Protocellular Heme and Iron-Sulfur Clusters

ConspectusCentral to the quest of understanding the emergence of life is to uncover the role of metals, particularly iron, in shaping prebiotic chemistry. Iron, as the most abundant of the accessible transition metals on the prebiotic Earth, played a pivotal role in early biochemical processes and continues to be indispensable to modern biology. Here, we discuss our recent contributions to probing the plausibility of prebiotic complexes with iron, including heme and iron-sulfur clusters, in mediating chemistry beneficial to a protocell. Laboratory experiments and spectroscopic findings suggest plausible pathways, often facilitated by UV light, for the synthesis of heme and iron-sulfur clusters. Once formed, heme displays catalytic, peroxidase-like activity when complexed with amphiphiles. This activity could have been beneficial in two ways. First, heme could have catalytically removed a molecule (H2O2) that could have had degradative effects on a protocell. Second, heme could have helped in the synthesis of the building blocks of life by coupling the reduction of H2O2 with the oxidation of organic substrates. The necessity of amphiphiles to avoid the formation of inactive complexes of heme is telling, as the modern-day electron transport chain possesses heme embedded within a lipid membrane. Conversely, prebiotic iron-sulfur peptides have yet to be reported to partition into lipid membranes, nor have simple iron-sulfur peptides been found to be capable of participating in the synthesis of organic molecules. Instead, iron-sulfur peptides span a wide range of reduction potentials complementary to the reduction potentials of hemes. The reduction potential of iron-sulfur peptides can be tuned by the type of iron-sulfur cluster formed, e.g., [2Fe-2S] versus [4Fe-4S], or by the substitution of ligands to the metal center. Since iron-sulfur clusters easily form upon stochastic encounters between iron ions, hydrosulfide, and small organic molecules possessing a thiolate, including peptides, the likelihood of soluble iron-sulfur clusters seems to be high. What remains challenging to determine is if iron-sulfur peptides participated in early prebiotic chemistry or were recruited later when protocellular membranes evolved that were compatible with the exploitation of electron transfer for the storage of energy as a proton gradient. This problem mirrors in some ways the difficulty in deciphering the origins of metabolism as a whole. Chemistry that resembles some facets of extant metabolism must have transpired on the prebiotic Earth, but there are few clues as to how and when such chemistry was harnessed to support a (proto)cell. Ultimately, unraveling the roles of hemes and iron-sulfur clusters in prebiotic chemistry promises to deepen our understanding of the origins of life on Earth and aids the search for life elsewhere in the universe.

Unveiling the role of inorganic nanoparticles in Earth's biochemical evolution through electron transfer dynamics

This article explores the intricate interplay between inorganic nanoparticles and Earth's biochemical history, with a focus on their electron transfer properties. It reveals how iron oxide and sulfide nanoparticles, as examples of inorganic nanoparticles, exhibit oxidoreductase activity similar to proteins. Termed "life fossil oxidoreductases," these inorganic enzymes influence redox reactions, detoxification processes, and nutrient cycling in early Earth environments. By emphasizing the structural configuration of nanoparticles and their electron conformation, including oxygen defects and metal vacancies, especially electron hopping, the article provides a foundation for understanding inorganic enzyme mechanisms. This approach, rooted in physics, underscores that life's origin and evolution are governed by electron transfer principles within the framework of chemical equilibrium. Today, these nanoparticles serve as vital biocatalysts in natural ecosystems, participating in critical reactions for ecosystem health. The research highlights their enduring impact on Earth's history, shaping ecosystems and interacting with protein metal centers through shared electron transfer dynamics, offering insights into early life processes and adaptations.

Electrochemical detection of glutathione based on accelerated CRISPR/Cas12a trans-cleavage with MnO2 nanosheets

The CRISPR/Cas12a system is accelerated by glutathione-mediated reduction of MnO2 nanosheets. By monitoring the trans-cleavage of the DNA probe, an electrochemical method for glutathione assay is fabricated, with the detection limit of 3.5 pM. It provides a promising tool for plasma analysis with satisfactory performance, indicating the broad application prospects of this glutathione assay.

