The Last Universal Common Ancestor (LUCA) and the Ancestors of Archaea and Bacteria were Progenotes

The time of appearance of the genetic code

I support the hypothesis that the origin of the genetic code occurred simultaneously with the evolution of cellularity. That is to say, I favour the hypothesis that the origin of the genetic code is a very, very late event in the history of life on Earth. I corroborate this hypothesis with observations favouring the progenote's stage for the Last Universal Common Ancestor (LUCA), for the ancestor of bacteria and that of archaea. Indeed, these progenotic stages would imply that - at that time - the origin of the genetic code was still ongoing simply because this origin would fall within the very definition of progenote. Therefore, if the evolution of cellularity had truly been coeval with the origin of the genetic code - at least in its terminal part - then this would favour theories such as the coevolution theory of the origin of the genetic code because this theory would postulate that this origin must have occurred in extremely complex protocellular conditions and not concerning stereochemical or physicochemical interactions having to do with other stages of the origin of life. In this sense, the coevolution theory would be corroborated while the stereochemical and physicochemical theories would be damaged. Therefore, the origin of the genetic code would be linked to the origin of the cell and not to the origin of life as sometimes asserted. Therefore, I will discuss the late hypothesis of the origin of the genetic code in the context of the theories proposed to explain this origin and more generally of its implications for the early evolution of life.

The absence of the evolutionary state of the Prokaryote would imply a polyphyletic origin of proteins and that LUCA, the ancestor of bacteria and that of archaea were progenotes

I analysed the similarity gradient observed in protein families - of phylogenetically deep fundamental traits - of bacteria and archaea, ranging from cases such as the core of the DNA replication apparatus where there is no sequence similarity between the proteins involved, to cases in which, as in the translation initiation factors, only some proteins involved would be homologs, to cases such as for aminoacyl-tRNA synthetases in which most of the proteins involved would be homologs. This pattern of similarity between bacteria and archaea would seem to be a very clear indication of a transitional evolutionary stage that preceded both the Last Bacterial Common Ancestor and the Last Archaeal Common Ancestor, i.e. progenotic stages. Indeed, this similarity pattern would seem to exemplify an ongoing transition as all the evolutionary phases would be represented in it. Instead, in the cellular stage it is expected that these evolutionary phases should have already been overcome, i.e. completed, and therefore no longer detectable. In fact, if we had really been in the presence of the prokaryotic stage then we should not have observed this similarity pattern in proteins involved in defining the ancestral characters of bacteria and archaea, as the completion of the different cellular structures should have required a very low number of proteins to be late evolved in lineages leading to bacteria and archaea. Indeed, the already reached state of the Prokaryote would have determined complete cellular structures therefore a total absence of proteins to evolve independently in the two main phyletic lineages and able to complete the evolution of a particular character already evidently in a definitive state, which, on the other hand, does not appear to have been the case. All this would have prevented the formation of this pattern of similarity which instead would appear to be real. In conclusion, the existence of this pattern of similarity observed in the families of homologous proteins of bacteria and archaea would imply the absence of the evolutionary stage of the Prokaryote and consequently a progenotic status to be assigned to the LUCA. Indeed, the LUCA stage would have been a stage of evolutionary transition because it is belatedly marked by the presence of all the different evolutionary phases, evidently more easily interpretable within the definition of progenote than that of genote precisely because they are inherent in an evolutionary transition and not to an evolution that has already been achieved. Finally, I discuss the importance of these arguments for the polyphyletic origin of proteins.

Biological Catalysis and Information Storage Have Relied on N-Glycosyl Derivatives of β-D-Ribofuranose since the Origins of Life

Most naturally occurring nucleotides and nucleosides are N-glycosyl derivatives of β-d-ribose. These N-ribosides are involved in most metabolic processes that occur in cells. They are essential components of nucleic acids, forming the basis for genetic information storage and flow. Moreover, these compounds are involved in numerous catalytic processes, including chemical energy production and storage, in which they serve as cofactors or coribozymes. From a chemical point of view, the overall structure of nucleotides and nucleosides is very similar and simple. However, their unique chemical and structural features render these compounds versatile building blocks that are crucial for life processes in all known organisms. Notably, the universal function of these compounds in encoding genetic information and cellular catalysis strongly suggests their essential role in the origins of life. In this review, we summarize major issues related to the role of N-ribosides in biological systems, especially in the context of the origin of life and its further evolution, through the RNA-based World(s), toward the life we observe today. We also discuss possible reasons why life has arisen from derivatives of β-d-ribofuranose instead of compounds based on other sugar moieties.

