Genetic code: Difference between revisions

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Hypotheses have addressed a variety of scenarios:<ref name="pmid10366854">{{cite journal | vauthors = Knight RD, Freeland SJ, Landweber LF | title = Selection, history and chemistry: the three faces of the genetic code | journal = Trends in Biochemical Sciences | volume = 24 | issue = 6 | pages = 241–7 | date = Jun 1999 | pmid = 10366854|doi=10.1016/S0968-0004(99)01392-4|url=https://www.sciencedirect.com/science/article/abs/pii/S0968000499013924| url-access = subscription }}</ref>

* Chemical principles govern specific RNA interaction with amino acids. Experiments with [[aptamer]]s showed that some amino acids have a selective chemical affinity for their codons.<ref name="pmid9751648">{{cite journal | vauthors = Knight RD, Landweber LF | title = Rhyme or reason: RNA-arginine interactions and the genetic code | journal = Chemistry & Biology | volume = 5 | issue = 9 | pages = R215–20 | date = Sep 1998 | pmid = 9751648 | doi = 10.1016/S1074-5521(98)90001-1 | doi-access = free }}</ref> Experiments showed that of 8 amino acids tested, 6 show some RNA triplet-amino acid association.<ref name="isbn0-674-05075-4" /><ref name="pmid19795157">{{cite journal | vauthors = Yarus M, Widmann JJ, Knight R | title = RNA-amino acid binding: a stereochemical era for the genetic code | journal = Journal of Molecular Evolution | volume = 69 | issue = 5 | pages = 406–29 | date = Nov 2009 | pmid = 19795157 | doi = 10.1007/s00239-009-9270-1 | bibcode = 2009JMolE..69..406Y | doi-access = free }}</ref>

