RNA World Hypothesis

10 Key excerpts on "RNA World Hypothesis"

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  Life's Origin

  The Beginnings of Biological Evolution

  • J. William Schopf(Author)
  • 2002(Publication Date)
  • University of California Press

    (Publisher)

  According to this hypothesis, RNA could go it alone—functioning both as a genetic material in the man-ner of modern DNA and as the basis for various types of catalysis, in-cluding the catalysis of RNA replication. These theoretical ideas re-ceived a great boost from the discovery of ribozymes, enzyme-like catalysts composed entirely of RNA (Kruger et al. 1982; Guerrier-Takada et al. 1983 ). The idea that there was once a protein-independent biological world, the so-called RNA World, has by now come to be widely accepted (although it remains unproven). If we accept the RNA World Hypothesis, we can restate the prob-lem of the origin of life in a very simple two-part question: How did the RNA World come into existence, and how did this world invent the DNA–RNA–protein world? We can say very little in answer to the second part of the question, so from now on let’s concentrate on the first part, the origin and development of the hypothesized RNA World. the rna world It would be a mistake to think of the RNA World as fixed and un-changing. Presumably, it started simple, but it finished complicated enough to invent protein synthesis. Very different opinions about the complexity of the RNA World have been expressed, probably because some workers focus on its primitive beginnings while others concen-trate on its mature state, just prior to the invention of ribosomal protein synthesis. In the following, we first consider a very optimistic scenario that explains how a simple RNA World could get started under very favorable conditions—conditions admittedly different from those prevail-ing on the primitive Earth. This is “The Molecular Biologist’s Dream” (Joyce and Orgel 1999 ), which posits a primitive pool loaded with chemically activated nucleotides waiting to be polymerized into RNA. Later, we will take a more realistic view of the problem.

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  Prebiotic Evolution and Astrobiology

  • J. Tze-Fei Wong, Antonio Lazcano(Authors)
  • 2009(Publication Date)
  • CRC Press

    (Publisher)

  E) The RNA World. When the RNA pool contains molecules that are also catalysts of their own copying, as well as those of any other functional RNAs, a full-fledged RNA World is achieved. processes must have intrinsically yielded RNA pools containing a large fraction of catalytically active molecules (by what is thus far an unknown process). (ii) E nvironm ental Conditions Unfortunately, few clues about the original environmental conditions on primitive Earth remain due to the activity of the biosphere and plate tectonics. However, recent investigations suggest the presence of liquid water and continents as far back as 4.3 x 10 9 years ago. Higher volcanic activity and lower sunlight levels than today can also be expected. Thus life producing reac­ tions could have occurred over a broad spectrum of conditions in terms of temperature, pressure, ionic strength, pH, etc. and have been located on land, deep within the Earth, in the oceans, or at interfaces between these regions. 10.3 RNA Monomers Although the synthesis of the different RNA monomers from prebiotic molecules is mosdy beyond the scope of this chapter (see ref. 2 ), a quick summary of research efforts on this topic is necessary. The implication of monomer syntheses (or the lack thereof) for the de novo emergence of an RNA World from prebiotic organic mixtures is essential for our discussion. (i) Synthesis o f the R ibonucleotides RNA monomers, P-D-ribonucleotides, are rather complex mol­ ecules formed by three different types of molecules—a nucleobase, a ribose and aphosphate group (see Box 10.1), each ofwhich needs to be synthesized as an intermediate product (or made available in the case of the phosphate group) before being assembled into the ribonucleotide.

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  Ribozymes

  Principles, Methods, Applications

  • Sabine Müller, Benoît Masquida, Wade Winkler, Sabine Müller, Benoît Masquida, Wade Winkler(Authors)
  • 2021(Publication Date)
  • Wiley-VCH

    (Publisher)

  4 ).

  Figure 14.1

  Stages of the RNA world. Between the two well‐defined endpoints of the origin of life lies the RNA world. Nonenzymatic RNA replication could have led to the evolution of a self‐replicating enzyme, which kick‐started metabolism. This stage was probably still unfolded on mineral surfaces. Cellular life marks the beginning of life. The error catastrophe was overcome when the chromosome evolved. This led to complex metabolism, which could recruit amino acids and then evolve peptide synthesis, thus leading to the RNA–peptide world stage. With the invention of DNA genome, the RNA world yielded to the now present DNA–peptide world.

