RNA world hypothesis

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RNA (left) and DNA (right) in comparison.
Structural model of a ribozyme, part of the RNA world hypothesis, with strands paired in sections

The RNA world hypothesis states that today's forms of life were preceded by a world whose life was based on ribonucleic acids  (RNA) as universal building blocks for information storage and catalysis of chemical reactions. Under this hypothesis that free or cell-bound RNA is assumed within the framework of evolution from chemically stable information storage medium deoxyribonucleic acid  (DNA) and of the functionally more flexible proteins has been replaced or supplemented by this.

Ribozymes (catalytically active RNA) are regarded as an indication of the existence of the RNA world , which as chemical (also: molecular ) fossils could represent evolutionary remnants from this early period (similar to living fossils ); an example of this is ribosomal RNA  (rRNA). The order of the biosynthetic pathways gives another clue. The deoxyribonucleotides that make up DNA are made in the cell from ribonucleotides , the building blocks of RNA, by removing the 2'- hydroxy group . So the cell must first be able to build RNA before it can produce DNA.

The main difference between RNA and DNA is the hydroxyl group at the 2 'position on RNA. DNA has just one more hydrogen atom there instead.

The four ribonucleotides can arise spontaneously under certain environmental conditions. The RNA world hypothesis is thus a link between the hypotheses of chemical evolution , which explain the formation of organic molecules from inorganic compounds , and the cooperation of several RNAs that initiate biological selection , as well as today's biological evolution based on DNA -Genome. The emergence of cellular life forms may not be at the end of this process, because cellular organisms based on RNA ( ribocytes ) could already have emerged in the RNA world.

concept

The concept of a postulated RNA world is based on two fundamental properties of RNA. On the one hand, like DNA, it serves as a medium for storing genetic information. On the other hand, RNA as well as proteins are able to catalyze chemical reactions.

Emergence

Although RNA is a very complex molecule, which consists of ribonucleotide units, which in turn are condensation products of ribose , a nucleobase and phosphate , its abiotic formation in the primordial soup is considered possible. Direct condensation is catalytically very complex and therefore unlikely for an abiotic formation, but in 2009 it was experimentally shown that pyrimidine ribonucleotides were formed in a few reaction steps from the simple molecules cyanamide , cyanoacetylene , glycolaldehyde , glyceraldehyde and phosphate, which were possible components of the primordial soup can be. Interestingly, in this reaction, phosphate is not only important as a starting material (starting material) in the esterification of the nucleoside to form the nucleotide. Rather, the presence of phosphate seems to selectively control several sub-steps of the reaction by z. B. acts as a pH buffer and catalyst with nucleophilic properties. This suppresses the combinatorial diversity so that hardly any undesired by-products occur.

The more complex purine nucleosides could be produced in 2016 with small molecules such as those still found on comets today via the formamidopyrimidine (FaPy) reaction path. Finally it was shown how the pyrimidines and purines can also be formed together under the same, plausible conditions.

Information storage

Due to its chemical and physical properties, RNA is considered to be the older storage medium for genetic information than DNA. For example, the RNA building block ribose, in contrast to the deoxyribose of DNA, can easily be formed by aldol condensation . Like DNA, RNA is also able to assemble into double-stranded macromolecules. For long-term storage of information, however, RNA is inferior to DNA, since RNA is error-prone and therefore energy-intensive.

catalysis

With the discovery that the ribosomal RNA of the eyelash animal Tetrahymena can splice itself, the first evidence of catalytic properties of ribonucleic acids ( ribozymes ) was provided in 1982 . In principle, almost any nucleic acid can evolve into a catalytic sequence under suitable conditions. This was particularly successful for DNA under laboratory conditions (so-called deoxyribozymes , also DNAzymes). However, this has not yet been observed in nature. In contrast, natural RNA molecules (in addition to artificially generated ribozymes) have been found that produce important components of cell metabolism, including their own building blocks, and even those that are capable of identical replication .