Natural History of DNA-Dependent DNA Polymerases: Multiple Pathways to the Origins of DNA

One of the major evolutionary transitions that led to DNA replacing RNA as the primary informational molecule in biological systems is still the subject of an intense debate in the scientific community. DNA polymerases are currently split into various families. Families A, B, and C are the most significant. In bacteria and some types of viruses, enzymes from families A and C predominate, whereas family B enzymes are more common in Archaea, Eukarya, and some types of viruses. A phylogenetic analysis of these three families of DNA polymerase was carried out. We assumed that reverse transcriptase was the ancestor of DNA polymerases. Our findings suggest that families A and C emerged and organized themselves when the earliest bacterial lineages had diverged, and that these earliest lineages had RNA genomes that were in transition—that is, the information was temporally stored in DNA molecules that were continuously being produced by reverse transcription. The origin of DNA and the apparatus for its replication in the mitochondrial ancestors may have occurred independently of DNA and the replication machinery of other bacterial lineages, according to these two alternate modes of genetic material replication. The family C enzymes emerged in a particular bacterial lineage before being passed to viral lineages, which must have functioned by disseminating this machinery to the other lineages of bacteria. Bacterial DNA viruses must have evolved at least twice independently, in addition to the requirement that DNA have arisen twice in bacterial lineages. We offer two possible scenarios based on what we know about bacterial DNA polymerases. One hypothesis contends that family A was initially produced and spread to the other lineages through viral lineages before being supplanted by the emergence of family C and acquisition at that position of the principal replicative polymerase. The evidence points to the independence of these events and suggests that the viral lineage’s acquisition of cellular replicative machinery was crucial for the establishment of a DNA genome in the other bacterial lineages, since these viral lineages may have served as a conduit for the machinery’s delivery to other bacterial lineages that diverged with the RNA genome. Our data suggest that family B initially established itself in viral lineages and was transferred to ancestral Archaea lineages before the group diversified; thus, the DNA genome must have emerged first in this cellular lineage. Our data point to multiple evolutionary steps in the origins of DNA polymerase, having started off at least twice in the bacterial lineage and once in the archaeal lineage. Given that viral lineages are implicated in a significant portion of the distribution of DNA replication equipment in both bacterial (families A and C) and Archaeal lineages (family A), our data point to a complex scenario.

The RNase P, LUCA, the ancestors of the life domains, the progenote, and the tree of life

I have tried to interpret the phylogenetic distribution of the RNase P with the aim of helping to clarify the stage reached by the evolution of cellularity in the Last Universal Common Ancestor (LUCA); that is to say, if the evolutionary stage of the LUCA was represented by a protocell (progenote) or by a complete cell (genote). Since there are several arguments that lead one to believe that only the RNA moiety of the RNase P was present in the LUCA, this might imply that this evolutionary stage was actually the RNA world. If true this would imply that the LUCA was a progenote because the RNA world being a world subject to multiple evolutionary transitions that would involve a high noise at many its levels, which would fall within the definition of the progenote. Furthermore, since RNA-mediated catalysis is much less efficient than protein-mediated catalysis, then the only RNA moiety that was present in the LUCA could imply - by per se, without invoking the existence of the RNA world - that the LUCA was a progenote because an inefficient catalysis might have characterized this evolutionary stage. This evolutionary stage would still fall under the definition of the progenote. In addition, the observation that the protein moieties of the RNase P of bacteria and archaea are not-homologs would imply that these originated independently in the two main phyletic lineages. In turn, this would imply the progenotic nature of the ancestors of both archaea and bacteria. Indeed, it is admissible that such a late origin - in the main phyletic lineages - of the protein moieties of the RNase P is witness to an evolutionary transition towards a more efficient catalysis, evidently made clear precisely by the evolution of the protein moieties of the RNase P which would have helped the RNA of the RNase P to a more efficient catalysis. Hence, this would date that evolutionary moment as a transition to a much more efficient catalysis and consequently would imply which in that evolutionary stage there was the actual transition from the progenotic to genotic status. Finally, this late origin of the RNase P protein moieties in the bacterial and archaeal domains per se could imply the presence of a progenotic stage for their ancestors, or at least that a cell stage would have been much less likely. In fact, it is true that genes can originate both in a cellular and in a progenotic stage, but they mainly typify the latter because they are, by definition, in formation. Then it is expected that in the evolutionary stage of the formation of the main phyletic lineages - that is to say, in an evolutionary time in which the formation of genes might be expected - that the origin of proteins is to be related to a rapid and progressive evolution typical of the progenote precisely because in such an evolutionary stage the origin of genes is more easily and simply explained as reflecting a progenotic rather than a genotic stage. Indeed, if instead the evolutionary stage of the ancestors of bacteria and archaea had been the cellular one, then observing the origin of the protein moieties of the RNase P would have been, to some extent, anomalous because this completion should have already occurred, simply because the transformation of a ribozyme into an enzyme should have already taken place precisely because it falls within the very definition of the cellular status. The conclusion is that both the LUCA and the ancestor of archaea and that of bacteria may have been progenotes. If these arguments were true then either the tree of life as commonly understood would not exist and therefore the main phyletic lineages would have originated directly from the LUCA, or there would have been at least two different populations of progenotes that would have finally defined the domain of bacteria and that of archaea.

