Why the Lipid Divide? Membrane Proteins as Drivers of the Split between the Lipids of the Three Domains of Life

A call for research on the basis for polygonal pleomorphism in archaea

Morphogenesis is a major unsolved problem. It is usually tackled in the embryogenesis of multicellular organisms, but rarely leans on studies of single-cell organisms. But the latter often have fascinating, puzzling shapes, whose understanding may be key to multicellular embryogenesis, wound healing, and regeneration. Here, I call for new directions in studying what may have been the first shaped, single-celled organisms, the Domain of Archaea, which might have been LUCA (Last Universal Common Ancestor), the first organisms at the origin of life. While their shaping is usually attributed to the "crystallinity" of the S-layer, this may have the liquidity of a bubble raft.

Archaeal Lipids: Extraction, Separation, and Identification via Natural Product Chemistry Perspective

Archaeal lipids, defining a primordial life domain alongside Bacteria and Eukarya, are distinguished by their unique glycerol-1-phosphate backbone and ether-linked isoprenoid chains. Serving as critical geochemical biomarkers, archaeal lipids like glycerol dialkyl glycerol tetraethers (GDGTs) underpin paleoclimate proxies, while their phylum-specific distributions illuminate phylogenetic divergence. Despite the maturity of Mass Spectrometry-based quantitative biomarkers-predominantly those with established structures-becoming well-established in geochemical research, systematic investigation of archaeal lipids as natural products has notably lagged. This deficit manifests across three key dimensions: (1) Extraction methodology lacks universal protocols adapted to diverse archaeal taxa and sample matrices. While comparative studies exist, theoretical frameworks guiding method selection remain underexplored. (2) Purification challenges persist due to the unique structures and complex isomerization profiles of archaeal lipids, hindering standardized separation protocols. (3) Most critically, structural characterization predominantly depends on decades-old foundational studies. However, the existing reviews prioritize chemical structural, biosynthetic, and applied aspects of archaeal lipids over analytical workflows. This review addresses this gap by adopting a natural product chemistry perspective, integrating three key aspects: (1) the clarification of applicable objects, scopes, and methodological mechanisms of various extraction technologies for archaeal lipids, encompassing both cultured and environmental samples; (2) the elucidation of separation principles underlying polar-gradient lipid fractionation processes, leveraging advanced chromatographic technologies; (3) the detailed exploration of applications for NMR in resolving complex lipid structures, with specialized emphasis on determining the stereochemical configuration. By synthesizing six decades of methodological evolution, we establish a comprehensive analytical framework, from lipids extraction to structural identification. This integrated approach constructs a systematic methodological paradigm for archaeal lipid analysis, bridging theoretical principles with practical implementation.

A tuneable minimal cell membrane reveals that two lipid species suffice for life

All cells are encapsulated by a lipid membrane that facilitates their interactions with the environment. How cells manage diverse mixtures of lipids, which dictate membrane property and function, is experimentally challenging to address. Here, we present an approach to tune and minimize membrane lipid composition in the bacterium Mycoplasma mycoides and its derived 'minimal cell' (JCVI-Syn3A), revealing that a two-component lipidome can support life. Systematic reintroduction of phospholipids with different features demonstrates that acyl chain diversity is more important for growth than head group diversity. By tuning lipid chirality, we explore the lipid divide between Archaea and the rest of life, showing that ancestral lipidomes could have been heterochiral. However, in these simple organisms, heterochirality leads to impaired cellular fitness. Thus, our approach offers a tunable minimal membrane system to explore the fundamental lipidomic requirements for life, thereby extending the concept of minimal life from the genome to the lipidome.

A tuneable minimal cell membrane reveals that two lipid species suffice for life

All cells are encapsulated by a lipid membrane which facilitates the interaction between life and its environment. How life exploits the diverse mixtures of lipids that dictate membrane property and function has been experimentally challenging to address. We introduce an approach to tune and minimize lipidomes in Mycoplasma mycoides and the Minimal Cell (JCVI-Syn3A) revealing that a 2-component lipidome can support life. Systematically reintroducing phospholipid features demonstrated that acyl chain diversity is more critical for growth than head group diversity. By tuning lipid chirality, we explored the lipid divide between Archaea and the rest of life, showing that ancestral lipidomes could have been heterochiral. Our approach offers a tunable minimal membrane system to explore the fundamental lipidomic requirements for life, thereby extending the concept of minimal life from the genome to the lipidome.

