Mutually stabilizing interactions between proto-peptides and RNA

Intellectual frameworks to understand complex biochemical systems at the origin of life

Understanding the emergence of complex biochemical systems, such as protein translation, is a great challenge. Although synthetic approaches can provide insight into the potential early stages of life, they do not address the equally important question of why the complex systems of life would have evolved. In particular, the intricacies of the mechanisms governing the transfer of information from nucleic acid sequences to proteins make it difficult to imagine how coded protein synthesis could have emerged from a prebiotic soup. Here we discuss the use of intellectual frameworks in studying the emergence of life. We discuss how one such framework, namely the RNA world theory, has spurred research, and provide an overview of its limitations. We suggest that the emergence of coded protein synthesis could be broken into experimentally tractable problems by treating it as a molecular bricolage-a complex system integrating many different parts, each of which originally evolved for uses unrelated to its modern function-to promote a concrete understanding of its origin.

Did organs precede organisms in the origin of life?

Evolutionary processes acting on populations of organized molecules preceded the origin of living organisms. These prebiotic entities were independently and repeatedly produced [i.e. (re)-produced] by the assembly of their components, following an iterative process giving rise to nearly but not fully identical replicas, allowing for a prebiotic form of Darwinian evolution. Natural selection favored the more persistent assemblies, some possibly modifying their own internal structure, or even their environment, thereby acquiring function. We refer to these assemblies as proto-organs. In association with other assemblies (e.g. in a coacervate or encapsulated within a vesicle), such proto-organs could evolve and acquire a role within the collective when their coexistence favored the selection of the ensemble. Along millions of years, an extraordinarily small number of successful combinations of those proto-organs co-occurring in spatially individualizing compartments might have co-evolved forming a proto-metabolic and proto-genetic informative network, eventually leading to the selfreplication of a very few. Thus, interactions between encapsulated proto-organs would have had a much higher probability of evolving into proto-organisms than interactions among simpler molecules. Multimolecular forms evolve functions; thus, functional organs would have preceded organisms.

Mutualistic Synthesis from Orthogonal Dynamic Covalent Reactions

Mutualisms are interactions that benefit all species involved. It has been widely investigated in neighbouring subjects, such as biology, ecology, sociology, and economics. However, such a reciprocal relationship in synthetic chemical systems has rarely been studied. Here, we demonstrate a mutualistic synthesis where byproducts from two orthogonal chemical reactions aid each other's production. Disulfide exchange and hydrazone exchange were chosen to generate two dynamic combinatorial libraries. A minor tetrameric macrocycle from the active disulfide library was quantitatively amplified in the presence of the hydrazone library. This incorporation also turned on the previously inert hydrazone reaction, producing a linear species that formed a "handcuffs" catenane with the disulfide tetramer. These findings not only lend robust support to the hypothesis of "RNA-peptide coevolution" for the origin of life but also broaden the scope of synthetic chemistry, highlighting the untapped potential of minor products from different reactions. Additionally, the co-self-assembly of these mutualistic entities to form supramolecular structures opens new avenues for future development of composite nanosystems with synergistic properties.

Weak effects of prebiotically plausible peptides on self-triphosphorylation ribozyme function

Catalytic RNAs (ribozymes) were central to early stages of life on earth. The first ribozymes probably emerged in the presence of prebiotically generated peptides because amino acids can be generated under abiotic conditions, and amino acids can oligomerize into peptides under prebiotically plausible conditions. Here we tested whether the presence of prebiotically plausible peptides could have aided the emergence of ribozymes, by an in vitro selection of self-triphosphorylation ribozymes from random sequence in the presence of ten different octapeptides. These peptides were composed of ten different, prebiotically plausible amino acids, each as mixture of d- and l-stereoisomers. After five rounds of selection and high throughput sequencing analysis, ten ribozymes that appeared most promising for peptide benefits were tested biochemically for possible benefits from each of the ten peptides. The strongest peptide benefit enhanced ribozyme activity by 2.6-fold, similar to the effect from an increase in the pH by one-half unit. Four arbitrarily chosen ribozymes from a previous selection without peptides showed no significant change in their activity in the presence of the ten peptides. Therefore, the used prebiotically plausible peptides - peptides without evolutionarily optimized sequence, without cationic or aromatic side chains - did not provide a strong benefit for the emergence of ribozyme activity. This finding stands in contrast to previously identified polycationic peptides, conjugates between peptides and polyaromatic hydrocarbons, and modern mRNA encoded proteins, all of which can strongly increase ribozyme function. The results are discussed in the context of origins of life.

The prebiotic emergence of biological evolution

The origin of life must have been preceded by Darwin-like evolutionary dynamics that could propagate it. How did that adaptive dynamics arise? And from what prebiotic molecules? Using evolutionary invasion analysis, we develop a universal framework for describing any origin story for evolutionary dynamics. We find that cooperative autocatalysts, i.e. autocatalysts whose per-unit reproductive rate grows as their population increases, have the special property of being able to cross a barrier that separates their initial degradation-dominated state from a growth-dominated state with evolutionary dynamics. For some model parameters, this leap to persistent propagation is likely, not rare. We apply this analysis to the Foldcat Mechanism, wherein peptides fold and help catalyse the elongation of each other. Foldcats are found to have cooperative autocatalysis and be capable of emergent evolutionary dynamics.

Amino acid analogues provide multiple plausible pathways to prebiotic peptides

Prebiotic peptide synthesis has consistently been a prominent topic within the field of the origin of life. While research predominantly centres on the 20 classical amino acids, the synthesis process encounters significant thermodynamic barriers. Consequently, amino acid analogues are being explored as potential building blocks for prebiotic peptide synthesis. This review delves into the pathway of polypeptide formation, identifying specific amino acid analogues that might have existed on early Earth, potentially participating in peptide synthesis and chemical evolution. Moreover, considering the complexity and variability of the environment on early Earth, we propose the plausibility of coevolution between amino acids and their analogues.

