Iron: Life's primeval transition metal

Modern life requires many different metal ions, which enable diverse biochemical functions. It is commonly assumed that metal ions' environmental availabilities controlled the evolution of early life. We argue that evolution can only explore the chemistry that life encounters, and fortuitous chemical interactions between metal ions and biological compounds can only be selected for if they first occur sufficiently frequently. We calculated maximal transition metal ion concentrations in the ancient ocean, determining that the amounts of biologically important transition metal ions were orders of magnitude lower than ferrous iron. Under such conditions, primitive bioligands would predominantly interact with Fe(II). While interactions with other metals in certain environments may have provided evolutionary opportunities, the biochemical capacities of Fe(II), Fe-S clusters, or the plentiful magnesium and calcium could have satisfied all functions needed by early life. Primitive organisms could have used Fe(II) exclusively for their transition metal ion requirements.

Prebiotic thiol-catalyzed thioamide bond formation

Thioamide bonds are important intermediates in prebiotic chemistry. In cyanosulfidic prebiotic chemistry, they serve as crucial intermediates in the pathways that lead to the formation of many important biomolecules (e.g., amino acids). They can also serve as purine and pyrimidine precursors, the two classes of heterocycle employed in genetic molecules. Despite their importance, the formation of thioamide bonds from nitriles under prebiotic conditions has required large excesses of sulfide or compounds with unknown prebiotic sources. Here, we describe the thiol-catalyzed formation of thioamide bonds from nitriles. We show that the formation of the simplest of these compounds, thioformamide, forms readily in spark-discharge experiments from hydrogen cyanide, sulfide, and a methanethiol catalyst, suggesting potential accumulation on early Earth. Lastly, we demonstrate that thioformamide has a Gibbs energy of hydrolysis ( Δ G r ∘ ) comparable to other energy-currencies on early Earth such as pyrophosphate and thioester bonds. Overall, our findings imply that thioamides might have been abundant on early Earth and served a variety of functions during chemical evolution.

Chapter 4: A Geological and Chemical Context for the Origins of Life on Early Earth

Within the first billion years of Earth's history, the planet transformed from a hot, barren, and inhospitable landscape to an environment conducive to the emergence and persistence of life. This chapter will review the state of knowledge concerning early Earth's (Hadean/Eoarchean) geochemical environment, including the origin and composition of the planet's moon, crust, oceans, atmosphere, and organic content. It will also discuss abiotic geochemical cycling of the CHONPS elements and how these species could have been converted to biologically relevant building blocks, polymers, and chemical networks. Proposed environments for abiogenesis events are also described and evaluated. An understanding of the geochemical processes under which life may have emerged can better inform our assessment of the habitability of other worlds, the potential complexity that abiotic chemistry can achieve (which has implications for putative biosignatures), and the possibility for biochemistries that are vastly different from those on Earth.

Chapter 1: The Astrobiology Primer 3.0

The Astrobiology Primer 3.0 (ABP3.0) is a concise introduction to the field of astrobiology for students and others who are new to the field of astrobiology. It provides an entry into the broader materials in this supplementary issue of Astrobiology and an overview of the investigations and driving hypotheses that make up this interdisciplinary field. The content of this chapter was adapted from the other 10 articles in this supplementary issue and thus represents the contribution of all the authors who worked on these introductory articles. The content of this chapter is not exhaustive and represents the topics that the authors found to be the most important and compelling in a dynamic and changing field.

One-Pot De Novo Synthesis of [4Fe-4S] Proteins Using a Recombinant SUF System under Aerobic Conditions

Fe-S clusters are essential cofactors mediating electron transfer in respiratory and metabolic networks. However, obtaining active [4Fe-4S] proteins with heterologous expression is challenging due to (i) the requirements for [4Fe-4S] cluster assembly, (ii) the O2 lability of [4Fe-4S] clusters, and (iii) copurification of undesired proteins (e.g., ferredoxins). Here, we established a facile and efficient protocol to express mature [4Fe-4S] proteins in the PURE system under aerobic conditions. An enzyme aconitase and thermophilic ferredoxin were selected as model [4Fe-4S] proteins for functional verification. We first reconstituted the SUF system in vitro via a stepwise manner using the recombinant SUF subunits (SufABCDSE) individually purified from E. coli. Later, the incorporation of recombinant SUF helper proteins into the PURE system enabled mRNA translation-coupled [4Fe-4S] cluster assembly under the O2-depleted conditions. To overcome the O2 lability of [4Fe-4S] Fe-S clusters, an O2-scavenging enzyme cascade was incorporated, which begins with formate oxidation by formate dehydrogenase for NADH regeneration. Later, NADH is consumed by flavin reductase for FADH2 regeneration. Finally, bifunctional flavin reductase, along with catalase, removes O2 from the reaction while supplying FADH2 to the SufBC2D complex. These amendments enabled a one-pot, two-step synthesis of mature [4Fe-4S] proteins under aerobic conditions, yielding holo-aconitase with a maximum concentration of ∼0.15 mg/mL. This renovated system greatly expands the potential of the PURE system, paving the way for the future reconstruction of redox-active synthetic cells and enhanced cell-free biocatalysis.

