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View source for RNA world - Wikipedia
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[[Alexander Rich]] first proposed the concept of the RNA world in 1962,<ref name="Neveu et al">{{cite journal | vauthors = Neveu M, Kim HJ, Benner SA | title = The "strong" RNA world hypothesis: fifty years old | journal = Astrobiology | volume = 13 | issue = 4 | pages = 391–403 | date = April 2013 | pmid = 23551238 | doi = 10.1089/ast.2012.0868 | quote = [The RNA world's existence] has broad support within the community today. | bibcode = 2013AsBio..13..391N }}</ref> and [[Walter Gilbert]] coined the term in 1986.<ref name="Cech2012">{{cite journal | vauthors = Cech TR | title = The RNA worlds in context | journal = Cold Spring Harbor Perspectives in Biology | volume = 4 | issue = 7 | pages = a006742 | date = July 2012 | pmid = 21441585 | pmc = 3385955 | doi = 10.1101/cshperspect.a006742 }}</ref> Among the characteristics of RNA that suggest its original prominence are that: * Like DNA, RNA can store and replicate genetic information. Although RNA is considerably more fragile than DNA, some ancient RNAs may have evolved the ability to [[RNA methylation|methylate]] other RNAs to protect them.<ref name="Rana">{{cite journal | vauthors = Rana AK, Ankri S | title = Reviving the RNA World: An Insight into the Appearance of RNA Methyltransferases | journal = Frontiers in Genetics | volume = 7 | pages = 99 | year = 2016 | pmid = 27375676 | pmc = 4893491 | doi = 10.3389/fgene.2016.00099 | doi-access = free }}</ref> The concurrent formation of all four RNA building blocks further strengthens the hypothesis.<ref>{{cite journal | vauthors = Becker S, Feldmann J, Wiedemann S, Okamura H, Schneider C, Iwan K, Crisp A, Rossa M, Amatov T, Carell T | display-authors = 6 | title = Unified prebiotically plausible synthesis of pyrimidine and purine RNA ribonucleotides | journal = Science | volume = 366 | issue = 6461 | pages = 76–82 | date = October 2019 | pmid = 31604305 | doi = 10.1126/science.aax2747 | s2cid = 203719976 | doi-access = free | bibcode = 2019Sci...366...76B }}</ref> * Enzymes made of RNA ([[ribozyme]]s) can [[catalyze]] (start or accelerate) chemical reactions that are critical for [[life]],<ref name="NYT-20140925-CZ">{{cite news |last= Zimmer |first= Carl |author-link= Carl Zimmer |title= A Tiny Emissary from the Ancient Past |url= https://www.nytimes.com/2014/09/25/science/a-tiny-emissary-from-the-ancient-past.html |date= September 25, 2014 |work= [[The New York Times]] |access-date= September 26, 2014 |url-status= live |archive-url= https://web.archive.org/web/20140927022738/http://www.nytimes.com/2014/09/25/science/a-tiny-emissary-from-the-ancient-past.html |archive-date= September 27, 2014 }}</ref> so it is conceivable that in an RNA world, ribozymes might have preceded [[enzyme]]s made of protein. * Many coenzymes that have fundamental roles in cellular life, such as [[acetyl-CoA]], [[nicotinamide adenine dinucleotide|NADH]], [[flavin adenine dinucleotide|FADH]], and [[coenzyme F420|F420]], are structurally strikingly similar to RNA and so may be surviving remnants of covalently bound coenzymes in an RNA world.<ref name="hong">{{cite journal | vauthors = White HB 3rd | title = Coenzymes as fossils of an earlier metabolic state. | journal = J Mol Evol | volume = 7 | issue = 2 | pages = 101–104 | year = 1976 | pmid = 1263263 | doi = 10.1007/BF01732468 | bibcode = 1976JMolE...7..101W | s2cid = 22282629 }}</ref> * One of the most critical components of cells, the [[ribosome]], is composed primarily of RNA. Although alternative chemical paths to life have been proposed,<ref name="NC-20150316">{{cite journal | vauthors = Patel BH, Percivalle C, Ritson DJ, Duffy CD, Sutherland JD | title = Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism | journal = Nature Chemistry | volume = 7 | issue = 4 | pages = 301–307 | date = April 2015 | pmid = 25803468 | pmc = 4568310 | doi = 10.1038/nchem.2202 | bibcode = 2015NatCh...7..301P }}</ref> and RNA-based life may not have been the first life to exist, <ref name="Cech2012" /><ref name="Robertson2012">{{cite journal | vauthors = Robertson MP, Joyce GF | title = The origins of the RNA world | journal = Cold Spring Harbor Perspectives in Biology | volume = 4 | issue = 5 | pages = a003608 | date = May 2012 | pmid = 20739415 | pmc = 3331698 | doi = 10.1101/cshperspect.a003608 }}</ref> the RNA world hypothesis seems to be the most favored abiogenesis paradigm. However, even proponents agree that there is still has not conclusive evidence to completely falsify other paradigms and hypotheses.<ref name="Neveu et al" /><ref name="NYT-20150504">{{cite news |last= Wade |first= Nicholas |author-link= Nicholas Wade |title= Making Sense of the Chemistry That Led to Life on Earth |url= https://www.nytimes.com/2015/05/05/science/making-sense-of-the-chemistry-that-led-to-life-on-earth.html |date= May 4, 2015 |work= [[The New York Times]] |access-date= May 10, 2015 |url-status= live |archive-url= https://web.archive.org/web/20170709115606/https://www.nytimes.com/2015/05/05/science/making-sense-of-the-chemistry-that-led-to-life-on-earth.html |archive-date= July 9, 2017 }}</ref><ref>{{cite journal | vauthors = Copley SD, Smith E, Morowitz HJ | title = The origin of the RNA world: co-evolution of genes and metabolism | journal = Bioorganic Chemistry | volume = 35 | issue = 6 | pages = 430–443 | date = December 2007 | pmid = 17897696 | doi = 10.1016/j.bioorg.2007.08.001 | quote = The proposal that life on Earth arose from an RNA World is the one most researched in the topic of Abiogenesis. }}</ref> Regardless of its plausibility in a [[prebiotic (chemistry)|prebiotic]] scenario, the RNA world can serve as a model system for studying the origin of life.<ref>{{cite journal | vauthors = Pressman A, Blanco C, Chen IA | title = The RNA World as a Model System to Study the Origin of Life | language = English | journal = Current Biology | volume = 25 | issue = 19 | pages = R953–R963 | date = October 2015 | pmid = 26439358 | doi = 10.1016/j.cub.2015.06.016 | s2cid = 43793294 | doi-access = free | bibcode = 2015CBio...25.R953P }}</ref> If the RNA world existed, it was probably followed by an age characterized by the evolution of [[ribonucleoprotein]]s ([[RNP world]]),<ref name="Cech2012"/> which in turn ushered in the era of DNA and longer proteins. DNA has greater stability and durability than RNA, which may explain why it became the predominant [[information storage]] molecule.<ref name="PiP"> {{cite journal | title = Patterns In Palaeontology: The first 3 billion years of evolution | first = Russell J. | last = Garwood | name-list-style = vanc | year = 2012 | journal = Palaeontology Online | volume = 2 | issue = 11 | pages = 1–14 | url = https://www.palaeontologyonline.com/articles/2012/patterns-in-palaeontology-the-first-3-billion-years-of-evolution/ | access-date = June 25, 2015 | url-status = live | archive-url = https://web.archive.org/web/20150626104131/http://www.palaeontologyonline.com/articles/2012/patterns-in-palaeontology-the-first-3-billion-years-of-evolution/ | archive-date = June 26, 2015 }} </ref> Protein enzymes may have replaced RNA-based ribozymes as [[Biocatalysis|biocatalysts]] because the greater abundance and diversity of the [[monomers]] of which they are built makes them more versatile. As some [[Cofactor (biochemistry)|cofactor]]s contain both nucleotide and amino-acid characteristics, it may be that amino acids, peptides, and finally proteins initially were cofactors for ribozymes.<ref name="hong"/> == History == One of the challenges in studying [[abiogenesis]] is that the system of reproduction and metabolism utilized by all extant life involves three distinct types of interdependent macromolecules ([[DNA]], [[RNA]], and [[protein|proteins]]). This suggests that life could not have arisen in its current form, which has led researchers to hypothesize mechanisms whereby the current system might have arisen from a simpler precursor system.<ref>{{cite journal | vauthors = Orgel LE | title = Prebiotic chemistry and the origin of the RNA world | journal = Critical Reviews in Biochemistry and Molecular Biology | volume = 39 | issue = 2 | pages = 99–123 | date = 2004 | pmid = 15217990 | doi = 10.1080/10409230490460765 | s2cid = 4939632 }}</ref> American molecular biologist [[Alexander Rich]] was the first to posit a coherent hypothesis on the origin of nucleotides as precursors of life.<ref>{{cite journal | vauthors = Lehman N | title = The RNA World: 4,000,000,050 years old | journal = Life | volume = 5 | issue = 4 | pages = 1583–1586 | date = October 2015 | pmid = 26791312 | pmc = 4695837 | doi = 10.3390/life5041583 | bibcode = 2015Life....5.1583L | doi-access = free }}</ref> In an article he contributed to a volume issued in honor of Nobel-laureate physiologist [[Albert Szent-Györgyi]], he explained that the primitive Earth's environment could have produced RNA molecules (polynucleotide monomers) that eventually acquired enzymatic and self-replicating functions.<ref>{{Cite book|last=Rich|first=Alexander|url=https://books.google.com/books?id=WCq2AAAAIAAJ|title=Horizons in Biochemistry: Albert Szent-Györgyi Dedicatory Volume|date=1962|publisher=Academic Press|isbn=978-0-12-400450-4|editor-last=Kasha|editor-first=Michael|pages=103–126|language=en|chapter=On the problems of evolution and biochemical information transfer|editor-last2=Pullman|editor-first2=Bernard}}</ref> Other mentions of RNA as a primordial molecule can be found in papers by [[Francis Crick]]<ref>{{cite journal | vauthors = Crick FH | title = The origin of the genetic code | journal = Journal of Molecular Biology | volume = 38 | issue = 3 | pages = 367–379 | date = December 1968 | pmid = 4887876 | doi = 10.1016/0022-2836(68)90392-6 | s2cid = 4144681 }}</ref> and [[Leslie Orgel]],<ref>{{cite journal | vauthors = Orgel LE | title = Evolution of the genetic apparatus | journal = Journal of Molecular Biology | volume = 38 | issue = 3 | pages = 381–393 | date = December 1968 | pmid = 5718557 | doi = 10.1016/0022-2836(68)90393-8 }}</ref> as well as in [[Carl Woese]]'s 1967 book ''The Genetic Code''.<ref>Woese C.R. (1967). The genetic code: The molecular basis for genetic expression. p. 186. Harper & Row</ref> [[Hans Kuhn (chemist)|Hans Kuhn]] in 1972 laid out a possible process by which the modern genetic system might have arisen from a nucleotide-based precursor, and this led Harold White in 1976 to observe that many of the cofactors essential for enzymatic function are either nucleotides or could have been derived from nucleotides. He proposed a scenario whereby the critical electrochemistry of enzymatic reactions would have necessitated retention of the specific nucleotide moieties of the original RNA-based enzymes carrying out the reactions, while the remaining structural elements of the enzymes were gradually replaced by protein, until all that remained of the original RNAs were these nucleotide cofactors, "fossils of nucleic acid enzymes".<ref>{{cite journal | vauthors = White HB | title = Coenzymes as fossils of an earlier metabolic state | journal = Journal of Molecular Evolution | volume = 7 | issue = 2 | pages = 101–104 | date = March 1976 | pmid = 1263263 | doi = 10.1007/BF01732468 | s2cid = 22282629 | bibcode = 1976JMolE...7..101W }}</ref> == Properties of RNA == The properties of RNA make the idea of the RNA world hypothesis conceptually plausible, though its general acceptance as an explanation for the origin of life requires further evidence.