Reflections on the Origin of Coded Protein Biosynthesis

The principle of continuity posits that some central features of primordial biocatalytic mechanisms should still be present in the genetically dependent pathway of protein synthesis, a crucial step in the emergence of life. Key bimolecular reactions of this process are catalyzed by DNA-dependent RNA polymerases, aminoacyl-tRNA synthetases, and ribosomes. Remarkably, none of these biocatalysts contribute chemically active groups to their respective reactions. Instead, structural and functional studies have demonstrated that nucleotidic α-phosphate and β-d-ribosyl 2' OH and 3' OH groups can help their own catalysis, a process which, consequently, has been called "substrate-assisted". Furthermore, upon binding, the substrates significantly lower the entropy of activation, exclude water from these catalysts' active sites, and are readily positioned for a reaction. This binding mode has been described as an "entropy trap". The combination of this effect with substrate-assisted catalysis results in reactions that are stereochemically and mechanistically simpler than the ones found in most modern enzymes. This observation is consistent with the way in which primordial catalysts could have operated; it may also explain why, thanks to their complementary reactivities, β-d-ribose and phosphate were naturally selected to be the central components of early coding polymers.

Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy Transduction

How Nature discovered genetic coding is a largely ignored question, yet the answer is key to explaining the transition from biochemical building blocks to life. Other, related puzzles also fall inside the aegis enclosing the codes themselves. The peptide bond is unstable with respect to hydrolysis. So, it requires some form of chemical free energy to drive it. Amino acid activation and acyl transfer are also slow and must be catalyzed. All living things must thus also convert free energy and synchronize cellular chemistry. Most importantly, functional proteins occupy only small, isolated regions of sequence space. Nature evolved heritable symbolic data processing to seek out and use those sequences. That system has three parts: a memory of how amino acids behave in solution and inside proteins, a set of code keys to access that memory, and a scoring function. The code keys themselves are the genes for cognate pairs of tRNA and aminoacyl-tRNA synthetases, AARSs. The scoring function is the enzymatic specificity constant, kcat/kM, which measures both catalysis and specificity. The work described here deepens the evidence for and understanding of an unexpected consequence of ancestral bidirectional coding. Secondary structures occur in approximately the same places within antiparallel alignments of their gene products. However, the polar amino acids that define the molecular surface of one are reflected into core-defining non-polar side chains on the other. Proteins translated from base-paired coding strands fold up inside out. Bidirectional genes thus project an inverted structural duality into the proteome. I review how experimental data root the scoring functions responsible for the origins of coding and catalyzed activation of unfavorable chemical reactions in that duality.

Assembly-driven protection from hydrolysis as key selective force during chemical evolution

The origins of biopolymers pose fascinating questions in prebiotic chemistry. The marvelous assembly proficiencies of biopolymers suggest they are winners of a competitive evolutionary process. Sophisticated molecular assembly is ubiquitous in life where it is often emergent upon polymerization. We focus on the influence of molecular assembly on hydrolysis rates in aqueous media and suggest that assembly was crucial for biopolymer selection. In this model, incremental enrichment of some molecular species during chemical evolution was partially driven by the interplay of kinetics of synthesis and hydrolysis. We document a general attenuation of hydrolysis by assembly (i.e., recalcitrance) for all universal biopolymers and highlight the likely role of assembly in the survival of the 'fittest' molecules during chemical evolution.

The First Nucleic Acid Strands May Have Grown on Peptides via Primeval Reverse Translation

The central dogma of molecular biology dictates that, with only a few exceptions, information proceeds from DNA to protein through an RNA intermediate. Examining the enigmatic steps from prebiotic to biological chemistry, we take another road suggesting that primordial peptides acted as template for the self-assembly of the first nucleic acids polymers. Arguing in favour of a sort of archaic "reverse translation" from proteins to RNA, our basic premise is a Hadean Earth where key biomolecules such as amino acids, polypeptides, purines, pyrimidines, nucleosides and nucleotides were available under different prebiotically plausible conditions, including meteorites delivery, shallow ponds and hydrothermal vents scenarios. Supporting a protein-first scenario alternative to the RNA world hypothesis, we propose the primeval occurrence of short two-dimensional peptides termed "selective amino acid- and nucleotide-matching oligopeptides" (henceforward SANMAOs) that noncovalently bind at the same time the polymerized amino acids and the single nucleotides dispersed in the prebiotic milieu. In this theoretical paper, we describe the chemical features of this hypothetical oligopeptide, its biological plausibility and its virtues from an evolutionary perspective. We provide a theoretical example of SANMAO's selective pairing between amino acids and nucleosides, simulating a poly-Glycine peptide that acts as a template to build a purinic chain corresponding to the glycine's extant triplet codon GGG. Further, we discuss how SANMAO might have endorsed the formation of low-fidelity RNA's polymerized strains, well before the appearance of the accurate genetic material's transmission ensured by the current translation apparatus.

An Analysis of Nucleotide-Amyloid Interactions Reveals Selective Binding to Codon-Sized RNA

Interactions between RNA and proteins are the cornerstone of many important biological processes from transcription and translation to gene regulation, yet little is known about the ancient origin of said interactions. We hypothesized that peptide amyloids played a role in the origin of life and that their repetitive structure lends itself to building interfaces with other polymers through avidity. Here, we report that short RNA with a minimum length of three nucleotides binds in a sequence-dependent manner to peptide amyloids. The 3'-5' linked RNA backbone appears to be well-suited to support these interactions, with the phosphodiester backbone and nucleobases both contributing to the affinity. Sequence-specific RNA-peptide interactions of the kind identified here may provide a path to understanding one of the great mysteries rooted in the origin of life: the origin of the genetic code.

Peptide conjugates with polyaromatic hydrocarbons can benefit the activity of catalytic RNAs

Early stages of life likely employed catalytic RNAs (ribozymes) in many functions that are today filled by proteins. However, the earliest life forms must have emerged from heterogenous chemical mixtures, which included amino acids, short peptides, and many other compounds. Here we explored whether the presence of short peptides can help the emergence of catalytic RNAs. To do this, we conducted an in vitro selection for catalytic RNAs from randomized sequence in the presence of ten different peptides with a prebiotically plausible length of eight amino acids. This in vitro selection generated dozens of ribozymes, one of them with ∼900-fold higher activity in the presence of one specific peptide. Unexpectedly, the beneficial peptide had retained its N-terminal Fmoc protection group, and this group was required to benefit ribozyme activity. The same, or higher benefit resulted from peptide conjugates with prebiotically plausible polyaromatic hydrocarbons (PAHs) such as fluorene and naphthalene. This shows that PAH-peptide conjugates can act as potent cofactors to enhance ribozyme activity. The results are discussed in the context of the origin of life.

