Recreating ancient metabolic pathways before enzymes

An ancestral fold reveals the evolutionary link between RNA polymerase and ribosomal proteins

Numerous molecular machines are required to drive the central dogma of molecular biology. However, the means by which these numerous proteins emerged in the early evolutionary stage of life remains enigmatic. Many of them possess small β-barrel folds with different topologies, represented by double-psi β-barrels (DPBBs) conserved in DNA and RNA polymerases, and similar but topologically distinct six-stranded β-barrel RIFT or five-stranded β-barrel folds such as OB and SH3 in ribosomal proteins. Here, we discover that the previously reconstructed ancient DPBB sequence could also adopt a β-barrel fold named Double-Zeta β-barrel (DZBB), as a metamorphic protein. The DZBB fold is not found in any modern protein, although its structure shares similarities with RIFT and OB. Indeed, DZBB could be transformed into them through simple engineering experiments. Furthermore, the OB designs could be further converted into SH3 by circular-permutation as previously predicted. These results indicate that these β-barrels diversified quickly from a common ancestor at the beginning of the central dogma evolution.

Major evolutionary transitions before cells: A journey from molecules to organisms

Basing on logical assumptions and necessary steps of complexification along biological evolution, we propose here an evolutionary path from molecules to cells presenting four ages and three major transitions. At the first age, the basic biomolecules were formed and become abundant. The first transition happened with the event of a chemical symbiosis between nucleic acids and peptides worlds, which marked the emergence of both life and the process of organic encoding. FUCA, the first living process, was composed of self-replicating RNAs linked to amino acids and capable to catalyze their binding. The second transition, from the age of FUCA to the age of progenotes, involved the duplication and recombination of proto-genomes, leading to specialization in protein production and the exploration of protein to metabolite interactions in the prebiotic soup. Enzymes and metabolic pathways were incorporated into biology from protobiotic reactions that occurred without chemical catalysts, step by step. Then, the fourth age brought origin of organisms and lineages, occurring when specific proteins capable to stackle together facilitated the formation of peptidic capsids. LUCA was constituted as a progenote capable to operate the basic metabolic functions of a cell, but still unable to interact with lipid molecules. We present evidence that the evolution of lipid interaction pathways occurred at least twice, with the development of bacterial-like and archaeal-like membranes. Also, data in literature suggest at least two paths for the emergence of DNA biosynthesis, allowing the stabilization of early life strategies in viruses, archaeas and bacterias. Two billion years later, the eukaryotes arouse, and after 1,5 billion years of evolution, they finally learn how to evolve multicellularity via tissue specialization.

Actomonas aquatica gen. nov., sp. nov., a marine lineage in the phylum Verrucomicrobiota with genetic potential for carbon and nitrogen fixation

A novel bacterial strain, designated WL0086T, was isolated from a marine sediment sample collected in Lianyungang city, Jiangsu province, PR China. This strain showed the highest 16S rRNA gene sequence similarity to Geminisphaera colitermitum TAV2T (92.7 %) of the family Opitutaceae, and all the unclassified cultured and uncultured isolates with similarities >95 % were from marine environments. Cells were Gram-stain-negative, aerobic, non-motile cocci with a size of 0.6-0.8 µm in diameter. Strain WL0086T was positive for both oxidase and catalase, and grew at 20-37 °C (optimum, 28 °C), with 1.5-11.0 % NaCl (w/v; optimum, 2.5-4.0 %) and at pH 5.0-9.0 (optimum, pH 7.0). The major polar lipid profile of strain WL0086T consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylcholine. The major isoprenoid quinone was menaquinone-7 and the predominant fatty acids were iso-C14 : 0, anteiso-C15 : 0, C16 : 0 and C16 : 1  ω9c. The complete genome consisted of a chromosome with 6 109 182 bp. The G+C content of genomic DNA was 64.0%. Results of phylogenomic analysis based on the 16S rRNA gene sequence and the whole genome suggested that strain WL0086T formed a distinct clade closely neighbouring the members of the family Opitutaceae. On the basis of phylogenetic, phenotypic, and chemotaxonomic evidences, strain WL0086T should represent a novel genus of the family Opitutaceae, for which the name Actomonas aquatica gen. nov., sp. nov. is proposed. The type strain is WL0086T (=MCCC 1K05844T=JCM 34677T=GDMCC 1.2411T).