<ref name="Atk06">{{cite book|last1=Atkins|first1=John F.|title=The RNA world: the nature of modern RNA suggests a prebiotic RNA world|last2=Gesteland|first2=Raymond F.|last3=Cech|first3=Thomas|publisher=Cold Spring Harbor Laboratory Press|year=2006|isbn=978-0-87969-739-6|location=Plainview, N.Y|name-list-style=vanc}}</ref> RNA is known to form efficient catalysts, and its similarity to DNA makes clear its ability to store information. Opinions differ, however, as to whether RNA constituted the first autonomous self-replicating system or was a derivative of a still-earlier system.<ref name= Cech2012 /> One version of the hypothesis is that a different type of [[nucleic acid]], termed ''[[#Alternative hypotheses|pre-RNA]]'', was the first one to emerge as a self-reproducing molecule, to be replaced by RNA only later. On the other hand, the discovery in 2009 that activated [[pyrimidine]] [[ribonucleotides]] can be synthesized under plausible [[Abiogenesis|prebiotic]] conditions<ref name="Powner2009">{{cite journal | vauthors = Powner MW, Gerland B, Sutherland JD | title = Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions | journal = Nature | volume = 459 | issue = 7244 | pages = 239–242 | date = May 2009 | pmid = 19444213 | doi = 10.1038/nature08013 | s2cid = 4412117 | bibcode = 2009Natur.459..239P }}</ref> suggests that it is premature to dismiss the RNA-first scenarios.<ref name= Cech2012 /> Suggestions for 'simple' ''pre-RNA'' nucleic acids have included [[peptide nucleic acid]] (PNA), [[threose nucleic acid]] (TNA) or [[glycol nucleic acid]] (GNA).<ref>{{cite journal | vauthors = Orgel L | title = Origin of life. A simpler nucleic acid | journal = Science | volume = 290 | issue = 5495 | pages = 1306–1307 | date = November 2000 | pmid = 11185405 | doi = 10.1126/science.290.5495.1306 | s2cid = 83662769 }}</ref><ref>{{cite journal | vauthors = Nelson KE, Levy M, Miller SL | title = Peptide nucleic acids rather than RNA may have been the first genetic molecule | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 97 | issue = 8 | pages = 3868–3871 | date = April 2000 | pmid = 10760258 | pmc = 18108 | doi = 10.1073/pnas.97.8.3868 | doi-access = free | bibcode = 2000PNAS...97.3868N }}</ref> Despite their structural simplicity and possession of properties comparable with RNA, the chemically plausible generation of "simpler" nucleic acids under prebiotic conditions has yet to be demonstrated.<ref>{{cite journal | vauthors = Anastasi C, Buchet FF, Crowe MA, Parkes AL, Powner MW, Smith JM, Sutherland JD | title = RNA: prebiotic product, or biotic invention? | journal = Chemistry & Biodiversity | volume = 4 | issue = 4 | pages = 721–739 | date = April 2007 | pmid = 17443885 | doi = 10.1002/cbdv.200790060 | s2cid = 23526930 }}</ref> === RNA as an enzyme === {{Further|Ribozyme}} In the 1980s, RNA structures capable of self-processing were discovered,<ref>{{Cite journal |last1=Kruger |first1=Kelly |last2=Grabowski |first2=Paula J. |last3=Zaug |first3=Arthur J. |last4=Sands |first4=Julie |last5=Gottschling |first5=Daniel E. |last6=Cech |first6=Thomas R. |date=November 1982 |title=Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena |url=http://dx.doi.org/10.1016/0092-8674(82)90414-7 |journal=Cell |volume=31 |issue=1 |pages=147–157 |doi=10.1016/0092-8674(82)90414-7 |pmid=6297745 |s2cid=14787080 |issn=0092-8674}}</ref> with the RNA moiety of RNase P acting as its catalytic subunit.<ref>{{Cite journal |last1=Guerrier-Takada |first1=Cecilia |last2=Gardiner |first2=Katheleen |last3=Marsh |first3=Terry |last4=Pace |first4=Norman |last5=Altman |first5=Sidney |date=December 1983 |title=The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme |url=http://dx.doi.org/10.1016/0092-8674(83)90117-4 |journal=Cell |volume=35 |issue=3 |pages=849–857 |doi=10.1016/0092-8674(83)90117-4 |pmid=6197186 |s2cid=39111511 |issn=0092-8674}}</ref> These catalytic RNAs were referred to as [[Ribozyme|RNA enzymes]], or ribozymes, are found in today's DNA-based life and could be examples of [[living fossil]]s. Ribozymes play vital roles, such as that of the [[ribosome]]. The large subunit of the ribosome includes an [[Ribosomal RNA|rRNA]] responsible for the peptide bond-forming [[peptidyl transferase]] activity of protein synthesis. Many other ribozyme activities exist; for example, the [[hammerhead ribozyme]] performs self-cleavage<ref>{{cite journal | vauthors = Forster AC, Symons RH | title = Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites | journal = Cell | volume = 49 | issue = 2 | pages = 211–220 | date = April 1987 | pmid = 2436805 | doi = 10.1016/0092-8674(87)90562-9 | s2cid = 33415709 }}</ref> and an [[RNA-dependent RNA polymerase|RNA polymerase]] ribozyme can synthesize a short RNA strand from a primed RNA template.<ref>{{cite journal | vauthors = Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP | title = RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension | journal = Science | volume = 292 | issue = 5520 | pages = 1319–1325 | date = May 2001 | pmid = 11358999 | doi = 10.1126/science.1060786 | url = http://web.wi.mit.edu/bartel/pub/publication_reprints/Johnston_Science01.pdf | url-status = live | s2cid = 14174984 | citeseerx = 10.1.1.70.5439 | bibcode = 2001Sci...292.1319J | archive-url = https://web.archive.org/web/20120227163451/http://web.wi.mit.edu/bartel/pub/publication_reprints/Johnston_Science01.pdf | archive-date = 2012-02-27 }}</ref> Among the enzymatic properties important for the beginning of life are: ;Self-replication :The ability to [[self-replication|self-replicate]] or synthesize other RNA molecules; relatively short RNA molecules that can synthesize others have been artificially produced in the lab. The shortest was 165 bases long, though it has been estimated that only part of the molecule was crucial for this function. One version, 189 bases long, had an error rate of just 1.1% per nucleotide when synthesizing an 11-nucleotide long RNA strand from primed template strands.<ref>{{cite journal | vauthors = Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP | title = RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension | journal = Science | volume = 292 | issue = 5520 | pages = 1319–1325 | date = May 2001 | pmid = 11358999 | doi = 10.1126/science.1060786 | s2cid = 14174984 | citeseerx = 10.1.1.70.5439 | bibcode = 2001Sci...292.1319J }}</ref> This 189-base pair ribozyme could polymerize a template of at most 14 nucleotides in length, which is too short for self-replication, but is a potential lead for further investigation. The longest [[primer extension]] performed by a ribozyme polymerase was 20 bases.<ref name="pmid17586759">{{cite journal | vauthors = Zaher HS, Unrau PJ | title = Selection of an improved RNA polymerase ribozyme with superior extension and fidelity | journal = RNA | location = New York, N.Y. | volume = 13 | issue = 7 | pages = 1017–26 | date = July 2007 | pmid = 17586759 | pmc = 1894930 | doi = 10.1261/rna.548807 }}</ref> In 2016, researchers reported the use of in vitro evolution to improve dramatically the activity and generality of an RNA polymerase ribozyme by selecting variants that can synthesize functional RNA molecules from an RNA template.<ref name="Horning-2016" /> Each RNA polymerase ribozyme was engineered to remain linked to its new, synthesized RNA strand; this allowed the team to isolate successful polymerases. The isolated RNA polymerases were again used for another round of evolution. After several rounds of evolution, they obtained one RNA polymerase ribozyme called 24-3 that was able to copy almost any other RNA, from small catalysts to long RNA-based enzymes. Particular RNAs were amplified up to 10,000 times, a first RNA version of the [[polymerase chain reaction]] (PCR).<ref name="Horning-2016">{{cite journal | vauthors = Horning DP, Joyce GF | title = Amplification of RNA by an RNA polymerase ribozyme | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 113 | issue = 35 | pages = 9786–9791 | date = August 2016 | pmid = 27528667 | pmc = 5024611 | doi = 10.1073/pnas.1610103113 | bibcode = 2016PNAS..113.9786H | doi-access = free }}</ref> ;Catalysis :The ability to [[Catalysis|catalyze]] simple chemical reactions—which would enhance creation of molecules that are building blocks of RNA molecules (i.e., a strand of RNA that would make creating more strands of RNA easier). Relatively short RNA molecules with such abilities have been artificially formed in the lab.<ref name="pmid9831528">{{cite journal | vauthors = Huang F, Yang Z, Yarus M |authorlink3=Michael Yarus| title = RNA enzymes with two small-molecule substrates | journal = Chemistry & Biology | volume = 5 | issue = 11 | pages = 669–678 | date = November 1998 | pmid = 9831528 | doi = 10.1016/s1074-5521(98)90294-0 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Unrau PJ, Bartel DP | title = RNA-catalysed nucleotide synthesis | journal = Nature | volume = 395 | issue = 6699 | pages = 260–263 | date = September 1998 | pmid = 9751052 | doi = 10.1038/26193 | s2cid = 9734076 | bibcode = 1998Natur.395..260U }}</ref> A recent study showed that almost any nucleic acid can evolve into a catalytic sequence under appropriate selection. For instance, an arbitrarily chosen 50-nucleotide DNA fragment encoding for the ''[[Taurine cattle|Bos taurus]]'' (cattle) [[albumin]] mRNA was subjected to test-tube evolution to derive a catalytic DNA ([[Deoxyribozyme]], also called DNAzyme) with RNA-cleavage activity. After only a few weeks, a DNAzyme with significant catalytic activity had evolved.<ref name="Gysbers">{{cite journal | vauthors = Gysbers R, Tram K, Gu J, Li Y | title = Evolution of an Enzyme from a Noncatalytic Nucleic Acid Sequence | journal = Scientific Reports | volume = 5 | pages = 11405 | date = June 2015 | pmid = 26091540 | pmc = 4473686 | doi = 10.1038/srep11405 | bibcode = 2015NatSR...511405G }}</ref> In general, DNA is much more chemically inert than RNA and hence much more resistant to obtaining catalytic properties. If in vitro evolution works for DNA it will happen much more easily with RNA. In 2022, Nick Lane and coauthors showed in a computational simulation that short RNA sequences could have been capable of catalyzing {{CO2}} fixation which supported protocell replication and growth.<ref>{{cite journal | vauthors = Nunes Palmeira R, Colnaghi M, Harrison SA, Pomiankowski A, Lane N | title = The limits of metabolic heredity in protocells | journal = Proceedings. Biological Sciences | volume = 289 | issue = 1986 | pages = 20221469 | date = November 2022 | pmid = 36350219 | pmc = 9653231 | doi = 10.1098/rspb.2022.1469 }}</ref> ;Amino acid-RNA ligation :The ability to conjugate an amino acid to the 3'-end of an RNA in order to use its chemical groups or provide a long-branched [[aliphatic]] sidechain.<ref name="pmid21779963">{{cite journal | vauthors = Erives A | title = A model of proto-anti-codon RNA enzymes requiring L-amino acid homochirality | journal = Journal of Molecular Evolution | volume = 73 | issue = 1–2 | pages = 10–22 | date = August 2011 | pmid = 21779963 | pmc = 3223571 | doi = 10.1007/s00239-011-9453-4 | bibcode = 2011JMolE..73...10E }}</ref> ;Peptide bond formation :The ability to catalyse the formation of [[peptide bonds]] between amino acids to produce short [[peptide]]s or longer [[protein]]s. This is done in modern cells by ribosomes, a complex of several RNA molecules known as [[rRNA]] together with many proteins. The rRNA molecules are thought responsible for its enzymatic activity, as no amino-acid residues lie within 18[[Ångström|Å]] of the enzyme's [[active site]],<ref name="Atk06" /> and, when the majority of the amino-acid residues in the ribosome were stringently removed, the resulting ribosome retained its full [[peptidyl transferase]] activity, fully able to catalyze the formation of peptide bonds between amino acids.