The evolutionary arch of bioenergetics from prebiotic mechanisms to the emergence of a cellular respiratory chain

This article proposes an evolutionary trajectory for the development of biological energy producing systems. Six main stages of energy producing system evolution are described, from early evolutionary pyrite-pulled mechanism through the Last Universal Common Ancestor (LUCA) to contemporary systems. We define the Last Pure Chemical Entity (LPCE) as the last completely non-enzymatic entity. LPCE could have had some life-like properties, but lacked genetic information carriers, thus showed greater instability and environmental dependence than LUCA. A double bubble model is proposed for compartmentalization and cellularization as a prerequisite to both highly efficient protein synthesis and transmembrane ion-gradient. The article finds that although LUCA predominantly functioned anaerobically, it was a non-exclusive anaerobe, and sulfur dominated metabolism preceded phosphate dominated one.

Evolution of Cellular Organization Along the First Branches of the Tree of Life

Current evidence suggests that some form of cellular organization arose well before the time of the last universal common ancestor (LUCA). Standard phylogenetic analyses have shown that several protein families associated with membrane translocation, membrane transport, and membrane bioenergetics were very likely present in the proteome of the LUCA. Despite these cellular systems emerging prior to the LUCA, extant archaea, bacteria, and eukaryotes have significant differences in cellular infrastructure and the molecular functions that support it, leading some researchers to argue that true cellularity did not evolve until after the LUCA. Here, we use recently reconstructed minimal proteomes of the LUCA as well as the last archaeal common ancestor (LACA) and the last bacterial common ancestor (LBCA) to characterize the evolution of cellular systems along the first branches of the tree of life. We find that a broad set of functions associated with cellular organization were already present by the time of the LUCA. The functional repertoires of the LACA and LBCA related to cellular organization nearly doubled along each branch following the divergence of the LUCA. These evolutionary trends created the foundation for similarities and differences in cellular organization between the taxonomic domains that are still observed today.

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

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

Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome

Most in silico evolutionary studies commonly assumed that core genes are essential for cellular function, while accessory genes are dispensable, particularly in nutrient-rich environments. However, this assumption is seldom tested genetically within the pangenome context. In this study, we conducted a robust pangenomic Tn-seq analysis of fitness genes in a nutrient-rich medium for Sinorhizobium strains with a canonical open pangenome. To evaluate the robustness of fitness category assignment, Tn-seq data for three independent mutant libraries per strain were analyzed by three methods, which indicates that the Hidden Markov Model (HMM)-based method is most robust to variations between mutant libraries and not sensitive to data size, outperforming the Bayesian and Monte Carlo simulation-based methods. Consequently, the HMM method was used to classify the fitness category. Fitness genes, categorized as essential (ES), advantage (GA), and disadvantage (GD) genes for growth, are enriched in core genes, while nonessential genes (NE) are over-represented in accessory genes. Accessory ES/GA genes showed a lower fitness effect than core ES/GA genes. Connectivity degrees in the cofitness network decrease in the order of ES, GD, and GA/NE. In addition to accessory genes, 1599 out of 3284 core genes display differential essentiality across test strains. Within the pangenome core, both shared quasi-essential (ES and GA) and strain-dependent fitness genes are enriched in similar functional categories. Our analysis demonstrates a considerable fuzzy essential zone determined by cofitness connectivity degrees in Sinorhizobium pangenome and highlights the power of the cofitness network in understanding the genetic basis of ever-increasing prokaryotic pangenome data.