Interaction between Cu and Thiols of Biological and Environmental Importance: Case Study Using Combined Spectrophotometric/Bathocuproine Sulfonate Disodium Salt Hydrate (BCS) Assay

Considering the biological and ecological importance of Cu-thiol interactions and the discrepancies in previous research, this study focuses on Cu interactions with biologically and ecologically relevant thiols: glutathione (GSH), L-cysteine (L-cys), 3-mercaptopropionic acid (MPA), and thioacetic acid (TAA) in aqueous solution. The addition of Cu(II) to a thiol-containing solution led to a rapid reduction of Cu(II) and the formation of a Cu(I)-thiol complex. The mechanism of Cu(II) reduction and Cu(I) complex formation as well as the kinetics of Cu(I) oxidation strongly depend on the structural properties of the individual thiols investigated. The reducing power of the investigated thiols can be summarized as follows: L-cys ≅ GSH > MPA > TAA. The reaction order, with respect to Cu(I) oxidation, also changes over the time of the reaction course. The deviation of the reaction kinetics from the first order with respect to Cu(I) in the later stages of the reaction course can be attributed to a Fenton-like reaction occurring under low thiol concentration conditions. At high Cu:thiol ratios, in the case of GSH, L-cys, and MPA, the early stage of the reaction course is characterized by high Cu(I) stability, most likely as a result of Cu(I) complexation by the thiols present in excess in the reaction mixture.

Investigation of thiol compounds (L-cysteine, thioacetic acid and ethanethiol) with V(V) and V(IV) using combined spectroscopy and chromatography

The interactions of V(V) and L-cysteine, thioacetic acid and ethanethiol were studied in aqueous solution using chromatographic and spectral analysis. The chromatographic determination of V(V) and V(IV) species in the presence of thiols was enabled by inducing the ligand exchange reaction with EDTA as the competing ligand. Analytical setup allowed investigation of the possible redox and structural transformations of V(V) in the presence of thiols used over a wide pH range. Obtained data strongly suggest that the reduction of V(V) is proton catalyzed in case of L-cysteine and thioacetic acid. In the case of ethanethiol, the reduction did not seem to be proton dependent, as no reduction was observed above pH = 2. Thus, reduction was inhibited by the deprotonation of L-cysteine and thioacetic acid, with L-cysteine being the strongest reducing agent of V(V), followed by thioacetic acid and finally ethanethiol. Apart from structural thiol properties, the reduction reaction seems to be influenced by the aqueous V(V) speciation due to the observed nonlinear kinetics. In the case of all investigated thiols, the formation of V(V)-thioester intermediate species was an essential step for V(V) reduction. The structural properties of the V(IV)-thiol complexes were also found to be pH-dependent.

Thioesters provide a plausible prebiotic path to proto-peptides

It is widely assumed that the condensation of building blocks into oligomers and polymers was important in the origins of life. High activation energies, unfavorable thermodynamics and side reactions are bottlenecks for abiotic peptide formation. All abiotic reactions reported thus far for peptide bond formation via thioester intermediates have relied on high energy molecules, which usually suffer from short half-life in aqueous conditions and therefore require constant replenishment. Here we report plausible prebiotic reactions of mercaptoacids with amino acids that result in the formation of thiodepsipeptides, which contain both peptide and thioester bonds. Thiodepsipeptide formation was achieved under a wide range of pH and temperature by simply drying and heating mercaptoacids with amino acids. Our results offer a robust one-pot prebiotically-plausible pathway for proto-peptide formation. These results support the hypothesis that thiodepsipeptides and thiol-terminated peptides formed readily on prebiotic Earth and were possible contributors to early chemical evolution.

