transferase center (PTC). The evolution of peptides to proteins would occur from small motif to domains and finally— folded proteins.
Felix Müller (2022): The ability to grow peptides on RNA with the help of non-canonical vestige nucleosides offers the possibility of an early co-evolution of covalently connected RNAs and peptides, which then could have dissociated at a higher level of sophistication to create the dualistic nucleic acid–protein world that is the hallmark of all life on Earth. It is difficult to imagine how an RNA world with complex RNA molecules could have emerged without the help of proteins and it is hard to envision how such an RNA world transitions into the modern dualistic RNA and protein world, in which RNA predominantly encodes information whereas proteins are the key catalysts of life.22
This story, when it comes to elucidating the trajectory from these small RNA-peptides, to fully developed proteins is very "sketchy" and superficial. This is a common modus operandi to uphold a story, that by looking closer, does not withstand scrutiny.
Charles Carter, structural biologist (2017): For life to take hold, the mystery polymer would have had to coordinate the rates of chemical reactions that could differ in speed by as much as 20 orders of magnitude. 24
Marcel Filoche (2019): Enzymes speed up biochemical reactions at the core of life by as much as 15 orders of magnitude. Yet, despite considerable advances, the fine dynamical determinants at the microscopic level of their catalytic proficiency are still elusive. Rate-promoting vibrations in the picosecond range, specifically encoded in the 3D protein structure, are localized vibrations optimally coupled to the chemical reaction coordinates at the active site. Remarkably, our theory also exposes a hitherto unknown deep connection between the unique localization fingerprint and a distinct partition of the 3D fold into independent, foldspanning subdomains that govern long-range communication. The universality of these features is demonstrated on a pool of more than 900 enzyme structures, comprising a total of more than 10,000 experimentally annotated catalytic sites. Our theory provides a unified microscopic rationale for the subtle structure-dynamics-function link in proteins. The intricate networks of metabolic cascades that power living organisms ultimately rest on the exquisite ability of enzymes to increase the rate of chemical reactions by many orders of magnitude. Although many molecular machines contain intrinsically disordered domains, the 3D fold is central to enzyme functioning. In particular, increasing evidence is accumulating in the literature in favor of the existence of specific fold-encoded motions believed to govern the relevant collective coordinate(s) that are coupled to the chemical transformation. These motions typically correspond to localized vibrations of the protein scaffold that contribute to the catalytic reaction, i.e., modes that, if impeded, would lead to a deterioration of the catalytic efficiency.
The more the function of a machine depends on its precise setup and arrangement respecting very limited tolerances, the more efforts have to be undertaken to achieve the required precision, demanding engineering solutions where nothing can be left to chance. That is precisely the case with proteins. There is an extraordinarily limited tolerance upon which proteins have to be engineered and designed, a requirement to achieve the necessary catalytic functions. That sets the bar for the cause to instantiate this state of affairs very high, for which random events are entirely inadequate!! The situation becomes even worse when we consider what Mathieu E. Rebeaud described as (2021): the challenge of reaching and maintaining properly folded and functional proteomes. Most proteins must fold to their native structure in order to function, and their folding is largely imprinted in their primary amino acid sequence. However, many proteins, especially large multidomain polypeptides, or certain protein types such as all-beta or repeat proteins, tend to misfold and aggregate into inactive species that may also be toxic. Life met this challenge by evolving employing molecular chaperones that can minimize protein misfolding and aggregation, even under stressful out-of-equilibrium conditions favoring aggregation. 25
Hays S. Rye (2013): Protein folding is a spontaneous process that is essential for life, yet the concentrated and complex interior of a cell is an inherently hostile environment for the efficient folding of many proteins. Some proteins—constrained by sequence, topology, size, and function—simply cannot fold by themselves and are instead prone to misfolding and aggregation. This problem is so deeply entrenched that a specialized family of proteins, known as molecular chaperones assists in protein folding. The bacterial chaperonin GroEL, along with its co-chaperonin GroES, is probably the best-studied example of this family of protein-folding machine. 27
Chaperones do bear no function unless there are misfolded proteins, that need to be re-folded in order to function. But non-functional proteins accumulating in the cell would be toxic waste and eventually kill the cell. So this creates another chicken & egg problem. What came first: Protein synthesis, or chaperones helping proteins to fold correctly? Consider as well, that, as Jörg Martin puts it (2000): The intracellular assembly of GroEL-type chaperonins appears to be a chaperone-dependent process itself and requires functional preformed chaperonin complexes !! 26 There are machines in the cell, that help other machines to be folded correctly, and these machines are also employed to help other machines to fold in order to be able to operate properly! Amazing!