Evolution at the Origins of Life?

The role of evolutionary theory at the origin of life is an extensively debated topic. The origin and early development of life is usually separated into a prebiotic phase and a protocellular phase, ultimately leading to the Last Universal Common Ancestor. Most likely, the Last Universal Common Ancestor was subject to Darwinian evolution, but the question remains to what extent Darwinian evolution applies to the prebiotic and protocellular phases. In this review, we reflect on the current status of evolutionary theory in origins of life research by bringing together philosophy of science, evolutionary biology, and empirical research in the origins field. We explore the various ways in which evolutionary theory has been extended beyond biology; we look at how these extensions apply to the prebiotic development of (proto)metabolism; and we investigate how the terminology from evolutionary theory is currently being employed in state-of-the-art origins of life research. In doing so, we identify some of the current obstacles to an evolutionary account of the origins of life, as well as open up new avenues of research.

Co-fermented milk beverage has better stability and contains more health-promoting amino acid metabolites than single-strain-fermented milk beverage over one-month storage

Few studies investigated the effects of co-fermentation with bifidobacteria on post-storage changes of probiotic fermented beverages (PFBs). Thus, this study compared the post-storage changes in physicochemical index and metabolomes of PFBs produced singly by Lacticaseibacillus paracasei PC-01 (PC-01) or in combination with Bifidobacterium adolescentis B8589 (B8589). No significant differences were observed in the pH, titratable acidity, and viable cell counts between the two PFBs over 30-day storage. However, adding B8589 not only increased the stability of PFB (based on evaluating differences in PFBs metabolomics), but also the contents of beneficial amino acid metabolites, including 4-hydroxystyrene, gamma-aminobutyric acid, N-acetyl-l-aspartic acid, d-alanyl-d-alanine, and l-malic acid, after storage. Our study showed that B8589 is preferred to single-strain fermentation by PC-01. This study supports the concept of using bifidobacteria as starter culture in PFB production.

Origin of life: Drawing the big picture

Trying to provide a broad overview about the origin of life in Earth, the most significant transitions of life before cells are listed and discussed. The current approach emphasizes the symbiotic relationships that emerged with life. We propose a rational, stepwise scenario for the origin of life that starts with the origin of the first biomolecules and steps forward until the origins of the first cells. Along this path, we aim to provide a brief, though comprehensive theoretical model that will consider the following steps: (i) how nucleotides and other biomolecules could be made prebiotically in specific prebiotic refuges; (ii) how the first molecules of RNAs were formed; (iii) how the proto-peptidyl transferase center was built by the concatenation of proto-tRNAs; (iv) how the ribosome and the genetic code could be structured; (v) how progenotes could live and reproduce as "naked" ribonucleoprotein molecules; (vi) how peptides started to bind molecules in the prebiotic soup allowing biochemical pathways to evolve from those bindings; (vii) how genomes got bigger by the symbiotic relationship of progenotes and lateral transference of genetic material; (viii) how the progenote LUCA has been formed by assembling most biochemical routes; (ix) how the first virion capsids probably emerged and evolved; (x) how phospholipid membranes emerged probably twice by the evolution of lipid-binding proteins; (xi) how DNA synthesis have been formed in parallel in Bacteria and Archaea; and, finally, (xii) how DNA-based cells of Bacteria and Archaeabacteria have been constituted. The picture provided is conjectural and present epistemological gaps. Future research will help to advance into the elucidation of gaps and confirmation/refutation of current statements.

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.

On the evolution of coenzyme biosynthesis

Covering: up to 2022The report provides a broad approach to deciphering the evolution of coenzyme biosynthetic pathways. Here, these various pathways are analyzed with respect to the coenzymes required for this purpose. Coenzymes whose biosynthesis relies on a large number of coenzyme-mediated reactions probably appeared on the scene at a later stage of biological evolution, whereas the biosyntheses of pyridoxal phosphate (PLP) and nicotinamide (NAD⁺) require little additional coenzymatic support and are therefore most likely very ancient biosynthetic pathways.