<ref name="pmid1604315">{{cite journal | vauthors = Noller HF, Hoffarth V, Zimniak L | title = Unusual resistance of peptidyl transferase to protein extraction procedures | journal = Science | volume = 256 | issue = 5062 | pages = 1416–1419 | date = June 1992 | pmid = 1604315 | doi = 10.1126/science.1604315 | bibcode = 1992Sci...256.1416N }}</ref> A pseudo 2 fold symmetry of the region surrounding the peptidyl transferase center led to the hypothesis of the Proto-Ribosome, that a vestige of an ancient dimeric molecule from the RNA world is functioning within the ribosome.<ref name="pmid21930590">{{cite journal | vauthors = Krupkin M, Matzov D, Tang H, Metz M, Kalaora R, Belousoff MJ, Zimmerman E, Bashan A, Yonath A | display-authors = 6 | title = A vestige of a prebiotic bonding machine is functioning within the contemporary ribosome | journal = Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences | volume = 366 | issue = 1580 | pages = 2972–2978 | date = October 2011 | pmid = 21930590 | pmc = 3158926 | doi = 10.1098/rstb.2011.0146 | doi-access = free }}</ref> An RNA molecule with the ribosomal RNA sequence has been synthesized in the lab to test the Proto-ribosome hypothesis and was able to dimerize and to form peptide bonds.<ref name="pmid35137169">{{cite journal | vauthors = Bose T, Fridkin G, Davidovich C, Krupkin M, Dinger N, Falkovich AH, Peleg Y, Agmon I, Bashan A, Yonath A | display-authors = 6 | title = Origin of life: protoribosome forms peptide bonds and links RNA and protein dominated worlds | journal = Nucleic Acids Research | volume = 50 | issue = 4 | pages = 1815–1828 | date = February 2022 | pmid = 35137169 | pmc = 8886871 | doi = 10.1093/nar/gkac052 | doi-access = free }}</ref> A much shorter RNA molecule has been synthesized in the laboratory with the ability to form [[peptide bonds]], and it has been suggested that rRNA has evolved from a similar molecule.<ref>{{cite journal | vauthors = Zhang B, Cech TR | title = Peptide bond formation by in vitro selected ribozymes | journal = Nature | volume = 390 | issue = 6655 | pages = 96–100 | date = November 1997 | pmid = 9363898 | doi = 10.1038/36375 | s2cid = 4398830 | bibcode = 1997Natur.390...96Z }}</ref> It has also been suggested that amino acids may have initially been involved with RNA molecules as cofactors enhancing or diversifying their enzymatic capabilities, before evolving into more complex peptides. Similarly, [[tRNA]] is suggested to have evolved from RNA molecules that began to catalyze amino acid transfer.<ref>{{cite journal | vauthors = Szathmáry E | title = The origin of the genetic code: amino acids as cofactors in an RNA world | journal = Trends in Genetics | volume = 15 | issue = 6 | pages = 223–229 | date = June 1999 | pmid = 10354582 | doi = 10.1016/S0168-9525(99)01730-8 }}</ref> ==== Cofactors ==== :Protein enzymes catalyze various chemical reactions, but over half of them incorporate cofactors to facilitate and diversify their catalytic activities.<ref>{{Cite journal |last=Decker |first=Karl |date=2006-01-17 |title=The Pyridine Nucleotide Coenzymes. Herausgegeben von J. Everse, B. Anderson und K.-S. You. Academic Press, New York 1982. XXXV, 389 S., geb. $ 46.00 |url=http://dx.doi.org/10.1002/ange.19830951241 |journal=Angewandte Chemie |volume=95 |issue=12 |pages=1033–1034 |doi=10.1002/ange.19830951241 |issn=0044-8249}}</ref> Cofactors are essential in biology, as they are based largely on nucleotides rather than amino acids. Ribozymes use nucleotide cofactors to create metabolism, with two basic choices: non-covalent binding or covalent attachment. Both approaches have been demonstrated using directed evolution to reinvent RNA dupes of protein-catalyzed processes. Lorsch and Szostak <ref>{{Cite journal |last1=Ekland |first1=Eric H. |last2=Szostak |first2=Jack W. |last3=Bartel |first3=David P. |date=1995-07-21 |title=Structurally Complex and Highly Active RNA Ligases Derived from Random RNA Sequences |url=http://dx.doi.org/10.1126/science.7618102 |journal=Science |volume=269 |issue=5222 |pages=364–370 |doi=10.1126/science.7618102 |pmid=7618102 |bibcode=1995Sci...269..364E |s2cid=40795082 |issn=0036-8075}}</ref> investigated ribozymes that could phosphorylate themselves and use ATP-γS as a substrate. However, only one of the seven classes of selected ribozymes had detectable ATP affinity, indicating that the ability to bind ATP was compromised. NAD<sup>+</sup>- dependent redox ribozymes were also evaluated.<ref>{{Cite journal |last1=Tsukiji |first1=Shinya |last2=Pattnaik |first2=Swetansu B |last3=Suga |first3=Hiroaki |date=2003-08-10 |title=An alcohol dehydrogenase ribozyme |url=http://dx.doi.org/10.1038/nsb964 |journal=Nature Structural & Molecular Biology |volume=10 |issue=9 |pages=713–717 |doi=10.1038/nsb964 |pmid=12910259 |s2cid=41081956 |issn=1545-9993}}</ref> The select ribozyme had a rate of enhancement of more than 10<sup>7</sup> fold and was proven to catalyze the reverse reaction - benzaldehyde reduction by NADH.<ref>{{Cite journal |last1=Tsukiji |first1=Shinya |last2=Pattnaik |first2=Swetansu B. |last3=Suga |first3=Hiroaki |date=2004-04-06 |title=Reduction of an Aldehyde by a NADH/Zn<sup>2+</sup>-Dependent Redox Active Ribozyme |url=http://dx.doi.org/10.1021/ja0495213 |journal=Journal of the American Chemical Society |volume=126 |issue=16 |pages=5044–5045 |doi=10.1021/ja0495213 |pmid=15099068 |issn=0002-7863}}</ref> Since the usage of adenosine as a cofactor is prevalent in current metabolism and is likely to have been common in the RNA world, these discoveries are essential for the evolution of metabolism in the RNA world. === RNA in information storage === RNA is a very similar molecule to DNA, with only two significant chemical differences (the backbone of RNA uses ribose instead of deoxyribose and its nucleobases include [[uracil]] instead of [[thymine]]). The overall structure of RNA and DNA are immensely similar—one strand of DNA and one of RNA can bind to form a double helical structure. This makes the storage of information in RNA possible in a very similar way to the storage of information in DNA. However, RNA is less stable, being more prone to hydrolysis due to the presence of a hydroxyl group at the ribose 2' position. [[File:Ribonucleic acid chemical structure.svg|thumb|The major difference between RNA and DNA is the presence of a [[hydroxyl]] group at the 2'-position.]] ==== Comparison of DNA and RNA structure ==== {{Main|RNA|DNA}} The major difference between RNA and DNA is the presence of a [[hydroxyl]] group at the 2'-position of the [[ribose]] sugar in RNA (illustration, right).<ref name="Atk06" /> This group makes the molecule less stable because, when not constrained in a double helix, the 2' hydroxyl can chemically attack the adjacent [[phosphodiester bond]] to cleave the phosphodiester backbone. The hydroxyl group also forces the ribose into the C3'-''endo'' sugar conformation unlike the C2'-''endo'' conformation of the [[deoxyribose]] sugar in DNA. This forces an RNA double helix to change from a [[B-DNA]] structure to one more closely resembling [[A-DNA]]. RNA also uses a different set of bases than DNA—[[adenine]], [[guanine]], [[cytosine]] and [[uracil]], instead of adenine, guanine, cytosine and [[thymine]]. Chemically, uracil is similar to thymine, differing only by a [[methyl group]], and its production requires less energy.<ref>{{cite web |title=Uracil |url=http://www.humpath.com/spip.php?article7304 |access-date=2020-07-24 |url-status=live |archive-url=https://web.archive.org/web/20150908055138/http://www.humpath.com/spip.php?article7304 |archive-date=2015-09-08}}</ref> In terms of base pairing, this has no effect. Adenine readily binds uracil or thymine. Uracil is, however, one product of damage to cytosine that makes RNA particularly susceptible to mutations that can replace a '''GC''' base pair with a '''GU''' ([[wobble base pair|wobble]]) or '''AU''' [[base pair]]. RNA is thought to have preceded DNA, because of their ordering in the biosynthetic pathways.<ref name="Robertson2012" /> The deoxyribonucleotides used to make DNA are made from ribonucleotides, the building blocks of RNA, by removing the 2'-hydroxyl group. As a consequence, a cell must have the ability to make RNA before it can make DNA. ==== Limitations of information storage in RNA ==== The chemical properties of RNA make large RNA [[molecule]]s inherently fragile, and they can easily be broken down into their constituent nucleotides through [[hydrolysis]].<ref>{{cite journal | vauthors = Lindahl T | title = Instability and decay of the primary structure of DNA | journal = Nature | volume = 362 | issue = 6422 | pages = 709–715 | date = April 1993 | pmid = 8469282 | doi = 10.1038/362709a0 | s2cid = 4283694 | bibcode = 1993Natur.362..709L }}</ref><ref>{{cite journal | vauthors = Pääbo S | title = Ancient DNA | journal = Scientific American | volume = 269 | issue = 5 | pages = 86–92 | date = November 1993 | pmid = 8235556 | doi = 10.1038/scientificamerican1193-86 | s2cid = 5288515 | bibcode = 1993SciAm.269e..86P }}</ref> These limitations do not make use of RNA as an [[information storage]] system impossible, simply energy intensive (to repair or replace damaged RNA molecules) and prone to mutation. While this makes it unsuitable for current 'DNA optimised' life, it may have been acceptable for more primitive life. === RNA as a regulator === {{Main|Riboswitch}} Riboswitches have been found to act as regulators of gene expression, particularly in bacteria, but also in plants and [[archaea]]. Riboswitches alter their [[secondary structure]] in response to the binding of a [[metabolite]]. Riboswitch classes have highly conserved aptamer domains, even among diverse organisms. When a target metabolite is bound to this aptamer, conformational changes occur, modulating the expression of genes carried by mRNA. These changes occur in an expression platform, located downstream from the aptamer.<ref>{{Cite journal |last1=Winkler |first1=Wade C. |last2=Breaker |first2=Ronald R. |date=2005-10-01 |title=Regulation of Bacterial Gene Expression by Riboswitches |url=http://dx.doi.org/10.1146/annurev.micro.59.030804.121336 |journal=Annual Review of Microbiology |volume=59 |issue=1 |pages=487–517 |doi=10.1146/annurev.micro.59.030804.121336 |pmid=16153177 |issn=0066-4227}}</ref> This change in structure can result in the formation or disruption of a [[Terminator (genetics)|terminator]], truncating or permitting transcription respectively.<ref>{{cite journal | vauthors = Nudler E, Mironov AS | title = The riboswitch control of bacterial metabolism | journal = Trends in Biochemical Sciences | volume = 29 | issue = 1 | pages = 11–17 | date = January 2004 | pmid = 14729327 | doi = 10.1016/j.tibs.2003.11.004 }}</ref> Alternatively, riboswitches may bind or occlude the [[Shine–Dalgarno sequence]], affecting translation.