Molecular Crowding Facilitates Ribozyme-Catalyzed RNA Assembly

Catalytic RNAs or ribozymes are considered to be central to primordial biology. Most ribozymes require moderate to high concentrations of divalent cations such as Mg2+ to fold into their catalytically competent structures and perform catalysis. However, undesirable effects of Mg2+ such as hydrolysis of reactive RNA building blocks and degradation of RNA structures are likely to undermine its beneficial roles in ribozyme catalysis. Further, prebiotic cell-like compartments bounded by fatty acid membranes are destabilized in the presence of Mg2+, making ribozyme function inside prebiotically relevant protocells a significant challenge. Therefore, we sought to identify conditions that would enable ribozymes to retain activity at low concentrations of Mg2+. Inspired by the ability of ribozymes to function inside crowded cellular environments with <1 mM free Mg2+, we tested molecular crowding as a potential mechanism to lower the Mg2+ concentration required for ribozyme-catalyzed RNA assembly. Here, we show that the ribozyme-catalyzed ligation of phosphorimidazolide RNA substrates is significantly enhanced in the presence of the artificial crowding agent polyethylene glycol. We also found that molecular crowding preserves ligase activity under denaturing conditions such as alkaline pH and the presence of urea. Additionally, we show that crowding-induced stimulation of RNA-catalyzed RNA assembly is not limited to phosphorimidazolide ligation but extends to the RNA-catalyzed polymerization of nucleoside triphosphates. RNA-catalyzed RNA ligation is also stimulated by the presence of prebiotically relevant small molecules such as ethylene glycol, ribose, and amino acids, consistent with a role for molecular crowding in primordial ribozyme function and more generally in the emergence of RNA-based cellular life.

Biomolecule-Based Coacervates with Modulated Physiological Functions

Liquid-liquid phase separation (LLPS) exists widely in living systems, and understanding the working mechanisms of the formed condensed droplets is of great significance for the prevention and treatment of diseases as well as for the development of biomimetic materials. Herein, in this Perspective we try to focus on the in vitro reconstructions of biomolecule-based coacervates and outline the associations between the functional components and droplets as well as the physiological and pathological functions associated with coacervates. Coacervates are formed by functional components through weak, multivalent interactions. The interaction strengths that determine coacervate properties such as electability and phase state, which in turn influence the functional components to limit their fluidity, stability, or diffusion coefficients, are specially discussed. At the end of this Perspective, the current challenges are summarized; progress will require our great efforts to reveal the mechanisms of action at the molecular level and then develop biomolecule-based coacervate models with complexity, integration of methods, and intellectualization.

Ribozyme activity modulates the physical properties of RNA-peptide coacervates

Condensed coacervate phases are now understood to be important features of modern cell biology, as well as valuable protocellular models in origin-of-life studies and synthetic biology. In each of these fields, the development of model systems with varied and tuneable material properties is of great importance for replicating properties of life. Here, we develop a ligase ribozyme system capable of concatenating short RNA fragments into long chains. Our results show that the formation of coacervate microdroplets with the ligase ribozyme and poly(L-lysine) enhances ribozyme rate and yield, which in turn increases the length of the anionic polymer component of the system and imparts specific physical properties to the droplets. Droplets containing active ribozyme sequences resist growth, do not wet or spread on unpassivated surfaces, and exhibit reduced transfer of RNA between droplets when compared to controls containing inactive sequences. These altered behaviours, which stem from RNA sequence and catalytic activity, constitute a specific phenotype and potential fitness advantage, opening the door to selection and evolution experiments based on a genotype-phenotype linkage.

Mixed anhydrides at the intersection between peptide and RNA autocatalytic sets: evolution of biological coding

We present a scenario for the origin of biological coding, a semiotic relationship between chemical information stored in one location that links to chemical information stored in a separate location. Coding originated from cooperation between two, originally separate, collectively autocatalytic sets (CASs), one for nucleic acids and one for peptides. Upon interaction, a series of RNA folding-directed processes led to their joint cooperativity. The aminoacyl adenylate was the first covalent association made by these two CASs and solidified their interdependence, and is a palimpsest of this era, a relic of the original semiotic relationship between RNA and proteins. Coding was driven by selection pressure to eliminate waste in CASs. Eventually a 1 : 1 relationship between single amino acids and short RNA pieces was established, i.e. the 'genetic code'. The two classes of aaRS enzymes are remnants of the complementary information in two RNA strands, as postulated by Rodin and Ohno. Every stage in the evolution of coding was driven by the downward selection on the components of a system to satisfy the Kantian whole. Coding was engendered because there were two chemically distinct classes of polymers needed for open-ended evolution; systems with only one polymer cannot exhibit this characteristic. Coding is thus synonymous with life as we know it.

Why we are made of proteins and nucleic acids: Structural biology views on extraterrestrial life

Is it a miracle that life exists on the Earth, or is it a common phenomenon in the universe? If extraterrestrial organisms exist, what are they like? To answer these questions, we must understand what kinds of molecules could evolve into life, or in other words, what properties are generally required to perform biological functions and store genetic information. This review summarizes recent findings on simple ancestral proteins, outlines the basic knowledge in textbooks, and discusses the generally required properties for biological molecules from structural biology viewpoints (e.g., restriction of shapes, and types of intra- and intermolecular interactions), leading to the conclusion that proteins and nucleic acids are at least one of the simplest (and perhaps very common) forms of catalytic and genetic biopolymers in the universe. This review article is an extended version of the Japanese article, On the Origin of Life: Coevolution between RNA and Peptide, published in SEIBUTSU BUTSURI Vol. 61, p. 232-235 (2021).

Dynamic exchange controls the assembly structure of nucleic-acid-peptide chimeras

Recent attempts to develop the next generation of functional biomaterials focus on systems chemistry approaches exploiting dynamic networks of hybrid molecules. This task is often found challenging, but we herein present ways for profiting from the multiple interaction interfaces forming Nucleic-acid-Peptide assemblies and tuning their formation. We demonstrate that the formation of well-defined structures by double-stranded DNA-peptide conjugates (dsCon) is restricted to a specific range of environmental conditions and that precise DNA hybridization, satisfying the interaction interfaces, is a crucial factor in this process. We further reveal the impact of external stimuli, such as competing free DNA elements or salt additives, which initiate dynamic interconversions, resulting in hybrid structures exhibiting spherical and fibrillar domains or a mixture of spherical and fibrillar particles. This extensive analysis of the co-assembly systems chemistry offers new insights into prebiotic hybrid assemblies that may now facilitate the design of new functional materials. We discuss the implications of these findings for the emergence of function in synthetic materials and during early chemical evolution.