* Biosynthetic expansion. The genetic code grew from a simpler earlier code through a process of "biosynthetic expansion". Primordial life "discovered" new amino acids (for example, as by-products of [[metabolism]]) and later incorporated some of these into the machinery of genetic coding.<ref>{{cite journal | vauthors = Sengupta S, Higgs PG | s2cid = 15542587 | year = 2015 | title = Pathways of genetic code evolution in ancient and modern organisms | journal = Journal of Molecular Evolution | volume = 80 | issue = 5–6| pages = 229–243 | doi=10.1007/s00239-015-9686-8 | pmid=26054480| bibcode = 2015JMolE..80..229S}}</ref> Although much circumstantial evidence has been found to suggest that fewer amino acid types were used in the past,<ref name="pmid12270892">{{cite journal | vauthors = Brooks DJ, Fresco JR, Lesk AM, Singh M | title = Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code | journal = Molecular Biology and Evolution | volume = 19 | issue = 10 | pages = 1645–55 | date = Oct 2002 | pmid = 12270892 | doi = 10.1093/oxfordjournals.molbev.a003988 | doi-access = free }}</ref> precise and detailed hypotheses about which amino acids entered the code in what order are controversial.<ref name="pmid9115171">{{cite journal | vauthors = Amirnovin R | s2cid = 23334860 | title = An analysis of the metabolic theory of the origin of the genetic code | journal = Journal of Molecular Evolution | volume = 44 | issue = 5 | pages = 473–6 | date = May 1997 | pmid = 9115171 | doi = 10.1007/PL00006170 | bibcode = 1997JMolE..44..473A }}</ref><ref name="pmid11087835">{{cite journal | vauthors = Ronneberg TA, Landweber LF, Freeland SJ | title = Testing a biosynthetic theory of the genetic code: fact or artifact? | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 97 | issue = 25 | pages = 13690–5 | date = Dec 2000 | pmid = 11087835 | pmc = 17637 | doi = 10.1073/pnas.250403097 | bibcode = 2000PNAS...9713690R | doi-access = free }}</ref> However, several studies have suggested that Gly, Ala, Asp, Val, Ser, Pro, Glu, Leu, Thr may belong to a group of early-addition amino acids, whereas Cys, Met, Tyr, Trp, His, Phe may belong to a group of later-addition amino acids.<ref>{{Cite journal|last=Trifonov|first=Edward N.|date=September 2009|title=The origin of the genetic code and of the earliest oligopeptides|url=https://linkinghub.elsevier.com/retrieve/pii/S0923250809000576|journal=Research in Microbiology|language=en|volume=160|issue=7|pages=481–486|doi=10.1016/j.resmic.2009.05.004|pmid=19524038|url-access=subscription}}</ref><ref>{{Cite journal|last1=Higgs|first1=Paul G.|last2=Pudritz|first2=Ralph E.|date=June 2009|title=A Thermodynamic Basis for Prebiotic Amino Acid Synthesis and the Nature of the First Genetic Code|url=http://www.liebertpub.com/doi/10.1089/ast.2008.0280|journal=Astrobiology|language=en|volume=9|issue=5|pages=483–490|doi=10.1089/ast.2008.0280|pmid=19566427|issn=1531-1074|arxiv=0904.0402|bibcode=2009AsBio...9..483H|s2cid=9039622}}</ref><ref>{{Cite journal|last1=Chaliotis|first1=Anargyros|last2=Vlastaridis|first2=Panayotis|last3=Mossialos|first3=Dimitris|last4=Ibba|first4=Michael|last5=Becker|first5=Hubert D.|last6=Stathopoulos|first6=Constantinos|last7=Amoutzias|first7=Grigorios D.|date=2017-02-17|title=The complex evolutionary history of aminoacyl-tRNA synthetases|url= |journal=Nucleic Acids Research|language=en|volume=45|issue=3|pages=1059–1068|doi=10.1093/nar/gkw1182|issn=0305-1048|pmc=5388404|pmid=28180287}}</ref><ref>{{Cite journal|last1=Ntountoumi|first1=Chrysa|last2=Vlastaridis|first2=Panayotis|last3=Mossialos|first3=Dimitris|last4=Stathopoulos|first4=Constantinos|last5=Iliopoulos|first5=Ioannis|last6=Promponas|first6=Vasilios|last7=Oliver|first7=Stephen G|last8=Amoutzias|first8=Grigoris D|date=2019-11-04|title=Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved|url= |journal=Nucleic Acids Research|language=en|volume=47|issue=19|pages=9998–10009|doi=10.1093/nar/gkz730|issn=0305-1048|pmc=6821194|pmid=31504783}}</ref> An alternative analysis of amino acid usage in the [[Last Universal Common Ancestor]] concluded that the amino acids came in the following order: Val, Gly, Ile, Met, Ala, Thr, His, Glu, Cys, Pro, Lys, Ser, Asp, Leu, Asn, Arg, Phe, Tyr, Gln, Trp.<ref name="wehbi2024">{{cite journal |last1=Wehbi |first1=Sawsan |last2=Wheeler |first2=Andrew |last3=Morel |first3=Benoit |last4=Manepalli |first4=Nandini |last5=Minh |first5=Bui Quang |last6=Lauretta |first6=Dante S. |last7=Masel |first7=Joanna |title=Order of amino acid recruitment into the genetic code resolved by last universal common ancestor’s protein domains |journal=Proceedings of the National Academy of Sciences |date=24 December 2024 |volume=121 |issue=52 |doi=10.1073/pnas.2410311121}}</ref> It was pointed out that the late appearance of sulfur-containing cysteine and methionine was concluded in part from their absence of the sulfur-free [[Miller–Urey experiment]], that early life is believed to have used [[S-adenosyl methionine]], and that while histidine is hard to make abiotically, it is straightforward to synthesize in an organism that already has sophisticated RNA and hence purine synthesis.<ref name="wehbi2024"></ref>