Historical Perspective of Pore-Forming Activity Studies of Voltage-Dependent Anion Channel (Eukaryotic or Mitochondrial Porin) Since Its Discovery in the 70th of the Last Century

Eukaryotic porin, also known as Voltage-Dependent Anion Channel (VDAC), is the most frequent protein in the outer membrane of mitochondria that are responsible for cellular respiration. Mitochondria are most likely descendants of strictly aerobic Gram-negative bacteria from the α-proteobacterial lineage. In accordance with the presumed ancestor, mitochondria are surrounded by two membranes. The mitochondrial outer membrane contains besides the eukaryotic porins responsible for its major permeability properties a variety of other not fully identified channels. It encloses also the TOM apparatus together with the sorting mechanism SAM, responsible for the uptake and assembly of many mitochondrial proteins that are encoded in the nucleus and synthesized in the cytoplasm at free ribosomes. The recognition and the study of electrophysiological properties of eukaryotic porin or VDAC started in the late seventies of the last century by a study of Schein et al., who reconstituted the pore from crude extracts of Paramecium mitochondria into planar lipid bilayer membranes. Whereas the literature about structure and function of eukaryotic porins was comparatively rare during the first 10years after the first study, the number of publications started to explode with the first sequencing of human Porin 31HL and the recognition of the important function of eukaryotic porins in mitochondrial metabolism. Many genomes contain more than one gene coding for homologs of eukaryotic porins. More than 100 sequences of eukaryotic porins are known to date. Although the sequence identity between them is relatively low, the polypeptide length and in particular, the electrophysiological characteristics are highly preserved. This means that all eukaryotic porins studied to date are anion selective in the open state. They are voltage-dependent and switch into cation-selective substates at voltages in the physiological relevant range. A major breakthrough was also the elucidation of the 3D structure of the eukaryotic pore, which is formed by 19 β-strands similar to those of bacterial porin channels. The function of the presumed gate an α-helical stretch of 20 amino acids allowed further studies with respect to voltage dependence and function, but its exact role in channel gating is still not fully understood.

The phylogenetic distribution of the cell division system would not imply a cellular LUCA but a progenotic LUCA

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.

Comparative Genomics Provides Insights into the Genetic Diversity and Evolution of the DPANN Superphylum