  14.1.1 Replication of the Genetic Information

  Evolution is a powerful mechanism that can produce novelty and considerable increase in complexity, but it requires reproduction, variation, and heredity. Reproduction is the capability of exponential growth achieved via autocatalysis [26 , 27 ], what chemical systems can exhibit [28 –32 ]. However, heredity and variation are characteristics that rarely are featured together in a system. The von Kiedrowski‐type replicators [33] , for example, exhibit heredity, but the reactants cannot be changed without destroying their ability for autocatalysis. Compositional information [34] , on the other hand, has ample variability but lacks heredity [35] . Modular polymers with complementary modules, such as RNA and DNA, have the potential for evolution. Variation in the form of mutations arises during RNA/DNA replication naturally (see below), and via complementarity, information is passed on. The copy of a strand is yielded in two steps: first, the complementary strand is produced, and by copying it, a replica of the original strand forms. However, without a mechanism for copying RNA, it also does not exhibit heredity and thus cannot evolve. For example, RNA molecules of intermediate length can form on clay surfaces [36 , 37

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  Evolutionarily Significant Biological Phenomena

  • (Author)
  • 2014(Publication Date)
  • White Word Publications

    (Publisher)

  ________________________ WORLD TECHNOLOGIES ________________________ modern organisms; and the ease of chemical synthesis of at least the components of the molecule under conditions approximating the early Earth. Relatively short RNA molecules which can duplicate others have been artificially produced in the lab. Such replicase RNA, which functions as both code and catalyst provides a template upon which copying can occur. Jack Szostak has shown that certain catalytic RNAs can, indeed, join smaller RNA sequences together, creating the potential, in the right conditions for self-replication. If these were present, Darwinian selection would favour the proliferation of such self-catalysing structures, to which further functionalities could be added. Lincoln and Joyce identified an RNA enzyme capable of self sustained replication. Researchers have pointed out difficulties for the abiotic synthesis of nucleotides from cytosine and uracil. Cytosine has a half-life of 19 days at 100 °C (212 °F) and 17,000 years in freezing water. Larralde et al., say that the generally accepted prebiotic synthesis of ribose, the formose reaction, yields numerous sugars without any selectivity. and they conclude that their results suggest that the backbone of the first genetic material could not have contained ribose or other sugars because of their instability. The ester linkage of ribose and phosphoric acid in RNA is known to be prone to hydrolysis. A slightly different version of the RNA-world hypothesis is that a different type of nucleic acid, such as PNA, TNA or GNA, was the first one to emerge as a self-reproducing molecule, to be replaced by RNA only later. Pyrimidine ribonucleosides and their respective nucleotides have been prebiotically synthesised by a sequence of reactions which by-pass the free sugars, and are assembled in a stepwise fashion by going against the dogma that nitrogenous and oxygenous chemistries should be avoided.

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  The Evolution of Biological Information

  How Evolution Creates Complexity, from Viruses to Brains

  • Christoph Adami(Author)
  • 2024(Publication Date)
  • Princeton University Press

    (Publisher)

  The idea that RNA constitutes the chemical cradle of all of life on Earth is called the “RNA world” hypothesis (Woese 1967; Orgel 1968; Crick 1968; Orgel and Sulston 1971; White 3rd. 1976). The idea is enticing because it solves a number of problems: information storage and replication machinery could be one and the same. However, the road to self-replication is—as far as our current evidence informs us—a difficult one, even if the monomers A, C, G, and U, along with the backbone molecules ribose and phosphate, can form easily. In order to obtain life—that is, polynucleotides that encode the information necessary to replicate that information—it is necessary for spe- cific sequences of ribonucleotides (or at a minimum the information encoded therein) to serve as a template for the synthesis of another such sequence. In present life, this duplication is achieved via enzymes, but before there is life such enzymes (even those made out of RNA, so called ribozymes) simply are not there, as the smallest highly active self-cleaving ribozymes are of the order ∼ fifty nucleotides (Ferré-D’Amaré and Scott 2010). Sequences of that length cannot arise by chance, as we will see further below. Thus, they cannot be there to help in the emergence of life. However, it is possible for templates to be copied passively, via a process where an RNA duplex opens up, and monomers aggregate on a strand: a C on a G, a U on a T, and so on, thus re-forming the duplex. This process is slow and error prone, because mismatched nucleotides (a T settling on a G rather than a U, for example) do occur. If the rate of production of correct copies was equal to the rate at which incorrect copies are made, then template-based copying is of no help at all: information could simply not emerge.

