title: Predicting stable functional peptides from the intergenic space ofE. coli.
abstract: Expression of synthetic proteins from intergenic regions ofE. coliand 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 reportedE. coliintergenic sequences, in search of novel peptides and proteins, unexpressed by nature. Overall, 2500E. coliintergenic 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 ofE. coligenome. 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.
authors.affiliation: Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, 695581 Kerala India.
authors.forename: Vipin
authors.initials: V
authors.lastname: Thomas
authors.affiliation: Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, 695581 Kerala India.
authors.forename: Navya
authors.initials: N
authors.lastname: Raj
authors.affiliation: Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, 695581 Kerala India.
authors.forename: Deepthi
authors.initials: D
authors.lastname: Varughese
authors.affiliation: Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, 201316 U.P. India.
authors.forename: Naveen
authors.initials: N
authors.lastname: Kumar
authors.affiliation: Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, 201316 U.P. India.
authors.forename: Seema
authors.initials: S
authors.lastname: Sehrawat
authors.affiliation: School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India.
authors.forename: Abhinav
authors.initials: A
authors.lastname: Grover
authors.affiliation: Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, 201316 U.P. India.
authors.forename: Shailja
authors.initials: S
authors.lastname: Singh
authors.affiliation: Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, 695581 Kerala India.|School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India.
authors.forename: Pawan K
authors.initials: PK
authors.lastname: Dhar
authors.affiliation: Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, 695581 Kerala India.
authors.forename: Achuthsankar S
authors.initials: AS
authors.lastname: Nair
keywords: Antimicrobial peptides; Functional annotation; Intergenic sequences; Structure prediction