Open questions in origin of life: experimental studies on the origin of nucleic acids and proteins with specific and functional sequences by a chemical synthetic biology approach

Prebiotic Peptide Synthesis: How Did Longest Peptide Appear?

The origin of proteins is a fundamental question in the study of the origin of life. Peptides, as the building blocks of proteins, necessarily preceded the first proteins in prebiotic chemical evolution. Prebiotic peptides may have also played crucial roles in early life's evolution, contributing to self-catalysis, interacting with nucleic acids, and stabilizing primitive cell compartments. Longer and more complicated prebiotic peptides often have greater structural flexibility and functional potential to support the emergence and evolution of early life. Since the Miller-Urey experiment demonstrated that amino acids can be synthesized in a prebiotic manner, the prebiotic synthesis route of peptides has garnered increasing attention from researchers. However, it is difficult for amino acids to condense into peptides in aqueous solutions spontaneously. Over the past few decades, researchers have explored various routes of prebiotic peptide synthesis in the plausible prebiotic Earth environment, such as thermal polymerization, clay mineral catalysis, wet-dry cycles, condensing agents, and lipid-mediated. This paper reviews advancements in prebiotic peptide synthesis research and discusses the conditions that may have facilitated the emergence of longer peptides.

The evolutionary arch of bioenergetics from prebiotic mechanisms to the emergence of a cellular respiratory chain

This article proposes an evolutionary trajectory for the development of biological energy producing systems. Six main stages of energy producing system evolution are described, from early evolutionary pyrite-pulled mechanism through the Last Universal Common Ancestor (LUCA) to contemporary systems. We define the Last Pure Chemical Entity (LPCE) as the last completely non-enzymatic entity. LPCE could have had some life-like properties, but lacked genetic information carriers, thus showed greater instability and environmental dependence than LUCA. A double bubble model is proposed for compartmentalization and cellularization as a prerequisite to both highly efficient protein synthesis and transmembrane ion-gradient. The article finds that although LUCA predominantly functioned anaerobically, it was a non-exclusive anaerobe, and sulfur dominated metabolism preceded phosphate dominated one.

A Bayesian Analysis of the Probability of the Origin of Life Per Site Conducive to Abiogenesis

The emergence of life from nonlife, or abiogenesis, remains a fundamental question in scientific inquiry. In this article, we investigate the probability of the origin of life (per conducive site) by leveraging insights from Earth's environments. If life originated endogenously on Earth, its existence is indeed endowed with informative value, although the interpretation of the attendant significance hinges critically upon prior assumptions. By adopting a Bayesian framework, for an agnostic prior, we establish a direct connection between the number of potential locations for abiogenesis on Earth and the probability of life's emergence per site. Our findings suggest that constraints on the availability of suitable environments for the origin(s) of life on Earth may offer valuable insights into the probability of abiogenesis and the frequency of life in the universe.

Additive and Emergent Catalytic Properties of Dimeric Unnatural Amino Acid Derivatives: Aldol and Conjugate Additions

Different densely substituted L- and D-proline esters were prepared by asymmetric (3+2) cycloaddition reactions catalyzed by conveniently selected EhuPhos chiral ligands. The γ-nitro-2-alkoxycarbonyl pyrrolidines thus obtained in either their endo or exo forms were functionalized and coupled to yield the corresponding γ-dipeptides. The catalytic properties of these latter dimers were examined using aldol and conjugate additions as case studies. When aldol reactions were analyzed, an additive behavior in terms of stereocontrol was observed on going from the monomers to the dimers. In contrast, in the case of the conjugate additions between ketones and nitroalkenes, the monomers did not catalyze this reaction, whereas the different γ-dipeptides promoted the formation of the corresponding Michael adducts. Therefore, in this latter case emergent catalytic properties were observed for these novel γ-dipeptides based on unnatural proline derivatives. Under certain conditions stoichiometric amounts of ketone, acid and nitroalkene), formation of N-acyloxy-2-oxooctahydro-1H-indoles was observed.