Boron-assisted abiotic polypeptide synthesis

The emergence of proteins and their interactions with RNAs were a key step in the origin and early evolution of life. The abiotic synthesis of peptides has been limited in short amino acid length and is favored in highly alkaline evaporitic conditions in which RNAs are unstable. This environment is also inconsistent with estimated Hadean Earth. Prebiotic environments rich in boron are reportedly ideal for abiotic RNA synthesis. However, the effects of boron on amino acid polymerization are unclear. We report that boric acid enables the polymerization of amino acids at acidic and near-neutral pH levels based on simple heating experiments of amino acid solutions containing borate/boric acid at various pH levels. Our study provides evidence for the boron-assisted synthesis of polypeptides in prebiotically plausible environments, where the same conditions would allow for the formation of RNAs and interactions of primordial proteins and RNAs that could be inherited by RNA-dependent protein synthesis during the evolution of life.

Origins of life: first came evolutionary dynamics

When life arose from prebiotic molecules 3.5 billion years ago, what came first? Informational molecules (RNA, DNA), functional ones (proteins), or something else? We argue here for a different logic: rather than seeking a molecule type, we seek a dynamical process. Biology required an ability to evolve before it could choose and optimise materials. We hypothesise that the evolution process was rooted in the peptide folding process. Modelling shows how short random peptides can collapse in water and catalyse the elongation of others, powering both increased folding stability and emergent autocatalysis through a disorder-to-order process.

How to build a protoribosome: structural insights from the first protoribosome constructs that have proven to be catalytically active

The modern ribosome catalyzes all coded protein synthesis in extant organisms. It is likely that its core structure is a direct descendant from the ribosome present in the last common ancestor (LCA). Hence, its earliest origins likely predate the LCA and therefore date further back in time. Of special interest is the pseudosymmetrical region (SymR) that lies deep within the large subunit (LSU) where the peptidyl transfer reaction takes place. It was previously proposed that two RNA oligomers, representing the P- and A-regions of extant ribosomes dimerized to create a pore-like structure, which hosted the necessary properties that facilitate peptide bond formation. However, recent experimental studies show that this may not be the case. Instead, several RNA constructs derived exclusively from the P-region were shown to form a homodimer capable of peptide bond synthesis. Of special interest will be the origin issues because the homodimer would have allowed a pre-LCA ribosome that was significantly smaller than previously proposed. For the A-region, the immediate issue will likely be its origin and whether it enhances ribosome performance. Here, we reanalyze the RNA/RNA interaction regions that most likely lead to SymR formation in light of these recent findings. Further, it has been suggested that the ability of these RNA constructs to dimerize and enhance peptide bond formation is sequence-dependent. We have analyzed the implications of sequence variations as parts of functional and nonfunctional constructs.

Novel Chimeric Amino Acid-Fatty Alcohol Ester Amphiphiles Self-Assemble into Stable Primitive Membranes in Diverse Geological Settings

Primitive cells are believed to have been self-assembled vesicular structures with minimal metabolic components, that were capable of self-maintenance and self-propagation in early Earth geological settings. The coevolution and self-assembly of biomolecules, such as amphiphiles, peptides, and nucleic acids, or their precursors, were essential for protocell emergence. Here, we present a novel class of amphiphiles-amino acid-fatty alcohol esters-that self-assemble into stable primitive membrane compartments under a wide range of geochemical conditions. Glycine n-octyl ester (GOE) and isoleucine n-octyl ester (IOE), the condensation ester products of glycine or isoleucine with octanol (OcOH), are expected to form at a mild temperature by wet-dry cycles. The GOE forms micelles in acidic aqueous solutions (pH 2-7) and vesicles at intermediate pH (pH 7.3-8.2). When mixed with cosurfactants (octanoic acid [OcA]; OcOH, or decanol) in different mole fractions [X_Cosurfactant = 0.1-0.5], the vesicle stability range expands significantly to span the extremely acidic to mildly alkaline (pH 2-8) and extremely alkaline (pH 10-11) regions. Only a small mole fraction of cosurfactant [X_Cosurfactant = 0.1] is needed to make stable vesicular structures. Notably, these GOE-based vesicles are also stable in the presence of high concentrations of divalent cations, even at low pHs and in simulated Hadean seawater composition (without sulfate). To better understand the self-assembly behavior of GOE-based systems, we devised complementary molecular dynamics computer simulations for a series of mixed GOE/OcA systems under simulated acidic pHs. The resulting calculated critical packing parameter values and self-assembly behavior were consistent with our experimental findings. The IOE is expected to show similar self-assembly behavior. Thus, amino acid-fatty alcohol esters, a novel chimeric amphiphile class composed of an amino acid head group and a fatty alcohol tail, may have aided in building protocell membranes, which were stable in a wide variety of geochemical circumstances and were conducive to supporting replication and self-maintenance. The present work contributes to our body of work supporting our hypothesis for synergism and coevolution of (proto)biomolecules on early Earth.

Selective Synthesis of Lysine Peptides and the Prebiotically Plausible Synthesis of Catalytically Active Diaminopropionic Acid Peptide Nitriles in Water

Why life encodes specific proteinogenic amino acids remains an unsolved problem, but a non-enzymatic synthesis that recapitulates biology's universal strategy of stepwise N-to-C terminal peptide growth may hold the key to this selection. Lysine is an important proteinogenic amino acid that, despite its essential structural, catalytic, and functional roles in biochemistry, has widely been assumed to be a late addition to the genetic code. Here, we demonstrate that lysine thioacids undergo coupling with aminonitriles in neutral water to afford peptides in near-quantitative yield, whereas non-proteinogenic lysine homologues, ornithine, and diaminobutyric acid cannot form peptides due to rapid and quantitative cyclization that irreversibly blocks peptide synthesis. We demonstrate for the first time that ornithine lactamization provides an absolute differentiation of lysine and ornithine during (non-enzymatic) N-to-C-terminal peptide ligation. We additionally demonstrate that the shortest lysine homologue, diaminopropionic acid, undergoes effective peptide ligation. This prompted us to discover a high-yielding prebiotically plausible synthesis of the diaminopropionic acid residue, by peptide nitrile modification, through the addition of ammonia to a dehydroalanine nitrile. With this synthesis in hand, we then discovered that the low basicity of diaminopropionyl residues promotes effective, biomimetic, imine catalysis in neutral water. Our results suggest diaminopropionic acid, synthesized by peptide nitrile modification, can replace or augment lysine residues during early evolution but that lysine's electronically isolated sidechain amine likely provides an evolutionary advantage for coupling and coding as a preformed monomer in monomer-by-monomer peptide translation.