A heterodimeric hyaluronate lyase secreted by the activated sludge bacterium Haliscomenobacter hydrossis

Haliscomenobacter hydrossis is a filamentous bacterium common in activated sludge. The bacterium was found to utilize hyaluronic acid, and hyaluronate lyase activity was detected in its culture. However, no hyaluronate lyase gene was found in the genome, suggesting the bacterium secretes a novel hyaluronate lyase. The purified enzyme exhibited two bands on SDS-PAGE and a single peak on gel filtration chromatography, suggesting a heterodimeric composition. N-terminal amino acid sequence and mass spectrometric analyses suggested that the subunits are molybdopterin-binding and [2Fe-2S]-binding subunits of a xanthine oxidase family protein. The presence of the cofactors was confirmed using spectrometric analysis. Oxidase activity was not detected, revealing that the enzyme is not an oxidase but a hyaluronate lyase. Nuclear magnetic resonance analysis of the enzymatic digest revealed that the enzyme breaks hyaluronic acid to 3-(4-deoxy-β-d-gluc-4-enuronosyl)-N-acetyl-d-glucosamine. As hyaluronate lyases (EC 4.2.2.1) are monomeric or trimeric, the enzyme is the first heterodimeric hyaluronate lyase.

Metals in Prebiotic Catalysis: A Possible Evolutionary Pathway for the Emergence of Metalloproteins

Proteinaceous catalysts found in extant biology are products of life that were potentially derived through prolonged periods of evolution. Given their complexity, it is reasonable to assume that they were not accessible to prebiotic chemistry as such. Nevertheless, the dependence of many enzymes on metal ions or metal-ligand cores suggests that catalysis relevant to biology could also be possible with just the metal centers. Given their availability on the Hadean/Archean Earth, it is fair to conjecture that metal ions could have constituted the first forms of catalysts. A slow increase of complexity that was facilitated through the provision of organic ligands and amino acids/peptides possibly allowed for further evolution and diversification, eventually demarcating them into specific functions. Herein, we summarize some key experimental developments and observations that support the possible roles of metal catalysts in shaping the origins of life. Further, we also discuss how they could have evolved into modern-day enzymes, with some suggestions for what could be the imminent next steps that researchers can pursue, to delineate the putative sequence of catalyst evolution during the early stages of life.

Structures of Atm1 provide insight into [2Fe-2S] cluster export from mitochondria

In eukaryotes, iron-sulfur clusters are essential cofactors for numerous physiological processes, but these clusters are primarily biosynthesized in mitochondria. Previous studies suggest mitochondrial ABCB7-type exporters are involved in maturation of cytosolic iron-sulfur proteins. However, the molecular mechanism for how the ABCB7-type exporters participate in this process remains elusive. Here, we report a series of cryo-electron microscopy structures of a eukaryotic homolog of human ABCB7, CtAtm1, determined at average resolutions ranging from 2.8 to 3.2 Å, complemented by functional characterization and molecular docking in silico. We propose that CtAtm1 accepts delivery from glutathione-complexed iron-sulfur clusters. A partially occluded state links cargo-binding to residues at the mitochondrial matrix interface that line a positively charged cavity, while the binding region becomes internalized and is partially divided in an early occluded state. Collectively, our findings substantially increase the understanding of the transport mechanism of eukaryotic ABCB7-type proteins.

Histidine Ligated Iron-Sulfur Peptides

Iron‐sulfur clusters are thought to be ancient cofactors that could have played a role in early protometabolic systems. Thus far, redox active, prebiotically plausible iron‐sulfur clusters have always contained cysteine ligands to the cluster. However, extant iron‐sulfur proteins can be found to exploit other modes of binding, including ligation by histidine residues, as seen with [2Fe‐2S] Rieske and MitoNEET proteins. Here, we investigated the ability of cysteine‐ and histidine‐containing peptides to coordinate a mononuclear Fe²⁺ center and a [2Fe‐2S] cluster and compare their properties with purified iron‐sulfur proteins. The iron‐sulfur peptides were characterized by UV‐vis, circular dichroism, and paramagnetic NMR spectroscopies and cyclic voltammetry. Small (≤6 amino acids) peptides can coordinate [2Fe‐2S] clusters through a combination of cysteine and histidine residues with similar reduction potentials as their corresponding proteins. Such complexes may have been important for early cell‐like systems.