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  Biophysics and Biology (Concepts, Elements and Applications)

  • (Author)
  • 2014(Publication Date)
  • Library Press

    (Publisher)

  ________________________ WORLD TECHNOLOGIES ________________________ and the ease of chemical synthesis of at least the components of the molecule under conditions approximating the early Earth. Relatively short RNA molecules which can duplicate others have been artificially produced in the lab. Such replicase RNA, which functions as both code and catalyst provides a template upon which copying can occur. Jack Szostak has shown that certain catalytic RNAs can, indeed, join smaller RNA sequences together, creating the potential, in the right conditions for self-replication. If these were present, Darwinian selection would favour the proliferation of such self-catalysing structures, to which further functionalities could be added. Lincoln and Joyce identified an RNA enzyme capable of self sustained replication. Researchers have pointed out difficulties for the abiotic synthesis of nucleotides from cytosine and uracil. Cytosine has a half-life of 19 days at 100 °C (212 °F) and 17,000 years in freezing water. Larralde et al., say that the generally accepted prebiotic synthesis of ribose, the formose reaction, yields numerous sugars without any selectivity. and they conclude that their results suggest that the backbone of the first genetic material could not have contained ribose or other sugars because of their instability. The ester linkage of ribose and phosphoric acid in RNA is known to be prone to hydrolysis. A slightly different version of the RNA-world hypothesis is that a different type of nucleic acid, such as PNA, TNA or GNA, was the first one to emerge as a self-reproducing molecule, to be replaced by RNA only later. Pyrimidine ribonucleosides and their respective nucleotides have been prebiotically synthesised by a sequence of reactions which by-pass the free sugars, and are assembled in a stepwise fashion by going against the dogma that nitrogenous and oxygenous chemistries should be avoided.

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  Evolutionary Biology (Concepts & Theories)

  • (Author)
  • 2014(Publication Date)
  • The English Press

    (Publisher)

  Virus self-assembly within host cells has implications for the study of the origin of life, as it lends further credence to the hypothesis that life could have started as self-assembling organic molecules. From organic molecules to protocells The question How do simple organic molecules form a protocell? is largely unanswered but there are many hypotheses. Some of these postulate the early appearance of nucleic acids (genes-first) whereas others postulate the evolution of biochemical reactions and pathways first (metabolism-first). Recently, trends are emerging to create hybrid models that combine aspects of both. Genes first models: the RNA world The RNA World Hypothesis describes an early Earth with self-replicating and catalytic RNA but no DNA or proteins. This has spurred scientists to try to determine if relatively short RNA molecules could have spontaneously formed that were capable of catalyzing their own continuing replication. A number of hypotheses of modes of formation have been put forward. Early cell membranes could have formed spontaneously from proteinoids, protein-like molecules that are produced when amino acid solutions are heated–when present at the correct concentration in aqueous solution, these form microspheres which are observed to behave similarly to membrane-enclosed compartments. Other possibilities include systems of chemical reactions taking place within clay substrates or on the surface of pyrite rocks. Factors supportive of an important role for RNA in early life include its ability to act both to store information and catalyse chemical reactions (as a ribozyme); its many important roles as an intermediate in the expression and maintenance of the genetic information (in the form of DNA) in modern organisms; and the ease of chemical synthesis of at least the components of the molecule under conditions approximating the early Earth. Relatively short RNA molecules which can duplicate others have been artificially produced in the lab.

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  Fundamental Molecular Biology

  • Lizabeth A. Allison(Author)
  • 2021(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  The change in free energy ( Δ G ) remains the same because the equilibrium position remains unaltered. In the induced-fit model, the catalyst changes shape upon binding substrates. The active site has a shape complementary to the substrates only after the substrates are bound. 3.4 The discovery of RNA catalysis 63 F o c u s B o x 3 . 1 The RNA world Molecular biologists who speculate on the origins of life on Earth are faced with a classic “chicken and egg problem.” Which came first, proteins or nucleic acids? In the modern world, the replica-tion of DNA and RNA is dependent on protein enzymes, and the synthesis of protein enzymes is dependent on DNA and RNA. The term “RNA world” was introduced by Walter Gilbert in 1986 to describe a hypothetical stage in the evolution of life some 4 billion years ago when RNA both carried the genetic informa-tion and catalyzed its own replication. The origin and prebiotic chemistry of this RNA world remains open to speculation. According to the RNA World Hypothesis , “life” first existed in the form of replicating RNA molecules (Figure 1). In this ancient world, neither protein nor DNA existed yet. Evidence in support of this hypothesis is that proteins cannot replicate themselves, except via mechanisms that involve an RNA intermediate. In contrast, RNA has all the structural pre-requisites necessary for self-replication. RNA genomes are widespread among viruses, and their replication in infected cells proceeds via complementary RNA chains. Compared with DNA or protein, RNA is clearly the most self-sufficient molecule. RNA molecules are capable of doing basically all that proteins can do. They can self-fold into specific three-dimensional structures, recognize other macromolecules and small ligands with precision, and perform catalysis of covalent reactions. Ribozymes can catalyze a diversity of reactions including polymerizing nucleotides, ligating DNA, cleaving DNA phosphodiester bonds, and synthesizing pep-tides.

