Origin of Life

Theories and evidence for chemical biopoieses

RNA world hypothesis

ScienceWeek: Modified: "The 'RNA world hypothesis' is the concept that RNA nucleotide sequences with catalytic and self-replicating capabilities predated catalytic protein systems in prebiological epochs. It is believed, however, that the nucleotides constituting RNA were scarce on early Earth. This requires that RNA-based life must have acquired the ability to synthesize RNA nucleotides from simpler and more readily available precursors -- such as sugars and nucleic acid bases. Apparently plausible prebiotic synthesis routes have been proposed for sugars, sugar phosphates, and the four RNA bases. However, the coupling of these molecules into nucleotides, specifically pyrimidine nucleotides, poses a challenge to the RNA world hypothesis."

Some consequences of the RNA world hypothesis. : "It is now generally accepted that our familiar biological world was preceded by an RNA world in which ribosome-catalyzed, nucleic-acid coded protein synthesis played no part. If the RNA world was the first biological world there is little that one can learn from biochemistry about prebiotic chemistry, except that the formation and polymerization of nucleotides were once prebiotic processes. If the RNA world was not the first biological world, the above conclusion may not be justified, and one can speculate that the monomers of earlier genetic polymers might be recognizable as important biochemicals. This suggests that the construction of replicating polymers from simple, not necessarily standard, aminoacids should be explored."
Orgel LE. Some consequences of the RNA world hypothesis. Orig Life Evol Biosph. 2003 Apr;33(2):211-8.

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): Asked about primordial conditions, participant UCLA paleobiologist William Schopf answered: 'We know the overall sequence of life's origin, from CHONSP (carbon, hydrogen, oxygen, nitrogen, sulfur, phosphorus), to monomers, to polymers, to cells; we know that the origin of life was early, microbial, and unicellular; and we know that an RNA world preceded today's DNA-protein world. "

[RNA world and its evolution] : "The early idea of A. N. Belozersky on the precedence of RNA in the origin of life on Earth is developed. Basing on the present knowledge of functional omnipotence of RNA, the author considers three novel mechanisms that could play a critical role in the origin and evolution of the ancient RNA world: (1) the reaction of spontaneous transesterification of polyribonucleotides in aqueous media, discovered by A.B. Chetverin, which could result in elongation of primary short oligoribonucleotides and generation of sequence variants for subsequent selection; (2) compartmentation of functional RNA ensembles in the form of mixed molecular colonies on moist solid surfaces, in the absence of membranes and any other coats; (3) systematic exponential enrichment of RNA population in functionally 'the best' molecules by means of alternately dissolving the colonies upon flooding and forming new ones upon drying a pool ('primordial natural SELEX')."
Sinrin AS. [RNA world and its evolution] Mol Biol (Mosk). 2005 Jul-Aug;39(4):550-6.

Hyperthermophily and the origin and earliest evolution of life.: "The possibility of a high-temperature origin of life has gained support based on indirect evidence of a hot, early Earth and on the basal position of hyperthermophilic organisms in rRNA-based phylogenies. However, although the availability of more than 80 completely sequenced cellular genomes has led to the identification of hyperthermophilic-specific traits, such as a trend towards smaller genomes, reduced protein-encoding gene sizes, and glutamic-acid-rich simple sequences, none of these characteristics are in themselves an indication of primitiveness. There is no geological evidence for the physical setting in which life arose, but current models suggest that the Earth's surface cooled down rapidly. Moreover, at 100 degrees C the half-lives of several organic compounds, including ribose, nucleobases, and amino acids, which are generally thought to have been essential for the emergence of the first living systems, are too short to allow for their accumulation in the prebiotic environment. Accordingly, if hyperthermophily is not truly primordial, then heat-loving lifestyles may be relics of a secondary adaptation that evolved after the origin of life, and before or soon after separation of the major lineages."
Islas S, Velasco AM, Becerra A, Delaye L, Lazcano A. Hyperthermophily and the origin and earliest evolution of life. Int Microbiol. 2003 Jun;6(2):87-94. Epub 2003 Jun 28.

