Genome analysis Advance Access publication September 17, 2014 Making novel proteins from pseudogenes

Motivation: Recently, we made synthetic proteins from non-coding DNA of Escherichia coli. Encouraged by this, we asked: can we arti-ficially express pseudogenes into novel and functional proteins? What kind of structures would be generated? Would these proteins be stable? How would the organism respond to the artificial reactivation of pseudogenes? Results: To answer these questions, we studied 16 full-length protein equivalents of pseudogenes. The sequence-based predictions indi-cated interesting molecular and cellular functional roles for pseudo-gene-derived proteins. Most of the proteins were predicted to be involved in the amino acid biosynthesis, energy metabolism, purines and pyrimidine biosynthesis, central intermediary metabolism, trans-port and binding. Interestingly, many of the pseudogene-derived pro-teins were predicted to be enzymes. Furthermore, proteins showed strong evidence of stable tertiary structures. The prediction scores for structure, function and stability were found to be favorable in most of the cases. Impact: To our best knowledge, this is the first such report that predicts the possibility of making functional and stable proteins from pseudogenes. In future, it would be interesting to experimentally synthesize and validate these predictions