In the Beginning was a Mutualism - On the Origin of Translation

The origin of translation is critical for understanding the evolution of life, including the origins of life. The canonical genetic code is one of the most dominant aspects of life on this planet, while the origin of heredity is one of the key evolutionary transitions in living world. Why the translation apparatus evolved is one of the enduring mysteries of molecular biology. Assuming the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity, we propose and discuss possible mechanisms, basic aspects of the emergence and subsequent molecular evolution of translation and ribosomes, as well as enzymes as we know them today. It is possible, in this sense, to view the ribosome as a digital-to-analogue information converter. The proposed mechanism is based on the abilities and tendencies of short RNA and polypeptides to fold and to catalyse biochemical reactions. The proposed mechanism is in concordance with the hypothesis of a possible chemical co-evolution of RNA and proteins in the origin of the genetic code or even more generally at the early evolution of life on Earth. The possible abundance and availability of monomers at prebiotic conditions are considered in the mechanism. The hypothesis that early polypeptides were folding on the RNA scaffold is also considered and mutualism in molecular evolutionary development of RNA and peptides is favoured.

Evolutionary convergence in the biosyntheses of the imidazole moieties of histidine and purines

Background

The imidazole group is an ubiquitous chemical motif present in several key types of biomolecules. It is a structural moiety of purines, and plays a central role in biological catalysis as part of the side-chain of histidine, the amino acid most frequently found in the catalytic site of enzymes. Histidine biosynthesis starts with both ATP and the pentose phosphoribosyl pyrophosphate (PRPP), which is also the precursor for the de novo synthesis of purines. These two anabolic pathways are also connected by the imidazole intermediate 5-aminoimidazole-4-carboxamide ribotide (AICAR), which is synthesized in both routes but used only in purine biosynthesis. Rather surprisingly, the imidazole moieties of histidine and purines are synthesized by different, non-homologous enzymes. As discussed here, this phenomenon can be understood as a case of functional molecular convergence.

Results

In this work, we analyze these polyphyletic processes and argue that the independent origin of the corresponding enzymes is best explained by the differences in the function of each of the molecules to which the imidazole moiety is attached. Since the imidazole present in histidine is a catalytic moiety, its chemical arrangement allows it to act as an acid or a base. On the contrary, the de novo biosynthesis of purines starts with an activated ribose and all the successive intermediates are ribotides, with the key β-glycosidic bondage joining the ribose and the imidazole moiety. This prevents purine ribonucleotides to exhibit any imidazole-dependent catalytic activity, and may have been the critical trait for the evolution of two separate imidazole-synthesizing-enzymes. We also suggest that, in evolutionary terms, the biosynthesis of purines predated that of histidine.

Conclusions

As reviewed here, other biosynthetic routes for imidazole molecules are also found in extant metabolism, including the autocatalytic cyclization that occurs during the formation of creatinine from creatine phosphate, as well as the internal cyclization of the Ala-Ser-Gly motif of some members of the ammonia-lyase and aminomutase families, that lead to the MIO cofactor. The diversity of imidazole-synthesizing pathways highlights the biological significance of this key chemical group, whose biosyntheses evolved independently several times.

Can an Imidazole Be Formed from an Alanyl-Seryl-Glycine Tripeptide under Possible Prebiotic Conditions?

The five-membered heterocyclic imidazole group, which is an essential component of purines, histidine and many cofactors, has been abiotically synthesized in different model experiments that attempt to simulate the prebiotic environment. The evolutionary significance of imidazoles is highlighted not only by its presence in nucleic acid components and in histidine, but also by experimental reports of its ability to restore the catalytic activity of ribozymes. However, as of today there are no reports of histidine in carbonaceous chondrites, and although the abiotic synthesis of His reported by Shen et al. (1987, 1990a) proceeds via an Amadori rearrangement, like in the biosynthesis of histidine, neither the reactants nor the conditions are truly prebiotic. Based on the autocatalytic biosynthesis of 4-methylidene-imidazole-one (MIO), a cofactor of some members of the amino acid aromatic ammonia-lyases and aminomutases, which occur via the self-condensation of a simple Ala-Ser-Gly motif within the sequence of the enzymes, we propose a possible prebiotic synthesis of an imidazolide.

