Predicting stable functional peptides from the intergenic space of E. coli

Abstract

Expression of synthetic proteins from intergenic regions of and their functional association was recently demonstrated (Dhar et al. in J Biol Eng 3:2, 2009. doi:10.1186/1754-1611-3-2). This gave birth to the question: if one can make 'user-defined' genes from non-coding genome-how big is the artificially translatable genome? (Dinger et al. in PLoS Comput Biol 4, 2008; Frith et al. in RNA Biol 3(1):40-48, 2006a; Frith et al. in PLoS Genet 2(4):e52, 2006b). To answer this question, we performed a bioinformatics study of all reported intergenic sequences, in search of novel peptides and proteins, unexpressed by nature. Overall, 2500 intergenic sequences were computationally translated into 'protein sequence equivalents' and matched against all known proteins. Sequences that did not show any resemblance were used for building a comprehensive profile in terms of their structure, function, localization, interactions, stability so on. A total of 362 protein sequences showed evidence of stable tertiary conformations encoded by the intergenic sequences of genome. Experimental studies are underway to confirm some of the key predictions. This study points to a vast untapped repository of functional molecules lying undiscovered in the non-expressed genome of various organisms.

Identification of Pseudo-R genes in Vitis vinifera and characterization of their role as immunomodulators in host-pathogen interactions

“…Plant antimicrobial peptides are a primary component of the barrier defense system against various phytopathogenic infections [15] . Studies involving pseudogene derived antimicrobial peptides were previously conducted in Drosophila melanogaster and Escherichia coli [16] , [17] . Although, the studies involving the artificial expression of pseudogene-based peptides are still in their infancy, but exhibit great potentials of pseudogenes being expressed as novel and functional proteins [18] .…”