<ref>{{cite journal | vauthors = Tucker BJ, Breaker RR | title = Riboswitches as versatile gene control elements | journal = Current Opinion in Structural Biology | volume = 15 | issue = 3 | pages = 342–348 | date = June 2005 | pmid = 15919195 | doi = 10.1016/j.sbi.2005.05.003 }}</ref> It has been suggested that these originated in an RNA-based world.<ref name="pmid18778966">{{cite journal | vauthors = Bocobza SE, Aharoni A | title = Switching the light on plant riboswitches | journal = Trends in Plant Science | volume = 13 | issue = 10 | pages = 526–533 | date = October 2008 | pmid = 18778966 | doi = 10.1016/j.tplants.2008.07.004 | bibcode = 2008TPS....13..526B }}</ref> In addition, [[RNA thermometer]]s regulate gene expression in response to temperature changes.<ref name="Nar06">{{cite journal | vauthors = Narberhaus F, Waldminghaus T, Chowdhury S | title = RNA thermometers | journal = FEMS Microbiology Reviews | volume = 30 | issue = 1 | pages = 3–16 | date = January 2006 | pmid = 16438677 | doi = 10.1111/j.1574-6976.2005.004.x | doi-access = free }}</ref> == Support and difficulties == The RNA world hypothesis is supported by RNA's ability to do all three of to store, to transmit, and to duplicate [[genetics|genetic]] information, as [[DNA]] does, and to perform enzymatic reactions, like protein-based enzymes. Because it can carry out the types of tasks now performed by proteins and DNA, RNA is believed to have once been capable of supporting independent life on its own.<ref name="Atk06" /> Some [[virus]]es use RNA as their genetic material, rather than DNA.<ref>Patton, John T. Editor (2008). Segmented Double-stranded RNA Viruses: Structure and Molecular Biology. Caister Academic Press. Editor's affiliation: Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD 20892-8026. {{ISBN|978-1-904455-21-9}}</ref> Further, while [[nucleotide]]s were not found in experiments based on [[Miller–Urey experiment|Miller-Urey experiment]], their formation in prebiotically plausible conditions was reported in 2009;<ref name="Powner2009"/> a [[purine]] base, adenine, is merely a [[pentamer]] of [[hydrogen cyanide]], and it happens that this particular base is used as omnipresent energy vehicle in the cell: [[adenosine triphosphate]] is used everywhere in preference to [[guanosine triphosphate]], [[cytidine triphosphate]], [[uridine triphosphate]] or even [[deoxythymidine triphosphate]], which could serve just as well but are practically never used except as building blocks for nucleic acid chains. Experiments with basic ribozymes, like [[Bacteriophage Qβ]] RNA, have shown that simple self-replicating RNA structures can withstand even strong selective pressures (e.g., opposite-chirality chain terminators).<!-- I don't want to link to Spiegelman Monster here because I'm not sure that this is what's being talked about, but it appears to be. --><ref>Bell, Graham: The Basics of Selection. Springer, 1997.{{page needed|date=March 2021}}</ref> Since there were no known chemical pathways for the abiogenic synthesis of nucleotides from [[pyrimidine]] nucleobases cytosine and uracil under prebiotic conditions, it is thought by some that nucleic acids did not contain these [[nucleobase]]s seen in life's nucleic acids.<ref>{{cite journal | vauthors = Orgel LE | title = The origin of life on the earth | journal = Scientific American | volume = 271 | issue = 4 | pages = 76–83 | date = October 1994 | pmid = 7524147 | doi = 10.1038/scientificamerican1094-76 | bibcode = 1994SciAm.271d..76O }}</ref> The nucleoside cytosine has a half-life in isolation of 19 days at {{convert|100|°C|°F|abbr=on}} and 17,000 years in freezing water, which some argue is too short on the [[geologic time scale]] for accumulation.<ref>{{cite journal | vauthors = Levy M, Miller SL | title = The stability of the RNA bases: implications for the origin of life | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 95 | issue = 14 | pages = 7933–7938 | date = July 1998 | pmid = 9653118 | pmc = 20907 | doi = 10.1073/pnas.95.14.7933 | doi-access = free | bibcode = 1998PNAS...95.7933L }}</ref> Others have questioned whether [[ribose]] and other backbone sugars could be stable enough to be found in the original genetic material,<ref>{{cite journal | vauthors = Larralde R, Robertson MP, Miller SL | title = Rates of decomposition of ribose and other sugars: implications for chemical evolution | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 92 | issue = 18 | pages = 8158–8160 | date = August 1995 | pmid = 7667262 | pmc = 41115 | doi = 10.1073/pnas.92.18.8158 | doi-access = free | bibcode = 1995PNAS...92.8158L }}</ref> and have raised the issue that all ribose molecules would have had to be the same [[enantiomer]], as any nucleotide of the wrong [[chirality (chemistry)|chirality]] acts as a chain [[terminator (genetics)|terminator]].<ref>{{cite journal | vauthors = Joyce GF, Visser GM, van Boeckel CA, van Boom JH, Orgel LE, van Westrenen J | title = Chiral selection in poly(C)-directed synthesis of oligo(G) | journal = Nature | volume = 310 | issue = 5978 | pages = 602–604 | year = 1984 | pmid = 6462250 | doi = 10.1038/310602a0 | s2cid = 4367383 | bibcode = 1984Natur.310..602J }}</ref> Pyrimidine ribonucleosides and their respective nucleotides have been prebiotically synthesised by a sequence of reactions that by-pass free sugars and assemble in a stepwise fashion by including nitrogenous and oxygenous chemistries. In a series of publications, [[John Sutherland (chemist)|John Sutherland]] and his team at the School of Chemistry, [[University of Manchester]], have demonstrated high yielding routes to [[cytidine]] and [[uridine]] ribonucleotides built from small 2- and 3-carbon fragments such as [[glycolaldehyde]], [[glyceraldehyde]] or glyceraldehyde-3-phosphate, [[cyanamide]], and [[cyanoacetylene]]. One of the steps in this sequence allows the isolation of [[enantiomer|enantiopure]] ribose aminooxazoline if the enantiomeric excess of glyceraldehyde is 60% or greater, of possible interest toward biological homochirality.<ref>Carole Anastasi, Michael A. Crowe, Matthew W. Powner, John D. Sutherland "Direct Assembly of Nucleoside Precursors from Two- and Three-Carbon Units ''Angewandte Chemie International Edition'' '''45'''(37):6176–79, 2006.</ref> This can be viewed as a prebiotic purification step, where the said compound spontaneously crystallised out from a mixture of the other pentose aminooxazolines. Aminooxazolines can react with cyanoacetylene in a mild and highly efficient manner, controlled by inorganic phosphate, to give the cytidine ribonucleotides. Photoanomerization with [[UV light]] allows for inversion about the 1' anomeric centre to give the correct beta stereochemistry; one problem with this chemistry is the selective phosphorylation of alpha-cytidine at the 2' position.<ref name="pmid18798212">{{cite journal | vauthors = Powner MW, Sutherland JD | title = Potentially prebiotic synthesis of pyrimidine beta-D-ribonucleotides by photoanomerization/hydrolysis of alpha-D-cytidine-2'-phosphate | journal = ChemBioChem | volume = 9 | issue = 15 | pages = 2386–2387 | date = October 2008 | pmid = 18798212 | doi = 10.1002/cbic.200800391 | s2cid = 5704391 }}</ref> However, in 2009, they showed that the same simple building blocks allow access, via phosphate controlled nucleobase elaboration, to 2',3'-cyclic pyrimidine nucleotides directly, which are known to be able to polymerise into RNA.<ref name=Powner2009 /> Organic chemist Donna Blackmond described this finding as "strong evidence" in favour of the RNA world.<ref>{{cite journal |title=RNA world easier to make |author=Van Noorden R |journal=Nature |year=2009 |url=https://www.nature.com/news/2009/090513/full/news.2009.471.html |doi=10.1038/news.2009.471 |url-status=live |archive-url=https://web.archive.org/web/20090516205806/http://www.nature.com/news/2009/090513/full/news.2009.471.html |archive-date=2009-05-16}}</ref> However, John Sutherland said that while his team's work suggests that nucleic acids played an early and central role in the origin of life, it did not necessarily support the RNA world hypothesis in the strict sense, which he described as a "restrictive, hypothetical arrangement".<ref>{{citation | last = Urquhart | first = James | name-list-style = vanc | title = Insight into RNA origins | magazine = Chemistry World | publisher = Royal Society of Chemistry | date = 13 May 2009 |url=https://www.chemistryworld.com/news/insight-into-rna-origins/3002171.article | url-status = live | archive-url = https://web.archive.org/web/20151004071059/http://www.rsc.org/chemistryworld/News/2009/May/13050902.asp | archive-date = 4 October 2015 }}</ref> The Sutherland group's 2009 paper also highlighted the possibility for the photo-sanitization of the pyrimidine-2',3'-cyclic phosphates.<ref name="Powner2009"/> A potential weakness of these routes is the generation of enantioenriched glyceraldehyde, or its 3-phosphate derivative (glyceraldehyde prefers to exist as its keto [[tautomer]] dihydroxyacetone).{{Citation needed|date=May 2009}} On August 8, 2011, a report, based on [[NASA]] studies with [[meteorite]]s found on [[Earth]], was published suggesting building blocks of RNA (adenine, guanine, and related [[organic molecules]]) may have been formed in [[outer space]].<ref name="Callahan">{{cite journal | vauthors = Callahan MP, Smith KE, Cleaves HJ, Ruzicka J, Stern JC, Glavin DP, House CH, Dworkin JP | display-authors = 6 | title = Carbonaceous meteorites contain a wide range of extraterrestrial nucleobases | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 108 | issue = 34 | pages = 13995–13998 | date = August 2011 | pmid = 21836052 | pmc = 3161613 | doi = 10.1073/pnas.1106493108 | doi-access = free | bibcode = 2011PNAS..10813995C }}</ref><ref name="Steigerwald">{{cite web | last = Steigerwald | first = John | name-list-style = vanc | title = NASA Researchers: DNA Building Blocks Can Be Made in Space |url=https://www.nasa.gov/topics/solarsystem/features/dna-meteorites.html | publisher = [[NASA]] | date = 8 August 2011 | access-date = 2011-08-10 | url-status = live | archive-url = https://web.archive.org/web/20150623004556/http://www.nasa.gov/topics/solarsystem/features/dna-meteorites.html | archive-date = 23 June 2015 }}</ref><ref name="DNA">{{cite web |author=ScienceDaily Staff |title=DNA Building Blocks Can Be Made in Space, NASA Evidence Suggests |url=https://www.sciencedaily.com/releases/2011/08/110808220659.htm |date=9 August 2011 |website=[[ScienceDaily]] |access-date=2011-08-09 |url-status=live |archive-url=https://web.archive.org/web/20110905105043/https://www.sciencedaily.com/releases/2011/08/110808220659.htm |archive-date=5 September 2011 }}</ref> In 2017, research using a [[computer simulation|numerical model]] suggested that a RNA world may have emerged in warm ponds on the early Earth, and that meteorites were a plausible and probable source of the RNA building blocks ([[ribose]] and nucleic acids) to these environments.<ref>{{cite journal | vauthors = Pearce BK, Pudritz RE, Semenov DA, Henning TK | title = Origin of the RNA world: The fate of nucleobases in warm little ponds | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 114 | issue = 43 | pages = 11327–11332 | date = October 2017 | pmid = 28973920 | pmc = 5664528 | doi = 10.1073/pnas.1710339114 | arxiv = 1710.00434 | doi-access = free | bibcode = 2017PNAS..11411327P }}</ref> On August 29, 2012, astronomers at [[Copenhagen University]] reported the detection of a specific sugar molecule, [[glycolaldehyde]], in a distant star system. The molecule was found around the [[protostar|protostellar]] binary ''IRAS 16293-2422'', which is located 400 light years from Earth.