Surveying the sequence diversity of model prebiotic peptides by mass spectrometry

The rise of peptides with secondary structures and functions would have been a key step in the chemical evolution which led to life. As with modern biology, amino acid sequence would have been a primary determinant of peptide structure and activity in an origins-of-life scenario. It is a commonly held hypothesis that unique functional sequences would have emerged from a diverse soup of proto-peptides, yet there is a lack of experimental data in support of this. Whereas the majority of studies in the field focus on peptides containing only one or two types of amino acids, here we used modern mass spectrometry (MS)-based techniques to separate and sequence de novo proto-peptides containing broader combinations of prebiotically plausible monomers. Using a dry-wet environmental cycling protocol, hundreds of proto-peptide sequences were formed over a mere 4 d of reaction. Sequence homology diagrams were constructed to compare experimental and theoretical sequence spaces of tetrameric proto-peptides. MS-based analyses such as this will be increasingly necessary as origins-of-life researchers move toward systems-level investigations of prebiotic chemistry.

Flexible Proteins at the Origin of Life

Almost all modern proteins possess well-defined, relatively rigid scaffolds that provide structural preorganization for desired functions. Such scaffolds require the sufficient length of a polypeptide chain and extensive evolutionary optimization. How ancestral proteins attained functionality, even though they were most likely markedly smaller than their contemporary descendants, remains a major, unresolved question in the origin of life. On the basis of evidence from experiments and computer simulations, we argue that at least some of the earliest water-soluble and membrane proteins were markedly more flexible than their modern counterparts. As an example, we consider a small, evolved in vitro ligase, based on a novel architecture that may be the archetype of primordial enzymes. The protein does not contain a hydrophobic core or conventional elements of the secondary structure characteristic of modern water-soluble proteins, but instead is built of a flexible, catalytic loop supported by a small hydrophilic core containing zinc atoms. It appears that disorder in the polypeptide chain imparts robustness to mutations in the protein core. Simple ion channels, likely the earliest membrane protein assemblies, could also be quite flexible, but still retain their functionality, again in contrast to their modern descendants. This is demonstrated in the example of antiamoebin, which can serve as a useful model of small peptides forming ancestral ion channels. Common features of the earliest, functional protein architectures discussed here include not only their flexibility, but also a low level of evolutionary optimization and heterogeneity in amino acid composition and, possibly, the type of peptide bonds in the protein backbone.

Engineering genetic circuit interactions within and between synthetic minimal cells

Genetic circuits and reaction cascades are of great importance for synthetic biology, biochemistry and bioengineering. An open question is how to maximize the modularity of their design to enable the integration of different reaction networks and to optimize their scalability and flexibility. One option is encapsulation within liposomes, which enables chemical reactions to proceed in well-isolated environments. Here we adapt liposome encapsulation to enable the modular, controlled compartmentalization of genetic circuits and cascades. We demonstrate that it is possible to engineer genetic circuit-containing synthetic minimal cells (synells) to contain multiple-part genetic cascades, and that these cascades can be controlled by external signals as well as inter-liposomal communication without crosstalk. We also show that liposomes that contain different cascades can be fused in a controlled way so that the products of incompatible reactions can be brought together. Synells thus enable a more modular creation of synthetic biology cascades, an essential step towards their ultimate programmability.

