For decades scientists believed that large regions within metazoan genomes are nonfunctional relicts from evolution because they do not encode proteins. However, we also knew that significant parts of these regions are transcribed into non-coding RNA (ncRNA). The view that ncRNAs have no function changed dramatically with the discovery of regulatory RNAs, such as microRNAs. However, most ncRNAs discovered so far lack any obvious function. Among them are poly A-containing RNAs that have only short open reading frames, some of which encode small peptides. However, the function of these peptides remains largely elusive. In a recent Science paper, French and Japanese scientists led by François Payre and Yuji Kageyama report the function of peptides derived from the polished rice (pri) gene in Drosophila development.
The pri gene was originally identified in the red flour beetle (Tribolium castaneum) and shown to encode multiple peptides rather than one single protein. When pri expression is silenced in Tribolium, the abdominal segments of the embryos turn into thoracic segments, providing the embryos with additional pairs of legs. Likewise, pri mutations display prominent defects in Drosophila embryogenesis, including defects in leg formation and epidermis differentiation. But how can the lack of small peptides produce such complex developmental phenotypes?
In Drosophila, epidermal cells form a distinct pattern of bristles known as trichomes on the body surface of the embryo. Mutants that are unable to form trichomes helped to identify some of the genes controlling this process and the team used one – known as shavenbaby (svb) due to the embryo's lack of trichomes and smooth appearance when the svb gene is defective – to identify the function of pri encoded peptides.
The svb gene is a master regulator and encodes a transcription factor, which controls the expression of other genes required for trichome formation. To examine the function of pri in epidermis differentiation, the French/Japanese team analyzed mutant embryos defective in pri, and observed that similar to svb mutants they lack trichomes. Knowing that the expression of svb target genes was lost while svb expression itself was unaffected, the team concluded that the pri encoded peptides must somehow act on the Svb transcription factor.
The key to understanding pri function was the multiple domain structure of the Svb transcription factor which contains an amino-terminal repression domain, a central activation domain and a carboxy-terminal DNA binding domain. The team carefully analyzed the ability of svb and ovoB (an activated version of Svb that lacks the repressor domain) to induce trichome formation in epidermal cells that usually lack trichomes. As expected, when svb was expressed in smooth epidermal cells, they formed trichomes, but not when these cells lacked pri. In contrast, ovoB (lacking the repressor domain) induced trichome formation even in cells lacking pri. These findings indicate that the pri encoded peptides act by triggering the removal of Svb's repressor domain to activate the transcription factor. Finally, immune blots and micro-sequencing showed that the mobility of Svb on electrophoretic gels varied depending on whether or not pri was present, and the repressor domain gets lost when the Pri peptides trigger the switch of Svb's transcriptional activity.
Payre, Kageyama and their colleagues have provided exciting evidence for a novel mode of gene regulation mediated by small peptides that trigger cleavage of their target proteins. Possibly, they function as small adaptors guiding proteases to their specific cleavage sites. If so, these peptides create fascinating possibilities to control gene expression and hence facilitate new therapeutic approaches.