<ref name="NG-20120829">{{cite journal |title=Sugar Found In Space |journal=National Geographic |last=Than |first=Ker |date=August 29, 2012 |url=https://www.nationalgeographic.com/news/2012/8/120829-sugar-space-planets-science-life/ |access-date=August 31, 2012 |url-status=dead |archive-url=https://web.archive.org/web/20150714073830/http://news.nationalgeographic.com/news/2012/08/120829-sugar-space-planets-science-life/ |archive-date=July 14, 2015 }}</ref><ref name="AP-20120829">{{cite web |author=Staff |title=Sweet! Astronomers spot sugar molecule near star |url=http://apnews.excite.com/article/20120829/DA0V31D80.html |date=August 29, 2012 |publisher=[[AP News]] |access-date=August 31, 2012 |url-status=live |archive-url=https://web.archive.org/web/20150714101929/http://apnews.excite.com/article/20120829/DA0V31D80.html |archive-date=July 14, 2015 }}</ref> Because glycolaldehyde is needed to form RNA, this finding suggests that complex organic molecules may form in stellar systems prior to the formation of planets, eventually arriving on young planets early in their formation.<ref>{{cite journal | title = Detection of the simplest sugar, glycolaldehyde, in a solar-type protostar with ALMA | last1 = Jørgensen | first1 = J. K. | last2 = Favre | first2 = C. | last3 = Bisschop | first3 = S. | last4 = Bourke | first4 = T. | last5 = Dishoeck | first5 = E. | last6 = Schmalzl | first6 = M. | name-list-style = vanc | version = eprint | year = 2012 | url = http://www.eso.org/public/archives/releases/sciencepapers/eso1234/eso1234a.pdf | bibcode = 2012ApJ...757L...4J | volume = 757 | issue = 1 | pages = L4 | journal = The Astrophysical Journal Letters | doi = 10.1088/2041-8205/757/1/L4 | url-status = live | archive-url = https://web.archive.org/web/20150924021240/http://www.eso.org/public/archives/releases/sciencepapers/eso1234/eso1234a.pdf | archive-date = 2015-09-24 | arxiv = 1208.5498 | s2cid = 14205612 }}</ref> [[Nitrile]]s, key molecular precursors of the RNA World scenario, are among the most abundant chemical families in the universe and have been found in molecular clouds in the center of the Milky Way, protostars of different masses, meteorites and comets, and also in the atmosphere of Titan, the largest moon of Saturn.<ref>{{Cite journal |last1=Rivilla |first1=Víctor M. |last2=Jiménez-Serra |first2=Izaskun |last3=Martín-Pintado |first3=Jesús |last4=Colzi |first4=Laura |last5=Tercero |first5=Belén |last6=de Vicente |first6=Pablo |last7=Zeng |first7=Shaoshan |last8=Martín |first8=Sergio |last9=García de la Concepción |first9=Juan |last10=Bizzocchi |first10=Luca |last11=Melosso |first11=Mattia |date=2022 |title=Molecular Precursors of the RNA-World in Space: New Nitriles in the G+0.693−0.027 Molecular Cloud |journal=Frontiers in Astronomy and Space Sciences |volume=9 |page=876870 |doi=10.3389/fspas.2022.876870 |arxiv=2206.01053 |bibcode=2022FrASS...9.6870R |issn=2296-987X|doi-access=free }}</ref><ref>{{Cite web |date=2022-07-08 |title=Building blocks for RNA-based life abound at center of our galaxy |url=https://www.eurekalert.org/news-releases/957827 |access-date=2022-07-11 |website=EurekAlert! |language=en}}</ref> A study in 2001 shows that nicotinic acid and its precursor, quinolinic acid can be "produced in yields as high as 7% in a six-step nonenzymatic sequence from aspartic acid and dihydroxyacetone phosphate (DHAP). The biosynthesis of ribose phosphate could have produced DHAP and other three carbon compounds. Aspartic acid could have been available from prebiotic synthesis or from the ribozyme synthesis of pyrimidines." This supports that NAD could have originated in the RNA world.<ref>{{Cite journal |last1=Cleaves |first1=H. James |last2=Miller |first2=Stanley L. |date=2001-01-01 |title=The Nicotinamide Biosynthetic Pathway Is a By-Product of the RNA World |url=https://doi.org/10.1007/s002390010135 |journal=Journal of Molecular Evolution |language=en |volume=52 |issue=1 |pages=73–77 |doi=10.1007/s002390010135 |pmid=11139296 |bibcode=2001JMolE..52...73C |s2cid=25458439 |issn=1432-1432}}</ref> RNA sequences at lengths of 30 nucleotides, 60 nucleotides, 100 nucleotides, and 140 nucleotides, were capable of catalysis of "the synthesis of three common coenzymes, CoA, NAD, and FAD, from their precursors, 4‘-phosphopantetheine, NMN, and FMN, respectively".<ref>{{Cite journal |last1=Huang |first1=Faqing |last2=Bugg |first2=Charles Walter |last3=Yarus |first3=Michael |date=2000-12-01 |title=RNA-Catalyzed CoA, NAD, and FAD Synthesis from Phosphopantetheine, NMN, and FMN |url=https://pubs.acs.org/doi/10.1021/bi002061f |journal=Biochemistry |language=en |volume=39 |issue=50 |pages=15548–15555 |doi=10.1021/bi002061f |pmid=11112541 |issn=0006-2960}}</ref> == Prebiotic RNA synthesis == [[File:Etls-2019-0024c.01.png|thumb|upright=2|The RNA world hypothesis proposes that spontaneous polymerization of ribonucleotides led to the emergence of [[ribozyme]]s and including an [[RNA-dependent RNA polymerase|RNA replicase]].]] Nucleotides are the fundamental molecules that combine in series to form RNA. They consist of a nitrogenous base attached to a sugar-phosphate backbone. RNA is made of long stretches of specific nucleotides arranged so that their sequence of bases carries information. The RNA world hypothesis holds that in the [[primordial soup]] (or [[primordial sandwich|sandwich]]), there existed free-floating nucleotides. These nucleotides regularly formed bonds with one another, which often broke because the change in energy was so low. However, certain sequences of base pairs have catalytic properties that lower the energy of their chain being created, enabling them to stay together for longer periods of time. As each chain grew longer, it attracted more matching nucleotides faster, causing chains to now form faster than they were breaking down. These chains have been proposed by some as the first, primitive forms of life. In an RNA world, different sets of RNA strands would have had different replication outputs, which would have increased or decreased their frequency in the population, i.e., [[natural selection]]. As the fittest sets of RNA molecules expanded their numbers, novel catalytic properties added by mutation, which benefitted their persistence and expansion, could accumulate in the population. Such an [[autocatalytic set]] of ribozymes, capable of self-replication in about an hour, has been identified. It was produced by molecular competition ([[Directed evolution|''in vitro'' evolution]]) of candidate enzyme mixtures.<ref>{{cite journal | vauthors = Lincoln TA, Joyce GF | title = Self-sustained replication of an RNA enzyme | journal = Science | volume = 323 | issue = 5918 | pages = 1229–1232 | date = February 2009 | pmid = 19131595 | pmc = 2652413 | doi = 10.1126/science.1167856 | bibcode = 2009Sci...323.1229L }} * {{cite web |date=January 12, 2009 |title=First Examples Of RNA That Replicates Itself Indefinitely Developed By Scripps Scientists |website=Medical News Today |url=http://www.medicalnewstoday.com/articles/135031.php |archive-url=https://web.archive.org/web/20090731234701/http://www.medicalnewstoday.com/articles/135031.php |archive-date=2009-07-31}}</ref> Competition between RNA may have favored the emergence of cooperation between different RNA chains, opening the way for the formation of the first [[protocell]]. Eventually, RNA chains developed with catalytic properties that help [[amino acid]]s bind together (a process called [[peptide bond|peptide-bonding]]). These amino acids could then assist with RNA synthesis, giving those RNA chains that could serve as ribozymes the selective advantage. The ability to catalyze one step in protein synthesis, [[Transfer RNA#Aminoacylation|aminoacylation]] of RNA, has been demonstrated in a short (five-nucleotide) segment of RNA.<ref>{{cite journal | vauthors = Turk RM, Chumachenko NV, Yarus M | title = Multiple translational products from a five-nucleotide ribozyme | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 107 | issue = 10 | pages = 4585–4589 | date = March 2010 | pmid = 20176971 | pmc = 2826339 | doi = 10.1073/pnas.0912895107 | doi-access = free | bibcode = 2010PNAS..107.4585T }} * {{cite press release |date=February 24, 2010 |title=Scientists create tiny RNA molecule with big implications for life's origins |website=ScienceDaily |url=https://www.sciencedaily.com/releases/2010/02/100222162009.htm}}</ref> In March 2015, NASA scientists reported that, for the first time, complex DNA and RNA organic compounds of [[life]], including uracil, cytosine, and thymine, have been formed in the laboratory under conditions found only in [[outer space]], using starting chemicals, like [[pyrimidine]], found in [[meteorite]]s. Pyrimidine, like [[polycyclic aromatic hydrocarbons]] (PAHs), may have been formed in [[red giant]] stars or in [[cosmic dust|interstellar dust]] and gas clouds, according to the scientists.<ref name="NASA-20150303">{{cite web |last=Marlaire |first=Ruth |name-list-style=vanc |title=NASA Ames Reproduces the Building Blocks of Life in Laboratory |url=https://www.nasa.gov/content/nasa-ames-reproduces-the-building-blocks-of-life-in-laboratory |date=3 March 2015 |work=[[NASA]] |access-date=5 March 2015 |url-status=live |archive-url=https://web.archive.org/web/20150305083306/http://www.nasa.gov/content/nasa-ames-reproduces-the-building-blocks-of-life-in-laboratory/ |archive-date=5 March 2015 }}</ref> In 2018, researchers at [[Georgia Institute of Technology]] identified three molecular candidates for the bases that might have formed an earliest version of proto-RNA: [[barbituric acid]], [[melamine]], and [[pyrimidine|2,4,6-triaminopyrimidine]] (TAP). These three molecules are simpler versions of the four bases in current RNA, which could have been present in larger amounts and could still be [[forward compatibility|forward-compatible]] with them but may have been discarded by evolution in exchange for more optimal base pairs.<ref>{{Cite web | url=https://www.astrobio.net/news-exclusive/new-study-identifies-possible-ancestors-of-rna/ | title=New Study Identifies Possible Ancestors of RNA| date=2018-09-14 |archive-url=https://web.archive.org/web/20201109042024/https://www.astrobio.net/news-exclusive/new-study-identifies-possible-ancestors-of-rna/ |archive-date=2020-11-09 |url-status=usurped}}</ref> Specifically, TAP can form nucleotides with a large range of sugars.<ref>{{cite journal | vauthors = Fialho DM, Clarke KC, Moore MK, Schuster GB, Krishnamurthy R, Hud NV | title = Glycosylation of a model proto-RNA nucleobase with non-ribose sugars: implications for the prebiotic synthesis of nucleosides | journal = Organic & Biomolecular Chemistry | volume = 16 | issue = 8 | pages = 1263–1271 | date = February 2018 | pmid = 29308815 | doi = 10.1039/c7ob03017g | bibcode = 2018OrgBC..16.1263F }}</ref> Both TAP and melamine base pair with barbituric acid. All three spontaneously form nucleotides with ribose.