In the context of the RNA world hypothesis, it is assumed that ribozymes, which were able to translate their genetic information through the synthesis of proteins ( translation ), initiated the triumphant advance of proteins as functional carriers. Proteins are superior to RNA in terms of their catalytic abilities and the rate of catalysis. This assumption was supported by the discovery that the important catalytic centers of the ribosomes are provided by RNA and not, as previously assumed, proteins.

Cellular RNA

Compartmentalization is seen as an important prerequisite for the development of the RNA world under the conditions of Darwinian evolution . It is assumed that these first RNA-based hypothetical forms of life, the ribocytes , which were surrounded by a cell membrane , developed rapidly and were able to control elementary cell functions such as the transport of substances through the cell membrane and the cell shape.

Two ages of the RNA world

Modern ribosomes (the protein factories of the cell) are made up of ribosomal RNA ( rRNA ) and proteins (rProtein). The proteins seem to only have an auxiliary function here, which make the translation of the messenger RNA ( mRNA ) into a protein faster and / or more reliable; in principle, the rRNA is sufficient as a ribozyme for this process. The RNA world can then be divided into two ages: an early phase without ribosomes (primordial RNA world, with short peptide chains of abiotic origin from the primordial soup ), and a later phase with protein biosynthesis by ribosomes ( RNP world, ribonucleoprotein). In between there is the genesis and evolution of the genetic code . When the organisms were dependent on the proteins produced in this way, the evolution of the genetic code had to be (largely) completed, since a change in the code means a change and possible inoperability of almost all proteins produced. Therefore, only very small natural deviations in the genetic code are observed today.

Alanine World Hypothesis

The alanine world hypothesis states that the genetic code that emerged in the RNA world operates with alanine derivatives as the most widely used amino acids; other possibilities are conceivable, but are not used in nature.

There are several scenarios of how the canonical amino acids were chosen for protein synthesis in the RNA world. The "alanine world" hypothesis places the canonical amino acid alanine at the center of the so-called protein world. The α-helix and the β-sheet are predominant as secondary structures of proteins . The amino acids most frequently selected as monomers for the ribosomal synthesis of the polypeptide chains can be regarded as chemical derivatives of alanine. They are best suited for building α-helices and β-sheets in proteins. The alanine world hypothesis is practically confirmed by alanine scanning , since with this method amino acids are exchanged by point mutations to Ala, while the secondary structure remains intact. This principle is also used in classic X-ray crystallography , since the polyalanine basic framework model is often used to determine three-dimensional structures of proteins.

In transmembrane proteins , the membrane -spanning parts, which anchor the protein in the lipid bilayer of a biomembrane as a transmembrane domain, consist mainly of these secondary structures, as far as is known.

Pre-RNA world

Since RNA is already a very complex molecule, both alternative and complementary hypotheses have been developed about the development of life on earth. In particular, this includes a possible role for proteinoids , peptide nucleic acids (PNA), threose nucleic acids (TNA) and glycerol nucleic acids (GNA). Because they are chemically more simply built, they are either viewed as possible predecessors of RNA, or a chemical coevolution is assumed. It has been shown that peptide nucleic acids can replicate themselves and serve as a template for the RNA. The formation of peptide nucleic acids in the primordial soup is considered possible. The polycyclic aromatic hydrocarbons (PAHs) suspected in the primordial soup are also viewed as possible predecessors of RNA.

The following hypotheses were discussed, which suggest other nucleic acid worlds (Xeno-nucleic acids, XNA) as the predecessors of an RNA world:

Alternative hypotheses

Not all of the suggested alternative hypotheses are mutually exclusive and mutually exclusive to the RNA world hypothesis; rather, these scenarios could mostly have played a role in the development of modern cells. A selection:

Iron-sulfur world

The iron-sulfur world theory proposed by Günter Wächtershäuser assumes that simple metabolic processes developed before nucleic acids were used as genetic material, and that these energy-generating cycles catalyzed the production of genetic information, i.e. genes.

Protein hypothesis

Sidney W. Fox suggested that proteinoids , protein-like amino acid chains formed abiotic by condensation reactions , could represent a precursor of living beings in the sense of an abiogenesis , in which they also create microspheres and later a storage structure for the genetic information.

