Antonio Lazcano

The Origin and Early Evolution of Life: Prebiotic Chemistry, the Pre-RNA World, and Time

If it is assumed that life arose in a prebiotic soup containing most, if not all, of the necessary small molecules, then there was a large potential energy supply available on the primitive Earth from different fermentations. It is clear that such compounds could provide both the growth and energy supply of a large number of organisms, but this would rapidly result in the depletion of the available nutrients. Although the usual example of a primordial fermentation is that of glucose (Oparin 1938xOparin, A.I. See all ReferencesOparin 1938), it is unlikely that large quantities of this sugar were available in the primitive environment because of its instability. As noted by Clarke and Elsden 1980xThe earliest catabolic pathways. Clarke, P.H. and Elsden, S.R. J. Mol. Evol. 1980; 15: 333–338Crossref | PubMed | Scopus (11)See all ReferencesClarke and Elsden 1980, a more likely early fermentation reaction was that of glycine: The primitive ocean may have had a glycine concentration between 10−8–10−4 M, depending on the efficiency of prebiotic synthesis and whether the ultimate source of organic compounds was endogenous or not. At one mole ATP per mole of glycine, these values correspond to 1025–1028 cells. Such high numbers of cells would lead to an exponential decrease in the concentration of the available fermentable organic compounds of prebiotic origin and would bring about a metabolic crisis that could only be overcome by the evolutionary development of light-harvesting autotrophic organisms with CO2-fixing abilities (Lazcano and Miller 1994xHow long did it take for life to begin and evolve to cyanobacteria?. Lazcano, A. and Miller, S.L. J. Mol. Evol. 1994; 39: 546–554Crossref | PubMed | Scopus (74)See all ReferencesLazcano and Miller 1994).The time for evolution of the first DNA/protein organisms to oscillatorian-like cyanobacteria is usually thought to be very long, because the latter have rather large genomes of 6 × 103 kb to 8 × 103 kb (Herdman 1985xSee all ReferencesHerdman 1985) and are usually considered to be very complex. However, many of the evolutionary novelties required for the emergence of oxygenic photosynthesis are the result of duplication and divergence of genes. Assuming that Archean cells had a random rate of duplicon fixation, and a rate of spontaneous gene duplications comparable with the present values of 10−5–10−3 gene duplications (Anderson and Roth 1977xTandem genetic duplications in phage and bacteria. Anderson, R.P. and Roth, J.R. Annu. Rev. Microbiol. 1977; 31: 473–505Crossref | PubMedSee all ReferencesAnderson and Roth 1977), the time required for the development of a 100 kb genome of a DNA/protein primitive heterotroph into a 7,000-genes filamentous cyanobacteria would require only 7 × 106 years (Lazcano and Miller 1994xHow long did it take for life to begin and evolve to cyanobacteria?. Lazcano, A. and Miller, S.L. J. Mol. Evol. 1994; 39: 546–554Crossref | PubMed | Scopus (74)See all ReferencesLazcano and Miller 1994).It is well known that only a few weeks are required for the rapid spread of duplicates in bacterial populations under the stress conditions of directed evolution experiments. There appear to be no experimental measurements of the rate of formation and fixation of new enzyme activities resulting from gene duplication. However, recent results on the organophosphate and phosphonate hydrolyzing phosphotriesterase from Pseudomonas diminuta and other soil eubacteria suggest that this new enzyme diverged by duplication from the α/β barrel family and reached the diffusion limit in only 40 years (Scanlan and Reid 1995xEvolution in action. Scanlan, T.S. and Reid, R.C. Chemistry and Biology. 1995; 2: 71–75Abstract | Full Text PDF | PubMed | Scopus (40)See all ReferencesScanlan and Reid 1995). Thus, the rate of duplication and fixation of new genes can be surprisingly fast on the geological timescale.There are a number of additional mechanisms that could have increased the rate of metabolic evolution, including the modular assembly of new proteins, gene fusion events, and horizontal gene transfer as seen in extensive antibiotic resistance in bacteria. Directed evolution experiments have shown that new substrate specificities appear in a few weeks from existing enzymes by recombination events within a gene (Hall and Zuzel 1980xEvolution of a new enzymatic function by recombination within a gene. Hall, B. and Zuzel, T. Proc. Natl. Acad. Sci. USA. 1980; 77: 3529–3533Crossref | PubMedSee all ReferencesHall and Zuzel 1980). This suggests that mosaic proteins may have enhanced the catalytic repertoire of ancient organisms.It is likely that the widespread belief that the origin and early evolution of life were slow processes requiring billions and billions of years stems from the classical Darwinian approach that major changes are slow and proceed in a stepwise manner over extended periods of time. All the evidence reviewed here suggests that stability of monomers and polymers essential for the origin of life strongly limited the possibility of a slow emergence of life. After the explosive metabolic evolution that took place soon after the beginning of life, the basic genetic processes and major molecular traits have persisted essentially unchanged for more than three-and-a-half billion years, perhaps owing to the linkages of the genes involved and the complex interactions between different metabolic routes. At a macroevolutionary level, this represents a case of conservatism that is even more striking than the maintenance of the major animal body plans that appeared at the base of the Cambrian, and which have remained basically unchanged for 600 million years.

