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Start codon

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Start codon (blue circle) of the human mitochondrial DNA MT-ATP6 gene. For each nucleotide triplet (square brackets), the corresponding amino acid is given (one-letter code), either in the +1 reading frame for MT-ATP8 (in red) or in the +3 frame for MT-ATP6 (in blue). In this genomic region, the two genes overlap.

The start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon always codes for methionine in eukaryotes and archaea and a N-formylmethionine (fMet) in bacteria, mitochondria and plastids.

The start codon is often preceded by a 5' untranslated region (5' UTR). In prokaryotes this includes the ribosome binding site.

Decoding

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In all three domains of life, the start codon is decoded by a special "initiation" transfer RNA different from the tRNAs used for elongation. There are important structural differences between an initiating tRNA and an elongating one, with distinguish features serving to satisfy the constraints of the translation system. In bacteria and organelles, an acceptor stem C1:A72 mismatch guide formylation, which directs recruitment by the 30S ribosome into the P site; so-called "3GC" base pairs allow assembly into the 70S ribosome.[1] In eukaryotes and archaea, the T stem prevents the elongation factors from binding, while eIF2 specifically recognizes the attached methionine and a A1:U72 basepair.[2]

In any case, the natural initiating tRNA only codes for methionine.[3] Knowledge of the key recognizing features has allowed researchers to construct alternative initiating tRNAs that code for different amino acids; see below.

Alternative start codons

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Alternative start codons are different from the standard AUG codon and are found in both prokaryotes (bacteria and archaea) and eukaryotes. Alternate start codons are still translated as Met when they are at the start of a protein (even if the codon encodes a different amino acid otherwise). This is because a separate tRNA is used for initiation.[3]

Eukaryotes

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Alternate start codons (non-AUG) are very rare in eukaryotic genomes: a wide range of mechanisms work to guarantee the relative fidelity of AUG initiation.[4] However, naturally occurring non-AUG start codons have been reported for some cellular mRNAs.[5] Seven out of the nine possible single-nucleotide substitutions at the AUG start codon of dihydrofolate reductase are functional as translation start sites in mammalian cells.[6]

Bacteria

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Bacteria do not generally have the wide range of translation factors monitoring start codon fidelity. GUG and UUG are the main, even "canonical", alternate start codons.[4] GUG in particular is important to controlling the replication of plasmids.[4]

E. coli uses 83% AUG (3542/4284), 14% (612) GUG, 3% (103) UUG[7] and one or two others (e.g., an AUU and possibly a CUG).[8][9]

Well-known coding regions that do not have AUG initiation codons are those of lacI (GUG)[10][11] and lacA (UUG)[12] in the E. coli lac operon. Two more recent studies have independently shown that 17 or more non-AUG start codons may initiate translation in E. coli.[13][14]

Mitochondria

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Mitochondrial genomes use alternate start codons more significantly (AUA and AUG in humans).[15] Many such examples, with codons, systematic range, and citations, are given in the NCBI list of translation tables.[16]

Archaea

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Archaea, which are prokaryotes with a translation machinery similar to but simpler than that of eukaryotes, allow initiation at UUG and GUG.[4]

Upstream start codons

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These are "alternative" start codons in the sense that they are upstream of the regular start codons and thus could be used as alternative start codons. More than half of all human mRNAs have at least one AUG codon upstream (uAUG) of their annotated translation initiation starts (TIS) (58% in the current versions of the human RefSeq sequence). Their potential use as TISs could result in translation of so-called upstream Open Reading Frames (uORFs). uORF translation usually results in the synthesis of short polypeptides, some of which have been shown to be functional, e.g., in ASNSD1, MIEF1, MKKS, and SLC35A4.[17] However, it is believed that most translated uORFs only have a mild inhibitory effect on downstream translation because most uORF starts are leaky (i.e. don't initiate translation or because ribosomes terminating after translation of short ORFs are often capable of reinitiating).[17]

Standard genetic code

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Amino-acid biochemical properties Nonpolar Polar Basic Acidic Termination: stop codon
Standard genetic code (NCBI table 1)[18]
1st
base 		2nd base 3rd
base
U C A G
U UUU (Phe/F) Phenylalanine UCU (Ser/S) Serine UAU (Tyr/Y) Tyrosine UGU (Cys/C) Cysteine U
UUC UCC UAC UGC C
UUA (Leu/L) Leucine UCA UAA Stop (Ochre)[B] UGA Stop (Opal)[B] A
UUG[A] UCG UAG Stop (Amber)[B] UGG (Trp/W) Tryptophan G
C CUU CCU (Pro/P) Proline CAU (His/H) Histidine CGU (Arg/R) Arginine U
CUC CCC CAC CGC C
CUA CCA CAA (Gln/Q) Glutamine CGA A
CUG CCG CAG CGG G
A AUU (Ile/I) Isoleucine ACU (Thr/T) Threonine AAU (Asn/N) Asparagine AGU (Ser/S) Serine U
AUC ACC AAC AGC C
AUA ACA AAA (Lys/K) Lysine AGA (Arg/R) Arginine A
AUG[A] (Met/M) Methionine ACG AAG AGG G
G GUU (Val/V) Valine GCU (Ala/A) Alanine GAU (Asp/D) Aspartic acid GGU (Gly/G) Glycine U
GUC GCC GAC GGC C
GUA GCA GAA (Glu/E) Glutamic acid GGA A
GUG[A] GCG GAG GGG G
A Possible start codons in NCBI table 1. AUG is most common.[19] The two other start codons listed by table 1 (GUG and UUG) are rare in eukaryotes.[20] Prokaryotes have less strigent start codon requirements; they are described by NCBI table 11.
B ^ ^ ^ The historical basis for designating the stop codons as amber, ochre and opal is described in an autobiography by Sydney Brenner[21] and in a historical article by Bob Edgar.[22]