* Natural selection has led to codon assignments of the genetic code that minimize the effects of [[mutation]]s.<ref name="pmid14604186">{{cite journal | vauthors = Freeland SJ, Wu T, Keulmann N | s2cid = 18823745 | title = The case for an error minimizing standard genetic code | journal = Origins of Life and Evolution of the Biosphere | volume = 33 | issue = 4–5 | pages = 457–77 | date = Oct 2003 | pmid = 14604186 | doi = 10.1023/A:1025771327614 | bibcode = 2003OLEB...33..457F }}</ref> A recent hypothesis<ref name="pmid19479032">{{cite journal | vauthors = Baranov PV, Venin M, Provan G | title = Codon size reduction as the origin of the triplet genetic code | journal = PLOS ONE | volume = 4 | issue = 5 | pages = e5708 | date = 2009 | pmid = 19479032 | pmc = 2682656 | doi = 10.1371/journal.pone.0005708 | editor1-last = Gemmell | bibcode = 2009PLoSO...4.5708B | editor1-first = Neil John | doi-access = free }}</ref> suggests that the triplet code was derived from codes that used longer than triplet codons (such as quadruplet codons). Longer than triplet decoding would increase codon redundancy and would be more error resistant. This feature could allow accurate decoding absent complex translational machinery such as the [[ribosome]], such as before cells began making ribosomes.

* Information channels: [[information theory|Information-theoretic]] approaches model the process of translating the genetic code into corresponding amino acids as an error-prone information channel.<ref name="pmid17826800">{{cite journal | vauthors = Tlusty T | title = A model for the emergence of the genetic code as a transition in a noisy information channel | journal = Journal of Theoretical Biology | volume = 249 | issue = 2 | pages = 331–42 | date = Nov 2007 | pmid = 17826800 | doi = 10.1016/j.jtbi.2007.07.029 | arxiv = 1007.4122 | bibcode = 2007JThBi.249..331T | s2cid = 12206140 }}</ref> The inherent noise (that is, the error) in the channel poses the organism with a fundamental question: how can a genetic code be constructed to withstand noise<ref>{{cite book | vauthors = Sonneborn TM | veditors =Bryson V, Vogel H | title = Evolving genes and proteins |publisher=Academic Press|___location=New York |date=1965|pages=377–397}}</ref> while accurately and efficiently translating information? These [[rate-distortion theory|"rate-distortion"]] models<ref name="pmid 18352335">{{cite journal | vauthors = Tlusty T | title = Rate-distortion scenario for the emergence and evolution of noisy molecular codes | journal = Physical Review Letters | volume = 100 | issue = 4 | pages = 048101 | date = Feb 2008 | pmid = 18352335 | doi = 10.1103/PhysRevLett.100.048101 | arxiv = 1007.4149 | bibcode = 2008PhRvL.100d8101T | s2cid = 12246664 }}</ref> suggest that the genetic code originated as a result of the interplay of the three conflicting evolutionary forces: the needs for diverse amino acids,<ref name="pmid16838217">{{cite journal | vauthors = Sella G, Ardell DH | s2cid = 1260806 | title = The coevolution of genes and genetic codes: Crick's frozen accident revisited | journal = Journal of Molecular Evolution | volume = 63 | issue = 3 | pages = 297–313 | date = Sep 2006 | pmid = 16838217 | doi = 10.1007/s00239-004-0176-7 | bibcode = 2006JMolE..63..297S }}</ref> for error-tolerance<ref name="pmid14604186" /> and for minimal resource cost. The code emerges at a transition when the mapping of codons to amino acids becomes nonrandom. The code's emergence is governed by the [[topology]] defined by the probable errors and is related to the [[map coloring problem]].<ref name="pmid 20558115">{{cite journal | vauthors = Tlusty T | title = A colorful origin for the genetic code: information theory, statistical mechanics and the emergence of molecular codes | journal = Physics of Life Reviews | volume = 7 | issue = 3 | pages = 362–76 | date = Sep 2010 | pmid = 20558115 | doi = 10.1016/j.plrev.2010.06.002 | arxiv = 1007.3906 | bibcode = 2010PhLRv...7..362T | s2cid = 1845965 }}</ref>