One of the early processes enabling the origins of life is thought to be the condensation of building blocks into oligomers and polymers. In this article, the authors report the synthesis of thiodepsipeptides and HS-peptides under mild temperatures and various pH, suggesting they could have formed on early prebiotic Earth.

Determining the "Biosignature Threshold" for Life Detection on Biotic, Abiotic, or Prebiotic Worlds

The field of prebiotic chemistry has demonstrated that complex organic chemical systems that exhibit various life-like properties can be produced abiotically in the laboratory. Understanding these chemical systems is important for astrobiology and life detection since we do not know the extent to which prebiotic chemistry might exist or have existed on other worlds. Nor do we know what signatures are diagnostic of an extant or "failed" prebiotic system. On Earth, biology has suppressed most abiotic organic chemistry and overprints geologic records of prebiotic chemistry; therefore, it is difficult to validate whether chemical signatures from future planetary missions are remnant or extant prebiotic systems. The "biosignature threshold" between whether a chemical signature is more likely to be produced by abiotic versus biotic chemistry on a given world could vary significantly, depending on the particular environment, and could change over time, especially if life were to emerge and diversify on that world. To interpret organic signatures detected during a planetary mission, we advocate for (1) gaining a more complete understanding of prebiotic/abiotic chemical possibilities in diverse planetary environments and (2) involving experimental prebiotic samples as analogues when generating comparison libraries for "life-detection" mission instruments.

Methods to identify and characterize iron-sulfur oligopeptides in water

Iron-sulfur clusters are ubiquitous cofactors that mediate central biological processes. However, despite their long history, these metallocofactors remain challenging to investigate when coordinated to small (≤ six amino acids) oligopeptides in aqueous solution. In addition to being often unstable in vitro, iron-sulfur clusters can be found in a wide variety of forms with varied characteristics, which makes it difficult to easily discern what is in solution. This difficulty is compounded by the dynamics of iron-sulfur peptides, which frequently coordinate multiple types of clusters simultaneously. To aid investigations of such complex samples, a summary of data from multiple techniques used to characterize both iron-sulfur proteins and peptides is provided. Although not all spectroscopic techniques are equally insightful, it is possible to use several, readily available methods to gain insight into the complex composition of aqueous solutions of iron-sulfur peptides.

Testing Abiotic Reduction of NAD+ Directly Mediated by Iron/Sulfur Minerals

Life emerged in a geochemical context, possibly in the midst of mineral substrates. However, it is not known to what extent minerals and dissolved inorganic ions could have facilitated the evolution of biochemical reactions. Herein, we have experimentally shown that iron sulfide minerals can act as electron transfer agents for the reduction of the ubiquitous biological protein cofactor nicotinamide adenine dinucleotide (NAD⁺) under anaerobic prebiotic conditions, observing the NAD⁺/NADH redox transition by using ultraviolet-visible spectroscopy and ¹H nuclear magnetic resonance. This reaction was mediated with iron sulfide minerals, which were likely abundant on early Earth in seafloor and hydrothermal settings; and the NAD⁺/NADH redox reaction occurred in the absence of UV light, peptide ligand(s), or dissolved mediators. To better understand this reaction, thermodynamic modeling was also performed. The ability of an iron sulfide mineral to transfer electrons to a biochemical cofactor that is found in every living cell demonstrates how geologic materials could have played a direct role in the evolution of certain cofactor-driven metabolic pathways.

Ynamide-Mediated Thioester Synthesis

A novel ynamide-mediated thioester synthesis strategy was developed. Importantly, no detectable racemization was observed for the thioesterifications of carboxylic acids containing an α-chiral center, enabling it to be useful for the synthesis of peptide thioester, which is the key component of native chemical ligation. It is worth mentioning that amino acid side chain functional groups such as -OH and indole -NH are compatible with the reaction conditions, rendering their protection unnecessary. Moreover, this method was also amenable to selenoesters.

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.