<ref>{{cite journal | vauthors = Cafferty BJ, Fialho DM, Khanam J, Krishnamurthy R, Hud NV | title = Spontaneous formation and base pairing of plausible prebiotic nucleotides in water | journal = Nature Communications | volume = 7 | issue = 1 | pages = 11328 | date = April 2016 | pmid = 27108699 | pmc = 4848480 | doi = 10.1038/ncomms11328 | bibcode = 2016NatCo...711328C }}</ref> ==Evolution of DNA== One of the challenges posed by the RNA world hypothesis is to discover the pathway by which an RNA-based system transitioned to one based on DNA. Geoffrey Diemer and Ken Stedman, at Portland State University in Oregon, may have found a solution. While conducting a survey of viruses in a hot acidic lake in Lassen Volcanic National Park, California, they uncovered evidence that a simple DNA virus had acquired a gene from a completely unrelated RNA-based virus. Virologist Luis Villareal of the University of California Irvine also suggests that viruses capable of converting an RNA-based gene into DNA and then incorporating it into a more complex DNA-based genome might have been common in the virus world during the RNA to DNA transition some 4 billion years ago.<ref>Holmes, Bob (2012) "First Glimpse at the birth of DNA" (New Scientist April 12, 2012)</ref><ref>{{cite journal | vauthors = Diemer GS, Stedman KM | title = A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses | journal = Biology Direct | volume = 7 | issue = 1 | pages = 13 | date = June 2012 | pmid = 22515485 | pmc = 3372434 | doi = 10.1186/1745-6150-7-13 | doi-access = free }}</ref> This finding bolsters the argument for the transfer of information from the RNA world to the emerging DNA world before the emergence of the [[last universal common ancestor]]. From the research, the diversity of this virus world is still with us. == Viroids == {{Main|Viroid}} Additional evidence supporting the concept of an RNA world has resulted from research on [[viroid]]s, the first representatives of a novel domain of "subviral pathogens".<ref name="pmid5095900">{{cite journal | vauthors = Diener TO | title = Potato spindle tuber "virus". IV. A replicating, low molecular weight RNA | journal = Virology | volume = 45 | issue = 2 | pages = 411–428 | date = August 1971 | pmid = 5095900 | doi = 10.1016/0042-6822(71)90342-4 }}</ref><ref name="ARS_timeline">{{cite web |url=https://www.ars.usda.gov/oc/timeline/viroid/ |title=ARS Research Timeline – Tracking the Elusive Viroid |date=2006-03-02 |access-date=2007-07-18 |url-status=live |archive-url=https://web.archive.org/web/20070706190644/http://www.ars.usda.gov/is/timeline/viroid.htm |archive-date=2007-07-06 }}</ref> Viroids infect plants, where most are pathogens, and consist of short stretches of highly complementary, circular, single-stranded and non-coding RNA without a protein coat. They are extremely small, ranging from 246 to 467 nucleobases, compared to the smallest known viruses capable of causing an infection, with genomes about 2,000 nucleobases in length.<ref>{{cite journal | vauthors = Sanger HL, Klotz G, Riesner D, Gross HJ, Kleinschmidt AK | title = Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 73 | issue = 11 | pages = 3852–3856 | date = November 1976 | pmid = 1069269 | pmc = 431239 | doi = 10.1073/pnas.73.11.3852 | doi-access = free | bibcode = 1976PNAS...73.3852S }}</ref> Based on their characteristic properties, in 1989 plant biologist [[Theodor Otto Diener|Theodor Diener]] argued that viroids are more plausible living relics of the RNA world than [[introns]] and other RNAs considered candidates at the time.<ref>{{cite journal | vauthors = Diener TO | title = Circular RNAs: relics of precellular evolution? | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 86 | issue = 23 | pages = 9370–9374 | date = December 1989 | pmid = 2480600 | pmc = 298497 | doi = 10.1073/pnas.86.23.9370 | doi-access = free | bibcode = 1989PNAS...86.9370D }}</ref> Diener's hypothesis would be expanded by the research group of Ricardo Flores,<ref>{{cite journal | vauthors = Daròs JA, Elena SF, Flores R | title = Viroids: an Ariadne's thread into the RNA labyrinth | journal = EMBO Reports | volume = 7 | issue = 6 | pages = 593–598 | date = June 2006 | pmid = 16741503 | pmc = 1479586 | doi = 10.1038/sj.embor.7400706 }}</ref><ref name="Flores, R. 2014">{{cite journal | vauthors = Flores R, Gago-Zachert S, Serra P, Sanjuán R, Elena SF | title = Viroids: survivors from the RNA world? | journal = Annual Review of Microbiology | volume = 68 | pages = 395–414 | year = 2014 | pmid = 25002087 | doi = 10.1146/annurev-micro-091313-103416 | hdl-access = free | hdl = 10261/107724 }}</ref> and gained a broader audience when in 2014, a ''[[New York Times]]'' science writer published a popularized version of the proposal.<ref name=Zimmer>{{cite news |last=Zimmer |first=Carl |author-link=Carl Zimmer |title=A Tiny Emissary From the Ancient Past |url=https://www.nytimes.com/2014/09/25/science/a-tiny-emissary-from-the-ancient-past.html?partner=rss&emc=rss |date=September 25, 2014 |work=[[The New York Times]] |access-date=November 22, 2014 |url-status=live |archive-url=https://web.archive.org/web/20141129180354/http://www.nytimes.com/2014/09/25/science/a-tiny-emissary-from-the-ancient-past.html?partner=rss&emc=rss |archive-date=November 29, 2014 }}</ref> The characteristics of viroids highlighted as consistent with an RNA world were their small size, high guanine and cytosine content, circular structure, structural periodicity, the lack of protein-coding ability and, in some cases, ribozyme-mediated replication.<ref name="Flores, R. 2014" /> One aspect critics of the hypothesis have focused on is that the exclusive hosts of all known viroids, [[angiosperm]]s, did not evolve until billions of years after the RNA world was replaced, making viroids more likely to have arisen through later evolutionary mechanisms unrelated to the RNA world than to have survived via a cryptic host over that extended period.<ref>{{citation|vauthors=Diener TO |year=2016 |title=Viroids: "living fossils" of primordial RNAs? |journal=Biology Direct |volume=11 |issue=1 |page=15 |doi=10.1186/s13062-016-0116-7|pmid=27016066 |pmc=4807594 |doi-access=free }}</ref> Whether they are relics of that world or of more recent origin, their function as autonomous naked RNA is seen as analogous to that envisioned for an RNA world. == Origin of sexual reproduction == {{Further|Evolution of sexual reproduction}} Eigen ''et al''.<ref>{{cite journal | vauthors = Eigen M, Gardiner W, Schuster P, Winkler-Oswatitsch R | title = The origin of genetic information | journal = Scientific American | volume = 244 | issue = 4 | pages = 88–92, 96, et passim | date = April 1981 | pmid = 6164094 | doi = 10.1038/scientificamerican0481-88 | bibcode = 1981SciAm.244a..88H }}</ref> and Woese<ref>Woese CR (1983). The primary lines of descent and the universal ancestor. Chapter in {{cite book | last = Bendall | first = D. S. | name-list-style = vanc | title = Evolution from molecules to men | publisher = Cambridge University Press | location = Cambridge, UK | year = 1983 | isbn = 978-0-521-28933-7 | url-access = registration | url = https://archive.org/details/evolutionfrommol0000unse }} pp. 209-233.</ref> proposed that the genomes of early [[protocell]]s were composed of single-stranded RNA, and that individual genes corresponded to separate RNA segments, rather than being linked end-to-end as in present-day DNA genomes. A protocell that was haploid (one copy of each RNA gene) would be vulnerable to damage, since a single lesion in any RNA segment would be potentially lethal to the protocell (e.g., by blocking replication or inhibiting the function of an essential gene). Vulnerability to damage could be reduced by maintaining two or more copies of each RNA segment in each protocell, i.e., by maintaining diploidy or polyploidy. Genome redundancy would allow a damaged RNA segment to be replaced by an additional replication of its homolog. However, for such a simple organism, the proportion of available resources tied up in the genetic material would be a large fraction of the total resource budget. Under limited resource conditions, the protocell reproductive rate would likely be inversely related to ploidy number. The protocell's fitness would be reduced by the costs of redundancy. Consequently, coping with damaged RNA genes while minimizing the costs of redundancy would likely have been a fundamental problem for early protocells. A cost-benefit analysis was carried out in which the costs of maintaining redundancy were balanced against the costs of genome damage.<ref name=Bernstein84>{{cite journal | vauthors = Bernstein H, Byerly HC, Hopf FA, Michod RE | title = Origin of sex | journal = Journal of Theoretical Biology | volume = 110 | issue = 3 | pages = 323–351 | date = October 1984 | pmid = 6209512 | doi = 10.1016/S0022-5193(84)80178-2 | bibcode = 1984JThBi.110..323B }}</ref> This analysis led to the conclusion that, under a wide range of circumstances, the selected strategy would be for each protocell to be haploid, but to periodically fuse with another haploid protocell to form a transient diploid. The retention of the haploid state maximizes the growth rate. The periodic fusions permit mutual reactivation of otherwise lethally damaged protocells. If at least one damage-free copy of each RNA gene is present in the transient diploid, viable progeny can be formed. For two, rather than one, viable daughter cells to be produced would require an extra replication of the intact RNA gene homologous to any RNA gene that had been damaged prior to the division of the fused protocell. The cycle of haploid reproduction, with occasional fusion to a transient diploid state, followed by splitting to the haploid state, can be considered to be the sexual cycle in its most primitive form.<ref name=Bernstein84 /><ref>{{cite book | last1 = Bernstein | first1 = Carol | last2 = Bernstein | first2 = Harris | name-list-style = vanc | title = Aging, sex, and DNA repair |publisher=Academic Press |location=Boston |year=1991 |isbn=978-0-12-092860-6 }} see pgs. 293-297</ref> In the absence of this sexual cycle, haploid protocells with damage in an essential RNA gene would simply die. This model for the early sexual cycle is hypothetical, but it is very similar to the known sexual behavior of the segmented RNA viruses, which are among the simplest organisms known. [[Orthomyxoviridae|Influenza virus]], whose genome consists of 8 physically separated single-stranded RNA segments,<ref>{{cite journal | vauthors = Lamb RA, Choppin PW | title = The gene structure and replication of influenza virus | journal = Annual Review of Biochemistry | volume = 52 | pages = 467–506 | year = 1983 | pmid = 6351727 | doi = 10.1146/annurev.bi.52.070183.002343 }}</ref> is an example of this type of virus. In segmented RNA viruses, "mating" can occur when a host cell is infected by at least two virus particles. If these viruses each contain an RNA segment with a lethal damage, multiple infection can lead to reactivation providing that at least one undamaged copy of each virus gene is present in the infected cell. This phenomenon is known as "multiplicity reactivation". Multiplicity reactivation has been reported to occur in influenza virus infections after induction of RNA damage by [[Ultraviolet germicidal irradiation|UV-irradiation]],<ref>{{cite journal | vauthors = Barry RD | title = The multiplication of influenza virus. II. Multiplicity reactivation of ultraviolet irradiated virus | journal = Virology | volume = 14 | issue = 4 | pages = 398–405 | date = August 1961 | pmid = 13687359 | doi = 10.1016/0042-6822(61)90330-0 | hdl-access = free | hdl = 1885/109240 }}</ref> and ionizing radiation.