Prebiotic Environments with Mg2+ and Thiophilic Metal Ions Increase the Thermal Stability of Cysteine and Non-cysteine Peptides

Wet-dry cycles driven by heating to high temperatures are frequently invoked for the prebiotic synthesis of peptides. Similarly, iron-sulfur clusters are often cited as an example of an ancient catalyst that helped prune early chemical systems into metabolic-like pathways. Because extant iron-sulfur clusters are metallocofactors of protein enzymes and nearly ubiquitous across biology, a reasonable hypothesis is that prebiotic iron-sulfur peptides formed on the early Earth. However, iron-sulfur clusters are coordinated by multiple cysteine residues, and the stability of cysteines to the heat steps of wet-dry cycles has not been determined. It, therefore, has remained unclear if the peptides needed to stabilize the formation of iron-sulfur clusters could have formed. If not, then iron-sulfur-dependent activity may have emerged later, when milder, more biological-like peptide synthesis machinery took hold. Here, we report the thermal stability of cysteine-containing peptides. We show that temperatures of 150 °C lead to the rapid degradation of cysteinyl peptides. However, the presence of Mg²⁺ at environmentally reasonable concentrations leads to significant protection. Thiophilic metal ions also protect against degradation at 150 °C but require concentrations not frequently observed in the environment. Nevertheless, cysteine-containing peptides are stable at lower, prebiotically plausible temperatures in seawater, carbonate lake, and ferrous lake conditions. The data are consistent with the persistence of cysteine-containing peptides on the early Earth in environments rich in metal ions. High concentrations of Mg²⁺ are common intra- and extra-cellularly, suggesting that the protection afforded by Mg²⁺ may reflect conditions that were present on the prebiotic Earth.

Metals Are Integral to Life as We Know It

Investigations of biology and the origins of life regularly focus on the components of the central dogma and thus the elements that compose nucleic acids and peptides. Less attention is given to the inorganic components of a biological cell, which are required for biological polymers to function. The Earth was and continues to be rich in metals, and so investigations of the emergence and evolution of life must account for the role that metal ions play. Evolution is shaped by what is present, and not all elements of the periodic table are equally accessible. The presence of metals, the solubility of their ions, and their intrinsic reactivity all impacted the composition of the cells that emerged. Geological and bioinformatic analyses clearly show that the suite of accessible metal ions changed over the history of the Earth; however, such analyses tend to be interpreted in comparison to average oceanic conditions, which do not represent well the many niche environments present on the Earth. While there is still debate concerning the sequence of events that led to extant biology, what is clear is that life as we know it requires metals, and that past and current metal-dependent events remain, at least partially, imprinted in the chemistry of the cell.

Porphyrin in prebiotic catalysis: Ascertaining a route for the emergence of early metalloporphyrins

Metal ions are known to catalyze certain prebiotic reactions. However, the transition from metal ions to extant metalloenzymes remains unclear. Porphyrins are found ubiquitously in the catalytic core of many ancient metalloenzymes. In this study, we evaluated the influence of porphyrin-based organic scaffold, on the catalysis, emergence and putative molecular evolution of prebiotic metalloporphyrins. We studied the effect of porphyrins on the transition metal ion-mediated oxidation of hydroquinone (HQ). We report a change in the catalytic activity of the metal ions in the presence of porphyrin. This was observed to be facilitated by the coordination between metal ions and porphyrins or by the formation of non-coordinated complexes. The metal-porphyrin complexes also oxidized NADH, underscoring its versatility at oxidizing more than one substrate. Our study highlights the selective advantage that some of the metal ions would have had in the presence of porphyrin, underscoring their role in shaping the evolution of protometalloenzymes.

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.

The pH dependence of emulsifying properties for glutathione disulfide at oil-water interfaces

Although peptides were widely used in many fields, their interface behaviors as surfactants have not been explored. The results of the surface tension experiments by an automatic surface tension meter indicate that the stability and emulsifying ability of glutathione disulfide (GSSG) under alkaline conditions were stronger than those under acidic conditions. With encoding the different oxygen and nitrogen atoms in GSSG, as well as the different hydrogen atoms bonded with oxygen and nitrogen atoms. The pH Dependence of the number of hydrogen bonds, affected by the protonation and deprotonation of the functional groups in GSSG, is calculated by LAMMPS software. The results demonstrate that GSSG forms twice as many hydrogen bonds under alkaline conditions as under acidic conditions, resulting in a better surface-interface activity in alkaline conditions. The interface properties of the GSSG surfactant can be regulated by pH. Therefore, GSSG is a potential pH-responsive surfactant.

