Speculations on the origin of life and thermophily: review of available information on reverse gyrase suggests that hyperthermophilic procaryotes are not so primitive

The Evolution of Reverse Gyrase Suggests a Nonhyperthermophilic Last Universal Common Ancestor

Reverse gyrase (RG) is the only protein found ubiquitously in hyperthermophilic organisms, but absent from mesophiles. As such, its simple presence or absence allows us to deduce information about the optimal growth temperature of long-extinct organisms, even as far as the last universal common ancestor of extant life (LUCA). The growth environment and gene content of the LUCA has long been a source of debate in which RG often features. In an attempt to settle this debate, we carried out an exhaustive search for RG proteins, generating the largest RG data set to date. Comprising 376 sequences, our data set allows for phylogenetic reconstructions of RG with unprecedented size and detail. These RG phylogenies are strikingly different from those of universal proteins inferred to be present in the LUCA, even when using the same set of species. Unlike such proteins, RG does not form monophyletic archaeal and bacterial clades, suggesting RG emergence after the formation of these domains, and/or significant horizontal gene transfer. Additionally, the branch lengths separating archaeal and bacterial groups are very short, inconsistent with the tempo of evolution from the time of the LUCA. Despite this, phylogenies limited to archaeal RG resolve most archaeal phyla, suggesting predominantly vertical evolution since the time of the last archaeal ancestor. In contrast, bacterial RG indicates emergence after the last bacterial ancestor followed by significant horizontal transfer. Taken together, these results suggest a nonhyperthermophilic LUCA and bacterial ancestor, with hyperthermophily emerging early in the evolution of the archaeal and bacterial domains.

Increase of positive supercoiling in a hyperthermophilic archaeon after UV irradiation

Diverse DNA repair mechanisms are essential to all living organisms. Some of the most widespread repair systems allow recovery of genome integrity in the face of UV radiation. Here, we show that the hyperthermophilic archaeon Thermococcus nautili possesses a remarkable ability to recovery from extreme chromosomal damage. Immediately following UV irradiation, chromosomal DNA of T. nautili is fragmented beyond recognition. However, the extensive UV-induced double-stranded breaks (DSB) are repaired over the course of several hours, allowing restoration of growth. DSBs also disrupted plasmid DNA in this species. Similar to the chromosome, plasmid integrity was restored during an outgrowth period. Intriguingly, the topology of recovered pTN1 plasmids differed from control strain by being more positively supercoiled. As reverse gyrase (RG) is the only enzyme capable of inducing positive supercoiling, our results suggest the activation of RG activity by UV-induced stress. We suggest simple UV stress could be used to study archaeal DNA repair and responses to DSB.

Environmental Adaptation from the Origin of Life to the Last Universal Common Ancestor

Extensive fundamental molecular and biological evolution took place between the prebiotic origins of life and the state of the Last Universal Common Ancestor (LUCA). Considering the evolutionary innovations between these two endpoints from the perspective of environmental adaptation, we explore the hypothesis that LUCA was temporally, spatially, and environmentally distinct from life's earliest origins in an RNA world. Using this lens, we interpret several molecular biological features as indicating an environmental transition between a cold, radiation-shielded origin of life and a mesophilic, surface-dwelling LUCA. Cellularity provides motility and permits Darwinian evolution by connecting genetic material and its products, and thus establishing heredity and lineage. Considering the importance of compartmentalization and motility, we propose that the early emergence of cellularity is required for environmental dispersal and diversification during these transitions. Early diversification and the emergence of ecology before LUCA could be an important pre-adaptation for life's persistence on a changing planet.

Genetic manipulation in Sulfolobus islandicus and functional analysis of DNA repair genes

Recently, a novel gene-deletion method was developed for the crenarchaeal model Sulfolobus islandicus, which is a suitable tool for addressing gene essentiality in depth. Using this technique, we have investigated functions of putative DNA repair genes by constructing deletion mutants and studying their phenotype. We found that this archaeon may not encode a eukarya-type of NER (nucleotide excision repair) pathway because depleting each of the eukaryal NER homologues XPD, XPB and XPF did not impair the DNA repair capacity in their mutants. However, among seven homologous recombination proteins, including RadA, Hel308/Hjm, Rad50, Mre11, HerA, NurA and Hjc, only the Hjc nuclease is dispensable for cell viability. Sulfolobus encodes redundant BER (base excision repair) enzymes such as two uracil DNA glycosylases and two putative apurinic/apyrimidinic lyases, but inactivation of one of the redundant enzymes already impaired cell growth, highlighting their important roles in archaeal DNA repair. Systematically characterizing these mutants and generating mutants lacking two or more DNA repair genes will yield further insights into the genetic mechanisms of DNA repair in this model organism.