The Origin of Translation: Bridging the Nucleotides and Peptides

Extant biology uses RNA to record genetic information and proteins to execute biochemical functions. Nucleotides are translated into amino acids via transfer RNA in the central dogma. tRNA is essential in translation as it connects the codon and the cognate amino acid. To reveal how the translation emerged in the prebiotic context, we start with the structure and dissection of tRNA, followed by the theory and hypothesis of tRNA and amino acid recognition. Last, we review how amino acids assemble on the tRNA and further form peptides. Understanding the origin of life will also promote our knowledge of artificial living systems.

A liquid crystal world for the origins of life

Nucleic acids (NAs) in modern biology accomplish a variety of tasks, and the emergence of primitive nucleic acids is broadly recognized as a crucial step for the emergence of life. While modern NAs have been optimized by evolution to accomplish various biological functions, such as catalysis or transmission of genetic information, primitive NAs could have emerged and been selected based on more rudimental chemical-physical properties, such as their propensity to self-assemble into supramolecular structures. One such supramolecular structure available to primitive NAs are liquid crystal (LC) phases, which are the outcome of the collective behavior of short DNA or RNA oligomers or monomers that self-assemble into linear aggregates by combinations of pairing and stacking. Formation of NA LCs could have provided many essential advantages for a primitive evolving system, including the selection of potential genetic polymers based on structure, protection by compartmentalization, elongation, and recombination by enhanced abiotic ligation. Here, we review recent studies on NA LC assembly, structure, and functions with potential prebiotic relevance. Finally, we discuss environmental or geological conditions on early Earth that could have promoted (or inhibited) primitive NA LC formation and highlight future investigation axes essential to further understanding of how LCs could have contributed to the emergence of life.

On the Evolutionary History of the Twenty Encoded Amino Acids

α-Amino acids are essential molecular constituents of life, twenty of which are privileged because they are encoded by the ribosomal machinery. The question remains open as to why this number and why this 20 in particular, an almost philosophical question that cannot be conclusively resolved. They are closely related to the evolution of the genetic code and whether nucleic acids, amino acids, and peptides appeared simultaneously and were available under prebiotic conditions when the first self-sufficient complex molecular system emerged on Earth. This report focuses on prebiotic and metabolic aspects of amino acids and proteins starting with meteorites, followed by their formation, including peptides, under plausible prebiotic conditions, and the major biosynthetic pathways in the various kingdoms of life. Coenzymes play a key role in the present analysis in that amino acid metabolism is linked to glycolysis and different variants of the tricarboxylic acid cycle (TCA, rTCA, and the incomplete horseshoe version) as well as the biosynthesis of the most important coenzymes. Thus, the report opens additional perspectives and facets on the molecular evolution of primary metabolism.

Collective adaptability in a replication network of minimal nucleobase sequences

A major challenge for understanding the origins of life is to explore how replication networks can engage in an evolutionary process. Herein, we shed light on this problem by implementing a network constituted by two different types of extremely simple biological components: the amino acid cysteine and the canonical nucleobases adenine and thymine, connected through amide bonds to the cysteine amino group and oxidation of its thiol into three possible disulfides. Supramolecular and kinetic analyses revealed that both self- and mutual interactions between such dinucleobase compounds drive their assembly and replication pathways. Those pathways involving sequence complementarity led to enhanced replication rates, suggesting a potential bias for selection. The interplay of synergistic dynamics and competition between replicators was then simulated, under conditions that are not easily accessible with experiments, in an open reactor parametrized and constrained with the unprecedentedly complete experimental kinetic data obtained for our replicative network. Interestingly, the simulations show bistability, as a selective amplification of different species depending on the initial mixture composition. Overall, this network configuration can favor a collective adaptability to changes in the availability of feedstock molecules, with disulfide exchange reactions serving as 'wires' that connect the different individual auto- and cross-catalytic pathways.

Role of Mutations in Differential Recognition of Viral RNA Molecules by Peptides

The conserved noncoding RNA elements in viral genomes interact with proteins to regulate various events during viral replication. We report studies on the recognition mechanisms of two helical peptides, namely, a native (Rev) peptide and a lab-evolved (RSG1.2) peptide, by a highly conserved viral RNA element from the human immunodeficiency virus 1 genome. Specifically, we investigated the physical interactions between the viral RNA molecule and helical peptides by computing free energy changes on mutating key amino acid residues involved in recognition of an internal loop in the viral RNA molecule.

Frontiers in Prebiotic Chemistry and Early Earth Environments

The Prebiotic Chemistry and Early Earth Environments (PCE₃) Consortium is a community of researchers seeking to understand the origins of life on Earth and in the universe. PCE₃ is one of five Research Coordination Networks (RCNs) within NASA’s Astrobiology Program. Here we report on the inaugural PCE₃ workshop, intended to cross-pollinate, transfer information, promote cooperation, break down disciplinary barriers, identify new directions, and foster collaborations. This workshop, entitled, “Building a New Foundation”, was designed to propagate current knowledge, identify possibilities for multidisciplinary collaboration, and ultimately define paths for future collaborations. Presentations addressed the likely conditions on early Earth in ways that could be incorporated into prebiotic chemistry experiments and conceptual models to improve their plausibility and accuracy. Additionally, the discussions that followed among workshop participants helped to identify within each subdiscipline particularly impactful new research directions. At its core, the foundational knowledge base presented in this workshop should underpin future workshops and enable collaborations that bridge the many disciplines that are part of PCE₃.

Phase-specific RNA accumulation and duplex thermodynamics in multiphase coacervate models for membraneless organelles

Liquid-liquid phase separation has emerged as an important means of intracellular RNA compartmentalization. Some membraneless organelles host two or more compartments serving different putative biochemical roles. The mechanisms for, and functional consequences of, this subcompartmentalization are not yet well understood. Here we show that adjacent phases of decapeptide-based multiphase model membraneless organelles differ markedly in their interactions with RNA. Single- and double-stranded RNAs preferentially accumulate in different phases within the same droplet, and one phase is more destabilizing for RNA duplexes than the other. Single-phase peptide droplets did not capture this behaviour. Phase coexistence introduces new thermodynamic equilibria that alter RNA duplex stability and RNA sorting by hybridization state. These effects require neither biospecific RNA-binding sites nor full-length proteins. As such, they are more general and point to primitive versions of mechanisms operating in extant biology that could aid understanding and enable the design of functional artificial membraneless organelles.