<ref>{{cite journal | vauthors = Gilker JC, Pavilanis V, Ghys R | title = Multiplicity reactivation in gamma irradiated influenza viruses | journal = Nature | volume = 214 | issue = 5094 | pages = 1235–1237 | date = June 1967 | pmid = 6066111 | doi = 10.1038/2141235a0 | s2cid = 4200194 | bibcode = 1967Natur.214.1235G }}</ref> == Further developments == {{Further|Viral eukaryogenesis}} [[Patrick Forterre]] has been working on a novel hypothesis, called "three viruses, three domains":<ref name=3V3D /> that viruses were instrumental in the transition from RNA to DNA and the evolution of [[Bacteria]], [[Archaea]], and [[Eukaryote|Eukaryota]]. He believes the [[last universal common ancestor]]<ref name=3V3D /> was RNA-based and evolved RNA viruses. Some of the viruses evolved into DNA viruses to protect their genes from attack. Through the process of viral infection into hosts the three domains of life evolved.<ref name=3V3D>{{cite journal | vauthors = Forterre P | title = Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 103 | issue = 10 | pages = 3669–3674 | date = March 2006 | pmid = 16505372 | pmc = 1450140 | doi = 10.1073/pnas.0510333103 | doi-access = free | bibcode = 2006PNAS..103.3669F }}</ref><ref>{{cite journal | vauthors = Zimmer C | title = Did DNA come from viruses? | journal = Science | volume = 312 | issue = 5775 | pages = 870–872 | date = May 2006 | pmid = 16690855 | doi = 10.1126/science.312.5775.870 | s2cid = 39984425 }}</ref> Another interesting proposal is the idea that RNA synthesis might have been driven by temperature gradients, in the process of [[thermosynthesis]].<ref>{{cite journal | vauthors = Muller AW | title = Thermosynthesis as energy source for the RNA World: a model for the bioenergetics of the origin of life | journal = Bio Systems | volume = 82 | issue = 1 | pages = 93–102 | date = October 2005 | pmid = 16024164 | doi = 10.1016/j.biosystems.2005.06.003 | arxiv = q-bio/0501013 | bibcode = 2005BiSys..82...93M }}</ref> Single nucleotides have been shown to catalyze organic reactions.<ref>{{cite journal | last1 = Kumar | first1 = Atul | first2 = Siddharth | last2 = Sharma | first3 = Ram Awatar | last3 = Maurya | name-list-style = vanc | title = Single Nucleotide-Catalyzed Biomimetic Reductive Amination | journal = Advanced Synthesis and Catalysis | volume = 352 | pages = 2227–2232 | year = 2010 | doi = 10.1002/adsc.201000178 | issue = 13 }}</ref> [[Steven Benner]] has argued that chemical conditions on the planet [[Mars]], such as the presence of [[boron]], [[molybdenum]], and [[oxygen]], may have been better for initially producing RNA molecules than those on [[Earth]]. If so, life-suitable molecules, originating on Mars, may have later migrated to Earth via mechanisms of [[panspermia]] or similar process.<ref name="NYT-20130912">{{cite news |last=Zimmer |first=Carl |author-link=Carl Zimmer |title=A Far-Flung Possibility for the Origin of Life |url=https://www.nytimes.com/2013/09/12/science/space/a-far-flung-possibility-for-the-origin-of-life.html |date=September 12, 2013 |work=[[The New York Times]] |access-date=September 12, 2013 |url-status=live |archive-url=https://web.archive.org/web/20150708122622/http://www.nytimes.com/2013/09/12/science/space/a-far-flung-possibility-for-the-origin-of-life.html |archive-date=July 8, 2015 }}</ref><ref name="NS-20130829">{{cite web |last=Webb |first=Richard |name-list-style=vanc |title=Primordial broth of life was a dry Martian cup-a-soup |url=https://www.newscientist.com/article/dn24120-primordial-broth-of-life-was-a-dry-martian-cup-a-soup/ |date=August 29, 2013 |work=[[New Scientist]] |access-date=September 13, 2013 |url-status=live |archive-url=https://web.archive.org/web/20150424181341/http://www.newscientist.com/article/dn24120-primordial-broth-of-life-was-a-dry-martian-cupasoup.html |archive-date=April 24, 2015 }}</ref> == Alternative hypotheses == The hypothesized existence of an RNA world does not exclude a "Pre-RNA world", where a metabolic system based on a different nucleic acid is proposed to pre-date RNA. A candidate nucleic acid is peptide nucleic acid ([[Peptide nucleic acid|PNA]]), which uses simple [[peptide bond]]s to link nucleobases.<ref>{{cite journal | vauthors = Egholm M, Buchardt O, Christensen L, Behrens C, Freier SM, Driver DA, Berg RH, Kim SK, Norden B, Nielsen PE | display-authors = 6 | title = PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules | journal = Nature | volume = 365 | issue = 6446 | pages = 566–568 | date = October 1993 | pmid = 7692304 | doi = 10.1038/365566a0 | s2cid = 4318153 | bibcode = 1993Natur.365..566E }}</ref> PNA is more stable than RNA, but its ability to be generated under prebiological conditions has yet to be demonstrated experimentally.{{citation needed|date=September 2024}} Threose nucleic acid ([[TNA (nucleic acid)|TNA]]) or glycol nucleic acid ([[GNA (nucleic acid)|GNA]]) have also been proposed as a starting point, and like PNA, also lack experimental evidence for their respective abiogenesis.{{citation needed|date=September 2024}} An alternative—or complementary—theory of RNA origin is proposed in the [[PAH world hypothesis]], whereby [[polycyclic aromatic hydrocarbon]]s ([[PAHs]]) mediate the synthesis of RNA molecules.<ref>{{cite web | vauthors = Platts SN | url = http://www.pahworld.com/ | title = The PAH World – Discotic polynuclear aromatic compounds as a mesophase scaffolding at the origin of life | archive-url = https://web.archive.org/web/20110203045451/http://pahworld.com/ | archive-date = 2011-02-03 }}</ref> PAHs are the most common and abundant of the known polyatomic molecules in the visible [[Universe]] and are a likely constituent of the [[primordial sea]].<ref name=ames>{{cite web | vauthors = Allamandola L | url = http://amesteam.arc.nasa.gov/Research/cosmic.html | title = Cosmic Distribution of Chemical Complexity | archive-url = https://web.archive.org/web/20140227184503/http://amesteam.arc.nasa.gov/Research/cosmic.html | archive-date=2014-02-27 }}</ref> PAHs and [[fullerenes]] (also implicated in the [[origin of life]])<ref>{{cite news |last=Atkinson |first=Nancy |url=http://www.universetoday.com/76732/buckyballs-could-be-plentiful-in-the-universe |title=Buckyballs Could Be Plentiful in the Universe |work=[[Universe Today]] |date=2010-10-27 |access-date=2010-10-28 |url-status=live |archive-url=https://web.archive.org/web/20101029231622/http://www.universetoday.com/76732/buckyballs-could-be-plentiful-in-the-universe/ |archive-date=2010-10-29 }}</ref> have been detected in [[nebulae]].<ref>{{cite journal | vauthors = Cami J, Bernard-Salas J, Peeters E, Malek SE | title = Detection of C60 and C70 in a young planetary nebula | journal = Science | volume = 329 | issue = 5996 | pages = 1180–1182 | date = September 2010 | pmid = 20651118 | doi = 10.1126/science.1192035 | s2cid = 33588270 | bibcode = 2010Sci...329.1180C }}</ref> The [[iron-sulfur world theory]] proposes that simple metabolic processes developed before genetic materials did, and these energy-producing cycles catalyzed the production of genes.{{citation needed|date=September 2024}} Some of the difficulties of producing the precursors on earth are bypassed by another alternative or complementary theory for their origin, [[panspermia]]. It discusses the possibility that the earliest life on this planet was carried here from somewhere else in the galaxy, possibly on meteorites similar to the [[Murchison meteorite]].<ref>{{cite journal | vauthors = Bernstein MP, Sandford SA, Allamandola LJ, Gillette JS, Clemett SJ, Zare RN | title = UV irradiation of polycyclic aromatic hydrocarbons in ices: production of alcohols, quinones, and ethers | journal = Science | volume = 283 | issue = 5405 | pages = 1135–1138 | date = February 1999 | pmid = 10024233 | doi = 10.1126/science.283.5405.1135 | bibcode = 1999Sci...283.1135B }}</ref> [[Sugar|Sugar molecules]], including [[ribose]], have been found in [[meteorite]]s.<ref name="NASA-20191118">{{cite news |last1=Steigerwald |first1=Bill |last2=Jones |first2=Nancy |last3=Furukawa |first3=Yoshihiro |title=First Detection of Sugars in Meteorites Gives Clues to Origin of Life |url=https://www.nasa.gov/press-release/goddard/2019/sugars-in-meteorites |date=18 November 2019 |work=[[NASA]] |access-date=18 November 2019 }}</ref><ref name="PNAS-20191118">{{cite journal | vauthors = Furukawa Y, Chikaraishi Y, Ohkouchi N, Ogawa NO, Glavin DP, Dworkin JP, Abe C, Nakamura T | display-authors = 6 | title = Extraterrestrial ribose and other sugars in primitive meteorites | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 116 | issue = 49 | pages = 24440–24445 | date = December 2019 | pmid = 31740594 | pmc = 6900709 | doi = 10.1073/pnas.1907169116 | doi-access = free | bibcode = 2019PNAS..11624440F }}</ref> Panspermia does not invalidate the concept of an RNA world, but posits that this world or its precursors originated not on Earth but rather another, probably older, planet.{{citation needed|date=September 2024}} The relative chemical complexity of the nucleotide and the unlikelihood of it spontaneously arising, along with the limited number of combinations possible among four base forms, as well as the need for RNA polymers of some length before seeing enzymatic activity, have led some to reject the RNA world hypothesis in favor of a metabolism-first hypothesis, where the chemistry underlying cellular function arose first, along with the ability to replicate and facilitate this metabolism.{{citation needed|date=September 2024}} === RNA-peptide coevolution === {{See also|RNP world}} Another proposal is that the dual-molecule system we see today, where a nucleotide-based molecule is needed to synthesize protein, and a peptide-based (protein) molecule is needed to make nucleic acid polymers, represents the original form of life.<ref>{{cite journal | vauthors = Kunin V | title = A system of two polymerases--a model for the origin of life | journal = Origins of Life and Evolution of the Biosphere | volume = 30 | issue = 5 | pages = 459–466 | date = October 2000 | pmid = 11002892 | doi = 10.1023/A:1006672126867 | s2cid = 5616924 | bibcode = 2000OLEB...30..459K }}</ref> This theory is called RNA-peptide coevolution,<ref name="pascal">{{Citation | last = Pascal| first = Robert | contribution = A scenario starting from the first chemical building blocks| year = 2007 | title = From Suns to Life: A Chronological Approach to the History of Life on Earth | editor-last = Reisse | editor-first = Jacques | pages = 163–166 | publisher = Springer Science & Business Media | isbn = 978-0-387-45083-4}}</ref> or the Peptide-RNA world, and offers a possible explanation for the rapid evolution of high-quality replication in RNA (since proteins are catalysts), with the disadvantage of having to postulate the coincident formation of two complex molecules, an enzyme (from peptides) and a RNA (from nucleotides). In this Peptide-RNA World scenario, RNA would have contained the instructions for life, while peptides (simple protein enzymes) would have accelerated key chemical reactions to carry out those instructions.<ref name="Urzymes 2013">{{cite journal |title=Challenging Assumptions About the Origin of Life |journal=Astrobiology Magazine |date=18 September 2013 |url=http://www.astrobio.net/pressrelease/5692/challenging-assumptions-about-the-origin-of-life |access-date=2014-05-07 |url-status=usurped |archive-url=https://web.archive.org/web/20140508042711/http://www.astrobio.net/pressrelease/5692/challenging-assumptions-about-the-origin-of-life |archive-date=8 May 2014 }}</ref> The study leaves open the question of exactly how those primitive systems managed to replicate themselves — something neither the RNA World hypothesis nor the Peptide-RNA World theory can yet explain, unless [[polymerase]]s (enzymes that rapidly assemble the RNA molecule) played a role.