Hello everyone,
Please, can anyone address me to any source where I can find the different starting codons for non coding rrnas in prokaryotes?
I know the known translation starting codons for protein coding genes are ATG, GTG, TTG (among the more abundant), and some times we can also find others such as ATT or CTG
I am looking into the starting sites of a bacterial genome, and found 4 different starting sites among the protein coding genes, ATG, GTG, TTG and GCG. But for non coding RNAs the list increase remarkably.
For rRNAs, I found the following 3: AGA, TGG and TTA. TTA seems to correspond in reality to the stop codon TAA, but as per the annotation, it is in the right coding direction and thus it is a starting site.
For tRNAs and ncRNAS the situation is more complicated, with up to 16 and 52 different starting sites, respectively.
Do you think this is possible? Or it must be something wrong with the genome annotation?
Thanks in advance for your help
Hello Cristina,
Broadly speaking, protein coding genes are transcribed and translated, while non coding genes are only transcribed, and the resulting RNA is folded and used simply as such. Only in the translation process the codon concept has a meaning, since it is the ribosome that "somehow knows" the genetic code. Thus, it makes no sense speaking of codons for non coding genes, and that is the reason why you can find stop codons within a non coding gene or that them do not start with the typical start codons. RNA polymerase do not "look" for start codons for starting the transcription process, but it recognize promoters, transcription start sites (TSS) and possibly other sequence patterns like the TATA box in the 5' UTR (untranslated region).
I hope that helps. Best regards.
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