Hydrophobic-cationic peptides modulate RNA polymerase ribozyme activity by accretion

Accretion and the resulting increase in local concentration is a widespread mechanism in biology to enhance biomolecular functions (for example, in liquid-liquid demixing phases). Such macromolecular aggregation phases (e.g., coacervates, amyloids) may also have played a role in the origin of life. Here, we report that a hydrophobic-cationic RNA binding peptide selected by phage display (P43: AKKVWIIMGGS) forms insoluble amyloid-containing aggregates, which reversibly accrete RNA on their surfaces in an RNA-length and Mg²⁺-concentration dependent manner. The aggregates formed by P43 or its sequence-simplified version (K₂V₆: KKVVVVVV) inhibited RNA polymerase ribozyme (RPR) activity at 25 mM MgCl₂, while enhancing it significantly at 400 mM MgCl₂. Our work shows that such hydrophobic-cationic peptide aggregates can reversibly concentrate RNA and enhance the RPR activity, and suggests that they could have aided the emergence and evolution of longer and functional RNAs in the fluctuating environments of the prebiotic earth.

The Bootstrap Model of Prebiotic Networks of Proteins and Nucleic Acids

It is not known how life arose from prebiotic physical chemistry. How did fruitful cell-like associations emerge from the two polymer types—informational (nucleic acids, xNAs = DNA or RNA) and functional (proteins)? Our model shows how functional networks could bootstrap from random sequence-independent initial states. For proteins, we adopt the foldamer hypothesis: through persistent nonequilibrium prebiotic syntheses, short random peptides fold and catalyze the elongation of others. The xNAs enter through random binding to the peptides, and all chains can mutate. Chains grow inside colloids that split when they’re large, coupling faster growth speeds to bigger populations. Random and useless at first, these folding and binding events grow protein—xNA networks that resemble today’s protein–protein networks.

Neuroepigenetic Mechanisms of Action of Ultrashort Peptides in Alzheimer's Disease

Epigenetic regulation of gene expression is necessary for maintaining higher-order cognitive functions (learning and memory). The current understanding of the role of epigenetics in the mechanism of Alzheimer’s disease (AD) is focused on DNA methylation, chromatin remodeling, histone modifications, and regulation of non-coding RNAs. The pathogenetic links of this disease are the misfolding and aggregation of tau protein and amyloid peptides, mitochondrial dysfunction, oxidative stress, impaired energy metabolism, destruction of the blood–brain barrier, and neuroinflammation, all of which lead to impaired synaptic plasticity and memory loss. Ultrashort peptides are promising neuroprotective compounds with a broad spectrum of activity and without reported side effects. The main aim of this review is to analyze the possible epigenetic mechanisms of the neuroprotective action of ultrashort peptides in AD. The review highlights the role of short peptides in the AD pathophysiology. We formulate the hypothesis that peptide regulation of gene expression can be mediated by the interaction of short peptides with histone proteins, cis- and transregulatory DNA elements and effector molecules (DNA/RNA-binding proteins and non-coding RNA). The development of therapeutic agents based on ultrashort peptides may offer a promising addition to the multifunctional treatment of AD.

Adaptation and Exaptation: From Small Molecules to Feathers

Evolution works by adaptation and exaptation. At an organismal level, exaptation and adaptation are seen in the formation of organelles and the advent of multicellularity. At the sub-organismal level, molecular systems such as proteins and RNAs readily undergo adaptation and exaptation. Here we suggest that the concepts of adaptation and exaptation are universal, synergistic, and recursive and apply to small molecules such as metabolites, cofactors, and the building blocks of extant polymers. For example, adenosine has been extensively adapted and exapted throughout biological evolution. Chemical variants of adenosine that are products of adaptation include 2' deoxyadenosine in DNA and a wide array of modified forms in mRNAs, tRNAs, rRNAs, and viral RNAs. Adenosine and its variants have been extensively exapted for various functions, including informational polymers (RNA, DNA), energy storage (ATP), metabolism (e.g., coenzyme A), and signaling (cyclic AMP). According to Gould, Vrba, and Darwin, exaptation imposes a general constraint on interpretation of history and origins; because of exaptation, extant function should not be used to explain evolutionary history. While this notion is accepted in evolutionary biology, it can also guide the study of the chemical origins of life. We propose that (i) evolutionary theory is broadly applicable from the dawn of life to the present time from molecules to organisms, (ii) exaptation and adaptation were important and simultaneous processes, and (iii) robust origin of life models can be constructed without conflating extant utility with historical basis of origins.

Origin of life: protoribosome forms peptide bonds and links RNA and protein dominated worlds

Although the mode of action of the ribosomes, the multi-component universal effective protein-synthesis organelles, has been thoroughly explored, their mere appearance remained elusive. Our earlier comparative structural studies suggested that a universal internal small RNA pocket-like segment called by us the protoribosome, which is still embedded in the contemporary ribosome, is a vestige of the primordial ribosome. Herein, after constructing such pockets, we show using the "fragment reaction" and its analyses by MALDI-TOF and LC-MS mass spectrometry techniques, that several protoribosome constructs are indeed capable of mediating peptide-bond formation. These findings present strong evidence supporting our hypothesis on origin of life and on ribosome's construction, thus suggesting that the protoribosome may be the missing link between the RNA dominated world and the contemporary nucleic acids/proteins life.

Differential Oligomerization of Alpha versus Beta Amino Acids and Hydroxy Acids in Abiotic Proto-Peptide Synthesis Reactions

The origin of biopolymers is a central question in origins of life research. In extant life, proteins are coded linear polymers made of a fixed set of twenty alpha-L-amino acids. It is likely that the prebiotic forerunners of proteins, or protopeptides, were more heterogenous polymers with a greater diversity of building blocks and linkage stereochemistry. To investigate a possible chemical selection for alpha versus beta amino acids in abiotic polymerization reactions, we subjected mixtures of alpha and beta hydroxy and amino acids to single-step dry-down or wet-dry cycling conditions. The resulting model protopeptide mixtures were analyzed by a variety of analytical techniques, including mass spectrometry and NMR spectroscopy. We observed that amino acids typically exhibited a higher extent of polymerization in reactions that also contained alpha hydroxy acids over beta hydroxy acids, whereas the extent of polymerization by beta amino acids was higher compared to their alpha amino acid analogs. Our results suggest that a variety of heterogenous protopeptide backbones existed during the prebiotic epoch, and that selection towards alpha backbones occurred later as a result of polymer evolution.