Primal eukaryogenesis: on the communal nature of precellular States, ancestral to modern life

This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) super-cells; (iv) a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v) multiple rounds of micro-cellular escape with streamlined reductive evolution-leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other.

Origin and evolution of life on terrestrial planets

The ultimate goal of terrestrial planet-finding missions is not only to discover terrestrial exoplanets inside the habitable zone (HZ) of their host stars but also to address the major question as to whether life may have evolved on a habitable Earth-like exoplanet outside our Solar System. We note that the chemical evolution that finally led to the origin of life on Earth must be studied if we hope to understand the principles of how life might evolve on other terrestrial planets in the Universe. This is not just an anthropocentric point of view: the basic ingredients of terrestrial life, that is, reduced carbon-based molecules and liquid H(2)O, have very specific properties. We discuss the origin of life from the chemical evolution of its precursors to the earliest life-forms and the biological implications of the stellar radiation and energetic particle environments. Likewise, the study of the biological evolution that has generated the various life-forms on Earth provides clues toward the understanding of the interconnectedness of life with its environment.

Kinetics and activation parameter analysis for the prebiotic oligocytidylate formation on Na(+)-montmorillonite at 0-100 degrees C

The kinetic analysis of the temperature dependence of the formation of oligocytidylate (oligo(C)) from the 5'-monophosphorimidazolide moiety of cytidine (ImpC) in the presence of Na (+)-montmorillonite (Na (+)-Mont) catalyst has been carried out at 0-100 degrees C. The rate constants for the formation of oligo(C), hydrolysis of ImpC with and without Na (+)-Mont and degradation of oligo(C) were determined. The apparent activation parameters were 30.8 +/- 3.9 kJ mol (-1) ( Ea), 28.3 +/- 4.0 kJ mol (-1) (Delta H++), and -231 +/- 13 J mol (-1) K (-1) (Delta S++) for the formation of the 2-mer; 45.6 +/- 2.9 kJ mol (-1) ( Ea), 43.0 +/- 3.0 kJ mol (-1) (Delta H++), -164 +/- 10 J mol (-1) K (-1) (Delta S++) for the 3-mer; and 45.2 +/- 0.6 kJ mol (-1) ( Ea), 42.7 +/- 0.7 kJ mol (-1) (Delta H++), -159 +/- 2 J mol (-1) K (-1) (Delta S++) for the 4-mer in the presence of Na (+)-Mont. An increasing trend for the rate constants for the formation of oligo(C) in the order 2-mer << 3-mer <4-mer was observed at high temperatures, which is consistent with that observed at low temperatures. These analyses implied for the first time that the associate formation between an activated nucleotide monomer and an elongating oligonucleotide prior to the phosphodiester bond formation during the elongation of an oligonucleotide on a clay surface would be based on the interaction between the two reactants at the phosphoester and/or ribose moieties rather than at the nucleotide bases. The hydrolysis rate of ImpC at 25-100 degrees C was 5.3-10.6 times greater in the presence of Na (+)-Mont than in its absence. Although the degradation of oligo(C) in the presence of Na (+)-Mont was slower than the formation of the 3-mer and longer oligo(C) on Na (+)-Mont, its yield decreased with temperature. This is mainly because the ratios of the rate constant of the 2-mer formation to those of ImpC hydrolysis and the 3-mer and 4-mer formation decrease with an increase in temperature, which is attributed to the enthalpy and entropy changes for the formation of the 2-mer. This trend resembles the case of the template-directed formation of oligo(G) on a poly(C) template but is different from the Pb (2+)-ion-catalyzed oligo(C) formation. According to the kinetics and activation parameter analyses regarding the clay reaction and other prebiotic polymerase models, the possible pathways for the oligonucleotide formation are discussed and compared.