<ref name="Urzymes 2013" /> A research project completed in March 2015 by the Sutherland group found that a network of reactions beginning with hydrogen cyanide and [[hydrogen sulfide]], in streams of water irradiated by UV light, could produce the chemical components of proteins and lipids, alongside those of RNA.<ref name="patel">{{cite journal | vauthors = Patel BH, Percivalle C, Ritson DJ, Duffy CD, Sutherland JD | title = Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism | journal = Nature Chemistry | volume = 7 | issue = 4 | pages = 301–307 | date = April 2015 | pmid = 25803468 | pmc = 4568310 | doi = 10.1038/nchem.2202 | bibcode = 2015NatCh...7..301P | author-link5 = John Sutherland (chemist) }}</ref><ref>{{cite news |last=Service |first=Robert F. |date=16 March 2015 |title=Researchers may have solved origin-of-life conundrum |url=https://www.science.org/content/article/researchers-may-have-solved-origin-life-conundrum |work=Science |type=News |location=Washington, D.C. |publisher=American Association for the Advancement of Science |issn=1095-9203 |access-date=2015-07-26 |url-status=live |archive-url=https://web.archive.org/web/20150812103559/http://news.sciencemag.org/biology/2015/03/researchers-may-have-solved-origin-life-conundrum |archive-date=12 August 2015 }}</ref> The researchers used the term "cyanosulfidic" to describe this network of reactions.<ref name="patel" /> In November 2017, a team at the [[Scripps Research Institute]] identified reactions involving the compound [[diamidophosphate]] which could have linked the chemical components into short peptide and lipid chains as well as short RNA-like chains of nucleotides.<ref>{{cite journal | vauthors = Gibard C, Bhowmik S, Karki M, Kim EK, Krishnamurthy R | title = Phosphorylation, oligomerization and self-assembly in water under potential prebiotic conditions | journal = Nature Chemistry | volume = 10 | issue = 2 | pages = 212–217 | date = February 2018 | pmid = 29359747 | pmc = 6295206 | doi = 10.1038/nchem.2878 }}</ref><ref>{{cite web|url=http://www.scripps.edu/news/press/2017/20171106krishnamurthy.html|title=Scientists Find Potential "Missing Link" in Chemistry That Led to Life on Earth|date=November 6, 2017|publisher=[[Scripps Research Institute]]|access-date=7 November 2017|url-status=live|archive-url=https://web.archive.org/web/20171107024003/http://www.scripps.edu/news/press/2017/20171106krishnamurthy.html|archive-date=7 November 2017}}</ref> == Implications == The RNA world hypothesis, if true, has important implications for the [[definition of life]] and the origin of life. For most of the time that followed [[Rosalind Franklin|Franklin]], [[James D. Watson|Watson]] and [[Francis Crick|Crick]]'s elucidation of DNA structure in 1953, life was largely defined in terms of DNA and proteins: DNA and proteins seemed the dominant macromolecules in the living cell, with RNA only aiding in creating proteins from the DNA blueprint. The RNA world hypothesis places RNA at center-stage when life originated. The RNA world hypothesis is supported by the observations that ribosomes are ribozymes:<ref>{{cite journal | vauthors = Fox GE | title = Origin and evolution of the ribosome | journal = Cold Spring Harbor Perspectives in Biology | volume = 2 | issue = 9 | pages = a003483 | date = September 2010 | pmid = 20534711 | pmc = 2926754 | doi = 10.1101/cshperspect.a003483 | doi-access = free }}</ref><ref>{{cite book | first1 = GE | last1 = Fox| veditors = Hernández G, Jagus R| year = 2016| title = Evolution of the Protein Synthesis Machinery and Its Regulation| chapter= Origins and early evolution of the ribosome |pages=31–60|location = Switzerland | publisher = Springer, Cham| doi = 10.1007/978-3-319-39468-8| isbn=978-3-319-39468-8 | s2cid = 27493054}}</ref> the catalytic site is composed of RNA, and proteins hold no major structural role and are of peripheral functional importance. This was confirmed with the deciphering of the 3-dimensional structure of the ribosome in 2001. Specifically, peptide bond formation, the reaction that binds [[amino acid]]s together into [[protein]]s, is now known to be catalyzed by an adenine residue in the [[rRNA]]. RNAs are known to play roles in other cellular catalytic processes, specifically in the targeting of enzymes to specific RNA sequences. In eukaryotes, the processing of [[pre-mRNA]] and [[RNA editing]] take place at sites determined by the base pairing between the target RNA and RNA constituents of [[snRNP|small nuclear ribonucleoproteins (snRNPs)]]. Such enzyme targeting is also responsible for gene down regulation through [[RNA interference]] (RNAi), where an enzyme-associated guide RNA targets specific mRNA for selective destruction. Likewise, in eukaryotes the maintenance of [[telomeres]] involves copying of an RNA template that is a constituent part of the [[telomerase]] ribonucleoprotein enzyme. Another cellular organelle, the [[Vault (organelle)|vault]], includes a ribonucleoprotein component, although the function of this organelle remains to be elucidated. == See also == * [[GADV-protein world hypothesis]] * ''[[The Major Transitions in Evolution]]'' *[[RNA-based evolution]] *[[Protocell]] or [[Pre-cell]], the primordial version of a cell which confined RNA and later, DNA *[[First universal common ancestor]] (FUCA) == References == <!--This article uses the Cite.php citation mechanism. If you would like more information on how to add references to this article, please see http://meta.wikimedia.org/wiki/Cite/Cite.php --> {{reflist}} == Further reading == {{refbegin|33em}} * {{cite journal | vauthors = Attwater J, Raguram A, Morgunov AS, Gianni E, Holliger P | title = Ribozyme-catalysed RNA synthesis using triplet building blocks | journal = eLife | volume = 7 | page = e35255 | date = May 2018 | pmid = 29759114 | pmc = 6003772 | doi = 10.7554/eLife.35255 | doi-access = free }} * {{cite book|title=Genetic Takeover: And the Mineral Origins of Life|url=https://archive.org/details/genetictakeover00cair|url-access=registration|first=A. G.|last=Cairns-Smith|name-list-style=vanc|year=1993|isbn=978-0-521-23312-5|publisher=Cambridge University Press}} * {{cite journal | vauthors = Orgel LE | title = The origin of life on the earth | journal = Scientific American | volume = 271 | issue = 4 | pages = 76–83 | date = October 1994 | pmid = 7524147 | doi = 10.1038/scientificamerican1094-76 | bibcode = 1994SciAm.271d..76O }} * {{cite journal | vauthors = Orgel LE | title = Prebiotic chemistry and the origin of the RNA world | journal = Critical Reviews in Biochemistry and Molecular Biology | volume = 39 | issue = 2 | pages = 99–123 | year = 2004 | pmid = 15217990 | doi = 10.1080/10409230490460765 | s2cid = 4939632 | citeseerx = 10.1.1.537.7679 }} * {{cite book|title=Life Without Genes|first=Adrian|last=Woolfson|name-list-style=vanc|date=September 2000|isbn=978-0-00-654874-4|publisher=Flamingo|location=London}} * {{cite journal | vauthors = Vlassov AV, Kazakov SA, Johnston BH, Landweber LF | title = The RNA world on ice: a new scenario for the emergence of RNA information | journal = Journal of Molecular Evolution | volume = 61 | issue = 2 | pages = 264–273 | date = August 2005 | pmid = 16044244 | doi = 10.1007/s00239-004-0362-7 | s2cid = 21096886 | bibcode = 2005JMolE..61..264V }} * {{cite journal | vauthors = Engelhart AE, Hud NV | title = Primitive genetic polymers | journal = Cold Spring Harbor Perspectives in Biology | volume = 2 | issue = 12 | pages = a002196 | date = December 2010 | pmid = 20462999 | pmc = 2982173 | doi = 10.1101/cshperspect.a002196 }} * {{cite journal | vauthors = Bernhardt HS | title = The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)(a) | journal = Biology Direct | volume = 7 | issue = 1 | pages = 23 | date = July 2012 | pmid = 22793875 | pmc = 3495036 | doi = 10.1186/1745-6150-7-23 | doi-access = free }} * {{cite journal | vauthors = Sutherland JD | title = Ribonucleotides | journal = Cold Spring Harbor Perspectives in Biology | volume = 2 | issue = 4 | pages = a005439 | date = April 2010 | pmid = 20452951 | pmc = 2845210 | doi = 10.1101/cshperspect.a005439 }} * {{cite journal|vauthors=Camprubí E, de Leeuw JW, House CH, Raulin F, Russell MJ, Spang A, Tirumalai MR, Westall F|title=The Emergence of Life|journal=Space Sci Rev|volume=215|date=Dec 2019|issue=56|page=56|doi=10.1007/s11214-019-0624-8|bibcode=2019SSRv..215...56C|doi-access=free}} * {{cite journal |last=Forster |first=Anthony C. |title=Revisiting the Extinction of the RNA World |journal=Biochemistry |date=2022-05-03 |volume=61 |issue=9 |pages=749–751 |doi=10.1021/acs.biochem.2c00121 |pmid=35389627 |pmc=9069686 }} {{refend}} == External links == * {{cite web |url=http://exploringorigins.org/rnaworld.html |title=Understanding the RNA World |website=Exploring Life's Origins |publisher=Exploring Origins Project}} * {{cite web |url=http://www.origins.rpi.edu/chem.html |title=The Formation of the RNA World |last=Ferris |first=James P. |author-link=James Ferris |publisher=The New York Center for Studies of the Origins of Life, [[Rensselaer Polytechnic Institute]] |archive-url=https://web.archive.org/web/20120301174206/http://www.origins.rpi.edu/chem.html |archive-date=March 1, 2012 |ref=none}} * {{cite web |url=https://www.nobelprize.org/nobel_prizes/chemistry/laureates/1989/altman-article.html |title=The RNA World |last=Altman |first=Sidney |author-link=Sidney Altman |year=2001 |website=NobelPrize.org |publisher=Nobel Media |ref=none}} * {{cite magazine |last=Kuska |first=Robert |date=June 2002 |title=A World Apart |url=http://www.hhmi.org/sites/default/files/Bulletin/2002/June/june2002_fulltext.pdf |magazine=HHMI Bulletin |publisher=[[Howard Hughes Medical Institute]] |pages=14–19 |archive-url=https://web.archive.org/web/20040522184700/http://www.hhmi.org/bulletin/pdf/june2002/RNA.pdf |archive-date=2004-05-22 |url-status=live |ref=none}} * {{cite web |url=https://www.nobelprize.org/nobel_prizes/chemistry/laureates/1989/cech-article.html |title=Exploring the New RNA World |last=Cech |first=Thomas R. |author-link=Thomas R. Cech |year=2004 |website=NobelPrize.org |publisher=Nobel Media |ref=none}} * {{cite journal | vauthors = Sutherland JD | title = Ribonucleotides | journal = Cold Spring Harbor Perspectives in Biology | volume = 2 | issue = 4 | pages = a005439 | date = April 2010 | pmid = 20452951 | pmc = 2845210 | doi = 10.1101/cshperspect.a005439 | ref = none }} * {{cite web | title = The Origins of the RNA World | date = August 5, 2016 | publisher = Library of Congress | website = YouTube | url = https://www.youtube.com/watch?v=2S7hlBmxO6s}} {{Origin of life}} {{Molecules detected in outer space}} {{Self-replicating organic structures}} [[Category:Biological hypotheses]] [[Category:Origin of life]] [[Category:Prebiotic chemistry]] [[Category:RNA]] [[Category:1962 in biology]] </textarea><div class="templatesUsed"><div class="mw-templatesUsedExplanation"><p><span id="templatesused">Pages transcluded onto the current version of this page<span class="posteditwindowhelplinks"> (<a 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