DPANN is known as highly diverse, globally widespread, and mostly ectosymbiotic archaeal superphylum. However, this group of archaea was overlooked for a long time, and there were limited in-depth studies reported. In this investigation, 41 metagenome-assembled genomes (MAGs) belonging to the DPANN superphylum were recovered (18 MAGs had average nucleotide identity [ANI] values of <95% and a percentage of conserved proteins [POCP] of >50%, while 14 MAGs showed a POCP of <50%), which were analyzed comparatively with 515 other published DPANN genomes. Mismatches to known 16S rRNA gene primers were identified among 16S rRNA genes of DPANN archaea. Numbers of gene families lost (mostly related to energy and amino acid metabolism) were over three times greater than those gained in the evolution of DPANN archaea. Lateral gene transfer (LGT; ∼45.5% was cross-domain) had facilitated niche adaption of the DPANN archaea, ensuring a delicate equilibrium of streamlined genomes with efficient niche-adaptive strategies. For instance, LGT-derived cytochrome bd ubiquinol oxidase and arginine deiminase in the genomes of “Candidatus Micrarchaeota” could help them better adapt to aerobic acidic mine drainage habitats. In addition, most DPANN archaea acquired enzymes for biosynthesis of extracellular polymeric substances (EPS) and transketolase/transaldolase for the pentose phosphate pathway from Bacteria.

IMPORTANCE The domain Archaea is a key research model for gaining insights into the origin and evolution of life, as well as the relevant biogeochemical processes. The discovery of nanosized DPANN archaea has overthrown many aspects of microbiology. However, the DPANN superphylum still contains a vast genetic novelty and diversity that need to be explored. Comprehensively comparative genomic analysis on the DPANN superphylum was performed in this study, with an attempt to illuminate its metabolic potential, ecological distribution and evolutionary history. Many interphylum differences within the DPANN superphylum were found. For example, Altiarchaeota had the biggest genome among DPANN phyla, possessing many pathways missing in other phyla, such as formaldehyde assimilation and the Wood-Ljungdahl pathway. In addition, LGT acted as an important force to provide DPANN archaeal genetic flexibility that permitted the occupation of diverse niches. This study has advanced our understanding of the diversity and genome evolution of archaea.

Errors of the ancestral translation, LUCA, and nature of its direct descendants

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 tRNA^Cys_GCA 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.

The late appearance of DNA, the nature of the LUCA and ancestors of the domains of 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.

LUCA as well as the ancestors of archaea, bacteria and eukaryotes were progenotes: Inference from the distribution and diversity of the reading mechanism of the AUA and AUG codons in the domains of life

Here I use the rationale assuming that if of a certain trait that exerts its function in some aspect of the genetic code or, more generally, in protein synthesis, it is possible to identify the evolutionary stage of its origin then it would imply that this evolutionary moment would be characterized by a high translational noise because this trait would originate for the first time during that evolutionary stage. That is to say, if this trait had a non-marginal role in the realization of the genetic code, or in protein synthesis, then the origin of this trait would imply that, more generally, it was the genetic code itself that was still originating. But if the genetic code were still originating - at that precise evolutionary stage - then this would imply that there was a high translational noise which in turn would imply that it was in the presence of a protocell, i.e. a progenote that was by definition characterized by high translational noise. I apply this rationale to the mechanism of modification of the base 34 of the anticodon of an isoleucine tRNA that leads to the reading of AUA and AUG codons in archaea, bacteria and eukaryotes. The phylogenetic distribution of this mechanism in these phyletic lineages indicates that this mechanism originated only after the evolutionary stage of the last universal common ancestor (LUCA), namely, during the formation of cellular domains, i.e., at the stage of ancestors of these main phyletic lineages. Furthermore, given that this mechanism of modification of the base 34 of the anticodon of the isoleucine tRNA would result to emerge at a stage of the origin of the genetic code - despite in its terminal phases - then all this would imply that the ancestors of bacteria, archaea and eukaryotes were progenotes. If so, all the more so, the LUCA would also be a progenote since it preceded these ancestors temporally. A consequence of all this reasoning might be that since these three ancestors were of the progenotes that were different from each other, if at least one of them had evolved into at least two real and different cells - basically different from each other - then the number of cellular domains would not be three but it would be greater than three.

The phylogenetic distribution of the glutaminyl-tRNA synthetase and Glu-tRNAGln amidotransferase in the fundamental lineages would imply that the ancestor of archaea, that of eukaryotes and LUCA were progenotes

