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There is some literature which shows that all start codons code for methionine. However, in the standard genetic code, the alternative start codons clearly code for leucine. Does that mean these codons will code for leucine when they are encountered during translation (after start codon has been initialised and translated).

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  • $\begingroup$ Duplicate biology.stackexchange.com/questions/604/… also biology.stackexchange.com/questions/1629/… It seems to be the case these codons are still recognised by fMet-tRNA in the context of a translational start. See also WP en.wikipedia.org/wiki/Start_codon $\endgroup$ – Alan Boyd Aug 23 '14 at 7:28
  • $\begingroup$ @AlanBoyd.. I always thought that it would be possible to map the translation start site only if the nascent polypeptide is captured. In many proteins the N-terminal is chopped off. Or otherwise stall the ribosome at translation initiation (by using lets say an analogue of $tRNA^{fMet}$ or $tRNA^{Met}_i$). Are you aware of any such studies? $\endgroup$ – WYSIWYG Aug 23 '14 at 8:02
  • $\begingroup$ Translation from the IRES can start from amino-acids other than methionine [Ref]. $\endgroup$ – WYSIWYG Aug 23 '14 at 8:11
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I commented that this was a duplicate, but reading the question more carefully you seem to be asking something slightly different.

In the context of a 'start' these codons will be recognised by fMet-tRNA and a formyl-methionine will be inserted as the first amino acid. Subsequent occurrences of the same codon within the open reading frame will be translated normally (e.g. GUG > valine).

The use of GTG as an initiation codon in the E. coli lacI gene

In this paper

Frottini et al. (2006) The Proteomics of N-terminal Methionine Cleavage. Molec. & Cell. Proteomics 5: 2336-2349

the authors report assays of E. coli methionine aminopeptidase with model peptides showing that when Lys is the 2nd residue, Met removal is very inefficient. They also show that when Pro is the 3rd residue, Met removal is very inefficient.

This explains the fact that when the lacI repressor protein was sequenced:

Beyreuther et al. (1973) The amino-acid sequence of lac repressor. PNAS 70: 3576-3580

it was found to have a Met residue at its N terminus (sequence Met-Lys-Pro-).

However, when the lacI gene was sequenced:

Farabaugh (1978) Sequence of the lacI gene. Nature 274: 765-769

the corresponding DNA sequence was GTG AAA CCA, demonstrating that the N-terminal residue is encoded by a GTG(Val) codon. LacI residue Val23 is encoded by a GTG codon, demonstrating the normal use of that codon in the body of the mRNA.

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  • $\begingroup$ Thanks! Do you have any literature that explains this? $\endgroup$ – user6417 Aug 23 '14 at 13:48

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