Short non-coded peptides interacting with cofactors facilitated the integration of early chemical networks

Independently developed iron-sulphur/thioester- and phosphate-driven chemical reactions would have set up two distinct reaction networks prior to coupling in a proto-metabolic system supporting a minimal organisation closure. Each chemical system assisted initially by simple catalysts and then by more complex cofactors would have provided the precursors of the small metabolites and monomer units along with their respective polymers through dehydrating template-independent assemblies. For example, acylation reactions mediated by activated thioester groups produced peptides, fatty acids and polyhydroxyalkanoates, while phosphorylation reactions by phosphorylating agents allowed the synthesis of polysaccharides, polyribonucleotides and polyphosphates. Here, we address how these independent chemical systems might fit together and shaped a proto-metabolic system, focusing specifically on cofactors as molecular fossils of metabolism. As a result, the proposed overview suggests that non-coded peptides capable of binding a variety of ligands, but in particular with a redox active versatility and/or group transfer potential could have facilitated the chemical connections that led to a minimal closure with a proto-metabolism. Later developments would have made it possible to establish a cellular organisation with more complex and interdependent metabolic pathways.

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.

Cysteine, glutathione and a new genetic code: biochemical adaptations of the primordial cells that spread into open water and survived biospheric oxygenation

Life most likely developed under hyperthermic and anaerobic conditions in close vicinity to a stable geochemical source of energy. Epitomizing this conception, the first cells may have arisen in submarine hydrothermal vents in the middle of a gradient established by the hot and alkaline hydrothermal fluid and the cooler and more acidic water of the ocean. To enable their escape from this energy-providing gradient layer, the early cells must have overcome a whole series of obstacles. Beyond the loss of their energy source, the early cells had to adapt to a loss of external iron-sulfur catalysis as well as to a formidable temperature drop. The developed solutions to these two problems seem to have followed the principle of maximum parsimony: Cysteine was introduced into the genetic code to anchor iron-sulfur clusters, and fatty acid unsaturation was installed to maintain lipid bilayer viscosity. Unfortunately, both solutions turned out to be detrimental when the biosphere became more oxidizing after the evolution of oxygenic photosynthesis. To render cysteine thiol groups and fatty acid unsaturation compatible with life under oxygen, numerous counter-adaptations were required including the advent of glutathione and the addition of the four latest amino acids (methionine, tyrosine, tryptophan, selenocysteine) to the genetic code. In view of the continued diversification of derived antioxidant mechanisms, it appears that modern life still struggles with the initially developed strategies to escape from its hydrothermal birthplace. Only archaea may have found a more durable solution by entirely exchanging their lipid bilayer components and rigorously restricting cysteine usage.

The curious case of peptide-coordinated iron-sulfur clusters: prebiotic and biomimetic insights

Iron-sulfur clusters are among the most ancient biological cofactors and are thought to have had an ancient role in mediating the chemical reactions that led to life. Two different, yet complementary approaches, based on bioinorganic chemistry and prebiotic chemistry, have already provided important clues for the formation and activity of biomimetic iron-sulfur analogues in aqueous solution. This frontier article discusses the efforts spent in the last 50 years in the context of peptide-coordinated iron-sulfur clusters, with a particular emphasis on insightful contributions from recent prebiotic chemistry research.

Quantifying Mineral-Ligand Structural Similarities: Bridging the Geological World of Minerals with the Biological World of Enzymes

Metal compounds abundant on Early Earth are thought to play an important role in the origins of life. Certain iron-sulfur minerals for example, are proposed to have served as primitive metalloenzyme cofactors due to their ability to catalyze organic synthesis processes and facilitate electron transfer reactions. An inherent difficulty with studying the catalytic potential of many metal compounds is the wide range of data and parameters to consider when searching for individual minerals and ligands of interest. Detecting mineral-ligand pairs that are structurally analogous enables more relevant selections of data to study, since structural affinity is a key indicator of comparable catalytic function. However, current structure-oriented approaches tend to be subjective and localized, and do not quantify observations or compare them with other potential targets. Here, we present a mathematical approach that compares structural similarities between various minerals and ligands using molecular similarity metrics. We use an iterative substructure search in the crystal lattice, paired with benchmark structural similarity methods. This structural comparison may be considered as a first stage in a more advanced analysis tool that will include a range of chemical and physical factors when computing mineral-ligand similarity. This approach will seek relationships between the mineral and enzyme worlds, with applications to the origins of life, ecology, catalysis, and astrobiology.