RNA-peptide coevolution

The RNA world hypothesis in the strict sense assumes that initially only ribozymes developed catalytic abilities, and that peptides or even the longer-chain proteins played no or only a marginal role. It was only to the extent that the biosynthesis of amino acid chains (on the ribosomes) emerged that the peptides produced in this way also took on their enzymatic function, and the RNA world became an RNP world (ribonucleoprotein world).

In contrast to this, the hypothesis of RNA-peptide coevolution assumes that, starting from abiotic primordial oligopeptides (short amino acid chains), there was a chemical coevolution of the peptides and the RNA and their catalytic abilities. However, the various primordial soup experiments show that short peptide chains ( oligopeptides ) could arise in the early days of chemical evolution. The theory therefore assumes the simultaneous emergence and development of two complex molecules (peptide as enzyme and RNA as carrier of genetic information). It thus describes an RNP world that has existed 'from the beginning': The current dual system, in which nucleic acids are required to produce proteins and, conversely, protein-based molecules that chain nucleic acids would have always existed, just an increase in efficiency and increase the respective chain lengths would be recorded. The assumption is supported, among other things, by the fact that there are apparently a number of evolutionarily very old protein-RNA complexes, including the ribosomes and telomerases . The hypothesis could explain the rapid evolution of the accuracy of RNA replication, since the proteins act as catalysts, as in recent ribosomes.

Lipid hypothesis

A research project completed in March 2015 by the John Sutherland group found that a network of reactions starting with hydrogen cyanide and hydrogen sulfide in flowing water that is irradiated by UV light could produce the chemical components of proteins and lipids along with RNA . In this scenario, a protocell was first created (with the help of the lipids), which then developed a metabolism by absorbing suitable molecules.

RNA-DNA coexistence

According to a new consideration by Jianfeng Xu, John Sutherland and colleagues (2020), there could also have been a coexistence of RNA and DNA very early on.

history

In his book "The Genetic Code" in 1967, Carl Woese presented the hypothesis of a simple life based on RNA. In 1968 Leslie Orgel also described RNA as an important stage in evolution. The term “RNA world” was first used by Walter Gilbert in 1986 and has since established itself.