The function of the glutaminyl-tRNA synthetase and Glu-tRNA^Gln amidotransferase might be related to the origin of the genetic code because, for example, glutaminyl-tRNA synthetase catalyses the fundamental reaction that makes the genetic code. If the evolutionary stage of the origin of these two enzymes could be unambiguously identified, then the genetic code should still have been originating at that particular evolutionary stage because the fundamental reaction that makes the code itself was still evidently evolving. This would result in that particular evolutionary moment being attributed to the evolutionary stage of the progenote because it would have a relationship between the genotype and the phenotype not yet fully realized because the genetic code was precisely still originating. I then analyzed the distribution of the glutaminyl-tRNA synthetase and Glu-tRNA^Gln aminodotrasferase in the main phyletic lineages. Since in some cases the origin of these two enzymes can be related to the evolutionary stages of ancestors of archaea and eukaryotes, this would indicate these ancestors as progenotes because at that evolutionary moment the genetic code was evidently still evolving, thus realizing the definition of progenote. The conclusion that the ancestor of archaea and that of eukaryotes were progenotes would imply that even the last universal common ancestor (LUCA) was a progenote because it appeared, on the tree of life, temporally before these ancestors.

Older Than Genes: The Acetyl CoA Pathway and Origins

For decades, microbiologists have viewed the acetyl CoA pathway and organisms that use it for H2-dependent carbon and energy metabolism, acetogens and methanogens, as ancient. Classical evidence and newer evidence indicating the antiquity of the acetyl CoA pathway are summarized here. The acetyl CoA pathway requires approximately 10 enzymes, roughly as many organic cofactors, and more than 500 kDa of combined subunit molecular mass to catalyze the conversion of H2 and CO2 to formate, acetate, and pyruvate in acetogens and methanogens. However, a single hydrothermal vent alloy, awaruite (Ni3Fe), can convert H2 and CO2 to formate, acetate, and pyruvate under mild hydrothermal conditions on its own. The chemical reactions of H2 and CO2 to pyruvate thus have a natural tendency to occur without enzymes, given suitable inorganic catalysts. This suggests that the evolution of the enzymatic acetyl CoA pathway was preceded by-and patterned along-a route of naturally occurring exergonic reactions catalyzed by transition metal minerals that could activate H2 and CO2 by chemisorption. The principle of forward (autotrophic) pathway evolution from preexisting non-enzymatic reactions is generalized to the concept of patterned evolution of pathways. In acetogens, exergonic reduction of CO2 by H2 generates acyl phosphates by highly reactive carbonyl groups undergoing attack by inert inorganic phosphate. In that ancient reaction of biochemical energy conservation, the energy behind formation of the acyl phosphate bond resides in the carbonyl, not in phosphate. The antiquity of the acetyl CoA pathway is usually seen in light of CO2 fixation; its role in primordial energy coupling via acyl phosphates and substrate-level phosphorylation is emphasized here.

Why Is AUG the Start Codon?: Theoretical Minimal RNA Rings: Maximizing Coded Information Biases 1st Codon for the Universal Initiation Codon AUG

The rational design of theoretical minimal RNA rings predetermines AUG as the universal start codon. This design maximizes coded amino acid diversity over minimal sequence length, defining in silico theoretical minimal RNA rings, candidate ancestral genes. RNA rings code for 21 amino acids and a stop codon after three consecutive translation rounds, and form a degradation-delaying stem-loop hairpin. Twenty-five RNA rings match these constraints, ten start with the universal initiation codon AUG. No first codon bias exists among remaining RNA rings. RNA ring design predetermines AUG as initiation codon. This is the only explanation yet for AUG as start codon. RNA ring design determines additional RNA ring gene- and tRNA-like properties described previously, because it presumably mimics constraints on life's primordial RNAs.

A Prerequisite for Life

The complex physicochemical structures and chemical reactions in living organism have some common features: (1) The life processes take place in the cytosol in the cells, which, from a physicochemical point of view is an emulsion of biomolecules in a dilute aqueous suspension. (2) All living systems are homochiral with respect to the units of amino acids and carbohydrates, but (some) proteins are chiral unstable in the cytosol. (3) And living organism are mortal. These three common features together give a prerequisite for the prebiotic self-assembly at the start of the Abiogenesis. Here we argue, that it all together indicates, that the prebiotic self-assembly of structures and reactions took place in a more saline environment, whereby the homochirality of proteins not only could be obtained, but also preserved. A more saline environment for the prebiotic self-assembly of organic molecules and establishment of biochemical reactions could have been the hydrothermal vents.

