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SH3 and OB are the simplest, oldest, and most common protein domains within the translation system. SH3 and OB domains are β-barrels that are structurally similar but are topologically distinct. To transform an OB domain to a SH3 domain, β-strands must be permuted in a multistep and evolutionarily implausible mechanism. Here, we explored relationships between SH3 and OB domains of ribosomal proteins, initiation, and elongation factors using a combined sequence- and structure-based approach. We detect a common core of SH3 and OB domains, as a region of significant structure and sequence similarity. The common core contains four β-strands and a loop, but omits the fifth β-strand, which is variable and is absent from some OB and SH3 domain proteins. The structure of the common core immediately suggests a simple permutation mechanism for interconversion between SH3 and OB domains, which appear to share an ancestor. The OB domain was formed by duplication and adaptation of the SH3 domain core, or vice versa, in a simple and probable transformation. By employing the folding algorithm AlphaFold2, we demonstrated that an ancestral reconstruction of a permuted SH3 sequence folds into an OB structure, and an ancestral reconstruction of a permuted OB sequence folds into a SH3 structure. The tandem SH3 and OB domains in the universal ribosomal protein uL2 share a common ancestor, suggesting that the divergence of these two domains occurred before the last universal common ancestor.

Among the enzyme lineages that undoubtedly emerged prior to the last universal common ancestor is the so-called HUP, which includes Class I aminoacyl tRNA synthetases (AARSs) as well as enzymes mediating NAD, FAD, and CoA biosynthesis. Here, we provide a detailed analysis of HUP evolution, from emergence to structural and functional diversification. The HUP is a nucleotide binding domain that uniquely catalyzes adenylation via the release of pyrophosphate. In contrast to other ancient nucleotide binding domains with the αβα sandwich architecture, such as P-loop NTPases, the HUP’s most conserved feature is not phosphate binding, but rather ribose binding by backbone interactions to the tips of β1 and/or β4. Indeed, the HUP exhibits unusual evolutionary plasticity and, while ribose binding is conserved, the location and mode of binding to the base and phosphate moieties of the nucleotide, and to the substrate(s) reacting with it, have diverged with time, foremost along the emergence of the AARSs. The HUP also beautifully demonstrates how a well- packed scaffold combined with evolvable surface elements promotes evolutionary innovation. Finally, we offer a scenario for the emergence of the HUP from a seed βαβ fragment, and suggest that despite an identical architecture, the HUP and the Rossmann represent independent emergences.

Production of molecular oxygen was a turning point in the Earth’s history. The geological record indicates the Great Oxidation Event, which marked a permanent transition to an oxidizing atmosphere around 2.4 Ga. However, the degree to which oxygen was available to life before oxygenation of the atmosphere remains unknown. Here, phylogenetic analysis of all known oxygen-utilizing and -producing enzymes (O2-enzymes) indicates that oxygen became widely available to living organisms well before the Great Oxidation Event. About 60% of the O2-enzyme families whose birth can be dated appear to have emerged at the separation of terrestrial and marine bacteria (22 families, compared to two families assigned to the last universal common ancestor). This node, dubbed the last universal oxygen ancestor, coincides with a burst of emergence of both oxygenases and other oxidoreductases, thus suggesting a wider availability of oxygen around 3.1 Ga. Phylogenetic dating of O2-utilizing enzymes indicates a burst of emergence several hundred million years before the Great Oxidation Event.

The origin of life is one of the most interesting and challenging questions in biology. This article discusses relevant contemporary theories and hypotheses about the origin of life, recent scientific evidence supporting them, and the main contributions of several scientists of different nationalities and specialties in different disciplines. Also discussed are several ideas about the characteristics of the most recent common ancestor, also called the “last universal common ancestor” (or LUCA), including cellular status (unicellular or community) and homogeneity level.

Prions, proteins that can convert between structurally and functionally distinct states and serve as non-Mendelian mechanisms of inheritance, were initially discovered and only known in eukaryotes, and consequently considered to likely be a relatively late evolutionary acquisition. However, the recent discovery of prions in bacteria and viruses has intimated a potentially more ancient evolutionary origin. Here, we provide evidence that prion-forming domains exist in the domain archaea, the last domain of life left unexplored with regard to prions. We searched for archaeal candidate prion-forming protein sequences computationally, described their taxonomic distribution and phylogeny, and analyzed their associated functional annotations. Using biophysical in vitro assays, cell-based and microscopic approaches, and dye-binding analyses, we tested select candidate prion-forming domains for prionogenic characteristics. Out of the 16 tested, eight formed amyloids, and six acted as protein-based elements of information transfer driving non-Mendelian patterns of inheritance. We also identified short peptides from our archaeal prion candidates that can form amyloid fibrils independently. Lastly, candidates that tested positively in our assays had significantly higher tyrosine and phenylalanine content than candidates that tested negatively, an observation that may help future archaeal prion predictions. Taken together, our discovery of functional prion-forming domains in archaea provides evidence that multiple archaeal proteins are capable of acting as prions—thus expanding our knowledge of this epigenetic phenomenon to the third and final domain of life and bolstering the possibility that they were present at the time of the last universal common ancestor.

Thermotoga are anaerobic hyperthermophiles that have a deep lineage to the last universal ancestor and produce biological hydrogen gas accompanying cell growth. In recent years, systems-level approaches have been used to elucidate their metabolic capacities, by integrating mathematical modeling and experimental results. To assist biochemical engineering studies of T. sp. strain RQ7, this work aims at building a metabolic model of the bacterium that quantitatively simulates its metabolism at the genome scale. The constructed model, RQ7_iJG408, consists of 408 genes, 692 reactions, and 538 metabolites. Constraint-based flux balance analyses were used to simulate cell growth in both the complex and defined media. Quantitative comparison of the predicted and measured growth rates resulted in good agreements. This model serves as a foundation for an integrated biochemical description of T. sp. strain RQ7. It is a useful tool in designing growth media, identifying metabolic engineering strategies, and exploiting the physiological potentials of this biotechnologically significant organism.

ABC ATPases form one of the largest clades of P-loop NTPase fold enzymes that catalyze ATP-hydrolysis and utilize its free energy for a staggering range of functions from transport to nucleoprotein dynamics. Using sensitive sequence and structure analysis with comparative genomics, for the first time we provide a comprehensive classification of the ABC ATPase superfamily. ABC ATPases developed structural hallmarks that unambiguously distinguish them from other P-loop NTPases such as an alternative to arginine-finger-based catalysis. At least five and up to eight distinct clades of ABC ATPases are reconstructed as being present in the last universal common ancestor. They underwent distinct phases of structural innovation with the emergence of inserts constituting conserved binding interfaces for proteins or nucleic acids and the adoption of a unique dimeric toroidal configuration for DNA-threading. Specifically, several clades have also extensively radiated in counter-invader conflict systems where they serve as nodal nucleotide-dependent sensory and energetic components regulating a diversity of effectors (including some previously unrecognized) acting independently or together with restriction-modification systems. We present a unified mechanism for ABC ATPase function across disparate systems like RNA editing, translation, metabolism, DNA repair, and biological conflicts, and some unexpected recruitments, such as MutS ATPases in secondary metabolism.