literature

Web links

Videos

Individual evidence

  1. ↑ a b Sidney Becker et al .: Unified prebiotically plausible synthesis of pyrimidine and purine RNA ribonucleotides. Science 366, 2019, doi: 10.1126 / science.aax2747 ( press release , review in Nature News ).
  2. ↑ Nilesh Vaidya, Michael L. Manapat, Irene A. Chen, Ramon Xulvi-Brunet, Eric J. Hayden: Spontaneous network formation among cooperative RNA replicators . In: Nature . tape 491 , no. 7422 , 2012, p. 72-77 , doi : 10.1038 / nature11549 .
  3. ↑ a b c Yarus M: Primordial genetics: phenotype of the ribocyte . In: Annu. Rev. Genet. . 36, 2002, pp. 125-51. doi : 10.1146 / annurev.genet.36.031902.105056 . PMID 12429689 .
  4. ↑ a b Powner MW, Gerland B, Sutherland JD: Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions . In: Nature . 459, No. 7244, May 2009, pp. 239-42. doi : 10.1038 / nature08013 . PMID 19444213 .
  5. ↑ Sidney Becker et al .: A high-yielding, strictly regioselective prebiotic purine nucleoside formation pathway . In: Science . tape 352 , 2016, doi : 10.1126 / science.aad2808 .
  6. ^ Robert F. Service: Chemists find a recipe that may have jump-started life on Earth. Science News, 2018, doi: 10.1126 / science.aav7778 .
  7. ↑ Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR: Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena . In: Cell . 31, No. 1, November 1982, pp. 147-57. PMID 6297745 .
  8. ^ Gysbers R, Tram K, Gu J, Li Y: Evolution of an Enzyme from a Noncatalytic Nucleic Acid Sequence . In: Scientific Reports . 5, 2015, p. 11405. doi : 10.1038 / srep11405 . PMID 26091540 . PMC 4473686 (free full text).
  9. ↑ Unrau PJ, Bartel DP: RNA-catalysed nucleotide synthesis . In: Nature . 395, No. 6699, September 1998, pp. 260-3. doi : 10.1038 / 26193 . PMID 9751052 .
  10. ^ Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP: RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension . In: Science . 292, No. 5520, May 2001, pp. 1319-25. doi : 10.1126 / science.1060786 . PMID 11358999 .
  11. ↑ Lincoln TA, Joyce GF : Self-sustained replication of an RNA enzyme . In: Science . 323, No. 5918, February 2009, pp. 1229-32. doi : 10.1126 / science.1167856 . PMID 19131595 . PMC 2652413 (free full text).
  12. ↑ Yusupov MM, Yusupova GZ, Baucom A, et al. : Crystal structure of the ribosome at 5.5 A resolution . In: Science . 292, No. 5518, May 2001, pp. 883-96. doi : 10.1126 / science.1060089 . PMID 11283358 .
  13. ^ Szostak JW, Bartel DP, Luisi PL: Synthesizing life . In: Nature . 409, No. 6818, January 2001, pp. 387-90. doi : 10.1038 / 35053176 . PMID 11201752 .
  14. ↑ P. Forterre: The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells. In: Biochemistry. Volume 87, Number 9-10, 2005 Sep-Oct, pp 793-803, doi : 10.1016 / j.biochi.2005.03.015 , PMID 16164990 .
  15. ^ NA Kovacs, AS Petrov, KA Lanier, LD Williams: Frozen in Time: The History of Proteins. In: Molecular biology and evolution. Volume 34, number 5, May 2017, pp. 1252-1260, doi : 10.1093 / molbev / msx086 , PMID 28201543 , PMC 5400399 (free full text).
  16. ^ TR Cech: The RNA worlds in context. In: Cold Spring Harbor perspectives in biology. Volume 4, number 7, July 2012, p. A006742, doi : 10.1101 / cshperspect.a006742 , PMID 21441585 , PMC 3385955 (free full text).
  17. ↑ PT van der Gulik, D. Speijer: How amino acids and peptides shaped the RNA world. In: Life. Volume 5, number 1, January 2015, pp. 230–246, doi : 10.3390 / life5010230 , PMID 25607813 , PMC 4390850 (free full text) (review).
  18. ↑ Vladimir Kubyshkin, Nediljko Budisa: Anticipating alien cells with alternative genetic codes: away from the alanine world! . In: Curr. Op. Biotechnol. . 60, July 3, 2019, pp. 242–249. doi : 10.1016 / j.copbio.2019.05.006 .
  19. ↑ Vladimir Kubyshkin, Nediljko Budisa: The Alanine World Model for the Development of the Amino Acid Repertoire in Protein Biosynthesis . In: Int. J. Mol. Sci. . 20, No. 21, September 24, 2019, p. 5507. doi : 10.3390 / ijms20215507 .
  20. ↑ AM Karmali, TL Blundell, N. Furnham: Model-building strategies for low-resolution X-ray crystallographic data . In: Acta Cryst. . 65, 2009, pp. 121-127. doi : 10.1107 / S0907444908040006 .