A Nonenzymatic Analog of Pyrimidine Nucleobase Biosynthesis

Metabolic theories for the origin of life posit that inorganic catalysts enabled self‐organized chemical precursors to the pathways of metabolism, including those that make genetic molecules. Recently, experiments showing nonenzymatic versions of a number of core metabolic pathways have started to support this idea. However, experimental demonstrations of nonenzymatic reaction sequences along the de novo ribonucleotide biosynthesis pathways are limited. Here we show that all three reactions of pyrimidine nucleobase biosynthesis that convert aspartate to orotate proceed at 60 °C without photochemistry under aqueous conditions in the presence of metals such as Cu²⁺ and Mn⁴⁺. Combining reactions into one‐pot variants is also possible. Life may not have invented pyrimidine nucleobase biosynthesis from scratch, but simply refined existing nonenzymatic reaction channels. This work is a first step towards uniting metabolic theories of life's origin with those centered around genetic molecules.

RNP-world: The ultimate essence of life is a ribonucleoprotein process

The fundamental essence of life is based on process of interaction between nucleic acids and proteins. In a prebiotic world, amino acids, peptides, ions, and other metabolites acted in protobiotic routes at the same time on which RNAs performed catalysis and self-replication. Nevertheless, it was only when nucleic acids and peptides started to interact together in an organized process that life emerged. First, the ignition was sparked with the formation of a Peptidyl Transferase Center (PTC), possibly by concatenation of proto-tRNAs. This molecule that would become the catalytic site of ribosomes started a process of self-organization that gave origin to a protoorganism named FUCA, a ribonucleic ribosomal-like apparatus capable to polymerize amino acids. In that sense, we review hypotheses about the origin and early evolution of the genetic code. Next, populations of open biological systems named progenotes were capable of accumulating and exchanging genetic material, producing the first genomes. Progenotes then evolved in two paths: some presented their own ribosomes and others used available ribosomes in the medium to translate their encoded information. At some point, two different types of organisms emerged from populations of progenotes: the ribosome-encoding organisms (cells) and the capsid-encoding organisms (viruses).

Computational Analysis of a Prebiotic Amino Acid Synthesis with Reference to Extant Codon-Amino Acid Relationships

Novel density functional theory calculations are presented regarding a mechanism for prebiotic amino acid synthesis from alpha-keto acids that was suggested to happen via catalysis by dinucleotide species. Our results were analysed with comparison to the original hypothesis (Copley et al., PNAS, 2005, 102, 4442–4447). It was shown that the keto acid–dinucleotide hypothesis for possible prebiotic amino acid synthesis was plausible based on an initial computational analysis, and details of the structures for the intermediates and transition states showed that there was wide scope for interactions between the keto acid and dinucleotide moieties that could affect the free energy profiles and lead to the required proto-metabolic selectivity.

Evolutionary Aspects of the Oxido-Reductive Network of Methylglyoxal

In the chemoautotrophic theory for the origin of life, offered as an alternative to broth theory, the archaic reductive citric acid cycle operating without enzymes is in the center. The non-enzymatic (methyl)glyoxalase pathway has been suggested to be the anaplerotic route for the reductive citric acid cycle. In the recent years, much has been learned about methylglyoxal, but its importance in the metabolic machinery is still uncovered. If methylglyoxal had been essential participant of the early stage of evolution, then it is a legitimate question whether it might have played a role in the early oxido-reduction network, too. Therefore, an oxido-reduction network of methylglyoxal that might have functioned under ancient circumstances without enzymes was constructed and analyzed by virtue of group contribution method. Taking methylglyoxal as input material, it turned out that the evolutionary value of reactions and biomolecules were not similar. Glycerol, glycerate, and tartonate, the output components, were conserved to different degrees. Although the tartonate route was similarly favorable from energetic point of view, its intermediates are almost not present in extant biochemistry. The presence of two carboxyl or aldehyde groups, or their combination in tricarbons of the constructed network seemed disadvantageous for selection, and the inductive effect, resulting in an asymmetry in electron cloud of chemicals, might have been important. The evolutionary role for cysteine, H₂S, and formaldehyde in the emergence of high-energy bonds in the form of thioesters and in Fe-S cluster formation as well as in imidazole synthesis was shown to bridge the gap between prebiotic chemistry and contemporary biochemistry. Overall, the ideas developed here represent an approach fitting to chemoautotrophic origin of life and implying to the role of methylglyoxal in triose formation. The proposed network is expected to have an impact upon how one may think of prebiological chemical processes on methylglyoxal, too. Finally, along the evolutionary time line, the network functioning without enzymes is situated between the formation of simple organic compounds and primeval cells, being closer to the former and well preceding the last common metabolic ancestor developed after primitive cells emerged.