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

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

Archaeal lipids

The major archaeal membrane glycerolipids are distinguished from those of bacteria and eukaryotes by the contrasting stereochemistry of their glycerol backbones, and by the use of ether-linked isoprenoid-based alkyl chains rather than ester-linked fatty acyl chains for their hydrophobic moieties. These fascinating compounds play important roles in the extremophile lifestyles of many species, but are also present in the growing numbers of recently discovered mesophilic archaea. The past decade has witnessed significant advances in our understanding of archaea in general and their lipids in particular. Much of the new information has come from the ability to screen large microbial populations via environmental metagenomics, which has revolutionised our understanding of the extent of archaeal biodiversity that is coupled with a strict conservation of their membrane lipid compositions. Significant additional progress has come from new culturing and analytical techniques that are gradually enabling archaeal physiology and biochemistry to be studied in real time. These studies are beginning to shed light on the much-discussed and still-controversial process of eukaryogenesis, which probably involved both bacterial and archaeal progenitors. Puzzlingly, although eukaryotes retain many attributes of their putative archaeal ancestors, their lipid compositions only reflect their bacterial progenitors. Finally, elucidation of archaeal lipids and their metabolic pathways have revealed potentially interesting applications that have opened up new frontiers for biotechnological exploitation of these organisms. This review is concerned with the analysis, structure, function, evolution and biotechnology of archaeal lipids and their associated metabolic pathways.

Biosynthesis of Hybrid Neutral Lipids with Archaeal and Eukaryotic Characteristics in Engineered Saccharomyces cerevisiae

Discovery of the Asgard superphylum of archaea provides new evidence supporting the two-domain model of life: eukaryotes originated from an Asgard-related archaeon that engulfed a bacterial endosymbiont. However, how eukaryotes acquired bacterial-like membrane lipids with a sn-glycerol-3-phosphate (G3P) backbone instead of the archaeal-like sn-glycerol-1-phosphate (G1P) backbone remains unknown. In this study, we reconstituted archaeal lipid production in Saccharomyces cerevisiae by expressing unsaturated archaeol-synthesizing enzymes. Using Golden Gate cloning for pathway assembly, modular gene replacement was performed, revealing the potential biosynthesis of both G1P- and G3P-based unsaturated archaeol by uncultured Asgard archaea. Unexpectedly, hybrid neutral lipids containing both archaeal isoprenoids and eukaryotic fatty acids were observed in recombinant S. cerevisiae. The ability of yeast and archaeal diacylglycerol acyltransferases to synthesize such hybrid lipids was demonstrated.

Self-assembly and biophysical properties of archaeal lipids

Archaea constitute one of the three fundamental domains of life. Archaea possess unique lipids in their cell membranes which distinguish them from bacteria and eukaryotes. This difference in lipid composition is referred to as 'Lipid Divide' and its origins remain elusive. Chemical inertness and the highly branched nature of the archaeal lipids afford the membranes stability against extremes of temperature, pH, and salinity. Based on the molecular architecture, archaeal polar lipids are of two types - monopolar and bipolar. Both monopolar and bipolar lipids have been shown to form vesicles and other well-defined membrane architectures. Bipolar archaeal lipids are among the most unique lipids found in nature because of their membrane-spanning nature and mechanical stability. The majority of the self-assembly studies on archaeal lipids have been carried out using crude polar lipid extracts or molecular mimics. The complexity of the archaeal lipids makes them challenging to synthesize chemically, and as a result, studies on pure lipids are few. There is an ongoing effort to develop simplified routes to synthesize complex archaeal lipids to facilitate diverse biophysical studies and pharmaceutical applications. Investigation on archaeal lipids may help us understand how life survives in extreme conditions and therefore unlock some of the mysteries surrounding the origins of cellular life.

Exploring the realm of soft matter biophysics: an early career perspective

This special issue of Emerging Topics in Life Sciences presents a selection of reviews that give insight into the vast array of research taking place in the fields of soft matter and biophysics, and where these two intersect. The reviews here cover the full range from the fundamentals of how biological systems may have assembled to how we can use this insight to develop and exploit new biomaterials for the future, all informed through the lens of the physical sciences. This issue has been both written and edited by early career researchers, highlighting the cutting-edge contributions that this generation of researchers is bringing to the field.