Comparative genomics and molecular phylogenetics are foundational for understanding biological evolution. Although many studies have been made with the aim of understanding the genomic contents of early life, uncertainty remains. A study by Weiss et al. (Weiss MC, Sousa FL, Mrnjavac N, Neukirchen S, Roettger M, Nelson-Sathi S, Martin WF. 2016. The physiology and habitat of the last universal common ancestor. Nat Microbiol. 1(9):16116.) identified a number of protein families in the last universal common ancestor of archaea and bacteria (LUCA) which were not found in previous works. Here, we report new research that suggests the clustering approaches used in this previous study undersampled protein families, resulting in incomplete phylogenetic trees which do not reflect protein family evolution. Phylogenetic analysis of protein families which include more sequence homologs rejects a simple LUCA hypothesis based on phylogenetic separation of the bacterial and archaeal domains for a majority of the previously identified LUCA proteins (∼82%). To supplement limitations of phylogenetic inference derived from incompletely populated orthologous groups and to test the hypothesis of a period of rapid evolution preceding the separation of the domains, we compared phylogenetic distances both within and between domains, for thousands of orthologous groups. We find a substantial diversity of interdomain versus intradomain branch lengths, even among protein families which exhibit a single domain separating branch and are thought to be associated with the LUCA. Additionally, phylogenetic trees with long interdomain branches relative to intradomain branches are enriched in information categories of protein families in comparison to those associated with metabolic functions. These results provide a new view of protein family evolution and temper claims about the phenotype and habitat of the LUCA.

Abstract Two apparently irreconcilable models dominate research into the origin of eukaryotes. In one model, amitochondrial proto-eukaryotes emerged autogenously from the last universal common ancestor of all cells. Proto-eukaryotes subsequently acquired mitochondrial progenitors by the phagocytic capture of bacteria. In the second model, two prokaryotes, probably an archaeon and a bacterial cell, engaged in prokaryotic endosymbiosis, with the species resident within the host becoming the mitochondrial progenitor. Both models have limitations. A search was therefore undertaken for alternative routes towards the origin of eukaryotic cells. The question was addressed by considering classes of potential pathways from prokaryotic to eukaryotic cells based on considerations of cellular topology. Among the solutions identified, one, called here the “third-space model”, has not been widely explored. A version is presented in which an extracellular space (the third-space), serves as a proxy cytoplasm for mixed populations of archaea and bacteria to “merge” as a transitionary complex without obligatory endosymbiosis or phagocytosis and to form a precursor cell. Incipient nuclei and mitochondria diverge by division of labour. The third-space model can accommodate the reorganization of prokaryote-like genomes to a more eukaryote-like genome structure. Nuclei with multiple chromosomes and mitosis emerge as a natural feature of the model. The model is compatible with the loss of archaeal lipid biochemistry while retaining archaeal genes and provides a route for the development of membranous organelles such as the Golgi apparatus and endoplasmic reticulum. Advantages, limitations and variations of the “third-space” models are discussed. Reviewers This article was reviewed by Damien Devos, Buzz Baum and Michael Gray.

We present a testable hypothesis related to an origin of life on land in which fluctuating volcanic hot spring pools play a central role. The hypothesis is based on experimental evidence that lipid-encapsulated polymers can be synthesized by cycles of hydration and dehydration to form protocells. Drawing on metaphors from the bootstrapping of a simple computer operating system, we show how protocells cycling through wet, dry, and moist phases will subject polymers to combinatorial selection and draw structural and catalytic functions out of initially random sequences, including structural stabilization, pore formation, and primitive metabolic activity. We propose that protocells aggregating into a hydrogel in the intermediate moist phase of wet-dry cycles represent a primitive progenote system. Progenote populations can undergo selection and distribution, construct niches in new environments, and enable a sharing network effect that can collectively evolve them into the first microbial communities. Laboratory and field experiments testing the first steps of the scenario are summarized. The scenario is then placed in a geological setting on the early Earth to suggest a plausible pathway from life's origin in chemically optimal freshwater hot spring pools to the emergence of microbial communities tolerant to more extreme conditions in dilute lakes and salty conditions in marine environments. A continuity is observed for biogenesis beginning with simple protocell aggregates, through the transitional form of the progenote, to robust microbial mats that leave the fossil imprints of stromatolites so representative in the rock record. A roadmap to future testing of the hypothesis is presented. We compare the oceanic vent with land-based pool scenarios for an origin of life and explore their implications for subsequent evolution to multicellular life such as plants. We conclude by utilizing the hypothesis to posit where life might also have emerged in habitats such as Mars or Saturn's icy moon Enceladus. "To postulate one fortuitously catalyzed reaction, perhaps catalyzed by a metal ion, might be reasonable, but to postulate a suite of them is to appeal to magic." -Leslie Orgel.

The distribution of all peptidase homologues across all phyla of organisms was analysed to determine within which kingdom each of the 271 families originated. No family was found to be ubiquitous and even peptidases thought to be essential for life, such as signal peptidase and methionyl aminopeptides are missing from some clades. There are 33 peptidase families common to archaea, bacteria and eukaryotes and are assumed to have originated in the last universal common ancestor (LUCA). These include peptidases with different catalytic types, exo- and endopeptidases, peptidases with different tertiary structures and peptidases from different families but with similar structures. This implies that the different catalytic types and structures pre-date LUCA. Other families have had their origins in the ancestors of viruses, archaea, bacteria, fungi, plants and animals, and a number of families have had their origins in the ancestors of particular phyla. The evolution of peptidases is compared to recent hypotheses about the evolution of organisms., Highlights • Sequences of proteolytic enzymes can be clustered into 271 families. • No family is present in all organisms. • Only 33 families are predicted to originate in the last universal common ancestor. • Different structures and activities predate the last universal common ancestor. • Other families have originated in organism kingdoms, phyla or even families.

In this paper the hypothesis that prions and prion-like molecules could have initiated the chemical evolutionary process which led to the eventual emergence of life is reappraised. The prions first hypothesis is a specific application of the protein-first hypothesis which asserts that protein-based chemical evolution preceded the evolution of genetic encoding processes. This genetics-first hypothesis asserts that an “RNA-world era” came before protein-based chemical evolution and rests on a singular premise that molecules such as RNA, acetyl-CoA, and NAD are relics of a long line of chemical evolutionary processes preceding the Last Universal Common Ancestor (LUCA). Nevertheless, we assert that prions and prion-like molecules may also be relics of chemical evolutionary processes preceding LUCA. To support this assertion is the observation that prions and prion-like molecules are involved in a plethora of activities in contemporary biology in both complex (eukaryotes) and primitive life forms. Furthermore, a literature survey reveals that small RNA virus genomes harbor information about prions (and amyloids). If, as has been presumed by proponents of the genetics-first hypotheses, small viruses were present during an RNA world era and were involved in some of the earliest evolutionary processes, this places prions and prion-like molecules potentially at the heart of the chemical evolutionary process whose eventual outcome was life. We deliberate on the case for prions and prion-like molecules as the frontier molecules at the dawn of evolution of living systems.