  21. ↑ Schöning K, Scholz P, Guntha S, Wu X, Krishnamurthy R, Eschenmoser A: Chemical etiology of nucleic acid structure: the alpha-threofuranosyl- (3 '→ 2') oligonucleotide system . In: Science . 290, No. 5495, November 2000, pp. 1347-51. PMID 11082060 .
  22. ↑ Zhang L, Peritz A, Meggers E: A simple glycol nucleic acid . In: J. Am. Chem. Soc. . 127, No. 12, March 2005, pp. 4174-5. doi : 10.1021 / ja042564z . PMID 15783191 .
  23. ↑ Böhler C, Nielsen PE, Orgel LE: Template switching between PNA and RNA oligonucleotides . In: Nature . 376, No. 6541, August 1995, pp. 578-81. doi : 10.1038 / 376578a0 . PMID 7543656 .
  24. ↑ Nelson KE, Levy M, Miller SL: Peptide nucleic acids rather than RNA may have been the first genetic molecule . In: Proc. Natl. Acad. Sci. USA . 97, No. 8, April 2000, pp. 3868-71. PMID 10760258 . PMC 18108 (free full text).
  25. ↑ Ehrenfreund P, Rasmussen S, Cleaves J, Chen L: Experimentally tracing the key steps in the origin of life: The aromatic world . In: Astrobiology . 6, No. 3, June 2006, pp. 490-520. doi : 10.1089 / ast.2006.6.490 . PMID 16805704 .
  26. ↑ Pascal, Robert: A scenario starting from the first chemical building blocks, in: Muriel Gargaud, Jaques Reisse et al .: From Suns to Life: A Chronological Approach to the History of Life on Earth , Springer Science & Business Media 2007, pages 163-166, ISBN 0-387-45083-1
  27. ^ Kunin V: A system of two polymerases - a model for the origin of life . In: Origins of Life and Evolution of the Biosphere . 30, No. 5, October 2000, pp. 459-466. bibcode : 2000OLEB ... 30..459K . doi : 10.1023 / A: 1006672126867 . PMID 11002892 .
  28. ↑ L. Li, C. Francklyn, CW Carter. Aminoacylating Urzymes Challenge the RNA World Hypothesis. Journal of Biological Chemistry, 2013; 288 (37): 26856 DOI: 10.1074 / jbc.M113.496125
  29. ^ CW Carter: What RNA World? Why a Peptide / RNA Partnership Merits Renewed Experimental Attention. In: Life. Volume 5, number 1, January 2015, pp. 294-320, doi : 10.3390 / life5010294 , PMID 25625599 , PMC 4390853 (free full text) (review).
  30. ↑ Peter TS van der Gulik et al .: How Amino Acids and Peptides Shaped the RNA World , in: Life, January 2015, 5, pages 230-246; doi : 10.3390 / life5010230
  31. ^ Joseph Flannery Sutherland: BC of Prehistory, Palaeontology and the Past. The author is an advocate of RNA-peptide coevolution. His blog contains the following articles on this topic:
    1. Updating The RNA World from June 24, 2015 4:03
    2. Lost In Translation dated June 24, 2015 3:18 am
    3. A Brilliant New Update For The RNA World Hypothesis of September 17, 2013 11:28 am
  32. ↑ Bhavesh H. Patel, Claudia Percivalle, Dougal J. Ritson, Colm D. Duffy, John D. Sutherland: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism . In: Nature Chemistry . 7, No. 4, April 2015, pp. 301-307. bibcode : 2015NatCh ... 7..301P . doi : 10.1038 / nchem.2202 . PMID 25803468 . PMC 4568310 (free full text).
  33. ^ Robert F. Service: Researchers may have solved the origin-of-life conundrum. In: Science . March 16, 2015, accessed on September 27, 2017 ( doi: 10.1126 / science.aab0325 ).
  34. ↑ Jianfeng Xu, Václav Chmela, Nicholas J. Green, David A. Russell, Mikołaj J. Janicki, Robert W. Góra, Rafał Szabla, Andrew D. Bond, John D. Sutherland: Selective prebiotic formation of RNA pyrimidine and DNA purine nucleosides , in: Nature Volume 582, June 3, 2020, pp. 60-66, doi: 10.1038 / s41586-020-2330-9
  35. ↑ Michael Marshall: First life on Earth may actually have been built from both RNA and DNA , on: NewScientist of June 3, 2020
  36. ↑ Did Life Emerge in the “Primordial Soup” via DNA or RNA? Surprising Answer From New Research , on: SciTechDaily June 7, 2020, Source: UK Research and Innovation
  37. ^ Woese C: The basic nature of the genetic code . In: The Genetic Code . Harper & Row, January 1967, ISBN 978-0-06-047176-7 , pp. 150-178.
  38. ↑ Organ LE: Evolution of the genetic apparatus . In: J. Mol. Biol. . 38, No. 3, December 1968, pp. 381-393. PMID 5718557 .
  39. ^ Gilbert W: The RNA World . In: Nature . 319, February 1986, p. 618. doi : 10.1038 / 319618a0 .