Astrophysical and astrochemical insights into the origin of life

Stellar nucleosynthesis of heavy elements such as carbon allowed the formation of organic molecules in space, which appear to be widespread in our Galaxy. The physical and chemical conditions—including density, temperature, ultraviolet (UV) radiation and energetic particles—determine reaction pathways and the complexity of organic molecules in different space environments. Dense interstellar clouds are the birth sites of stars of all masses and their planetary systems. During the protostellar collapse, interstellar organic molecules in gaseous and solid phases are integrated into protostellar disks from which planets and smaller solar

The Miller volcanic spark discharge experiment

Millers 1950s experiments used, besides the apparatus known in textbooks, one that generated a hot water mist in the spark flask, simulating a water vapor‐rich volcanic eruption. We found the original extracts of this experiment in Millers material and reanalyzed them. The volcanic apparatus produced a wider variety of amino acids than the classic one. Release of reduced gases in volcanic eruptions accompanied by lightning could have been common on the early Earth. Prebotic compounds synthesized in these environments could have locally accumulated, where they could have undergone further processing.

A Reassessment of Prebiotic Organic Synthesis in Neutral Planetary Atmospheres

The action of an electric discharge on reduced gas mixtures such as H2O, CH4 and NH3 (or N2) results in the production of several biologically important organic compounds including amino acids. However, it is now generally held that the early Earth’s atmosphere was likely not reducing, but was dominated by N2 and CO2. The synthesis of organic compounds by the action of electric discharges on neutral gas mixtures has been shown to be much less efficient. We show here that contrary to previous reports, significant amounts of amino acids are produced from neutral gas mixtures. The low yields previously reported appear to be the outcome of oxidation of the organic compounds during hydrolytic workup by nitrite and nitrate produced in the reactions. The yield of amino acids is greatly increased when oxidation inhibitors, such as ferrous iron, are added prior to hydrolysis. Organic synthesis from neutral atmospheres may have depended on the oceanic availability of oxidation inhibitors as well as on the nature of the primitive atmosphere itself. The results reported here suggest that endogenous synthesis from neutral atmospheres may be more important than previously thought.

The origin of life—did it occur at high temperatures?

A high-temperature origin of life has been proposed, largely for the reason that the hyperthermophiles are claimed to be the last common ancestor of modern organisms. Even if they are the oldest extant organisms, which is in dispute, their existence can say nothing about the temperatures of the origin of life, the RNA world, and organisms preceding the hyperthermophiles. There is no geological evidence for the physical setting of the origin of life because there are no unmetamorphosed rocks from that period. Prebiotic chemistry points to a low-temperature origin because most biochemicals decompose rather rapidly at temperatures of 100°C (e.g., half-lives are 73 min for ribose, 21 days for cytosine, and 204 days for adenine). Hyperthermophiles may appear at the base of some phylogenetic trees because they outcompeted the mesophiles when they adapted to lower temperatures, possibly due to enhanced production of heat-shock proteins.

On the Origin of Metabolic Pathways

Abstract. The heterotrophic theory of the origin of life is the only proposal available with experimental support. This comes from the ease of prebiotic synthesis under strongly reducing conditions. The prebiotic synthesis of organic compounds by reduction of CO2 to monomers used by the first organisms would also be considered an heterotrophic origin. Autotrophy means that the first organisms biosynthesized their cell constituents as well as assembling them. Prebiotic synthetic pathways are all different from the biosynthetic pathways of the last common ancestor (LCA). The steps leading to the origin of the metabolic pathways are closer to prebiotic chemistry than to those in the LCA. There may have been different biosynthetic routes between the prebiotic and the LCAs that played an early role in metabolism but have disappeared from extant organisms. The semienzymatic theory of the origin of metabolism proposed here is similar to the Horowitz hypothesis but includes the use of compounds leaking from preexisting pathways as well as prebiotic compounds from the environment.

Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment

Archived samples from a previously unreported 1958 Stanley Miller electric discharge experiment containing hydrogen sulfide (H2S) were recently discovered and analyzed using high-performance liquid chromatography and time-of-flight mass spectrometry. We report here the detection and quantification of primary amine-containing compounds in the original sample residues, which were produced via spark discharge using a gaseous mixture of H2S, CH4, NH3, and CO2. A total of 23 amino acids and 4 amines, including 7 organosulfur compounds, were detected in these samples. The major amino acids with chiral centers are racemic within the accuracy of the measurements, indicating that they are not contaminants introduced during sample storage. This experiment marks the first synthesis of sulfur amino acids from spark discharge experiments designed to imitate primordial environments. The relative yield of some amino acids, in particular the isomers of aminobutyric acid, are the highest ever found in a spark discharge experiment. The simulated primordial conditions used by Miller may serve as a model for early volcanic plume chemistry and provide insight to the possible roles such plumes may have played in abiotic organic synthesis. Additionally, the overall abundances of the synthesized amino acids in the presence of H2S are very similar to the abundances found in some carbonaceous meteorites, suggesting that H2S may have played an important role in prebiotic reactions in early solar system environments.

Molecular evolution of the lysine biosynthetic pathways

Among the different biosynthetic pathways found in extant organisms, lysine biosynthesis is peculiar because it has two different anabolic routes. One is the diaminopimelic acid pathway (DAP), and the other over the a-aminoadipic acid route (AAA). A variant of the AAA route that includes some enzymes involved in arginine and leucine biosyntheses has been recently reported in Thermus thermophilus (Nishida et al. 1999). Here we describe the results of a detailed genomic analysis of each of the sequences involved in the two lysine anabolic routes, as well as of genes from other routes related to them. No evidence was found of an evolutionary relationship between the DAP and AAA enzymes. Our results suggest that the DAP pathway is related to arginine metabolism, since the lysC, asd, dapC, dapE, and lysA genes from lysine biosynthesis are related to the argB, argC, argD, argE, and speAC genes, respectively, whose products catalyze different steps in arginine metabolism. This work supports previous reports on the relationship between AAA gene products and some enzymes involved in leucine biosynthesis and the tricarboxylic acid cycle (Irvin and Bhattacharjee 1998; Miyazaki et al. 2001). Here we discuss the significance of the recent finding that several genes involved in the arginine (Arg) and leucine (Leu) biosynthesis participate in a new alternative route of the AAA pathway (Miyazaki et al. 2001). Our results demonstrate a clear relationship between the DAP and Arg routes, and between the AAA and Leu pathways.

The roads to and from the RNA world

The historical existence of the RNA world, in which early life used RNA for both genetic information and catalytic ability, is widely accepted. However, there has been little discussion of whether protein synthesis arose before DNA or what preceded the RNA world (i.e. the pre-RNA world). We outline arguments of what route life may have taken out of the RNA world: whether DNA or protein followed. Metabolic arguments favor the possibility that RNA genomes preceded the use of DNA as the informational macromolecule. However, the opposite can also be argued based on the enhanced stability, reactivity, and solubility of 2-deoxyribose as compared to ribose. The possibility that DNA may have come before RNA is discussed, although it is a less parsimonious explanation than DNA following RNA.

How long did it take for life to begin and evolve to cyanobacteria

There is convincing paleontological evidence showing that stromatolite-building phototactic prokaryotes were already in existence 3.5 × 109 years ago. Late accretion impacts may have killed off life on our planet as late as 3.8 × 109 years ago. This leaves only 300 million years to go from the prebiotic soup to the RNA world and to cyanobacteria. However, 300 million years should be more than sufficient time. All known prebiotic reactions take place in geologically rapid time scales, and very slow prebiotic reactions are not feasible because the intermediate compounds would have been destroyed due to the passage of the entire ocean through deep-sea vents every 107 years or in even less time. Therefore, it is likely that self-replicating systems capable of undergoing Darwinian evolution emerged in a period shorter than the destruction rates of its components (<5 million years). The time for evolution from the first DNA/protein organisms to cyanobacteria is usually thought to be very long. However, the similarities of many enzymatic reactions, together with the analysis of the available sequence data, suggest that a significant number of the components involved in basic biological processes are the result of ancient gene duplication events. Assuming that the rate of gene duplication of ancient prokaryotes was comparable to todays present values, the development of a filamentous cyanobacterial-like genome would require approximately 7 × 106 years—or perhaps much less. Thus, in spite of the many uncertainties involved in the estimates of time for life to arise and evolve to cyanobacteria, we see no compelling reason to assume that this process, from the beginning of the primitive soup to cyanobacteria, took more than 10 million years.