Geological and Geochemical Constraints on the Origin and Evolution of Life

The traditional tree of life from molecular biology with last universal common ancestor (LUCA) branching into bacteria and archaea (though fuzzy) is likely formally valid enough to be a basis for discussion of geological processes on the early Earth. Biologists infer likely properties of nodal organisms within the tree and, hence, the environment they inhabited. Geologists both vet tenuous trees and putative origin of life scenarios for geological and ecological reasonability and conversely infer geological information from trees. The latter approach is valuable as geologists have only weakly constrained the time when the Earth became habitable and the later time when life actually existed to the long interval between ∼4.5 and ∼3.85 Ga where no intact surface rocks are known. With regard to vetting, origin and early evolution hypotheses from molecular biology have recently centered on serpentinite settings in marine and alternatively land settings that are exposed to ultraviolet sunlight. The existence of these niches on the Hadean Earth is virtually certain. With regard to inferring geological environment from genomics, nodes on the tree of life can arise from true bottlenecks implied by the marine serpentinite origin scenario and by asteroid impact. Innovation of a very useful trait through a threshold allows the successful organism to quickly become very abundant and later root a large clade. The origin of life itself, that is, the initial Darwinian ancestor, the bacterial and archaeal roots as free-living cellular organisms that independently escaped hydrothermal chimneys above marine serpentinite or alternatively from shallow pore-water environments on land, the Selabacteria root with anoxygenic photosynthesis, and the Terrabacteria root colonizing land are attractive examples that predate the geological record. Conversely, geological reasoning presents likely events for appraisal by biologists. Asteroid impacts may have produced bottlenecks by decimating life. Thermophile roots of bacteria and archaea as well as a thermophile LUCA are attractive.

The last universal common ancestor between ancient Earth chemistry and the onset of genetics

All known life forms trace back to a last universal common ancestor (LUCA) that witnessed the onset of Darwinian evolution. One can ask questions about LUCA in various ways, the most common way being to look for traits that are common to all cells, like ribosomes or the genetic code. With the availability of genomes, we can, however, also ask what genes are ancient by virtue of their phylogeny rather than by virtue of being universal. That approach, undertaken recently, leads to a different view of LUCA than we have had in the past, one that fits well with the harsh geochemical setting of early Earth and resembles the biology of prokaryotes that today inhabit the Earth's crust.

New insights into a hot environment for early life

Investigating the physical-chemical setting of early life is a challenging task. In this contribution, the author attempted to introduce a provocative concept from cosmology - cosmic microwave background (CMB), which is the residual thermal radiation from a hot early Universe - to the field. For this purpose, the author revisited a recently deduced biomarker, the 1,6-anhydro bond of sugars in bacteria. In vitro, the 1,6-anhydro bond of sugars reflects and captures residual thermal radiation in thermochemical processes and therefore is somewhat analogous to CMB. In vivo, the formation process of the 1,6-anhydro bond of sugars on the peptidoglycan of prokaryotic cell wall is parallel to in vitro processes, suggesting that the 1,6-anhydro bond is an ideal CMB-like analogue that suggests a hot setting for early life. The CMB-like 1,6-anhydro bond is involved in the life cycle of viruses and the metabolism of eukaryotes, underlying this notion. From a novel perspective, the application of the concept of the CMB to microbial ecology may give new insights into a hot environment, such as hydrothermal vents, supporting early life and providing hypotheses to test in molecular palaeontology.

Life before LUCA

We see the last universal common ancestor of all living organisms, or LUCA, at the evolutionary separation of the Archaea from the Eubacteria, and before the symbiotic event believed to have led to the Eukarya. LUCA is often implicitly taken to be close to the origin of life, and sometimes this is even stated explicitly. However, LUCA already had the capacity to code for many proteins, and had some of the same bioenergetic capacities as modern organisms. An organism at the origin of life must have been vastly simpler, and this invites the question of how to define a living organism. Even if acceptance of the giant viruses as living organisms forces the definition of LUCA to be revised, it will not alter the essential point that LUCA should be regarded as a recent player in the evolution of life.