Deep structural insights into RNA-binding disordered protein regions

Recent efforts to identify RNA binding proteins in various organisms and cellular contexts have yielded a large collection of proteins that are capable of RNA binding in the absence of conventional RNA recognition domains. Many of the recently identified RNA interaction motifs fall into intrinsically disordered protein regions (IDRs). While the recognition mode and specificity of globular RNA binding elements have been thoroughly investigated and described, much less is known about the way IDRs can recognize their RNA partners. Our aim was to summarize the current state of structural knowledge on the RNA binding modes of disordered protein regions and to propose a classification system based on their sequential and structural properties. Through a detailed structural analysis of the complexes that contain disordered protein regions binding to RNA, we found two major binding modes that represent different recognition strategies and, most likely, functions. We compared these examples with DNA binding disordered proteins and found key differences stemming from the nucleic acids as well as similar binding strategies, implying a broader substrate acceptance by these proteins. Due to the very limited number of known structures, we integrated molecular dynamics simulations in our study, whose results support the proposed structural preferences of specific RNA‐binding IDRs. To broaden the scope of our review, we included a brief analysis of RNA‐binding small molecules and compared their structural characteristics and RNA recognition strategies to the RNA‐binding IDRs.

This article is categorized under:

RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry

RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition

RNA Interactions with Proteins and Other Molecules > Small Molecule–RNA Interactions

Enhanced Ribozyme-Catalyzed Recombination and Oligonucleotide Assembly in Peptide-RNA Condensates

The ability of RNA to catalyze RNA ligation is critical to its central role in many prebiotic model scenarios, in particular the copying of information during self-replication. Prebiotically plausible ribozymes formed from short oligonucleotides can catalyze reversible RNA cleavage and ligation reactions, but harsh conditions or unusual scenarios are often required to promote folding and drive the reaction equilibrium towards ligation. Here, we demonstrate that ribozyme activity is greatly enhanced by charge-mediated phase separation with poly-L-lysine, which shifts the reaction equilibrium from cleavage in solution to ligation in peptide-RNA coaggregates and coacervates. This compartmentalization enables robust isothermal RNA assembly over a broad range of conditions, which can be leveraged to assemble long and complex RNAs from short fragments under mild conditions in the absence of exogenous activation chemistry, bridging the gap between pools of short oligomers and functional RNAs.

Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides

Interactions between RNA molecules and proteins are critical to many cellular processes and are implicated in various diseases. The RNA-peptide complexes are good model systems to probe the recognition mechanism of RNA by proteins. In this work, we report studies on the binding-unbinding process of a helical peptide from a viral RNA element using nonequilibrium molecular dynamics simulations. We explored the existence of various dissociation pathways with distinct free-energy profiles that reveal metastable states and distinct barriers to peptide dissociation. We also report the free-energy differences for each of the four pathways to be 96.47 ± 12.63, 96.1 ± 10.95, 91.83 ± 9.81, and 92 ± 11.32 kcal/mol. Based on the free-energy analysis, we further propose the preferred pathway and the mechanism of peptide dissociation. The preferred pathway is characterized by the formation of sequential hydrogen-bonding and salt-bridging interactions between several key arginine amino acids and the viral RNA nucleotides. Specifically, we identified one arginine amino acid (R8) of the peptide to play a significant role in the recognition mechanism of the peptide by the viral RNA molecule.

Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase

The extant complex proteins must have evolved from ancient short and simple ancestors. The double-ψ β-barrel (DPBB) is one of the oldest protein folds and conserved in various fundamental enzymes, such as the core domain of RNA polymerase. Here, by reverse engineering a modern DPBB domain, we reconstructed its plausible evolutionary pathway started by "interlacing homodimerization" of a half-size peptide, followed by gene duplication and fusion. Furthermore, by simplifying the amino acid repertoire of the peptide, we successfully created the DPBB fold with only seven amino acid types (Ala, Asp, Glu, Gly, Lys, Arg, and Val), which can be coded by only GNN and ARR (R = A or G) codons in the modern translation system. Thus, the DPBB fold could have been materialized by the early translation system and genetic code.

The microenvironment and pKa perturbation of aminoacyl-tRNA guided the selection of cationic amino acids

The proteinogenic lysine (Lys) and arginine (Arg) have multiple methylene groups between α-carbon and the terminal charged centre. Why nature did not select ornithine (Orn), 2,4-diamino butyric acid (Dab) and 2,3-diamino propionic acid (Dpr) with fewer methylene groups in the side chain remains an important question! The propensity of aminoacyl-tRNA (aa-tRNA) model substrates towards self-degradation via intramolecular lactamization was studied using UV spectroscopy and ¹H-NMR titration, which showed that Lys and Arg remain stable, and Orn and Dab cyclize to lactam. Hydrophobicity-assisted surface mediated model peptide formation highlighted that the microenvironment and pK_a perturbation led to poor regioselectivity (α-amine vs. terminal amine) in Dpr and other non-proteinogenic analogues. The α-selectivity became even poorer in the presence of phosphate, making them ill-suited for peptide synthesis. Superior regioselectivity of the Lys aa-tRNA model substrate suggests that the extra methylene bridge helped nature to separate the microenvironments of the α-amine and ε-amine to synthesize the peptide backbone.

Primitive selection of the fittest emerging through functional synergy in nucleopeptide networks

Many fundamental cellular and viral functions, including replication and translation, involve complex ensembles hosting synergistic activity between nucleic acids and proteins/peptides. There is ample evidence indicating that the chemical precursors of both nucleic acids and peptides could be efficiently formed in the prebiotic environment. Yet, studies on nonenzymatic replication, a central mechanism driving early chemical evolution, have focused largely on the activity of each class of these molecules separately. We show here that short nucleopeptide chimeras can replicate through autocatalytic and cross-catalytic processes, governed synergistically by the hybridization of the nucleobase motifs and the assembly propensity of the peptide segments. Unequal assembly-dependent replication induces clear selectivity toward the formation of a certain species within small networks of complementary nucleopeptides. The selectivity pattern may be influenced and indeed maximized to the point of almost extinction of the weakest replicator when the system is studied far from equilibrium and manipulated through changes in the physical (flow) and chemical (template and inhibition) conditions. We postulate that similar processes may have led to the emergence of the first functional nucleic-acid-peptide assemblies prior to the origin of life. Furthermore, spontaneous formation of related replicating complexes could potentially mark the initiation point for information transfer and rapid progression in complexity within primitive environments, which would have facilitated the development of a variety of functions found in extant biological assemblies.