Aminoacyl tRNA synthetases (aaRSs) are among the proposed proteins present in the Last Universal Common Ancestor (LUCA). There are two types of glycyl tRNA synthetases (GlyRSs), from which the archaeal-eukaryal type is the one suggested to be present in LUCA. Here we solved the crystal structure of a complete bacterial glycyl tRNA synthetase (bacGlyRS) and show that indeed, bacGlyRS carries several structural signals that point it at the origin of all aaRSs. Furthermore, if bacGlyRS is ancestral, it should help to build a reliable Tree of Life (ToL). Given the modular nature of protein evolution, we used only two sub-domain segments with duplicated ancestral topologies, no detected orthologs and an assumed limited horizontal gene transfer (HGT). These motifs correspond to the non-specific RNA binding regions of contemporary bacGlyRS, archaeal CCA-adding enzyme (arch-CCAadd), and eukaryotic rRNA processing enzyme (euk-rRNA). The calculated, rooted bacterial ToL agrees with several phyla relationships unaccounted by the available trees.

The stage reached by the evolution of cellularity in the Last Universal Common Ancestor (LUCA) has not yet been identified. In actual fact, it has not been clarified whether the LUCA was a cell (genote) or a protocell (progenote). Recently, Pende et al. (2021) analysed the phylogenetic distribution of the cell division system present in bacteria and archaea reaching the conclusion that LUCA was a cell and not a progenote. I find this conclusion unreasonable with respect to the observations they presented. One of the points is that the presence in the domains of life of many genes - some paralogs - which would define the membrane-remodeling superfamily would seem to imply a tempo and a mode of evolution for the LUCA more typical of the progenote than the genote. Indeed, the simultaneous presence of different genes - in a given evolutionary stage and with functions that are also partially correlated - would seem to define a heterogeneity that would appear to be the expression of a rapid and progressive evolution precisely because this evolution would have taken place in the diversification of all these genes. Furthermore, the presence of different genes coding for the function of cell division and related functions could reflect a progenotic status in LUCA, precisely because these functions might have originated from a single ancestral gene instead coding for a protein (or proteins) with multiple functions, and therefore an expression of a rapid and progressive evolution typical of the progenote. I also criticize other aspects of considerations made by Pende at al. (2021). The arguments presented here together with those existing in the literature make the hypothesis of a cellular LUCA favoured by Pende et al. (2021) unlikely.

RNA-peptide/protein interactions have been of utmost importance to life since its earliest forms, reaching even before the last universal common ancestor (LUCA). However, the ancient molecular mechanisms behind this key biological interaction remain enigmatic because extant RNA-protein interactions rely heavily on positively charged and aromatic amino acids that were absent (or heavily under-represented) in the early pre-LUCA evolutionary period. Here, an RNA-binding variant of the ribosomal L11 C-terminal domain was selected from a ∼1010 library of partially randomized sequences, all composed of 10 prebiotically plausible canonical amino acids. The selected variant binds to the cognate RNA with a similar overall affinity although it is less structured in the unbound form than the wild-type protein domain. The variant complex association and dissociation are both slower than for the wild-type, implying different mechanistic processes involved. The profile of the wild-type and mutant complex stabilities along with MD simulations uncover qualitative differences in the interaction modes. In the absence of positively charged and aromatic residues, the mutant L11 domain uses bridging ion (K+/Mg2+) interactions between the RNA sugar-phosphate backbone and glutamic acid residues as an alternative source of stabilization. This study presents experimental support to provide a new perspective on how early protein-RNA interactions evolved, where the lack of aromatic/basic residues was compensated by acidic residues plus metal ions.

Summary Membrane remodeling and repair are essential for all cells. Proteins that perform these functions include Vipp1/IM30 in photosynthetic plastids, PspA in bacteria, and ESCRT-III in eukaryotes. Here, using a combination of evolutionary and structural analyses, we show that these protein families are homologous and share a common ancient evolutionary origin that likely predates the last universal common ancestor. This homology is evident in cryo-electron microscopy structures of Vipp1 rings from the cyanobacterium Nostoc punctiforme presented over a range of symmetries. Each ring is assembled from rungs that stack and progressively tilt to form dome-shaped curvature. Assembly is facilitated by hinges in the Vipp1 monomer, similar to those in ESCRT-III proteins, which allow the formation of flexible polymers. Rings have an inner lumen that is able to bind and deform membranes. Collectively, these data suggest conserved mechanistic principles that underlie Vipp1, PspA, and ESCRT-III-dependent membrane remodeling across all domains of life., Graphical abstract, Highlights • PspA, Vipp1, and ESCRT-III are members of the same polymer-forming protein family • ESCRT-III-like polymers function to remodel membranes across all domains of life • Hinges in the Vipp1 monomer enable it to form a diverse set of flexible polymers • The inner lumen of the dome-shaped Vipp1 ring binds and deforms membranes, Phylogenetic and structural characterization of Vipp1 and PspA identifies them as ESCRT-III homologs and part of an ancient family of protein polymers that remodel membranes across the domains of life.

A powerful and concise concept of life is crucial for studies aiming to understand the characteristics that emerged from an inorganic world. Among biologists, the most accepted argument define life under a top-down strategy by looking into the shared characteristics observed in all cellular organisms. This is often made highlighting (i) autonomy and (ii) evolutionary capacity as fundamental characteristics observed in all cellular organisms. Along the present work, we assume the framework of code biology considering that biology started with the emergence of the first organic code by self-organization. We reinforces that the conceptual structure of life should be reallocated from the ontology class of Matter to its sister class of Process. Along the emergence and early evolution of biological systems, biological codes changed from open systems of "naked" molecules (at the progenote era), to close, encapsulated systems (at the organismic era). Living beings appeared at the very moment when nucleic acids with coding properties became encapsulated. This led to the origin of viruses and, then, to the origin of cells. In this context, we propose that the single character that makes a clear distinction between the abiotic and the biotic world is the capacity to process organic codes. Thus, life appears with the self-assembly of a genetic code and evolves by the emergence of other overlapping codes. Once life has been clearly conceptualized, we go further to conceptualize organisms, parents, lineages, and species in terms of code biology.