The relative ages of eukaryotes and akaryotes

The Last Eukaryote Common Ancestor (LECA) appears to have the genetics required for meiosis, mitosis, nucleus and nuclear substructures, an exon/intron gene structure, spliceosomes, many centres of DNA replication, etc. (and including mitochondria). Most of these features are not generally explained by models for the origin of the Eukaryotic cell based on the fusion of an Archeon and a Bacterium. We find that the term 'prokaryote' is ambiguous and the non-phylogenetic term akaryote should be used in its place because we do not yet know the direction of evolution between eukaryotes and akaryotes. We use the term 'protoeukaryote' for the hypothetical stem group ancestral eukaryote that took up a bacterium as an endosymbiont that formed the mitochondrion. It is easier to make detailed models with a eukaryote to an akaryote transition, rather than vice versa. So we really are at a phylogenetic impasse in not being confident about the direction of change between eukaryotes and akaryotes.

Biology of purinergic signalling: its ancient evolutionary roots, its omnipresence and its multiple functional significance

The purinergic signalling system, which utilises ATP, related nucleotides and adenosine as transmitter molecules, appeared very early in evolution: release mechanisms and ATP-degrading enzymes are operative in bacteria, and the first specific receptors are present in single cell eukaryotic protozoa and algae. Further evolution of the purinergic signalling system resulted in the development of multiple classes of purinoceptors, several pathways for release of nucleotides and adenosine, and a system of ectonucleotidases controlling extracellular levels of purinergic transmitters. The purinergic signalling system is expressed in virtually all types of tissues and cells, where it mediates numerous physiological reactions and contributes to pathological responses in a variety of diseases.

Type IV pili in Gram-positive bacteria

Type IV pili (T4P) are surface-exposed fibers that mediate many functions in bacteria, including locomotion, adherence to host cells, DNA uptake (competence), and protein secretion and that can act as nanowires carrying electric current. T4P are composed of a polymerized protein, pilin, and their assembly apparatuses share protein homologs with type II secretion systems in eubacteria and the flagella of archaea. T4P are found throughout Gram-negative bacterial families and have been studied most extensively in certain model Gram-negative species. Recently, it was discovered that T4P systems are also widespread among Gram-positive species, in particular the clostridia. Since Gram-positive and Gram-negative bacteria have many differences in cell wall architecture and other features, it is remarkable how similar the T4P core proteins are between these organisms, yet there are many key and interesting differences to be found as well. In this review, we compare the two T4P systems and identify and discuss the features they have in common and where they differ to provide a very broad-based view of T4P systems across all eubacterial species.

Novel molecular fossils of bacteria: insights into hydrothermal origin of life

Hydrothermal vents, in particular, alkaline submarine vents, are potential systems for the origin of life. Early hydrothermal vents may have imprinted on biochemical processes and housekeeping proteins of life and have hallmarked key molecules. This essay introduces new information to this discussion by focusing on newly identified sulfur-modified DNA and a heretofore ignored anhydro bond of the cell wall peptidoglycan in bacteria. It is suggested that they are novel molecular fossils that are relevant to the settings of alkaline submarine vents and harbor clues of early life. As DNA and the cell wall are bound up with genetic information and the integrity of cell, respectively, these two molecular fossils may provide insights into hydrothermal origin of life from a new angle.

Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC

BACKGROUND

Bacterial genomes displaying a strong bias between the leading and the lagging strand of DNA replication encode two DNA polymerases III, DnaE and PolC, rather than a single one. Replication is a highly unsymmetrical process, and the presence of two polymerases is therefore not unexpected. Using comparative genomics, we explored whether other processes have evolved in parallel with each polymerase.

RESULTS

Extending previous in silico heuristics for the analysis of gene co-evolution, we analyzed the function of genes clustering with dnaE and polC. Clusters were highly informative. DnaE co-evolves with the ribosome, the transcription machinery, the core of intermediary metabolism enzymes. It is also connected to the energy-saving enzyme necessary for RNA degradation, polynucleotide phosphorylase. Most of the proteins of this co-evolving set belong to the persistent set in bacterial proteomes, that is fairly ubiquitously distributed. In contrast, PolC co-evolves with RNA degradation enzymes that are present only in the A+T-rich Firmicutes clade, suggesting at least two origins for the degradosome.

CONCLUSION

DNA replication involves two machineries, DnaE and PolC. DnaE co-evolves with the core functions of bacterial life. In contrast PolC co-evolves with a set of RNA degradation enzymes that does not derive from the degradosome identified in gamma-Proteobacteria. This suggests that at least two independent RNA degradation pathways existed in the progenote community at the end of the RNA genome world.