Origin of cyanobacterial thylakoids via a non-vesicular glycolipid phase transition and their impact on the Great Oxygenation Event

The appearance of oxygenic photosynthesis in cyanobacteria is a major event in evolution. It had an irreversible impact on the Earth, promoting the Great Oxygenation Event (GOE) ~2.4 billion years ago. Ancient cyanobacteria predating the GOE were Gloeobacter-type cells lacking thylakoids, which hosted photosystems in their cytoplasmic membrane. The driver of the GOE was proposed to be the transition from unicellular to filamentous cyanobacteria. However, the appearance of thylakoids expanded the photosynthetic surface to such an extent that it introduced a multiplier effect, which would be more coherent with an impact on the atmosphere. Primitive thylakoids self-organize as concentric parietal uninterrupted multilayers. There is no robust evidence for an origin of thylakoids via a vesicular-based scenario. This review reports studies supporting that hexagonal II-forming glucolipids and galactolipids at the periphery of the cytosolic membrane could be turned, within nanoseconds and without any external source of energy, into membrane multilayers. Comparison of lipid biosynthetic pathways shows that ancient cyanobacteria contained only one anionic lamellar-forming lipid, phosphatidylglycerol. The acquisition of sulfoquinovosyldiacylglycerol biosynthesis correlates with thylakoid emergence, possibly enabling sufficient provision of anionic lipids to trigger a hexagonal II-to-lamellar phase transition. With this non-vesicular lipid-phase transition, a framework is also available to re-examine the role of companion proteins in thylakoid biogenesis.

Possible chemical and physical scenarios towards biological homochirality

The single chirality of biological molecules in terrestrial biology raises more questions than certitudes about its origin. The emergence of biological homochirality (BH) and its connection with the appearance of life have elicited a large number of theories related to the generation, amplification and preservation of a chiral bias in molecules of life under prebiotically relevant conditions. However, a global scenario is still lacking. Here, the possibility of inducing a significant chiral bias "from scratch", i.e. in the absence of pre-existing enantiomerically-enriched chemical species, will be considered first. It includes phenomena that are inherent to the nature of matter itself, such as the infinitesimal energy difference between enantiomers as a result of violation of parity in certain fundamental interactions, and physicochemical processes related to interactions between chiral organic molecules and physical fields, polarized particles, polarized spins and chiral surfaces. The spontaneous emergence of chirality in the absence of detectable chiral physical and chemical sources has recently undergone significant advances thanks to the deracemization of conglomerates through Viedma ripening and asymmetric auto-catalysis with the Soai reaction. All these phenomena are commonly discussed as plausible sources of asymmetry under prebiotic conditions and are potentially accountable for the primeval chiral bias in molecules of life. Then, several scenarios will be discussed that are aimed to reflect the different debates about the emergence of BH: extra-terrestrial or terrestrial origin (where?), nature of the mechanisms leading to the propagation and enhancement of the primeval chiral bias (how?) and temporal sequence between chemical homochirality, BH and life emergence (when?). Intense and ongoing theories regarding the emergence of optically pure molecules at different moments of the evolution process towards life, i.e. at the levels of building blocks of Life, of the instructed or functional polymers, or even later at the stage of more elaborated chemical systems, will be critically discussed. The underlying principles and the experimental evidence will be commented for each scenario with particular attention on those leading to the induction and enhancement of enantiomeric excesses in proteinogenic amino acids, natural sugars, and their intermediates or derivatives. The aim of this review is to propose an updated and timely synopsis in order to stimulate new efforts in this interdisciplinary field.

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

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

Changes in the distribution of membrane lipids during growth of Thermotoga maritima at different temperatures: Indications for the potential mechanism of biosynthesis of ether-bound diabolic acid (membrane-spanning) lipids