Selenium is an essential trace element whose compounds are widely metabolized by organisms from all three domains of life. Moreover, phylogenetic evidence indicates that selenium species, along with iron, molybdenum, tungsten, and nickel, were metabolized by the last universal common ancestor of all cellular lineages, primarily for the synthesis of the 21st amino acid selenocysteine. Thus, selenium metabolism is both environmentally ubiquitous and a physiological adaptation of primordial life. Selenium metabolic reactions comprise reductive transformations both for assimilation into macromolecules and dissimilatory reduction of selenium oxyanions and elemental selenium during anaerobic respiration. This review offers a comprehensive overview of the physiology and evolution of both assimilatory and dissimilatory selenium metabolism in bacteria and archaea, highlighting mechanisms of selenium respiration. This includes a thorough discussion of our current knowledge of the physiology of selenocysteine synthesis and incorporation into proteins in bacteria obtained from structural biology. Additionally, this is the first comprehensive discussion in a review of the incorporation of selenium into the tRNA nucleoside 5-methylaminomethyl-2-selenouridine and as an inorganic cofactor in certain molybdenum hydroxylase enzymes. Throughout, conserved mechanisms and derived features of selenium metabolism in both domains are emphasized and discussed within the context of the global selenium biogeochemical cycle.

We report evidence further supporting homology between proteins in the F1 FO -ATP synthetase and the bacterial flagellar motor (BFM). BFM proteins FliH, FliI, and FliJ have been hypothesized to be homologous to FO -b + F1 -δ, F1 -α/β, and F1 -γ, with similar structure and interactions. We conduct a further test by constructing a gene order dataset, examining the order of fliH, fliI, and fliJ genes across the phylogenetic breadth of flagellar and nonflagellar type 3 secretion systems, and comparing this to published surveys of gene order in the F1 FO -ATP synthetase, its N-ATPase relatives, and the bacterial/archaeal V- and A-type ATPases. Strikingly, the fliHIJ gene order was deeply conserved, with the few exceptions appearing derived, and exactly matching the widely conserved F-ATPase gene order atpFHAG, coding for subunits b-δ-α-γ. The V/A-type ATPases have a similar conserved gene order. Our results confirm homology between these systems, and suggest a rare case of synteny conserved over billions of years, predating the Last Universal Common Ancestor (LUCA).

Significance Orthologous proteins from the three superkingdoms have conserved their structures and functions over evolutionary time. We ask whether their folding mechanisms and the structures of their partially folded states are similarly conserved, using bacterial and archaeal representatives of the IGPS TIM barrel enzyme. Comparison of circular dichroism and fluorescence spectroscopic studies reveal a highly conserved mechanism, and hydrogen–deuterium exchange mass spectrometry analyses highlight similar cores of stability in regions dominated by clusters of branched aliphatic side chains. A bioinformatics analysis of hundreds of IGPS sequences from each superkingdom shows a very highly conserved sequence, V/ILLI, that nucleates the formation of a misfolded, microsecond intermediate and has existed since the last universal common ancestor of the IGPS family of proteins., The amino acid sequences of proteins have evolved over billions of years, preserving their structures and functions while responding to evolutionary forces. Are there conserved sequence and structural elements that preserve the protein folding mechanisms? The functionally diverse and ancient (βα)1–8 TIM barrel motif may answer this question. We mapped the complex six-state folding free energy surface of a ∼3.6 billion y old, bacterial indole-3-glycerol phosphate synthase (IGPS) TIM barrel enzyme by equilibrium and kinetic hydrogen–deuterium exchange mass spectrometry (HDX-MS). HDX-MS on the intact protein reported exchange in the native basin and the presence of two thermodynamically distinct on- and off-pathway intermediates in slow but dynamic equilibrium with each other. Proteolysis revealed protection in a small (α1β2) and a large cluster (β5α5β6α6β7) and that these clusters form cores of stability in Ia and Ibp. The strongest protection in both states resides in β4α4 with the highest density of branched aliphatic side chain contacts in the folded structure. Similar correlations were observed previously for an evolutionarily distinct archaeal IGPS, emphasizing a key role for hydrophobicity in stabilizing common high-energy folding intermediates. A bioinformatics analysis of IGPS sequences from the three superkingdoms revealed an exceedingly high hydrophobicity and surprising α-helix propensity for β4, preceded by a highly conserved βα-hairpin clamp that links β3 and β4. The conservation of the folding mechanisms for archaeal and bacterial IGPS proteins reflects the conservation of key elements of sequence and structure that first appeared in the last universal common ancestor of these ancient proteins.

Catalysis using iron–sulfur clusters and transition metals can be traced back to the last universal common ancestor. The damage to metalloproteins caused by reactive oxygen species (ROS) can prevent cell growth and survival when unmanaged, thus eliciting an essential stress response that is universal and fundamental in biology. Here we develop a computable multiscale description of the ROS stress response in Escherichia coli , called OxidizeME. We use OxidizeME to explain four key responses to oxidative stress: 1) ROS-induced auxotrophy for branched-chain, aromatic, and sulfurous amino acids; 2) nutrient-dependent sensitivity of growth rate to ROS; 3) ROS-specific differential gene expression separate from global growth-associated differential expression; and 4) coordinated expression of iron–sulfur cluster (ISC) and sulfur assimilation (SUF) systems for iron–sulfur cluster biosynthesis. These results show that we can now develop fundamental and quantitative genotype–phenotype relationships for stress responses on a genome-wide basis.

The attempt to delineate the essential features that characterized life in its beginnings and the understanding of how those features evolved, represent important scientific challenges. While there have been varied efforts in the elucidation of how the first biomolecules arose from a prebiotic environment, there remains important gaps towards the characterization of the complete repertoire of the Last Universal Common Ancestor (LUCA). We portray a step-wise proteome evolution, by looking at the phenotype encoded by each one of the genetic codes that were appearing along evolution, beginning with the primeval genetic code and then with two intermediate Extended RNA codes, which finally shaped the current Standard Genetic Code (SGC). Notably, all molecules involved in translation, such as ribosomal proteins and all tRNA synthetases, were already present before LUCA. The metabolism belonged to extremophiles as hinted by the presence of reverse gyrase and acetyl coenzyme A synthase. Furthermore, we predict the structure and possible ligands of the proteins retrieved. We have forged a bridge between the hitherto unknown proteome of progenotes and the proteome of LUCA.

Compartmentalization was likely essential for primitive chemical systems during the emergence of life, both for preventing leakage of important components, i.e., genetic materials, and for enhancing chemical reactions. Although life as we know it uses lipid bilayer-based compartments, the diversity of prebiotic chemistry may have enabled primitive living systems to start from other types of boundary systems. Here, we demonstrate membraneless compartmentalization based on prebiotically available organic compounds, α-hydroxy acids (αHAs), which are generally coproduced along with α-amino acids in prebiotic settings. Facile polymerization of αHAs provides a model pathway for the assembly of combinatorially diverse primitive compartments on early Earth. We characterized membraneless microdroplets generated from homo- and heteropolyesters synthesized from drying solutions of αHAs endowed with various side chains. These compartments can preferentially and differentially segregate and compartmentalize fluorescent dyes and fluorescently tagged RNA, providing readily available compartments that could have facilitated chemical evolution by protecting, exchanging, and encapsulating primitive components. Protein function within and RNA function in the presence of certain droplets is also preserved, suggesting the potential relevance of such droplets to various origins of life models. As a lipid amphiphile can also assemble around certain droplets, this further shows the droplets’ potential compatibility with and scaffolding ability for nascent biomolecular systems that could have coexisted in complex chemical systems. These model compartments could have been more accessible in a “messy” prebiotic environment, enabling the localization of a variety of protometabolic and replication processes that could be subjected to further chemical evolution before the advent of the Last Universal Common Ancestor.