Thermosynthesis as energy source for the RNA World: a new model for the origin of life: modified: The thermosynthesis concept, biological free energy gain from thermal cycling, is combined with the concept of the RNA World. The resulting overall origin of life model gives new explanations for the emergence of the genetic code and the ribosome. The first protein named pF1 obtains the energy to support the RNA world by a thermal variation of F1 ATP synthase's binding change mechanism. This pF1 is the single translation product during the emergence of the genetic machinery. During thermal cycling pF1 condenses many substrates with broad specificity, yielding NTPs and randomly constituted protein and RNA libraries that contain (self)-replicating RNA. The smallness of pF1 permits the emergence of the genetic machinery by selection of RNA that increases the fraction of pF1s in the protein library: (1) a progenitor of rRNA that concatenates amino acids bound to (2) a chain of 'positional tRNAs' linked by mutual recognition, yielding a pF1 (or its main motif); this positional tRNA set gradually evolves to a set of regular tRNAs functioning according to the genetic code, with concomitant emergence of (3) an mRNA coding for pF1.
Anthonie W. J. Muller Thermosynthesis as energy source for the RNA World: a new model for the origin of life. Full-text: PDF only

Effect of temperature on the adsorption of adenine. : "Equilibrium adsorption isotherms for the purine base adenine on the surface of graphite crystals have been obtained at 30, 40, 50, and 60 degrees C by frontal analysis using water as a mobile phase. These data were fitted to the Langmuir isotherm model and interpreted in terms of the well-characterized adsorbate monolayer structure. A van't Hoff plot was used to estimate the adsorption enthalpy, -delta H degree which we determined to be 20 kJ mol-1. The susceptibility of nucleic acid bases to aqueous-phase hydrolysis may have been a limiting feature for their inclusion in the primordial genetic architecture; our results suggest that the effects of temperature and the presence of inorganic solids must also be included when assessing the prebiotic availability of adenine."
Sowerby SJ, Morth CM, Holm NG. Effect of temperature on the adsorption of adenine. Astrobiology. 2001 Winter;1(4):481-7.

Survival of the fittest before the beginning of life: selection of the first oligonucleotide-like polymers by UV light. :"BACKGROUND: A key event in the origin of life on this planet has been formation of self-replicating RNA-type molecules, which were complex enough to undergo a Darwinian-type evolution (origin of the "RNA world"). However, so far there has been no explanation of how the first RNA-like biopolymers could originate and survive on the primordial Earth. RESULTS: As condensation of sugar phosphates and nitrogenous bases is thermodynamically unfavorable, these compounds, if ever formed, should have undergone rapid hydrolysis. Thus, formation of oligonucleotide-like structures could have happened only if and when these structures had some selective advantage over simpler compounds. It is well known that nitrogenous bases are powerful quenchers of UV quanta and effectively protect the pentose-phosphate backbones of RNA and DNA from UV cleavage. To check if such a protection could play a role in abiogenic evolution on the primordial Earth (in the absence of the UV-protecting ozone layer), we simulated, by using Monte Carlo approach, the formation of the first oligonucleotides under continuous UV illumination. The simulations confirmed that UV irradiation could have worked as a selective factor leading to a relative enrichment of the system in longer sugar-phosphate polymers carrying nitrogenous bases as UV-protectors. Partial funneling of the UV energy into the condensation reactions could provide a further boost for the oligomerization. CONCLUSION: These results suggest that accumulation of the first polynucleotides could be explained by their abiogenic selection as the most UV-resistant biopolymers."
Mulkidjanian AY, Cherepanov DA, Galperin MY. Survival of the fittest before the beginning of life: selection of the first oligonucleotide-like polymers by UV light. BMC Evol Biol. 2003 May 28;3:12. Epub 2003 May 28. Free Full Text article

Thermosynthesis as energy source for the RNA World: a model for the bioenergetics of the origin of life. : "The thermosynthesis concept, biological free energy gain from thermal cycling, is combined with the concept of the RNA World. The resulting overall origin of life model suggests new explanations for the emergence of the genetic code and the ribosome. It is proposed that the first protein named pF(1) obtained the energy to support the RNA World by a thermal variation of F(1) ATP synthase's binding change mechanism. It is further proposed that this pF(1) was the single translation product during the emergence of the genetic machinery. During thermal cycling pF(1) condensed many substrates with broad specificity, yielding NTPs and randomly constituted protein and RNA libraries that contained self-replicating RNA. The smallness of pF(1) permitted the emergence of the genetic machinery by selection of RNA that increased the fraction of pF(1)s in the protein library: (1) an amino acids concatenating progenitor of rRNA bound to (2) a chain of 'positional tRNAs' linked by mutual recognition, and yielded a pF(1) (or its main motif); this positional tRNA set gradually evolved to a set of regular tRNAs functioning according to the genetic code, with concomitant emergence of (3) an mRNA coding for pF(1)."
Muller AW. Thermosynthesis as energy source for the RNA World: a model for the bioenergetics of the origin of life. Biosystems. 2005 Oct;82(1):93-102.