The origin of modern terrestrial life

The study of the origin of life covers many areas of expertise and requires the input of various scientific communities. In recent years, this research field has often been viewed as part of a broader agenda under the name of "exobiology" or "astrobiology." In this review, we have somewhat narrowed this agenda, focusing on the origin of modern terrestrial life. The adjective "modern" here means that we did not speculate on different forms of life that could have possibly appeared on our planet, but instead focus on the existing forms (cells and viruses). We try to briefly present the state of the art about alternative hypotheses discussing not only the origin of life per se, but also how life evolved to produce the modern biosphere through a succession of steps that we would like to characterize as much as possible.

About a formamide-based origin of informational polymers: syntheses of nucleobases and favourable thermodynamic niches for early polymers

Formamide NH(2)CHO chemistry provides a unitary frame into which several pieces of the origin-of-life puzzle may be adjusted. Synthetic processes were uncovered which, starting from formamide and prebiotically easily available common catalysts, yield all the necessary nucleic bases precursors, including acyclonucleosides. Formamide allows phosphorylations and trans-phosphorylations, favours the micellar aggregation of surfactants and, most importantly, determines conditions in which the formation of nucleic polymers is thermodynamically favoured. In the detected conditions, the phosphoester bonds are more stable in the polymeric than in the monomeric form, thus allowing formation and survival of informational nucleic polymers.

Boron enhances the thermostability of carbohydrates

We have studied the effect of borate and pH upon the half-lives of ribose and glucose. Under acidic conditions the presence of boric acid increase the thermo-stability of ribose, while under basic conditions glucose is favored.

Origin of informational polymers. Differential stability of 3'- and 5'-phosphoester bonds in deoxy monomers and oligomers

To survive, an informational macromolecule must solve the major problem set by its very polymeric nature: instability. This is especially true in prebiotic terms because of the presumed initial absence of protective structures (proteins, lipids, etc.). We have analyzed the stability of the beta-glycosidic and of the 3'- and 5'-phosphoester bonds in both deoxy monomers and deoxy oligomers under a large set of conditions. The results show a strong dependence of the relative stability of these bonds on the physico-chemical environment. A set of conditions has been identified in which the stability of polymers becomes comparable with that of the precursor monomers. In certain instances the stability of the 5'-phosphoester bond is even higher in the polymer than in the mononucleotide.

Exo/Astrobiology in Europe

The question of the chemical origins of life is engraved in the European scientific patrimony as it can be traced back to the pioneer ideas of Charles Darwin, Louis Pasteur, and more recently to Alexander Oparin. During the last decades, the European community of origin of life scientists has organized seven out of the twelve International Conferences on the Origins of Life held since 1957. This community contributed also to enlarge the field of research to the study of life in extreme environments and to the search for extraterrestrial life, i.e. exobiology in its classical definition or astrobiology if one uses a more NASA-inspired terminology. The present paper aims to describe the European science background in exo/astrobiology as well as the project of a European Network of Exo/Astrobiology.

The late stage of genetic code structuring took place at a high temperature

The correlation between the optimal growth temperature of organisms and a thermophily index based on the propensity of amino acids to enter more frequently into (hyper)thermophile proteins is used to conduct an analysis aiming to establish whether genetic code structuring took place at a low or a high temperature. If the number of codons attributed to the various amino acids in the genetic code constitutes an estimate of the mean amino acid composition of proteins produced when the genetic code was definitively structured, then the thermophily index can also be associated to the genetic code. This value and the sampling of the variable thermophily index of different alignments of protein sequences from mesophile, thermophile and hyperthermophile species make it possible to establish, with an extremely high statistical confidence, that the late stage of genetic code structuring took place in a hyperthermophile (or thermophile) 'organism'. Moreover the 95% confidence interval of the temperature at which the genetic code was fixed turned out to be 91+/-24 degrees C. These observations seem to support the hypothesis that the origin of life might have taken place at a high temperature.

Early evolution: prokaryotes, the new kids on the block

Prokaryotes are generally assumed to be the oldest existing form of life on earth. This assumption, however, makes it difficult to understand certain aspects of the transition from earlier stages in the origin of life to more complex ones, and it does not account for many apparently ancient features in the eukaryotes. From a model of the RNA world, based on relic RNA species in modern organisms, one can infer that there was an absolute requirement for a high-accuracy RNA replicase even before proteins evolved. In addition, we argue here that the ribosome (together with the RNAs involved in its assembly) is so large that it must have had a prior function before protein synthesis. A model that connects and equates these two requirements (high-accuracy RNA replicase and prior function of the ribosome) can explain many steps in the origin of life while accounting for the observation that eukaryotes have retained more vestiges of the RNA world. The later derivation of prokaryote RNA metabolism and genome structure can be accounted for by the two complementary mechanisms of r-selection and thermoreduction.