Carbamoyl phosphate and its substitutes for the uracil synthesis in origins of life scenarios

The first step of pyrimidine synthesis along the orotate pathway is studied to test the hypothesis of geochemical continuity of protometabolic pathways at the origins of life. Carbamoyl phosphate (CP) is the first high-energy building block that intervenes in the in vivo synthesis of the uracil ring of UMP. Thus, the likelihood of its occurrence in prebiotic conditions is investigated herein. The evolution of carbamoyl phosphate in water and in ammonia aqueous solutions without enzymes was characterised using ATR-IR, ³¹P and ¹³C spectroscopies. Carbamoyl phosphate initially appears stable in water at ambient conditions before transforming to cyanate and carbamate/hydrogenocarbonate species within a matter of hours. Cyanate, less labile than CP, remains a potential carbamoylating agent. In the presence of ammonia, CP decomposition occurs more rapidly and generates urea. We conclude that CP is not a likely prebiotic reagent by itself. Alternatively, cyanate and urea may be more promising substitutes for CP, because they are both “energy-rich” (high free enthalpy molecules in aqueous solutions) and kinetically inert regarding hydrolysis. Energy-rich inorganic molecules such as trimetaphosphate or phosphoramidates were also explored for their suitability as sources of carbamoyl phosphate. Although these species did not generate CP or other carbamoylating agents, they exhibited energy transduction, specifically the formation of high-energy P–N bonds. Future efforts should aim to evaluate the role of carbamoylating agents in aspartate carbamoylation, which is the following reaction in the orotate pathway.

Chemical Basis of Carbon Fixation Autotrophic Paleometabolism

Abstract

On the basis of biomimetic, phylometabolic, and thermodynamic analysis of modern CO2 assimilation pathways, a paleophenotypic reconstruction of ancient autotrophic metabolism systems was carried out. As a chemical basis for CO2 fixation paleometabolism, metabolic networks capable of self-reproduction and evolution are considered, and the reversibility of the transformation reactions of its intermediates is the most important factor in self-development of this network. The substances of the C–H–O system, paragenetically associated with hydrocarbons, create a phase space, which is a set of universal intermediates of the autotrophic paleometabolism chemical network. The concept of two strategies for the origin and development of autotrophic carbon fixation paleometabolism in the oxidized (CO2) and reduced (CH4) redox regimes of degassing of the ancient Earth is proposed. It was shown that P, T, and the redox conditions of hydrothermal systems of the early Archean were favorable for the development of primary methanotrophic metabolism.

The Semi-Enzymatic Origin of Metabolic Pathways: Inferring a Very Early Stage of the Evolution of Life

The early evolution of life is a period with many important events with a lot of big and open questions. One of them is the evolution of metabolic pathways, which means the origin and assembly of enzymes that act together. The retrograde hypothesis was the first attempt to explain the origin and evolutionary history of metabolic pathways; Norman Horowitz developed this first significant hypothesis. This idea was followed by relevant proposals developed by Sam Granick, who proposed the "forward direction hypothesis," and then the successful idea of "Patchwork" assembly proposed independently by Martynas Yčas and Roy Jensen. Since then, a few new hypotheses were proposed; one of the most influential was made by Antonio Lazcano and Stanley Miller in the Journal Molecular Evolution, the "semi-enzymatic origin" of metabolic pathways. This article was cited more than 160 times, including in most papers published about the early evolution of metabolism, placing it as influential work in the field. The ideas proposed in this work and their effects on studying the origin and early evolution of life are analyzed.