A deoxyribozyme that harnesses light to repair thymine dimers in DNA -- Chinnapen and Sen 101 (1): 65 -- Proceedings of the National Academy of Sciences: "The RNA world hypothesis (1) postulates that RNA or RNA-like polymers, capable of genetic as well as catalytic function, may have constituted primitive "life" in the course of evolution. Currently, in vitro selection (2, 3) experiments from random sequence DNA and RNA libraries permit the identification of novel catalytic activities for nucleic acids, in support of the RNA world hypothesis. To date, such selections have indicated a substantially broader catalytic repertoire for RNA and DNA than found in naturally occurring ribozymes (4). We were interested in investigating whether reactions that use light energy could be catalyzed by nucleic acid enzymes.Thymine (or pyrimidine) dimers are the major lesions formed in DNA as a result of exposure to UV light. Two major kinds of dimer are known, the cyclobutane and the (6—4) photoproduct (5). Different organisms use a variety of strategies to repair these lesions, among the more interesting of which is the use of light of substantially lower energy (longer wavelength) than the natural absorption of thymine dimers (>250 nm wavelength) to reactivate the dimers back to monomers. Such "photolyase" enzymes for the repair of both cyclobutane and (6—4) dimers have been studied extensively (6). The cyclobutane (CPD) photolyases harness a broad spectrum of light by using a number of chromophores such as methenyltetrahydrofolate (MTHF), flavin nucleotides, and tryptophan side chains (7). Photoexcitation culminates in electron donation from the excited-state flavin directly to the thymine dimer, leading to destabilization of the 5—5 and 6—6 bonds of the dimer, and thus, reversion to base monomers. Interestingly, studies have shown that a single strategically positioned tryptophan residue in the Escherichia coli enzyme's active site is able to provide a significant photoreactivation, even in the absence of the FADH and MTHF cofactors (8). "
Chinnapen DJ, Sen D. A deoxyribozyme that harnesses light to repair thymine dimers in DNA. Proc Natl Acad Sci U S A. 2004 Jan 6;101(1):65-9. Epub 2003 Dec 22.

Concentration of simple aldehydes by sulfite-containing double-layer hydroxide minerals: implications for biopoesis.: "Environmental conditions play an important role in conceptual studies of prebiotically relevant chemical reactions that could have led to functional biomolecules. The necessary source compounds are likely to have been present in dilute solution, raising the question of how to achieve selective concentration and to reach activation. With the assumption of an initial 'RNA World', the questions of production, concentration, and interaction of aldehydes and aldehyde phosphates, potential precursors of sugar phosphates, come into the foreground. As a possible concentration process for simple, uncharged aldehydes, we investigated their adduct formation with sulfite ion bound in the interlayer of positively charged expanding-sheet-structure double-layer hydroxide minerals. Minerals of this type, initially with chloride as interlayer counter anion, have previously been shown to induce concentration and subsequent aldolization of aldehyde phosphates to form tetrose, pentose, and hexose phosphates. The reversible uptake of the simple aldehydes formaldehyde, glycolaldehyde, and glyceraldehyde by adduct formation with the immobilized sulfite ions is characterized by equilibrium constants of K=1.5, 9, and 11, respectively. This translates into an observable uptake at concentrations exceeding 50 mM."
Pitsch S, Krishnamurthy R, Arrhenius G. Concentration of simple aldehydes by sulfite-containing double-layer hydroxide minerals: implications for biopoesis.Helv Chim Acta. 2000 Sep-Oct;83(9):2398-411.

A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase.: "The modified nucleoside 1-methyladenosine (m(1)A) is found in the T-loop of many tRNAs from organisms belonging to the three domains of life (Eukaryota, Bacteria, Archaea). In the T-loop of eukaryotic and bacterial tRNAs, m(1)A is present at position 58, whereas in archaeal tRNAs it is present at position(s) 58 and/or 57, m(1)A57 being the obligatory intermediate in the biosynthesis of 1-methylinosine (m(1)I57). In yeast, the formation of m(1)A58 is catalysed by the essential tRNA (m(1)A58) methyltransferase (MTase), a tetrameric enzyme that is composed of two types of subunits (Gcd14p and Gcd10p), whereas in the bacterium Thermus thermophilus the enzyme is a homotetramer of the TrmI polypeptide. Here, we report that the TrmI enzyme from the archaeon Pyrococcus abyssi is also a homotetramer. However, unlike the bacterial site-specific TrmI MTase, the P.abyssi enzyme is region-specific and catalyses the formation of m(1)A at two adjacent positions (57 and 58) in the T-loop of certain tRNAs. The stabilisation of P.abyssi TrmI at extreme temperatures involves intersubunit disulphide bridges that reinforce the tetrameric oligomerisation, as revealed by biochemical and crystallographic evidences. The origin and evolution of m(1)A MTases is discussed in the context of different hypotheses of the tree of life."Roovers M, Wouters J, Bujnicki JM, Tricot C, Stalon V, Grosjean H, Droogmans L. A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase. Nucleic Acids Res. 2004 Jan 22;32(2):465-76. Print 2004. Free Full Text article

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