Finding mooonlighting proteins from genomes
Moonlighting proteins, proteins which have two or more independent functions, have drawn an increasing attention as more and more such examples have been discovered in recent years. However, the number of known moonlighting proteins is still not large enough to elucidate the overall landscape of their functional diversity. In this work, published on Biology Direct, Dr. Daisuke Kihara and his co-authors have developed a computational framework for finding moonlighting proteins in a genome scale.
Since the systematic study of moonlighting proteins is still in an early stage, in most of the cases they are not explicitly labeled in public databases with "moonlighting", "dual function", or related words, which make it difficult to collect and reuse existing knowledge of moonlighting proteins. Therefore, the researchers first analyzed the Gene Ontology (GO) terms (vocabulary for describing function of genes) assigned to known moonlighting proteins and found that GO terms can be clearly clustered into separate groups reflecting diverse functions of these proteins. The researchers further analyzed the GO term annotations of all protein genes in the Escherichia coli K-12 genome and found 33 novel moonlighting proteins by identifying genes with clear GO term separations followed by literature survey. Next, Dr. Kihara and colleagues analyzed moonlighting proteins based on protein-protein interaction, gene expression, phylogenetic profile, and genetic interaction networks and found that they have a higher number of interacting partners of distinct functions than non-moonlighting proteins in these networks.
The characteristics of known moonlighting proteins found in this work form foundation for identifying new moonlighting proteins in a genome-scale and open up a new opportunity to investigate the multi-functional nature of proteins at a systems level.
Four undergraduate students were involved in this research.
- Ishita K. Khan, Yuqian Chen, Tiange Dong, Xioawei Hong, Rikiya Takeuchi, Hirotada Mori, and Daisuke Kihara "Genome-scale Identification and Characterization of Moonlighting Proteins" Biology Direct 9(1): 30 (Dec. 2014).