A way to thioacetate esters compatible with non-oxidative prebiotic conditions

The centrality of pyruvate oxidative decarboxylation into acetyl-CoA in current biochemistry is a strong argument for proposing that a similar reaction have been necessary for the development of an effective protometabolism on the primitive Earth. However, such a decarboxylation requires the use of an oxidant and a catalyst, today enzymatic. Based on the mechanisms of the pyruvate dehydrogenase complex and pyruvate-ferredoxin oxidoreductase, we propose that the initial mechanism involved disulfides and occurred via radicals. A first disulfide is obtained by reacting glyoxylate with hydrogen sulfide. It is then possible to produce a wide variety of other disulfides by exchange reactions. When reacted with pyruvate under UV light they give thioesters. This process requires no oxidant and is therefore compatible with what is known of the redox conditions of the early Earth. Neither does it require any catalyst. It could be the first way to acetyl thioesters, a way that was later improved by the introduction of catalysts, first minerals, then enzymes.

Nonenzymatic Metabolic Reactions and Life's Origins

Prebiotic chemistry aims to explain how the biochemistry of life as we know it came to be. Most efforts in this area have focused on provisioning compounds of importance to life by multistep synthetic routes that do not resemble biochemistry. However, gaining insight into why core metabolism uses the molecules, reactions, pathways, and overall organization that it does requires us to consider molecules not only as synthetic end goals. Equally important are the dynamic processes that build them up and break them down. This perspective has led many researchers to the hypothesis that the first stage of the origin of life began with the onset of a primitive nonenzymatic version of metabolism, initially catalyzed by naturally occurring minerals and metal ions. This view of life's origins has come to be known as "metabolism first". Continuity with modern metabolism would require a primitive version of metabolism to build and break down ketoacids, sugars, amino acids, and ribonucleotides in much the same way as the pathways that do it today. This review discusses metabolic pathways of relevance to the origin of life in a manner accessible to chemists, and summarizes experiments suggesting several pathways might have their roots in prebiotic chemistry. Finally, key remaining milestones for the protometabolic hypothesis are highlighted.

Twenty Years of "Lipid World": A Fertile Partnership with David Deamer

"The Lipid World" was published in 2001, stemming from a highly effective collaboration with David Deamer during a sabbatical year 20 years ago at the Weizmann Institute of Science in Israel. The present review paper highlights the benefits of this scientific interaction and assesses the impact of the lipid world paper on the present understanding of the possible roles of amphiphiles and their assemblies in the origin of life. The lipid world is defined as a putative stage in the progression towards life's origin, during which diverse amphiphiles or other spontaneously aggregating small molecules could have concurrently played multiple key roles, including compartment formation, the appearance of mutually catalytic networks, molecular information processing, and the rise of collective self-reproduction and compositional inheritance. This review brings back into a broader perspective some key points originally made in the lipid world paper, stressing the distinction between the widely accepted role of lipids in forming compartments and their expanded capacities as delineated above. In the light of recent advancements, we discussed the topical relevance of the lipid worldview as an alternative to broadly accepted scenarios, and the need for further experimental and computer-based validation of the feasibility and implications of the individual attributes of this point of view. Finally, we point to possible avenues for exploring transition paths from small molecule-based noncovalent structures to more complex biopolymer-containing proto-cellular systems.

Provisioning the origin and early evolution of life

There is a lot of controversy in the origin and early evolution of life field, but most people agree that at the advent of genetically coded protein synthesis, cells must have had access to ribonucleotides, amino acids, lipids and some sort of energy source. However, the provenance of these materials is a contentious issue — did early life obtain its building blocks prefabricated from the environment, or did it synthesise them from feedstocks such as CO₂ and N₂? In the first case, synthesis conditions need not have been compatible with life and any kind of reaction network that furnished the building blocks — and not much else — could have provisioned the subsequent origin and early evolution of life. In the second case, synthesis must have been under life-compatible conditions, with the reaction network either along the same lines as extant biology or along different ones. On the basis of experimental evidence, we will argue in favour of prefabrication and against synthesis by life in its nascent state, especially synthesis that resembles extant biosynthesis, which we suggest would have been well-nigh impossible without biological catalysts.