Non-methionine start codons

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Natural

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Translation started by an internal ribosome entry site (IRES), which bypasses a number of regular eukaryotic initiation systems, can have a non-methinone start with GCU or CAA codons.[23]

Mammalian cells can initiate translation with leucine using a specific leucyl-tRNA that decodes the codon CUG. This mechanism is independent of eIF2. No secondary structure similar to that of an IRES is needed.[24][25][26]

Engineered start codons

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Engineered initiator tRNA (tRNAfMet
CUA, changed from a MetY tRNAfMet
CAU) have been used to initiate translation at the amber stop codon UAG in E. coli. Initiation with this tRNA not only inserts the traditional formylmethionine, but also formylglutamine, as glutamyl-tRNA synthase also recognizes the new tRNA.[27] (Recall from above that the bacterial translation initiation system does not specifically check for methionine, only the formyl modification).[1] One study has shown that the amber initiator tRNA does not initiate translation to any measurable degree from genomically-encoded UAG codons, only plasmid-borne reporters with strong upstream Shine-Dalgarno sites.[28]

See also

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References

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  1. ^ a b Shetty, S; Shah, RA; Chembazhi, UV; Sah, S; Varshney, U (28 February 2017). "Two highly conserved features of bacterial initiator tRNAs license them to pass through distinct checkpoints in translation initiation". Nucleic Acids Research. 45 (4): 2040–2050. doi:10.1093/nar/gkw854. PMC 5389676. PMID 28204695.
  2. ^ Kolitz, SE; Lorsch, JR (21 January 2010). "Eukaryotic initiator tRNA: finely tuned and ready for action". FEBS Letters. 584 (2): 396–404. doi:10.1016/j.febslet.2009.11.047. PMC 2795131. PMID 19925799.
  3. ^ a b Lobanov, A. V.; Turanov, A. A.; Hatfield, D. L.; Gladyshev, V. N. (2010). "Dual functions of codons in the genetic code". Critical Reviews in Biochemistry and Molecular Biology. 45 (4): 257–65. doi:10.3109/10409231003786094. PMC 3311535. PMID 20446809.
  4. ^ a b c d Asano, K (2014). "Why is start codon selection so precise in eukaryotes?". Translation (Austin, Tex.). 2 (1): e28387. doi:10.4161/trla.28387. PMC 4705826. PMID 26779403.
  5. ^ Ivanov IP, Firth AE, Michel AM, Atkins JF, Baranov PV (2011). "Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences". Nucleic Acids Research. 39 (10): 4220–4234. doi:10.1093/nar/gkr007. PMC 3105428. PMID 21266472.
  6. ^ Peabody, D. S. (1989). "Translation initiation at non-AUG triplets in mammalian cells". The Journal of Biological Chemistry. 264 (9): 5031–5. doi:10.1016/S0021-9258(18)83694-8. PMID 2538469.
  7. ^ Blattner, F. R.; Plunkett g, G.; Bloch, C. A.; Perna, N. T.; Burland, V.; Riley, M.; Collado-Vides, J.; Glasner, J. D.; Rode, C. K.; Mayhew, G. F.; Gregor, J.; Davis, N. W.; Kirkpatrick, H. A.; Goeden, M. A.; Rose, D. J.; Mau, B.; Shao, Y. (1997). "The Complete Genome Sequence of Escherichia coli K-12". Science. 277 (5331): 1453–1462. doi:10.1126/science.277.5331.1453. PMID 9278503.
  8. ^ Sacerdot, C.; Fayat, G.; Dessen, P.; Springer, M.; Plumbridge, J. A.; Grunberg-Manago, M.; Blanquet, S. (1982). "Sequence of a 1.26-kb DNA fragment containing the structural gene for E.coli initiation factor IF3: Presence of an AUU initiator codon". The EMBO Journal. 1 (3): 311–315. doi:10.1002/j.1460-2075.1982.tb01166.x. PMC 553041. PMID 6325158.
  9. ^ Missiakas, D.; Georgopoulos, C.; Raina, S. (1993). "The Escherichia coli heat shock gene htpY: Mutational analysis, cloning, sequencing, and transcriptional regulation". Journal of Bacteriology. 175 (9): 2613–2624. doi:10.1128/jb.175.9.2613-2624.1993. PMC 204563. PMID 8478327.
  10. ^ E.coli lactose operon with lacI, lacZ, lacY and lacA genes GenBank: J01636.1
