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. Homo sapiens-mtDNA~NC 012920-ATP8+ATP6 Overlap.svg
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.

Contents

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

Decoding

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

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

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

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

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

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

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

Amino-acid biochemical propertiesNonpolarPolarBasicAcidicTermination: stop codon
Standard genetic code (NCBI table 1) [18]
1st
base
2nd base3rd
base
UCAG
UUUU(Phe/F) Phenylalanine UCU(Ser/S) Serine UAU(Tyr/Y) Tyrosine UGU(Cys/C) Cysteine U
UUCUCCUACUGCC
UUA(Leu/L) Leucine UCAUAA Stop (Ochre) [B] UGA Stop (Opal) [B] A
UUG [A] UCGUAG Stop (Amber) [B] UGG(Trp/W) Tryptophan G
CCUUCCU(Pro/P) Proline CAU(His/H) Histidine CGU(Arg/R) Arginine U
CUCCCCCACCGCC
CUACCACAA(Gln/Q) Glutamine CGAA
CUGCCGCAGCGGG
AAUU(Ile/I) Isoleucine ACU(Thr/T) Threonine AAU(Asn/N) Asparagine AGU(Ser/S) Serine U
AUCACCAACAGCC
AUAACAAAA(Lys/K) Lysine AGA(Arg/R) Arginine A
AUG [A] (Met/M) Methionine ACGAAGAGGG
GGUU(Val/V) Valine GCU(Ala/A) Alanine GAU(Asp/D) Aspartic acid GGU(Gly/G) Glycine U
GUCGCCGACGGCC
GUAGCAGAA(Glu/E) Glutamic acid GGAA
GUG [A] GCGGAGGGGG
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

Natural

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. It proceeds by ribosomal scanning, and a Kozak context enhances initiation efficiency. [24] [25] [26]

Engineered start codons

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

References

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  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. 1 2 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.
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  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.
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  10. E.coli lactose operon with lacI, lacZ, lacY and lacA genes GenBank: J01636.1
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  12. NCBI Sequence Viewer v2.0
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  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.
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  21. Brenner S. A Life in Science (2001) Published by Biomed Central Limited ISBN   0-9540278-0-9 see pages 101-104
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