A diverse collection of enzymes comprising the protocatechuate dioxygenases (PCADs) has been characterized in several extradiol aromatic compound degradation pathways. Structural studies have shown a relationship between PCADs and the more broadly-distributed, functionally enigmatic Memo domain linked to several human diseases. To better understand the evolution of this PCAD–Memo protein superfamily, we explored their structural and functional determinants to establish a unified evolutionary framework, identifying 15 clearly-delineable families, including a previously-underappreciated diversity in five Memo clade families. We place the superfamily's origin within the greater radiation of the nucleoside phosphorylase/hydrolase-peptide/amidohydrolase fold prior to the last universal common ancestor of all extant organisms. In addition to identifying active-site residues across the superfamily, we describe three distinct, structurally-variable regions emanating from the core scaffold often housing conserved residues specific to individual families. These were predicted to contribute to the active-site pocket, potentially in substrate specificity and allosteric regulation. We also identified several previously-undescribed conserved genome contexts, providing insight into potentially novel substrates in PCAD clade families. We extend known conserved contextual associations for the Memo clade beyond previously-described associations with the AMMECR1 domain and a radical S-adenosylmethionine family domain. These observations point to two distinct yet potentially overlapping contexts wherein the elusive molecular function of the Memo domain could be finally resolved, thereby linking it to nucleotide base and aliphatic isoprenoid modification. In total, this report throws light on the functions of large swaths of the experimentally-uncharacterized PCAD–Memo families.

Motivation Histones form octameric complexes called nucleosomes, which organize the genomic DNA of eukaryotes into chromatin. Each nucleosome comprises two copies each of the histones H2A, H2B, H3 and H4, which share a common ancestry. Although histones were initially thought to be a eukaryotic innovation, the subsequent identification of archaeal homologs led to the notion that histones emerged before the divergence of archaea and eukaryotes. Results Here, we report the detection and classification of two new groups of histone homologs, which are present in both archaea and bacteria. Proteins in one group consist of two histone subunits welded into single-chain pseudodimers, whereas in the other they resemble eukaryotic core histone subunits and show sequence patterns characteristic of DNA binding. The sequences come from a broad spectrum of deeply-branching lineages, excluding their genesis by horizontal gene transfer. Our results extend the origin of histones to the last universal common ancestor. Supplementary information Supplementary data are available at Bioinformatics online.

In this study, we used a computational approach to investigate the early evolutionary history of a system of proteins that, together, embed and translocate other proteins across cell membranes. Cell membranes comprise the basis for cellularity, which is an ancient, fundamental organizing principle shared by all organisms and a key innovation in the evolution of life on Earth. Two related requirements for cellularity are that organisms are able to both embed proteins into membranes and translocate proteins across membranes. One system that accomplishes these tasks is the signal recognition particle (SRP) system, in which the core protein components are the paralogs, FtsY and Ffh. Complementary to the SRP system is the Sec translocation channel, in which the primary channel-forming protein is SecY. We performed phylogenetic analyses that strongly supported prior inferences that FtsY, Ffh, and SecY were all present by the time of the last universal common ancestor of life, the LUCA, and that the ancestor of FtsY and Ffh existed before the LUCA. Further, we combined ancestral sequence reconstruction and protein structure and function prediction to show that the LUCA had an SRP system and Sec translocation channel that were similar to those of extant organisms. We also show that the ancestor of Ffh and FtsY that predated the LUCA was more similar to FtsY than Ffh but could still have comprised a rudimentary protein translocation system on its own. Duplication of the ancestor of FtsY and Ffh facilitated the specialization of FtsY as a membrane bound receptor and Ffh as a cytoplasmic protein that could bind nascent proteins with specific membrane-targeting signal sequences. Finally, we analyzed amino acid frequencies in our ancestral sequence reconstructions to infer that the ancestral Ffh/FtsY protein likely arose prior to or just after the completion of the canonical genetic code. Taken together, our results offer a window into the very early evolutionary history of cellularity., Author summary Cellularity is an ancient, fundamental organizing principle of life. Central to cellularity is the cell membrane, which separates a cell from the outside environment. Cell membranes contain proteins that perform a range of functions including transport of compounds across the membrane barrier, sensing the external environment, and performing certain metabolic activities that must occur in proximity to the membrane. Therefore, embedding proteins into membranes and secreting proteins across membranes is an essential aspect of cellularity, not to mention an essential aspect of life itself. One cellular system that accomplishes embedding proteins into membranes and secreting proteins across membranes is the signal recognition particle (SRP) system. The SRP system has a core consisting of the proteins, FtsY and Ffh, which derive from a single FtsY/Ffh ancestral protein. The system is also associated with a protein-based passageway, the Sec channel, for embedding proteins within the membrane or allowing them to pass through it. To study the SRP system and the central protein of the Sec channel, SecY, in early life, we reconstructed evolutionary trees from protein sequences. Based on these trees, we infer that the last universal common ancestor (LUCA) of life had an SRP system and SecY channel that were similar to those in extant organisms, while an earlier ancestor of the LUCA possessed a more rudimentary system for embedding and secreting proteins. Moreover, the ancestral Ffh/FtsY protein probably arose prior to or soon after the final amino acids were added to the standard genetic code.

The twenty amino acids in the standard genetic code were fixed prior to the last universal common ancestor (LUCA). Factors that guided this selection included establishment of pathways for their metabolic synthesis and the concomitant fixation of substrate specificities in the emerging aminoacyl-tRNA synthetases (aaRSs). In this conceptual paper, we propose that the chemical reactivity of some amino acid side chains (e.g., lysine, cysteine, homocysteine, ornithine, homoserine, and selenocysteine) delayed or prohibited the emergence of the corresponding aaRSs and helped define the amino acids in the standard genetic code. We also consider the possibility that amino acid chemistry delayed the emergence of the glutaminyl- and asparaginyl-tRNA synthetases, neither of which are ubiquitous in extant organisms. We argue that fundamental chemical principles played critical roles in fixation of some aspects of the genetic code pre- and post-LUCA.