Cell-free transcription at 95 degrees: thermostability of transcriptional components and DNA topology requirements of Pyrococcus transcription

Cell-free transcription of archaeal promoters is mediated by two archaeal transcription factors, aTBP and TFB, which are orthologues of the eukaryotic transcription factors TBP and TFIIB. Using the cell-free transcription system described for the hyperthermophilic Archaeon Pyrococcus furiosus by Hethke et al., the temperature limits and template topology requirements of archaeal transcription were investigated. aTBP activity was not affected after incubation for 1 hr at 100 degrees. In contrast, the half-life of RNA polymerase activity was 23 min and that of TFB activity was 3 min. The half-life of a 328-nt RNA product was 10 min at 100 degrees. Best stability of RNA was observed at pH 6, at 400 mm K-glutamate in the absence of Mg(2+) ions. Physiological concentrations of K-glutamate were found to stabilize protein components in addition, indicating that salt is an important extrinsic factor contributing to thermostability. Both RNA and proteins were stabilized by the osmolyte betaine at a concentration of 1 m. The highest activity for RNA synthesis at 95 degrees was obtained in the presence of 1 m betaine and 400 mm K-glutamate. Positively supercoiled DNA, which was found to exist in Pyrococcus cells, can be transcribed in vitro both at 70 degrees and 90 degrees. However, negatively supercoiled DNA was the preferred template at all temperatures tested. Analyses of transcripts from plasmid topoisomers harboring the glutamate dehydrogenase promoter and of transcription reactions conducted in the presence of reverse gyrase indicate that positive supercoiling of DNA inhibits transcription from this promoter.

The stability of the RNA bases: implications for the origin of life

High-temperature origin-of-life theories require that the components of the first genetic material are stable. We therefore have measured the half-lives for the decomposition of the nucleobases. They have been found to be short on the geologic time scale. At 100 degreesC, the growth temperatures of the hyperthermophiles, the half-lives are too short to allow for the adequate accumulation of these compounds (t1/2 for A and G approximately 1 yr; U = 12 yr; C = 19 days). Therefore, unless the origin of life took place extremely rapidly (<100 yr), we conclude that a high-temperature origin of life may be possible, but it cannot involve adenine, uracil, guanine, or cytosine. The rates of hydrolysis at 100 degreesC also suggest that an ocean-boiling asteroid impact would reset the prebiotic clock, requiring prebiotic synthetic processes to begin again. At 0 degreesC, A, U, G, and T appear to be sufficiently stable (t1/2 >/= 10(6) yr) to be involved in a low-temperature origin of life. However, the lack of stability of cytosine at 0 degreesC (t1/2 = 17, 000 yr) raises the possibility that the GC base pair may not have been used in the first genetic material unless life arose quickly (<10(6) yr) after a sterilization event. A two-letter code or an alternative base pair may have been used instead.

Characterization of the reverse gyrase from the hyperthermophilic archaeon Pyrococcus furiosus

The reverse gyrase gene rgy from the hyperthermophilic archaeon Pyrococcus furiosus was cloned and sequenced. The gene is 3,642 bp (1,214 amino acids) in length. The deduced amino acid sequence has relatively high similarity to the sequences of the Methanococcus jannaschii reverse gyrase (48% overall identity), the Sulfolobus acidocaldarius reverse gyrase (41% identity), and the Methanopynrus kandleri reverse gyrase (37% identity). The P. furiosus reverse gyrase is a monomeric protein, containing a helicase-like module and a type I topoisomerase module, which resembles the enzyme from S. acidocaldarius more than that from M. kandleri, a heterodimeric protein encoded by two separate genes. The control region of the P. furiosus rgy gene contains a typical archaeal putative box A promoter element which is located at position -26 from the transcription start identified by primer extension experiments. The initiating ATG codon is preceded by a possible prokaryote-type ribosome-binding site. Purified P. furiosus reverse gyrase has a sedimentation coefficient of 6S, suggesting a monomeric structure for the native protein. The enzyme is a single polypeptide with an apparent molecular mass of 120 kDa, in agreement with the gene structure. The sequence of the N terminus of the protein corresponded to the deduced amino acid sequence. Phylogenetic analysis indicates that all known reverse gyrase topoisomerase modules form a subgroup inside subfamily IA of type I DNA topoisomerases (sensu Wang [J. C. Wang, Annu. Rev. Biochem. 65:635-692, 1996]). Our results suggest that the fusion between the topoisomerase and helicase modules of reverse gyrase occurred before the divergence of the two archaeal phyla, Crenoarchaeota and Euryarchaeota.