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  Science and Religion

  Understanding the Issues

  • Nancy Morvillo(Author)
  • 2010(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  A U G G A A G U U A U G G A A G U U 5 ′ end 3 ′ end A peptide bond joins MET to LEU: A transfer RNA coupled to lysine (LYS) binds to the next triplet codon, AAG, in the mRNA: A peptide bond joins LEU to LYS, extending the peptide chain: MET A U G G A A G U U MET LEU A U G G A A G U U MET LEU A U G G A A G U U LEU MET LYS A U G G A A G U U LEU MET LYS A U U G A A U ILE STOP 166 Evolution other than RNA. Since RNA can carry genetic information, it could substitute for DNA. But what about the metabolism component? It turns out that, because of the ability of RNA to base-pair with itself and fold into three-dimensional shapes, it can perform catalytic functions and act as enzymes. The notion that RNA was the first genetic material and also acted to catalyze its own existence (and other functions in the cell) is known as the RNA World Hypothesis. We have many examples in living organisms today of catalytic RNA, and we also know of many viruses that use RNA as their genetic material. So it is easy to envision how RNA could have been the molecule to carry out the basic necessary func-tions for the very first life forms. Thus the assembly of RNA, a genetic material, could have led to the formation of cells capable of metabolism, the genetics-first model. One of the key problems with the genetics-first idea is the structure of the RNA molecule: it has been difficult to explain how such a complex molecule could have been the original source of material for life. Some argue that simpler molecules must have started it all, eventually resulting in the RNA world. This view, which is known as the metabolism-first model, focuses on enzymatic pathways. The original organic molecules that started life may have been amino acids, which are chemically much simpler than nucleic acids (recall that Miller was able to produce them easily in his experiment). The amino acids could have formed proteins capable of catalytic activity.

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  Self And The Phenomenon Of Life: A Biologist Examines Life From Molecules To Humanity

  A Biologist Examines Life from Molecules to Humanity

  • Ramon Lim(Author)
  • 2017(Publication Date)
  • World Scientific

    (Publisher)

  Earth and Planetary Sci Lett 270: 130–136. Self and the Phenomenon of Life 70 16. Callahan MP, Smith KE, Cleaves HJ II, et al . (2011) Carbonaceous meteorites contain a wide range of extraterrestrial nucleobases. Proc Natl Acad Sci USA 108: 13995–13998. 17. Chemical and Engineering News (2007), 85: 41–42. 18. Miller SL. (1953) A production of amino acids under possible primitive earth conditions. Science 117: 528–529. 19. Oró J, Kimball AP. (1961) Synthesis of purines under possible primitive earth conditions. I. Adenine from hydrogen cyanide. Arch Bio Chem Bio-phys 94: 217–227. 20. Oró J, Kamat SS. (1961) Amino-acid synthesis from hydrogen cyanide under possible primitive earth conditions. Nature 190: 442–443; Oró J. (1967) Stages and mechanisms of prebiological organic synthesis. In Fox SW. ed. Origins of Prebiological Systems and of Their Molecular Matrices. Academic Press, New York, pp. 137–171. 21. Unlike DNA chains which are rigid except to coil around and form a dou-ble helix, RNA chains are highly flexible so that the various regions of a single chain can come together by base-pairing to produce highly irregular, three-dimensional structures unique for each RNA molecule (reminiscent of protein folding). Examples of RNA enzymes include self-splicing RNA from the protozoan Tetrahymena, and RNAseP, a nucleoprotein whose RNA part is responsible for RNA-cutting activity (nuclease) during the for-mation of tRNA. See: Kruger K, Grabowski PJ, Zaug AJ, et al . (1982) Auto excision and auto cyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31: 147–157; Guerrier-Takada C, Gardiner K, Marsh T, et al . (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35: 849–857. 22. Gilbert W. (1986) The RNA World. Nature 319: 618. 23. White HB. (1976) Coenzymes as fossils of an earlier metabolic state. J Mol Evolution 7: 101–104. 24. Bartel DP, Szostak JW.

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