  11. ^ Farabaugh, P. J. (1978). "Sequence of the lacI gene". Nature. 274 (5673): 765–769. Bibcode:1978Natur.274..765F. doi:10.1038/274765a0. PMID 355891. S2CID 4208767.
  12. ^ NCBI Sequence Viewer v2.0
  13. ^ Hecht, Ariel; Glasgow, Jeff; Jaschke, Paul R.; Bawazer, Lukmaan A.; Munson, Matthew S.; Cochran, Jennifer R.; Endy, Drew; Salit, Marc (2017). "Measurements of translation initiation from all 64 codons in E. coli". Nucleic Acids Research. 45 (7): 3615–3626. doi:10.1093/nar/gkx070. PMC 5397182. PMID 28334756.
  14. ^ Firnberg, Elad; Labonte, Jason; Gray, Jeffrey; Ostermeir, Marc A. (2014). "A comprehensive, high-resolution map of a gene's fitness landscape". Molecular Biology and Evolution. 31 (6): 1581–1592. doi:10.1093/molbev/msu081. PMC 4032126. PMID 24567513.
  15. ^ Watanabe, Kimitsuna; Suzuki, Tsutomu (2001). "Genetic Code and its Variants". Encyclopedia of Life Sciences. doi:10.1038/npg.els.0000810. ISBN 978-0470015902.
  16. ^ Elzanowski, Andrzej; Ostell, Jim. "The Genetic Codes". NCBI. Retrieved 29 March 2019.
  17. ^ a b Andreev, Dmitry E.; Loughran, Gary; Fedorova, Alla D.; Mikhaylova, Maria S.; Shatsky, Ivan N.; Baranov, Pavel V. (2022-05-09). "Non-AUG translation initiation in mammals". Genome Biology. 23 (1): 111. doi:10.1186/s13059-022-02674-2. ISSN 1474-760X. PMC 9082881. PMID 35534899.
  18. ^ Elzanowski A, Ostell J (7 January 2019). "The Genetic Codes". National Center for Biotechnology Information. Archived from the original on 5 October 2020. Retrieved 21 February 2019.
  19. ^ Nakamoto T (March 2009). "Evolution and the universality of the mechanism of initiation of protein synthesis". Gene. 432 (1–2): 1–6. doi:10.1016/j.gene.2008.11.001. PMID 19056476.
  20. ^ Asano, K (2014). "Why is start codon selection so precise in eukaryotes?". Translation (Austin, Tex.). 2 (1): e28387. doi:10.4161/trla.28387. PMID 26779403.
  21. ^ Brenner S. A Life in Science (2001) Published by Biomed Central Limited ISBN 0-9540278-0-9 see pages 101-104
  22. ^ Edgar B (2004). "The genome of bacteriophage T4: an archeological dig". Genetics. 168 (2): 575–82. PMC 1448817. PMID 15514035. see pages 580-581
  23. ^ RajBhandary, Uttam L. (15 February 2000). "More surprises in translation: Initiation without the initiator tRNA". Proceedings of the National Academy of Sciences. 97 (4): 1325–1327. Bibcode:2000PNAS...97.1325R. doi:10.1073/pnas.040579197. PMC 34295. PMID 10677458.
  24. ^ "Where to Start? Alternate Protein Translation Mechanism Creates Unanticipated Antigens". PLOS Biology. 2 (11): e397. 26 October 2004. doi:10.1371/journal.pbio.0020397. PMC 524256.
  25. ^ Starck, S. R.; Jiang, V; Pavon-Eternod, M; Prasad, S; McCarthy, B; Pan, T; Shastri, N (2012). "Leucine-tRNA initiates at CUG start codons for protein synthesis and presentation by MHC class I". Science. 336 (6089): 1719–23. Bibcode:2012Sci...336.1719S. doi:10.1126/science.1220270. PMID 22745432. S2CID 206540614.
  26. ^ Dever, T. E. (2012). "Molecular biology. A new start for protein synthesis". Science. 336 (6089): 1645–6. doi:10.1126/science.1224439. PMID 22745408. S2CID 44326947.
  27. ^ Varshney, U.; RajBhandary, U. L. (1990-02-01). "Initiation of protein synthesis from a termination codon". Proceedings of the National Academy of Sciences. 87 (4): 1586–1590. Bibcode:1990PNAS...87.1586V. doi:10.1073/pnas.87.4.1586. ISSN 0027-8424. PMC 53520. PMID 2406724.
  28. ^ Vincent, Russel M.; Wright, Bradley W.; Jaschke, Paul R. (2019-03-15). "Measuring Amber Initiator tRNA Orthogonality in a Genomically Recoded Organism" (PDF). ACS Synthetic Biology. 8 (4): 675–685. doi:10.1021/acssynbio.9b00021. ISSN 2161-5063. PMID 30856316. S2CID 75136654.
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  • The Genetic Codes. Compiled by Andrzej (Anjay) Elzanowski and Jim Ostell, National Center for Biotechnology Information (NCBI), Bethesda, Maryland, US [1]
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