I analyzed the implications of the observation that the methyltransferases, Trm5 and TrmD, which perform the methylation of the 37th base (m1G37) in tRNAs of bacteria and archaea respectively, are not homologous proteins. The first implication is that these methyltransferases originated very late only when the fundamental lineages leading to bacteria and archaea had separated, otherwise the two methyltransferases would have been homologous enzymes, which they are not. The conclusion that Trm5 and TrmD originated only when the main lineages were defined would imply that at least some aspects of the translation, such as +1 frameshifting, were still in rapid and progressive evolution, that is, they were still originating. This would in itself imply a high rate of translation errors because the absence of m1G37 from tRNAs could have determined a high rate of +1 translational frameshifting in the reading of mRNAs, identifying this stage as that of a phase of the origin of the genetic code. Furthermore, the observation that the frameshifting mechanism was still in rapid and progressive evolution in such an advanced evolutionary stage would imply that other mechanisms concerning translation were still rapidly evolving simply because it would be very unique if only the frameshifting mechanism were the only one still originating. Importantly, the observation that in archaea m1G37 also acts as a determinant of the identity of the tRNACysGCA would imply in itself that some aspects of the origin of the genetic code were still originating, greatly strengthening the hypothesis that other aspects of the translation apparatus were still in rapid and progressive evolution. Then, all this would imply a status of progenote for LUCA and ancestors of archaea and bacteria because a high rate of translation errors would fall within the definition of progenote.

All life on Earth is unified by its use of a shared set of component chemical compounds and reactions, providing a detailed model for universal biochemistry. However, this notion of universality is specific to currently observed biochemistry and does not allow quantitative predictions about examples not yet observed. Here we introduce a more generalizable concept of biochemical universality, more akin to the kind of universality discussed in physics. Using annotated genomic datasets including an ensemble of 11955 metagenomes and 1282 archaea, 11759 bacteria and 200 eukaryotic taxa, we show how four of the major enzyme functions - the oxidoreductases, transferases, hydrolases and ligases - form universality classes with common scaling behavior in their relative abundances observed across the datasets. We verify these universal scaling laws are not explained by the presence of compounds, reactions and enzyme functions shared across all known examples of life. We also demonstrate how a consensus model for the last universal common ancestor (LUCA) is consistent with predictions from these scaling laws, with the exception of ligases and transferases. Our results establish the existence of a new kind of biochemical universality, independent of the details of the component chemistry, with implications for guiding our search for missing biochemical diversity on Earth, or other for any biochemistries that might deviate from the exact chemical make-up of life as we know it, such as at the origins of life, in alien environments, or in the design of synthetic life.

All life forms on earth ultimately descended from a primordial population dubbed the last universal common ancestor or LUCA via Darwinian evolution. Extant living systems share two salient functional features, a metabolism extracting and transforming energy required for survival, and an evolvable, informational polymer – the genome – conferring heredity. Genome replication invariably generates essential and ubiquitous genetic parasites. Here we model the energetic, replicative conditions of LUCA-like organisms and their parasites, as well as adaptive problem solving of host-parasite pairs. We show using the Lotka-Volterra equations that three host-parasite pairs – individually a unit of a host and a parasite that is itself parasitized – are sufficient for robust and stable homeostasis, forming a life cycle. This catalytic life cycle efficiently captures, channels and transforms energy, enabling dynamic host survival and adaptation. We propose a Malthusian fitness model for an original quasispecies evolving through a host-parasite life cycle.

Speciation, an evolutionary process by which new species form, is ultimately responsible for the incredible biodiversity that we observe on Earth every day. Such biodiversity is one of the critical features which contributes to the survivability of biospheres and modern life. While speciation and biodiversity have been amply studied in organismic evolution and modern life, it has not yet been applied to a great extent to understanding the evolutionary dynamics of primitive life. In particular, one unanswered question is at what point in the history of life did speciation as a phenomenon emerge in the first place. Here, we discuss the mechanisms by which speciation could have occurred before the origins of life in the context of chemical evolution. Specifically, we discuss that primitive compartments formed before the emergence of the last universal common ancestor (LUCA) could have provided a mechanism by which primitive chemical systems underwent speciation. In particular, we introduce a variety of primitive compartment structures, and associated functions, that may have plausibly been present on early Earth, followed by examples of both discriminate and indiscriminate speciation affected by primitive modes of compartmentalization. Finally, we discuss modern technologies, in particular, droplet microfluidics, that can be applied to studying speciation phenomena in the laboratory over short timescales. We hope that this discussion highlights the current areas of need in further studies on primitive speciation phenomena while simultaneously proposing directions as important areas of study to the origins of life.

Extant protein-coding sequences span a huge range of ages, from those that emerged only recently in particular lineages, to those present in the last universal common ancestor. Because evolution has had less time to act on young sequences, there might be “phylostratigraphy” trends in any properties that evolve slowly with age. Indeed, a long-term reduction in hydrophobicity and in hydrophobic clustering has been found in previous, taxonomically restricted studies. Here we perform integrated phylostratigraphy across 435 fully sequenced and dated eukaryotic species, using sensitive HMM methods to detect homology of protein domains (which may vary in age within the same gene), and applying a variety of quality filters. We find that the reduction in hydrophobic clustering is universal across diverse lineages, showing limited sign of saturation. But the tendency for young domains to have higher protein structural disorder, driven primarily by more hydrophilic amino acids, is found only among young animal domains, and not young plant domains, nor ancient domains predating the existence of the last eukaryotic common ancestor. Among ancient domains, trends in amino acid composition reflect the order of recruitment into the genetic code, suggesting that events during the earliest stages of life on earth continue to have an impact on the composition of ancient sequences.

Building a live cell from non-living building blocks would be a fundamental breakthrough in biological sciences, and it would enable engineering new lineages of life, not directly descendant of the Last Universal Common Ancestor. Fully engineered synthetic cells will have architectures that can be radically different from the natural cells, yet most life processes reconstituted in synthetic cells so far are built from natural and biosimilar building blocks. Most natural processes have already been reconstituted in synthetic cell chassis. This paper summarizes recent advancements in using non-living building blocks to reconstitute some of the most crucial features of living systems in a fully engineerable chassis of a synthetic cell.

Evidence of homology between proteins in the ATP synthetase and the bacterial flagellar motor (BFM) has been accumulating since the 1980s. Specifically, the BFM’s Type 3 Secretion System (T3SS) export apparatus FliH, FliI, and FliJ are considered homologous to FO-b + F1-δ, F1-α/β, and F1-γ, and have similar structure and interactions. We review the discoveries that advanced the homology hypothesis and then conduct a further test by examining gene order in the two systems and their relatives. Conservation of gene order, or synteny, is often observed between closely related prokaryote species, but usually degrades with phylogenetic distance. As a result, observed conservation of synteny over vast phylogenetic distances can be evidence of shared ancestral coexpression, interaction, and function. We constructed a gene order dataset by examining the order offliH,fliI, andfliJgenes across the phylogenetic breadth of flagellar and nonflagellar T3SS. We compared this to published surveys of gene order in the F1FO-ATP synthetase, its N-ATPase relatives, and the bacterial/archaeal V- and A-type ATPases. Strikingly, thefliHIJgene order was deeply conserved, with the few exceptions appearing derived, and exactly matching the widely conserved F-ATPase gene orderatpFHAG, coding for subunitsb-δ-α-γ. The V/A-type ATPases have a similar conserved gene order shared for homologous components. Our results further strengthen the argument for homology between these systems, and suggest a rare case of synteny conserved over billions of years, dating back to well before the Last Universal Common Ancestor (LUCA).