'Whole Organism', Systems Biology, and Top-Down Criteria for Evaluating Scenarios for the Origin of Life

While most advances in the study of the origin of life on Earth (OoLoE) are piecemeal, tested against the laws of chemistry and physics, ultimately the goal is to develop an overall scenario for life's origin(s). However, the dimensionality of non-equilibrium chemical systems, from the range of possible boundary conditions and chemical interactions, renders the application of chemical and physical laws difficult. Here we outline a set of simple criteria for evaluating OoLoE scenarios. These include the need for containment, steady energy and material flows, and structured spatial heterogeneity from the outset. The Principle of Continuity, the fact that all life today was derived from first life, suggests favoring scenarios with fewer non-analog (not seen in life today) to analog (seen in life today) transitions in the inferred first biochemical pathways. Top-down data also indicate that a complex metabolism predated ribozymes and enzymes, and that full cellular autonomy and motility occurred post-LUCA. Using these criteria, we find the alkaline hydrothermal vent microchamber complex scenario with a late evolving exploitation of the natural occurring pH (or Na⁺ gradient) by ATP synthase the most compelling. However, there are as yet so many unknowns, we also advocate for the continued development of as many plausible scenarios as possible.

The Origin(s) of Cell(s): Pre-Darwinian Evolution from FUCAs to LUCA : To Carl Woese (1928-2012), for his Conceptual Breakthrough of Cellular Evolution

The coming of the Last Universal Cellular Ancestor (LUCA) was the singular watershed event in the making of the biotic world. If the coming of LUCA marked the crossing of the "Darwinian Threshold", then pre-LUCA evolution must have been Pre-Darwinian and at least partly non-Darwinian. But how did Pre-Darwinian evolution before LUCA actually operate? I broaden our understanding of the central mechanism of biological evolution (i.e., variation-selection-inheritance) and then extend this broadened understanding to its natural starting point: the origin(s) of the First Universal Cellular Ancestors (FUCAs) before LUCA. My hypothesis centers upon vesicles' making-and-remaking as variation and competition as selection. More specifically, I argue that vesicles' acquisition and merger, via breaking-and-repacking, proto-endocytosis, proto-endosymbiosis, and other similar processes had been a central force of both variation and selection in the pre-Darwinian epoch. These new perspectives shed important new light upon the origin of FUCAs and their subsequent evolution into LUCA.

In search of the RNA world on Mars

Advances in origins of life research and prebiotic chemistry suggest that life as we know it may have emerged from an earlier RNA World. However, it has been difficult to reconcile the conditions used in laboratory experiments with real-world geochemical environments that may have existed on the early Earth and hosted the origin(s) of life. This challenge is due to geologic resurfacing and recycling that have erased the overwhelming majority of the Earth's prebiotic history. We therefore propose that Mars, a planet frozen in time, comprised of many surfaces that have remained relatively unchanged since their formation > 4 Gya, is the best alternative to search for environments consistent with geochemical requirements imposed by the RNA world. In this study, we synthesize in situ and orbital observations of Mars and modeling of its early atmosphere into solutions containing a range of pHs and concentrations of prebiotically relevant metals (Fe²⁺ , Mg²⁺ , and Mn²⁺ ) spanning various candidate aqueous environments. We then experimentally determine RNA degradation kinetics due to metal-catalyzed hydrolysis (cleavage) and evaluate whether early Mars could have been permissive toward the accumulation of long-lived RNA polymers. Our results indicate that a Mg²⁺ -rich basalt sourcing metals to a slightly acidic (pH 5.4) environment mediates the slowest rates of RNA cleavage, though geologic evidence and basalt weathering models suggest aquifers on Mars would be near neutral (pH ~ 7). Moreover, the early onset of oxidizing conditions on Mars has major consequences regarding the availability of oxygen-sensitive metals (i.e., Fe²⁺ and Mn²⁺ ) due to increased RNA degradation rates and precipitation. Overall, (a) low pH decreases RNA cleavage at high metal concentrations; (b) acidic to neutral pH environments with Fe²⁺ or Mn²⁺ cleave more RNA than Mg²⁺ ; and (c) alkaline environments with Mg²⁺ dramatically cleaves more RNA while precipitates were observed for Fe²⁺ and Mn²⁺ .

Social Networking of Quasi-Species Consortia drive Virolution via Persistence

The emergence of cooperative quasi-species consortia (QS-C) thinking from the more accepted quasispecies equations of Manfred Eigen, provides a conceptual foundation from which concerted action of RNA agents can now be understood. As group membership becomes a basic criteria for the emergence of living systems, we also start to understand why the history and context of social RNA networks become crucial for survival and function. History and context of social RNA networks also lead to the emergence of a natural genetic code. Indeed, this QS-C thinking can also provide us with a transition point between the chemical world of RNA replicators and the living world of RNA agents that actively differentiate self from non-self and generate group identity with membership roles. Importantly the social force of a consortia to solve complex, multilevel problems also depend on using opposing and minority functions. The consortial action of social networks of RNA stem-loops subsequently lead to the evolution of cellular organisms representing a tree of life.

Helicase-like functions in phosphate loop containing beta-alpha polypeptides

The P-loop Walker A motif underlies hundreds of essential enzyme families that bind nucleotide triphosphates (NTPs) and mediate phosphoryl transfer (P-loop NTPases), including the earliest DNA/RNA helicases, translocases, and recombinases. What were the primordial precursors of these enzymes? Could these large and complex proteins emerge from simple polypeptides? Previously, we showed that P-loops embedded in simple βα repeat proteins bind NTPs but also, unexpectedly so, ssDNA and RNA. Here, we extend beyond the purely biophysical function of ligand binding to demonstrate rudimentary helicase-like activities. We further constructed simple 40-residue polypeptides comprising just one β-(P-loop)-α element. Despite their simplicity, these P-loop prototypes confer functions such as strand separation and exchange. Foremost, these polypeptides unwind dsDNA, and upon addition of NTPs, or inorganic polyphosphates, release the bound ssDNA strands to allow reformation of dsDNA. Binding kinetics and low-resolution structural analyses indicate that activity is mediated by oligomeric forms spanning from dimers to high-order assemblies. The latter are reminiscent of extant P-loop recombinases such as RecA. Overall, these P-loop prototypes compose a plausible description of the sequence, structure, and function of the earliest P-loop NTPases. They also indicate that multifunctionality and dynamic assembly were key in endowing short polypeptides with elaborate, evolutionarily relevant functions.