Protoenzymes: The Case of Hyperbranched Polymer-Scaffolded ZnS Nanocrystals

Enzymes are biological catalysts that are comprised of small-molecule, metal, or cluster catalysts augmented by biopolymeric scaffolds. It is conceivable that early in chemical evolution, ancestral enzymes opted for simpler, easier to assemble scaffolds. Herein, we describe such possible protoenzymes: hyperbranched polymer-scaffolded metal-sulfide nanocrystals. Hyperbranched polyethyleneimine (HyPEI) and glycerol citrate polymer-supported ZnS nanocrystals (NCs) are formed in a simple process. Transmission electron microscopy (TEM) analyses of HyPEI-supported NCs reveal spherical particles with an average size of 10 nm that undergo only a modest aggregation over a 14-day incubation. The polymer-supported ZnS NCs are shown to possess a high photocatalytic activity in an eosin B photodegradation assay, making them an attractive model for the study of the origin of life under the “Zn world” theory dominated by a photocatalytic proto-metabolic redox reaction network. The catalyst, however, could be easily adapted to apply broadly to different protoenzymatic systems.

Small protein folds at the root of an ancient metabolic network

Life on Earth is driven by electron transfer reactions catalyzed by a suite of enzymes that comprise the superfamily of oxidoreductases (Enzyme Classification EC1). Most modern oxidoreductases are complex in their structure and chemistry and must have evolved from a small set of ancient folds. Ancient oxidoreductases from the Archean Eon between ca. 3.5 and 2.5 billion years ago have been long extinct, making it challenging to retrace evolution by sequence-based phylogeny or ancestral sequence reconstruction. However, three-dimensional topologies of proteins change more slowly than sequences. Using comparative structure and sequence profile-profile alignments, we quantify the similarity between proximal cofactor-binding folds and show that they are derived from a common ancestor. We discovered that two recurring folds were central to the origin of metabolism: ferredoxin and Rossmann-like folds. In turn, these two folds likely shared a common ancestor that, through duplication, recruitment, and diversification, evolved to facilitate electron transfer and catalysis at a very early stage in the origin of metabolism.

Prebiotic Peptides: Molecular Hubs in the Origin of Life

The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.

Progress in synthesizing protocells

IMPACT STATEMENT

Advances in the understanding of the biophysics of membranes, the nonenzymatic and enzymatic polymerization of RNA, and in the design of complex chemical reaction networks have led to a new, integrated way of viewing the shared chemistry needed to sustain life. Although a protocell capable of Darwinian evolution has yet to be built, the seemingly disparate pieces are beginning to fit together. At the very least, better cellular mimics are on the horizon that will likely teach us much about the physicochemical underpinnings of cellular life.

Patterns of Ligands Coordinated to Metallocofactors Extracted from the Protein Data Bank

A new R tool is described that rapidly identifies, ranks, and clusters sequence patterns coordinated to metallocofactors. This tool, PdPDB, fills a void because, unlike currently available tools, PdPDB searches through sequences with metal coordination as the primary determinant and can identify patterns consisting of amino acids, nucleotides, and small molecule ligands at once. PdPDB was tested by analyzing structures that coordinate Fe^2+/3+, [2Fe-2S], [4Fe-4S], Zn²⁺, and Mg²⁺ cofactors. PdPDB confirmed previously identified sequence motifs and revealed which residues are enriched (e.g., glycine) and are under-represented (e.g., glutamine) near ligands to metal centers. The data show the similarities and differences between different metal-binding sites. The patterns that coordinate metallocofactors vary, depending upon whether the metal ions play a structural or catalytic role, with catalytic metal centers exhibiting partial coordination by small molecule ligands. PdPDB 2.0.1 is freely available as a CRAN package.

UV-light-driven prebiotic synthesis of iron-sulfur clusters

Iron-sulfur clusters are ancient cofactors that play a fundamental role in metabolism and may have impacted the prebiotic chemistry that led to life. However, it is unclear whether iron-sulfur clusters could have been synthesized on prebiotic Earth. Dissolved iron on early Earth was predominantly in the reduced ferrous state, but ferrous ions alone cannot form polynuclear iron-sulfur clusters. Similarly, free sulfide may not have been readily available. Here we show that UV light drives the synthesis of [2Fe-2S] and [4Fe-4S] clusters through the photooxidation of ferrous ions and the photolysis of organic thiols. Iron-sulfur clusters coordinate to and are stabilized by a wide range of cysteine-containing peptides and the assembly of iron-sulfur cluster-peptide complexes can take place within model protocells in a process that parallels extant pathways. Our experiments suggest that iron-sulfur clusters may have formed easily on early Earth, facilitating the emergence of an iron-sulfur-cluster-dependent metabolism.