Where are all the small peptides and what might they do?

RP Hellens1,2, WA Laing3, AM Bulley4 and RM Macknight2

  1. Queensland University of Technology, Institute for Future Environments, 2 George Street, Brisbane 4000, Queensland
  2. University of Otago, Department of Biochemistry, PO Box 56, Dunedin 9054, New Zealand
  3. The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Batchelar Road, Palmerston North 4474, New Zealand
  4. The New Zealand Institute for Plant & Food Research Limited, 412 No 1 Road, RD 2, Te Puke 3182, New Zealand

While genome sequencing is now commonplace, genome annotation and functional characterisation of components of the genome remains an enormous challenge. Like small regulatory RNAs, short open reading frames (sORFs) often reside in ‘non-coding’ regions of the genome that have long been considered to be ‘junk DNA [1]. Translatable sORFs of less than 100 amino acids are extremely difficult to predict from genome sequences as the number of potential ORFs increases exponentially as the potential peptide lengths get smaller [2]. This challenge is made more complicated by mounting evidence that these short proteins do not always comply with genetic convention, and are frequently encoded by short ORFs that use a translation start codon other than AUG[3].
References: 1. Waterhouse PM, Hellens RP (2015) Plant biology: Coding in non-coding RNAs. Nature 520: 41-42. 2. Hellens RP, Brown CM, Chisnall MA, Waterhouse PM, Macknight RC (2015) The Emerging World of Small ORFs. Trends Plant Sci. 3. Laing WA, Martinez-Sanches M, Wright M, Bulley S, Brewster D, et al. (2015) A non-canonical upstream open reading frame is essential for feedback regulation of ascorbate biosynthesis The Plant Cell 27: 772-786.