Sunday, September 9, 2007

Peptidomics of Really Small Peptides

Small sized RNA molecules, known as microRNA or miRNA in short, play vital physiological roles in cellular metabolism. These miRNAs do not have to be exact complementary sequence of their target messenger RNA (mRNA), thus, expanding the range of target mRNAs that a single miRNA can control. There are over 300 miRNA known to be coded by the mammalian genome. And they collectively regulate the levels of 25 percent of the genetic messages.
Having seen the formation and function of miRNA, I ask if it is a far-fetched idea to think of a naturally occurring peptidome in a cell, either as a result of protein translation from short but genuine ORFs or as a result of general protein degradation?
We know that majority of the protein-coding ORFs carry the canonical start codon, ATG. But, now and then, we do run into ORFs which use translation initiation codons other than ATG, although, at less frequency. Most transcripts carry extra nucleotide sequence (UTR) of varying lengths both at the 5’ and 3’ ends. What if these UTRS, beyond serving as stabilizing sequences, also carry hidden short ORFs with non canonical start codon that might be translated into small peptides?
We know that proteins have life-time. The span is dependent upon their susceptibility to the protein degradation machinery. So, during degradation, particularly the proteins with closely spaced arginine or lysine residues, very small peptides which might have vital biological function(s) may be generated.
A Japanese group did publish an article on this issue. They could find very small numbers, less than ten, of naturally occurring peptides in the cell. I think it was more due to their technical limitations. I think there is more. The field of peptidomics of really small peptides is definitely worth pursuing. Because, peptides can work wonders.

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