Membrane-spanning lipids are present in a wide variety of archaea but they are rarely in bacteria. Nevertheless, the (hyper)thermophilic members of the order Thermotogales harbor tetraester, tetraether, and mixed ether/ester membrane-spanning lipids mostly composed of core lipids derived from diabolic acids, C_30, C₃₂ and C₃₄ dicarboxylic acids with two adjacent mid-chain methyl substituents. Lipid analysis of Thermotoga maritima across growth phases revealed a decrease of the relative abundance of fatty acids together with an increase of diabolic acids with independence of growth temperature. We also identified isomers of C₃₀ and C₃₂ diabolic acids, i.e. dicarboxylic acids with only one methyl group at C-15. Their distribution suggests they are products of the condensation reaction but preferably produced when the length of the acyl chains is not optimal. In comparison with growth at the optimal temperature of 80°C, an increase of glycerol ether-derived lipids was observed at 55°C. Besides, our analysis only detected diabolic acid-containing intact polar lipids with phosphoglycerol (PG) headgroups. Considering these findings, we hypothesize a biosynthetic pathway for the synthesis of membrane-spanning lipids based on PG polar lipid formation, suggesting that the protein catalyzing this process could be a membrane protein. We also identified, by genomic and protein domain analyses, a gene coding for a putative plasmalogen synthase homologue in T. maritima, which is also present in other bacteria producing sn1-alkyl ether lipids but not plasmalogens, suggesting it could be involved in the conversion of the ester to ether bond in the diabolic acids bound in membrane-spanning lipids. Importance Membrane-spanning lipids are unique compounds found in most archaeal membranes, but they are also present in specific bacterial groups like the Thermotogales. The synthesis and physiological role of membrane-spanning lipids in bacteria represent an evolutionary and biochemical open question that points to the differentiation of the membrane lipids composition. Understanding the formation of membrane-spanning lipids is crucial to solving this question and identifying the enzymatic and biochemical mechanism performing this procedure. In the present work, we found changes at the core lipid level, and we propose that the growth phase drives the biosynthesis of these lipids rather than temperature. Our results identified physiological conditions influencing the membrane-spanning lipids biosynthetic process which can further clarify the pathway leading to the biosynthesis of these compounds.

Relational model of the standard genetic code

The genetic code is a set of rules that establishes mapping between triplets in messenger RNA and amino acids in proteins. The most common way to display these rules is the Standard Genetic Code (SGC) table. This paper takes an alternative approach, based on the relational data model by Edgar F. Codd (Commun. ACM, 13:377-387, 1970). The relational model (RM) proposes a distributed storage of data into a collection of tables (called relations), that can be connected by shared communality. Basic elements of the table are rows (called records or tuples), and columns (called fields or attributes). The SGC table, according to the relational data model, represents the so called unnormalized form of a table. Using normalization rules it is possible to subdivide the SGC table into four tables. The rows and columns of single tables are defined by the first and second base and individual tables by the third codon base. The result of this model is an approach to managing genetic code data, represented in terms of tuples and grouped into relations, with table structure and language consistent with first-order (predicate) logic. The RM explains that the final step in the development of the SGC was the adoption of coding function by the third base, which makes an informational/functional unit with the first base, despite the different physical location in a triplet. This enabled the synthesis of specific proteins without ambiguity, in accordance with the concept of ambiguity reduction and five phases of the general model on the origin of biological codes by Marcello Barbieri (BioSystems 181:11-19, 2019).

Probing the Role of Chirality in Phospholipid Membranes

Nucleotides, amino acids, sugars, and lipids are almost ubiquitously homochiral within individual cells on Earth. While oligonucleotides and proteins exist as one natural chirality throughout the tree of life, two stereoisomers of phospholipids have separately emerged in archaea and bacteria, an evolutionary divergence known as "the lipid divide". Within this review, we focus on the emergence of phospholipid homochirality and compare the stability of synthetic homochiral and heterochiral membranes in vitro. We discuss chemical probes designed to study the stereospecific interactions of lipid membranes in vitro. Overall, we aim to highlight studies that help elucidate the determinants of stereospecific interactions between lipids, peptides, and small molecule ligands. Continued work in understanding the drivers of favorable interactions between chiral molecules and biological membranes will lead to the design of increasingly selective chemical tools for bioorthogonal labeling of lipid membranes and safer membrane-associating pharmaceuticals.

The Origin(s) of Cell(s): Pre-Darwinian Evolution from FUCAs to LUCA : To Carl Woese (1928-2012), for his Conceptual Breakthrough of Cellular Evolution

The coming of the Last Universal Cellular Ancestor (LUCA) was the singular watershed event in the making of the biotic world. If the coming of LUCA marked the crossing of the "Darwinian Threshold", then pre-LUCA evolution must have been Pre-Darwinian and at least partly non-Darwinian. But how did Pre-Darwinian evolution before LUCA actually operate? I broaden our understanding of the central mechanism of biological evolution (i.e., variation-selection-inheritance) and then extend this broadened understanding to its natural starting point: the origin(s) of the First Universal Cellular Ancestors (FUCAs) before LUCA. My hypothesis centers upon vesicles' making-and-remaking as variation and competition as selection. More specifically, I argue that vesicles' acquisition and merger, via breaking-and-repacking, proto-endocytosis, proto-endosymbiosis, and other similar processes had been a central force of both variation and selection in the pre-Darwinian epoch. These new perspectives shed important new light upon the origin of FUCAs and their subsequent evolution into LUCA.