One of the most studied metabolic routes is the biosynthesis of histidine, especially in enterobacteria where a single compact operon composed of eight adjacent genes encodes the complete set of biosynthetic enzymes. It is still not clear how his genes were organized in the genome of the last universal common ancestor community. The aim of this work was to analyze the structure, organization, phylogenetic distribution, and degree of horizontal gene transfer (HGT) of his genes in the Bacteroidota-Rhodothermota-Balneolota-Chlorobiota superphylum, a group of phylogenetically close bacteria with different surviving strategies. The analysis of the large variety of his gene structures and organizations revealed different scenarios with genes organized in more or less compact—heterogeneous or homogeneous—operons, in suboperons, or in regulons. The organization of his genes in the extant members of the superphylum suggests that in the common ancestor of this group, genes were scattered throughout the chromosome and that different forces have driven the assembly of his genes in compact operons. Gene fusion events and/or paralog formation, HGT of single genes or entire operons between strains of the same or different taxonomic groups, and other molecular rearrangements shaped the his gene structure in this superphylum.

While gazing at the Earth from orbit, some astronauts have described a cognitive shift known as the overview effect. Here we describe an analogous biological overview effect produced by looking at the tiny twig of humanity on the tree of life. We describe the increasingly precise phylogenetic tree of all life on Earth and how it shows us our place in nature among the other eukaryotes, metazoa, vertebrates and apes. We discuss problems with this tree including the assumption of sexual isolation, purely vertical gene transmission and the dependence of the epoch of LUCA (Last Universal Common Ancestor) on the completeness of the tree. We compile and present the most concise taxonomic overview of the evolution of our lineage from LUCA to humans. We conclude with a description of how the biological overview effect might help us survive.

We discuss how environmental conditions of the early Earth about 4.5 billion years ago have been estimated from astronomy, geology and chemistry. Of major interest are the prebiotic chemical constituents from which life began. We discuss models for precursors of the first cells, including more detailed models: the hypercycle model, the metabolism first model, the protocell model and a model based on phylogenetic methods of a last universal common ancestor of cells.

Contains fulltext : 232020.pdf (Publisher’s version ) (Open Access) Archaea synthesize membranes of isoprenoid lipids that are ether-linked to glycerol-1-phosphate (G1P), while Bacteria/Eukarya produce membranes consisting of fatty acids ester-bound to glycerol-3-phosphate (G3P). This dichotomy in membrane lipid composition (i.e., the 'lipid divide') is believed to have arisen after the Last Universal Common Ancestor (LUCA). A leading hypothesis is that LUCA possessed a heterochiral 'mixed archaeal/bacterial membrane'. However, no natural microbial representatives supporting this scenario have been shown to exist today. Here, we demonstrate that bacteria of the Fibrobacteres-Chlorobi-Bacteroidetes (FCB) group superphylum encode a putative archaeal pathway for ether-bound isoprenoid membrane lipids in addition to the bacterial fatty acid membrane pathway. Key genes were expressed in the environment and their recombinant expression in Escherichia coli resulted in the formation of a 'mixed archaeal/bacterial membrane'. Genomic evidence and biochemical assays suggest that the archaeal-like lipids of members of the FCB group could possess either a G1P or G3P stereochemistry. Our results support the existence of 'mixed membranes' in natural environments and their stability over a long period in evolutionary history, thereby bridging a once-thought fundamental divide in biology.

Cells occupy a prominent place in the history of life on planet Earth. The central role of cellular organization is observed by the fact that “cellular life” is often used as a synonym for life itself. Thus, most characteristics used to define cells overlap with the ones used to define life. Notwithstanding, new scenarios about the origin of life are bringing alternative views to describe how cells may have evolved from the open biological systems named progenotes. Here, using a logical and conceptual analysis, we re-evaluate the characteristics used to infer a single origin for cells. We argue that some evidences used to support cell monophyly, such as the presence of elements from both the translation mechanism and the universality of the genetic code, actually indicate a unique origin for all “biological systems”, a term used to define not only cells, but also virus and progenotes. Besides, we present evidence that at least two biochemical pathways as important as (i) DNA replication and (ii) lipid biosynthesis may not homologous between Bacteria and Archaea. The identities observed between the proteins involved in those pathways along representatives of these two ancestral Domains are too low to indicate common genic ancestry. Altogether these facts can be seen as an indication that cellular organization has possibly evolved two or more times and that LUCA (the Last Universal Common Ancestor) might not have existed as a cellular entity. Thus, we aim to consider the possibility that different strategies acquired by biological systems to exist, such as viral, bacterial and archaeal were originated independently from the evolution of different progenote populations.

Dating back to the last universal common ancestor (LUCA), the P-loop NTPases and Rossmanns now comprise the most ubiquitous and diverse enzyme lineages. Intriguing similarities in their overall architecture and phosphate binding motifs suggest common ancestry; however, due to a lack of sequence identity and some fundamental structural differences, these families are considered independent emergences. To address this longstanding dichotomy, we systematically searched for ‘bridge proteins’ with structure and sequence elements shared by both lineages. We detected homologous segments that span the first βαβ segment of both lineages and include two key functional motifs: (i) a phosphate binding loop – the ‘Walker A’ motif of P-loop NTPases or the Rossmann equivalent, both residing at the N-terminus of α1; and (ii) an Asp at the tip of β2. The latter comprises the ‘Walker B’ aspartate that chelates the catalytic metal in P-loop NTPases, or the canonical Rossmann β2-Asp that binds the cofactor’s ribose moiety. Tubulin, a Rossmann GTPase, demonstrates the potential of the β2-Asp to take either one of these two roles. We conclude that common P-loops/Rossmann ancestry is plausible, although convergence cannot be completely ruled out. Regardless, both lineages most likely emerged from a polypeptide comprising a βαβ segment carrying the above two functional motifs, a segment that comprises the core of both enzyme families to this very day.

Jumbo phages have attracted much attention by virtue of their extraordinary genome size and unusual aspects of biology. By performing a comparative genomics analysis of 224 jumbo phages, we suggest an objective inclusion criterion based on genome size distributions and present a synthetic overview of their manifold adaptations across major biological systems. By means of clustering and principal component analysis of the phyletic patterns of conserved genes, all known jumbo phages can be classified into three higher-order groups, which include both myoviral and siphoviral morphologies indicating multiple independent origins from smaller predecessors. Our study uncovers several under-appreciated or unreported aspects of the DNA replication, recombination, transcription and virion maturation systems. Leveraging sensitive sequence analysis methods, we identify novel protein-modifying enzymes that might help hijack the host-machinery. Focusing on host&ndash, virus conflicts, we detect strategies used to counter different wings of the bacterial immune system, such as cyclic nucleotide- and NAD+-dependent effector-activation, and prevention of superinfection during pseudolysogeny. We reconstruct the RNA-repair systems of jumbo phages that counter the consequences of RNA-targeting host effectors. These findings also suggest that several jumbo phage proteins provide a snapshot of the systems found in ancient replicons preceding the last universal ancestor of cellular life.

