Enhanced synthesis of alkyl amino acids in Miller's 1958 H2S experiment

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.

Decoding viruses: An alternative perspective on their history, origins and role in nature

This article provides an alternative perspective on viruses, exploring their origins, ecology, and evolution. Viruses are recognized as the most prevalent biological entities on Earth, permeating nearly all environments and forming the virosphere-a significant biological layer. They play a crucial role in regulating bacterial populations within ecosystems and holobionts, influencing microbial communities and nutrient recycling. Viruses are also key drivers of molecular evolution, actively participating in the maintenance and regulation of ecosystems and cellular organisms. Many eukaryotic genomes contain genomic elements with viral origins, which contribute to organismal equilibrium and fitness. Viruses are involved in the generation of species-specific orphan genes, facilitating adaptation and the development of unique traits in biological lineages. They have been implicated in the formation of vital structures like the eukaryotic nucleus and the mammalian placenta. The presence of virus-specific genes absent in cellular organisms suggests that viruses may pre-date cellular life. Like progenotes, viruses are ribonucleoprotein entities with simpler capsid architectures compared to proteolipidic membranes. This article presents a comprehensive scenario describing major transitions in prebiotic evolution and proposes that viruses emerged prior to the Last Universal Common Ancestor (LUCA) during the progenote era. However, it is important to note that viruses do not form a monophyletic clade, and many viral taxonomic groups originated more recently as reductions of cellular structures. Thus, viral architecture should be seen as an ancient and evolutionarily stable strategy adopted by biological systems. The goal of this article is to reshape perceptions of viruses, highlighting their multifaceted significance in the complex tapestry of life and fostering a deeper understanding of their origins, ecological impact, and evolutionary dynamics.

Methyl Metabolism and the Clock: An Ancient Story With New Perspectives

Methylation, that is, the transfer or synthesis of a –CH₃ group onto a target molecule, is a pervasive biochemical modification found in organisms from bacteria to humans. In mammals, a complex metabolic pathway powered by the essential nutrients vitamin B9 and B12, methionine and choline, synthesizes S-adenosylmethionine, the methyl donor in the methylation of nucleic acids, proteins, fatty acids, and small molecules by over 200 substrate-specific methyltransferases described so far in humans. Methylations not only play a key role in scenarios for the origin and evolution of life, but they remain essential for the development and physiology of organisms alive today, and methylation deficiencies contribute to the etiology of many pathologies. The methylation of histones and DNA is important for circadian rhythms in many organisms, and global inhibition of methyl metabolism similarly affects biological rhythms in prokaryotes and eukaryotes. These observations, together with various pieces of evidence scattered in the literature on circadian gene expression and metabolism, indicate a close mutual interdependence between biological rhythms and methyl metabolism that may originate from prebiotic chemistry. This perspective first proposes an abiogenetic scenario for rhythmic methylations and then outlines mammalian methyl metabolism, before reanalyzing previously published data to draw a tentative map of its profound connections with the circadian clock.

Astrochemical Pathways to Complex Organic and Prebiotic Molecules: Experimental Perspectives for In Situ Solid-State Studies

A deep understanding of the origin of life requires the physical, chemical, and biological study of prebiotic systems and the comprehension of the mechanisms underlying their evolutionary steps. In this context, great attention is paid to the class of interstellar molecules known as "Complex Organic Molecules" (COMs), considered as possible precursors of prebiotic species. Although COMs have already been detected in different astrophysical environments (such as interstellar clouds, protostars, and protoplanetary disks) and in comets, the physical-chemical mechanisms underlying their formation are not yet fully understood. In this framework, a unique contribution comes from laboratory experiments specifically designed to mimic the conditions found in space. We present a review of experimental studies on the formation and evolution of COMs in the solid state, i.e., within ices of astrophysical interest, devoting special attention to the in situ detection and analysis techniques commonly used in laboratory astrochemistry. We discuss their main strengths and weaknesses and provide a perspective view on novel techniques, which may help in overcoming the current experimental challenges.

Are disulfide bonds resilient to double ionization? Insights from coincidence spectroscopy and ab initio calculations

Disulfide bonds (-S-S-) are commonly present in biomolecules and have also been detected in astrophysical environments. In this work, the stability of the disulfide bond towards double ionization is investigated using quantum chemical calculations and photoelectron photoion photoion coincidence (PEPIPICO) spectroscopy measurements on the prototype dimethyl disulfide (CH3SSCH3, DMDS) molecule. The experiments were performed using high energy synchrotron radiation photons before (2465.0 eV) and at (2470.9 eV) the first sigma resonance around the S 1s edge. We applied the multivariate normal distribution analysis to identify the most plausible ionic fragmentation mechanisms from the doubly ionized DMDS. By mapping the minimum energy structures on the dicationic C2H6S2 2+ potential energy surface, we show that disulfide bonds are only present in high-lying isomers, in contrast to their analogous neutral systems. Our results also indicate that the number of fragment ions containing a disulfide bond for both photon energies is negligible. Taken together, our results reveal that the disulfide bond is severely damaged as a consequence of sulfur core-shell ionization processes, due to the lowering of its thermodynamic stability in multiply-charged systems.

New insights into prebiotic chemistry from Stanley Miller's spark discharge experiments

1953 was a banner year for biological chemistry: The double helix structure of DNA was published by Watson and Crick, Sanger's group announced the first amino acid sequence of a protein (insulin) and the synthesis of key biomolecules using simulated primordial Earth conditions has demonstrated by Miller. Miller's studies in particular transformed the study of the origin of life into a respectable field of inquiry and established the basis of prebiotic chemistry, a field of research that investigates how the components of life as we know it can be formed in a variety of cosmogeochemical environments. In this review, I cover the continued advances in prebiotic syntheses that Miller's pioneering work has inspired. The main focus is on recent state-of-the-art analyses carried out on archived samples of Miller's original experiments, some of which had never before been analyzed, discovered in his laboratory material just before his death in May 2007. One experiment utilized a reducing gas mixture and an apparatus configuration (referred to here as the "volcanic" apparatus) that could represent a water-rich volcanic eruption accompanied by lightning. Another included H(2)S as a component of the reducing gas mixture. Compared to the limited number of amino acids Miller identified, these new analyses have found that over 40 different amino acids and amines were synthesized, demonstrating the potential robust formation of important biologic compounds under possible cosmogeochemical conditions. These experiments are suggested to simulate long-lived volcanic island arc systems, an environment that could have provided a stable environment for some of the processes thought to be involved in chemical evolution and the origin of life. Some of the alternatives to the Miller-based prebiotic synthesis and the "primordial soup" paradigm are evaluated in the context of their relevance under plausible planetary conditions.