A cell-free transcription system for the hyperthermophilic archaeon Pyrococcus furiosus

We describe here the establishment of a cell-free transcription system for the hyperthermophilic Archaeon Pyrococcus furiosus using the cloned glutamate dehydrogenase (gdh) gene as template. The in vitro system that operated up to a temperature of 85 degrees C initiated transcription 23 bp downstream of a TATA box located 45 bp upstream of the translational start codon of gdh mRNA, at the same site as in Pyrococcus cells. Mutational analyses revealed that this TATA box is essential for in vitro initiation of transcription. Pyrococcus transcriptional components were separated into at least two distinct transcription factor activities and RNA polymerase. One of these transcription factors could be functionally replaced by Methanococcus aTFB and Thermococcus TATA bind- ing protein (TBP). Immunochemical analyses demonstrated a structural relationship between Pyrococcus aTFB and Thermococcus TBP. These findings indicate that a TATA box and a TBP are essential components of the Pyrococcus transcriptional machinery.

The unique DNA topology and DNA topoisomerases of hyperthermophilic archaea

Hyperthermophilic archaea exhibit a unique pattern of DNA topoisomerase activities. They have a peculiar enzyme, reverse gyrase, which introduces positive superturns into DNA at the expense of ATP. This enzyme has been found in all hyperthermophiles tested so far (including Bacteria) but never in mesophiles. Reverse gyrases are formed by the association of a helicase-like domain and a 5'-type 1 DNA topoisomerase. These two domains might be located on the same polypeptide. However, in the methanogenic archaeon Methanopyrus kandleri, the topoisomerase domain is divided between two subunits. Besides reverse gyrase, Archaea contain other type 1 DNA topoisomerases; in particular, M. kandleri harbors the only known procaryotic 3'-type 1 DNA topoisomerase (Topo V). Hyperthermophilic archaea also exhibit specific type II DNA topoisomerases (Topo II), i.e. whereas mesophilic Bacteria have a Topo II that produces negative supercoiling (DNA gyrase), the Topo II from Sulfolobus and Pyrococcus lack gyrase activity and are the smallest enzymes of this type known so far. This peculiar pattern of DNA topoisomerases in hyperthermophilic archaea is paralleled by a unique DNA topology, i.e. whereas DNA isolated from Bacteria and Eucarya is negatively supercoiled, plasmidic DNA from hyperthermophilic archaea are from relaxed to positively supercoiled. The possible evolutionary implications of these findings are discussed in this review. We speculate that gyrase activity in mesophiles and reverse gyrase activity in hyperthermophiles might have originated in the course of procaryote evolution to balance the effect of temperature changes on DNA structure.

Looking for the most "primitive" organism(s) on Earth today: the state of the art

Molecular phylogenetic studies have revealed a tripartite division of the living world into two procaryotic groups, Bacteria and Archaea, and one eucaryotic group, Eucarya. Which group is the most "primitive"? Which groups are sister? The answer to these questions would help to delineate the characters of the last common ancestor to all living beings, as a first step to reconstruct the earliest periods of biological evolution on Earth. The current "Procaryotic dogma" claims that procaryotes are primitive. Since the ancestor of Archaea was most probably a hyperthermophile, and since bacteria too might have originated from hyperthermophiles, the procaryotic dogma has been recently connected to the hot origin of life hypothesis. However, the notion that present-day hyperthermophiles are primitive has been challenged by recent findings, in these unique microorganisms, of very elaborate adaptative devices for life at high temperature. Accordingly, I discuss here alternative hypotheses that challenge the procaryotic dogma, such as the idea of a universal ancestor with molecular features in between those of eucaryotes and procaryotes, or the origin of procaryotes via thermophilic adaptation. Clearly, major evolutionary questions about early cellular evolution on Earth remain to be settled before we can speculate with confidence about which kinds of life might have appeared on other planets.