It has been firmly observed that replicative DNA polymerases of bacteria, archaea and eukaryotes are not homologous proteins. This lack of homology in the replication apparatus among the domains of life is not only compatible with but would seem to imply the view that the emergence of DNA occurred in the fundamental cellular lineages. In consequence, this diversity of DNA polymerase would go back to the level of ancestors of the domains of life and to the evolutionary time in which the DNA emerged. Therefore, the presumed evolutionary stage linked to the RNA- > DNA transition would have occurred only at the level of ancestors of the main lineages of the tree of life. Thus, the high noise associated with this major evolutionary transition and the impossibility for a cellular stage to generate different fundamental genetically profound traits - such as the different replication apparatuses of bacteria, archaea and eukaryotes - would imply not only that the last universal common ancestor (LUCA) was a progenote but that the ancestors of the domains of life were also at this evolutionary stage. So, I criticize the hypotheses which want, instead, that completely different cells - such as, bacteria and archaea - could have originated from a cellular LUCA.

The Archaea present profound differences compared to Bacteria in fundamental molecular and cellular processes. While most Archaea divide by binary fission using an FtsZ-based system similar to Bacteria, they lack the majority of the components forming the complex bacterial divisome. Moreover, how FtsZ precisely functions and interacts with other proteins to assemble the archaeal division machinery remains largely unknown. Notably, among the multiple bacterial factors that tether FtsZ to the membrane during cell constriction, Archaea only possess SepF-like homologues, but their function has not been demonstrated. Here, we combine structural, cellular, and evolutionary approaches to demonstrate that SepF is the FtsZ anchor in the human-associated archaeon Methanobrevibacter smithii. 3D super-resolution microscopy of immunolabeled cells shows that M. smithii SepF co-localizes with FtsZ at the division plane. We also show that M. smithii SepF binds both to membranes and FtsZ, inducing filament bundling. High-resolution crystal structures of archaeal SepF alone and in complex with FtsZCTD reveal that SepF forms a dimer with a specific homodimerization interface. This drives a strikingly different binding mode from what is observed in Bacteria. Finally, analysis of the distribution and phylogeny of SepF and FtsZ indicates that these proteins date back to the Last Universal Common Ancestor (LUCA) and that Archaea may have retained features of an ancestral minimal cell division system, while Bacteria likely diverged to accommodate the emergence of the complex machinery required to coordinate cytokinesis with the rigid peptidoglycan cell wall and the appearance of additional FtsZ tethers. Our results contribute key insights into the largely understudied mechanisms of archaeal cell division, and pave the way for a better understanding of the processes underlying the divide between the two prokaryotic domains.

The phage shock protein (PSP) systems orchestrate a conserved stress response function by stabilizing the cell membrane and protecting bacteria from envelope stress. The full repertoire of PSP components remains poorly characterized. We combined comparative genomics and protein sequence-structure-function analyses to systematically identify homologs, phyletic patterns, domain architectures, and gene neighborhoods to trace the evolution of PSP components across the tree of life. This approach showed that the core component PspA/Snf7 (Psp/ESCRT systems) was present in the Last Universal Common Ancestor and that different clades co-opted a diverse range of partners to constitute distinct PSP systems. We identified several novel partners of the PSP system: (i) the Toastrack domain, which likely facilitates assembling diverse sub-membrane stress-sensing and signaling complexes, (ii) the newly-defined HAAS–PadR-like transcription regulator pair system, and (iii) multiple independent associations with ATPase or CesT/Tir-like chaperones, and Band-7 domain proteins that likely mediate sub-membrane dynamics. Our work also uncovered links between the PSP components and diverse SHOCT-like domains, suggesting a role in assembling membrane-associated complexes of proteins with disparate biochemical functions. Tracing the evolution of Psp cognate proteins provides new insights into the functions of the system and helps predict previously uncharacterized, often lineage-specific, membrane-dynamics and stress-response systems. The conservation of PSP systems across bacterial phyla emphasizes the importance of this stress response system in prokaryotes, while its modular diversity in various lineages indicates the emergence of lineage-specific cell-envelope structures, lifestyles, and adaptation mechanisms. The results can be accessed at https://jravilab.shinyapps.io/psp-evolution.

Membrane enclosed intracellular compartments have been exclusively associated with the eukaryotes, represented by the highly compartmentalized last eukaryotic common ancestor. Recent evidence showing the presence of membranous compartments with specific functions in archaea and bacteria makes it conceivable that the last universal common ancestor and its hypothetical precursor, the protocell, may have exhibited compartmentalization. To the authors' knowledge, there are no experimental studies yet that have tested this hypothesis. They report on an autonomous subcompartmentalization mechanism for protocells which results in the transformation of initial subcompartments to daughter protocells. The process is solely determined by the fundamental materials properties and interfacial events, and does not require biological machinery or chemical energy supply. In the light of the authors' findings, it is proposed that similar events may have taken place under early Earth conditions, leading to the development of compartmentalized cells and potentially, primitive division.

A fundamental concept in evolutionary theory is the last universal common ancestor (LUCA) from which all living organisms. While some authors have suggested a relatively complex LUCA 1 it is still widely assumed that LUCA must have been a very simple cell and that life has subsequently increased in complexity through time 2,3. However, while current thought does tend towards a general increase in complexity through time in Eukaryotes 4,5, there is increasing evidence that bacteria and archaea have undergone considerable genome reduction during their evolution 6,7. This raises the surprising possibility that LUCA, as the ancestor of bacteria and archaea may have been a considerably complex cell. While hypotheses regarding the phenotype of LUCA do exist, all are founded on gene presence/absence 1–3. Yet, despite recent attempts to link genes and phenotypic traits in prokaryotes 8,9, it is still inherently difficult to predict phenotype based on the presence or absence of genes alone. In response to this, we used Bayesian phylogenetic comparative methods 10,11 to predict ancestral traits. Testing for robustness to horizontal gene transfer (HGT) we inferred the phenotypic traits of LUCA using two robust published phylogenetic trees 12,13 and a dataset of 3,128 bacterial and archaeal species (Supplementary Information). Our results depict LUCA as a far more complex cell than has previously been proposed, challenging the evolutionary model of increased complexity through time in prokaryotes. Given current estimates for the emergence of LUCA we suggest that early life very rapidly evolved considerable cellular complexity.

It is puzzling why life on Earth consisted of prokaryotes for up to 2.5 ± 0.5 billion years (Gy) before the appearance of the first eukaryotes. This period, from LUCA (Last Universal Common Ancestor) to LECA (Last Eucaryotic Common Ancestor), we have named the Lucacene, to suggest all prokaryotic descendants of LUCA before the appearance of LECA. Here we present a simple model based on horizontal gene transfer (HGT). It is the process of HGT from Bacteria to Archaea and its reverse that we wish to simulate and estimate its duration until eukaryogenesis. Rough quantitation of its parameters shows that the model may explain the long duration of the Lucacene.