Small and Random Peptides: An Unexplored Reservoir of Potentially Functional Primitive Organocatalysts. The Case of Seryl-Histidine

Catalysis is an essential feature of living systems biochemistry, and probably, it played a key role in primordial times, helping to produce more complex molecules from simple ones. However, enzymes, the biocatalysts par excellence, were not available in such an ancient context, and so, instead, small molecule catalysis (organocatalysis) may have occurred. The best candidates for the role of primitive organocatalysts are amino acids and short random peptides, which are believed to have been available in an early period on Earth. In this review, we discuss the occurrence of primordial organocatalysts in the form of peptides, in particular commenting on reports about seryl-histidine dipeptide, which have recently been investigated. Starting from this specific case, we also mention a peptide fragment condensation scenario, as well as other potential roles of peptides in primordial times. The review actually aims to stimulate further investigation on an unexplored field of research, namely one that specifically looks at the catalytic activity of small random peptides with respect to reactions relevant to prebiotic chemistry and early chemical evolution.

Origin of Life and the Phosphate Transfer Catalyst

In this paper, we revisit several issues relevant to origin-of-life research and propose a Phosphate Transfer Catalyst hypothesis that furthers our understanding of some of the key events in prebiotic chemical evolution. In the Phosphate Transfer Catalyst hypothesis, we assume the existence of hypothetical metallopeptides with phosphate transfer activity that use abundant polyphosphates as both substrates and energy sources. Nonspecific catalysis by this phosphate transfer catalyst would provide a variety of different products such as phosphoryl amino acids, nucleosides, polyphosphate nucleotides, nucleic acids, and aminoacylated nucleic acids. Moreover, being an autocatalytic set and metabolic driver at the same time, it could possibly replicate itself and produce a collective system of two polymerases; a nucleic acid able to catalyze peptide bond formation and a peptide able to polymerize nucleic acids. The genetic code starts at first as a system that reduces the energy barrier by bringing substrates (2'/3' aminoacyl-nucleotides) together, an ancestral form of the catalysis performed by modern ribosomes. Key Words: Origin of life-Prebiotic chemistry-Catalysis-Nucleic acids. Astrobiology 17, 277-285.

CPe-III-S Metabolism in Vitro and in Vivo and Molecular Simulation of Its Metabolites Using a p53-R273H Mutant

It was previously found that CPe-III-S, synthesized according to the chickpea peptide CPe-III (RQSHFANAQP), exhibited an antiproliferative effect. The aim of this study was to investigate the antiproliferative mechanism of CPe-III-S. CPe-III-S was treated by pepsin and trypsin in a simulated gastrointestinal digestion environment as well as in an animal experiment. With HPLC-ESI-MS analysis, three peptide fragments of Ser-His, His-Phe, and Ala-Asn-Ala-Gln were identified. Ser-His was the only common product from both in vitro and in vivo environments. The specific bindings between three peptides and p53-R273H were performed by molecular docking, and the molecular dynamic simulation between Ser-His and p53-R273H revealed the stability of the binding complex. The binding free energy of the complex was -12.56 ± 1.03 kcal/mol with a reliable hydrogen bond between the ligand and Thr284 of p53. Ser-His may restore mutant p53-R273H activity or inhibit its binding with a downstream signal. This metabolite is a potential anticancer factor for suppressing cell proliferation.

Synergism and mutualism in non-enzymatic RNA polymerization

The link between non-enzymatic RNA polymerization and RNA self-replication is a key step towards the "RNA world" and still far from being solved, despite extensive research. Clay minerals, lipids and, more recently, peptides were found to catalyze the non-enzymatic synthesis of RNA oligomers. Herein, a review of the main models for the formation of the first RNA polymers is presented in such a way as to emphasize the cooperation between life's building blocks in their emergence and evolution. A logical outcome of the previous results is a combination of these models, in which RNA polymerization might have been catalyzed cooperatively by clays, lipids and peptides in one multi-component prebiotic soup. The resulting RNAs and oligopeptides might have mutualistically evolved towards functional RNAs and catalytic peptides, preceding the first RNA replication, thus supporting an RNA-peptide world. The investigation of such a system is a formidable challenge, given its complexity deriving from a tremendously large number of reactants and innumerable products. A rudimentary experimental design is outlined, which could be used in an initial attempt to study a quaternary component system.