Thorsten Hugel (2020): In a living cell, protein function is regulated in several ways, including post-translational modifications (PTMs), protein-protein interaction, or by the global environment (e.g. crowding or phase separation). While site-specific PTMs act very locally on the protein, specific protein interactions typically affect larger (sub-)domains, and global changes affect the whole protein non-specifically. Herein, we directly observe protein regulation under three different degrees of localization, and present the effects on the Hsp90 chaperone system at the levels of conformational steady states, kinetics and protein function. Interestingly using single-molecule FRET, we find that similar functional and conformational steady states are caused by completely different underlying kinetics. We disentangle specific and non-specific effects that control Hsp90’s ATPase function, which has remained a puzzle up to now. Lastly, we introduce a new mechanistic concept: functional stimulation through conformational confinement. Our results demonstrate how cellular protein regulation works by fine-tuning the conformational state space of proteins. 28
Susan Lindquist (2010): Cells also require a ubiquitin-proteasome system, targeting terminally misfolded proteins for degradation, and with translocation machineries to get proteins to their proper locations. These protein folding agents constitute a large, diverse, and structurally unrelated group. Many are upregulated in response to heat and are therefore termed heat shock proteins (HSPs). HSP90 is one of the most conserved HSPs, present from bacteria to mammals, and is an essential component of the protective heat shock response. The role of HSP90, however, extends well beyond stress tolerance. Even in nonstressed cells, HSP90 is highly abundant and associates with a wide array of proteins (known as clients) that depend on its chaperoning function to acquire their active conformations. 20% of yeast proteins are influenced by Hsp90 function, making it the most highly connected protein in the yeast genome, and GroES mediates the folding of ~10% of proteins in E. coli.29
Short RNA-peptides, or peptides on their own, are not functional and are useless in a supposed "proto-cell" unless they have the right size and sequence, able to fold into the functional 3D conformation. In face of this evidence, supposing and theorizing intermediate states and transitions of growing size and complexity over long periods of time until a functional state of affairs is achieved, is untenable. It opposes the evidence just described. Sophisticated exquisite mechanisms have to be instantiated from the get-go, to guarantee the right setup and folding of proteins of the full length. Such a hypothesized transition is never to work and going to happen. These RNA-peptides would simply lay around, and then sooner or later disintegrate. These explanations not including an intelligent agent are entirely inadequate to account for the origin of this kind of these high-tech engineering marvel implementations on a molecular scale!
George Church, Professor of Genetics, described the ribosome as "the most complicated thing that is present in all organisms". The peptidyl transferase center (PTC) is the core of the ribosome, where peptide bond formation occurs, which is a central catalytic reaction in life, where proteins are synthesized, and is as such of particular importance. The process is so intriguingly complex, that a science paper in 2015 had to admit that: "The detailed mechanism of peptidyl transfer, as well as the atoms and functional groups involved in this process are still in limbo." 19 The PTC is a ribozyme, which means it is composed of ribosomal RNAs ( rRNAs). Francisco Prosdocimi (2020): The PTC region has been considered crucial in the understanding about the origins of life. It has been described as the most significant trigger that engendered a mutualistic behavior between nucleic acids and peptides, allowing the emergence of biological systems. The emergence of this proto-PTC is a prerequisite to couple a chemical symbiosis between RNAs and peptides. Of 1434 complete sequences of 23S ribosomal RNAs analyzed, it was demonstrated that site A2451 from the 23S rRNA, which is the catalytic site of the PTC, is essential for the peptide bond to occur, and is absolutely preserved in each and every analyzed sequence. The PTC is known to be a flexible and efficient catalyst as it is capable of recognizing different, specific substrates (20 different amino acids bind to aminoacyl-tRNAs) and polymerizing proteins at a similar rate. 20
Sávio T.Farias (2014): Studies reveal that the PTC has a symmetrical structure comprising approximately 180 nucleotides. Molecular structure models suggest that the catalytic portion of the 23S rRNA entities of the symmetrical region possesses the common stem-elbow-stem (SES) structural motif. 21
Let's suppose that this structure would have emerged in an RNA-peptide world. Let's also not consider, that finding a functional sequence of 180 RNAs would vastly exceed the resources in sequence space, exhausting the maximum number of possible events in a universe that is 18 Billion years old (10^16 seconds) where every atom (10^80) is changing its state at the maximum rate of 10^40 times per second is 10^139. If we had such a core PTC, it would have no function whatsoever, unless all other players would be in place to perform translation from RNA to amino acids, having as well the genetic code implemented, and the entire chain from DNA to mRNA, to then coming to the events in translation. All these proposals, the RNA world, and the RNA-peptide world are based on silly pipe dreams - that they call theories when they are not more than ideas, based on fertile minds, and not results based on scientific evidence, experimentation, and tests in the lab. These are just invented scenarios - out of the need to keep an explanatory framework based on philosophical naturalism to find answers that do not require invoking a supernatural entity. All these proposals have been shown to be inadequate and doomed to failure. Biological cells are too complicated, sophisticated, integrated, and functional in order to warrant the belief that they could have originated by unguided means - the ribosome is a prime example to conclude this.