Spontaneous assembly of redox-active iron-sulfur clusters at low concentrations of cysteine

Iron-sulfur (FeS) proteins are ancient and fundamental to life, being involved in electron transfer and CO₂ fixation. FeS clusters have structures similar to the unit-cell of FeS minerals such as greigite, found in hydrothermal systems linked with the origin of life. However, the prebiotic pathway from mineral surfaces to biological clusters is unknown. Here we show that FeS clusters form spontaneously through interactions of inorganic Fe²⁺/Fe³⁺ and S^2- with micromolar concentrations of the amino acid cysteine in water at alkaline pH. Bicarbonate ions stabilize the clusters and even promote cluster formation alone at concentrations >10 mM, probably through salting-out effects. We demonstrate robust, concentration-dependent formation of [4Fe4S], [2Fe2S] and mononuclear iron clusters using UV-Vis spectroscopy, ⁵⁷Fe-Mössbauer spectroscopy and ¹H-NMR. Cyclic voltammetry shows that the clusters are redox-active. Our findings reveal that the structures responsible for biological electron transfer and CO₂ reduction could have formed spontaneously from monomers at the origin of life.

Electrochemically induced metal- vs. ligand-based redox changes in mackinawite: identification of a Fe3+- and polysulfide-containing intermediate

Under anaerobic conditions, ferrous iron reacts with sulfide producing FeS, which can then undergo a temperature, redox potential, and pH dependent maturation process resulting in the formation of oxidized mineral phases, such as greigite or pyrite. A greater understanding of this maturation process holds promise for the development of iron-sulfide catalysts, which are known to promote diverse chemical reactions, such as H+, CO2 and NO3- reduction processes. Hampering the full realization of the catalytic potential of FeS, however, is an incomplete knowledge of the molecular and redox processess ocurring between mineral and nanoparticulate phases. Here, we investigated the chemical properties of iron-sulfide by cyclic voltammetry, Raman and X-ray absorption spectroscopic techniques. Tracing oxidative maturation pathways by varying electrode potential, nanoparticulate n(Fe2+S2-)(s) was found to oxidize to a Fe3+ containing FeS phase at -0.5 V vs. Ag/AgCl (pH = 7). In a subsequent oxidation, polysulfides are proposed to give a material that is composed of Fe2+, Fe3+, S2- and polysulfide (Sn2-) species, with its composition described as Fe2+1-3xFe3+2xS2-1-y(Sn2-)y. Thermodynamic properties of model compounds calculated by density functional theory indicate that ligand oxidation occurs in conjunction with structural rearrangements, whereas metal oxidation may occur prior to structural rearrangement. These findings together point to the existence of a metastable FeS phase located at the junction of a metal-based oxidation path between FeS and greigite (Fe2+Fe3+2S2-4) and a ligand-based oxidation path between FeS and pyrite (Fe2+(S2)2-).

Spectral decomposition of iron-sulfur clusters

The near universal availability of UV-Visible spectrophotometers makes this instrument a highly exploited tool for the inexpensive, rapid examination of iron-sulfur clusters. Yet, the analysis of iron-sulfur cluster reconstitution experiments by UV-Vis spectroscopy is notoriously difficult due to the presence of broad, ill-defined peaks. Other types of spectroscopies, such as electron paramagnetic resonance spectroscopy and Mössbauer spectroscopy, are superior in characterizing the type of cluster present and their associated electronic transitions but require expensive, less readily available equipment. Here, we describe a tool that utilizes the accessible and convenient platform of Microsoft Excel to allow for the semi-quantitative analysis of iron-sulfur clusters by UV-Vis spectroscopy. This tool, which we call Fit-FeS, could potentially be used to additionally decompose spectra of solutions containing chromophores other than iron-sulfur clusters.

The Grayness of the Origin of Life

In the search for life beyond Earth, distinguishing the living from the non-living is paramount. However, this distinction is often elusive, as the origin of life is likely a stepwise evolutionary process, not a singular event. Regardless of the favored origin of life model, an inherent "grayness" blurs the theorized threshold defining life. Here, we explore the ambiguities between the biotic and the abiotic at the origin of life. The role of grayness extends into later transitions as well. By recognizing the limitations posed by grayness, life detection researchers will be better able to develop methods sensitive to prebiotic chemical systems and life with alternative biochemistries.

Autocatalytic Synthesis of Thioesters via Thiocarbonylation of gem-Difluoroalkenes

Herein, we report a new method for the synthesis of acyethanethioates via thiocarbonylation of gem-difluoroalkenes with thiols. This reaction provides a new pathway to prepare thioesters under mild conditions without the use of any additives. Mechanistic studies revealed that in situ generated HF facilitated the C-F bond cleavage in an autocatalytic manner.