Life and living beings under the perspective of organic macrocodes

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.

The requirement of cellularity for abiogenesis

The history of modern biochemistry started with the cellular theory of life. By putting aside the holistic protoplasmic theory, scientists of the XX century were able to advance the functional classification of cellular components significantly. The cell became the unit of the living. Current theories on the abiogenesis of life must account for a moment in evolution (chemical or biological) when this was not the case. Investigating the role of compartments and membranes along chemical and biotic evolution can lead a more generalised idea of living organisms that is fundamental to advance our efforts in astrobiology, origin of life and artificial life studies. Furthermore, it may provide insights in unexplained evolutionary features such as the lipid divide between Archaea and Eubacteria. By surveying our current understanding of the involvement of compartments in abiogenesis and evolution, the idea of cells as atomistic units of a general theory of biology will be discussed. The aim is not to undermine the validity of the cellular theory of life, but rather to elucidate possible biases with regards to cellularity and the origin of life. An open discussion in these regards could show the inherent limitations of non-cellular compartmentalization that may lead to the necessity of cellular structures to support complex life.

Is it possible that cells have had more than one origin?

Cells occupy a prominent place in the history of life in Earth. The central role of cellular organization can be understood by the fact that "cellular life" is often used as a synonym for life itself. Thus, most characteristics used to define cell overlap with those ones used to define life. However, innovative scenarios for 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 the translation mechanism together with 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 viruses and progenotes. Besides, we present evidence that at least two biochemical pathways as important as (i) DNA replication and (ii) lipid biosynthesis are not homologous between Bacteria and Archaea. The identities observed between the proteins involved in those pathways along representatives of these two ancestral domains of life 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) may 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 most likely originated independently from the evolution of different progenote populations.

Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)

Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.

Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)

Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.

The archaeal-bacterial lipid divide, could a distinct lateral proton route hold the answer?

The archaea-bacteria lipid divide is one of the big evolutionary enigmas concerning these two domains of life. In short, bacterial membranes are made of fatty-acid esters whereas archaeal ones contain isoprenoid ethers, though at present we do not have a good understanding on why they evolved differently. The lateral proton transfer mode of energy transduction in membranes posits that protons utilize the solvation layer of the membrane interface as the main route between proton pumps and ATPases, avoiding dissipation of energy to the bulk phase. In this article I present the hypothesis on a proton-transport route through the ester groups of bacterial phospholipids as an explanation for the evolutionary divergence seen between bacteria and archaea. REVIEWERS: This article was reviewed by Uri Gophna (Editorial Board member) and Víctor Sojo.

Isoprenoids enhance the stability of fatty acid membranes at the emergence of life potentially leading to an early lipid divide

Two key problems concern cell membranes during the emergence and early evolution of life: what was their initial composition, and why did the membranes of archaea and bacteria diverge? The composition of the first cell membranes could shed light on the most likely environment for the emergence of life. The opposing stereochemistry of modern lipid glycerol-phosphate headgroups in bacteria and archaea suggests that early membranes were composed of single chain amphiphiles, perhaps both fatty acids and isoprenoids. We investigated the effect of adding isoprenoids to fatty acid membranes using a combination of UV-visible spectroscopy, confocal microscopy and transmission electron microscopy. We tested the stability of these membranes across a pH range and under different concentrations of ionic species relevant to oceanic hydrothermal environments, including Na2+, Cl-, Mg2+, Ca2+, HC O 3 - , Fe3+, Fe2+ and S2-. We also tested the assembly of vesicles in the presence of Fe particles and FeS precipitates. We found that isoprenoids enhance the stability of membranes in the presence of salts but require 30-fold higher concentrations for membrane formation. Intriguingly, isoprenoids strongly inhibit the tendency of vesicles to aggregate together in the presence of either Fe particles or FeS precipitates. These striking physical differences in the stability and aggregation of protocells may have shaped the divergence of bacteria and archaea in early hydrothermal environments.