1. Suzan Mazur: The Origin of Life Circus: A How To Make Life Extravaganza November 30, 2014
2. PHILIP BALL: Flaws in the RNA world 12 FEBRUARY 2020
3. Eugene Koonin: The Logic of Chance: The Nature and Origin of Biological Evolution 31 agosto 2011
4. Natalia Szostak: Simulating the origins of life: The dual role of RNA replicases as an obstacle to evolution July 10, 2017
5. Jaroslaw Synak: RNA World Modeling: A Comparison of Two Complementary Approaches 11 April 2022
6. Jack W Szostak: The eightfold path to non-enzymatic RNA replication 03 February 2012
7. Hannes Mutschler: The difficult case of an RNA-only origin of life AUGUST 28 2019
8. Jordana Cepelewicz: Origin-of-Life Study Points to Chemical Chimeras, Not RNA September 16, 2019
9. Harris Bernstein: Origin of DNA Repair in the RNA World October 12th, 2020
10. Gerald F. Joyce: Protocells and RNA Self-Replication 2018
11. Steven A. Benner: The ‘‘Strong’’ RNA World Hypothesis: Fifty Years Old 2013 Apr;13
12. Harold S Bernhardt:[url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495036/#:~:text=However%2C the following objections have,of RNA is too limited.] The RNA world hypothesis: the worst theory of the early evolution of life[/url] (except for all the others) 2012 Jul 13
13. Eugene V Koonin: On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization 2007 May 31
14. Sami EL Khatib: Assumption and Criticism on RNA World Hypothesis from Ribozymes to Functional Cells March 12, 2021
15. Paul C. W. Davies: The algorithmic origins of life 2013 Feb 6
16. Charles W. Carter, Jr. What RNA World? Why a Peptide/RNA Partnership Merits Renewed Experimental Attention 23 January 2015
17. Dennis R. Salahub: Characterization of the active site of yeast RNA polymerase II by DFT and ReaxFF calculations 08 April 2008
18. Dimiter Kunnev: Possible Emergence of Sequence Specific RNA Aminoacylation via Peptide Intermediary to Initiate Darwinian Evolution and Code Through Origin of Life 2018 Oct 2;8
19. Hadieh Monajemi: The P-site A76 2′-OH acts as a peptidyl shuttle in a stepwise peptidyl transfer mechanism 2015
20. Francisco Prosdocimi: The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses 2020 Aug 5
21. Sávio T.Farias: Origin and evolution of the Peptidyl Transferase Center from proto-tRNAs 2014
22. Felix Müller: A prebiotically plausible scenario of an RNA–peptide world 11 May 2022
23. Stephen D. Fried: Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids 09 February 2022
24. Jordana Cepelewicz: The End of the RNA World Is Near, Biochemists Argue December 19, 2017
25. Mathieu E. Rebeaud: On the evolution of chaperones and cochaperones and the expansion of proteomes across the Tree of Life May 17, 2021
26. Jörg Martin: Assembly and Disassembly of GroEL and GroES Complexes 2000
27. Hays S. Rye: GroEL-Mediated Protein Folding: Making the Impossible, Possible 2013 Sep 25
28. Thorsten Hugel: Controlling protein function by fine-tuning conformational flexibility 2020 Jul 22
29. Susan Lindquist: HSP90 at the hub of protein homeostasis: emerging mechanistic insights 2010 Jul;11
30. F Egami: A working hypothesis on the interdependent genesis of nucleotide bases, protein amino acids, and primitive genetic code 1981 Sep;11
31. Charles W Carter, Jr: Interdependence, Reflexivity, Fidelity, Impedance Matching, and the Evolution of Genetic Coding 24 October 2017
32. Jessica C. Bowman: The Ribosome Challenge to the RNA World 20 February 2015
33. Jordana Cepelewicz: Life’s First Molecule Was Protein, Not RNA, New Model Suggests November 2, 2017
