title: Making novel proteins from pseudogenes.
abstract: BACKGROUND
  Recently, we made synthetic proteins from non-coding DNA of Escherichia coli. Encouraged by this, we asked: can we artificially 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 indicated interesting molecular and cellular functional roles for pseudogene-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, transport and binding. Interestingly, many of the pseudogene-derived proteins 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India.
authors.forename: P R
authors.initials: PR
authors.lastname: Shidhi
authors.affiliation: Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India.
authors.forename: Prashanth
authors.initials: P
authors.lastname: Suravajhala
authors.affiliation: Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India.
authors.forename: Aysha
authors.initials: A
authors.lastname: Nayeema
authors.affiliation: Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India.
authors.forename: Achuthsankar S
authors.initials: AS
authors.lastname: Nair
authors.affiliation: Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India.
authors.forename: Shailja
authors.initials: S
authors.lastname: Singh
authors.affiliation: Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India.
authors.forename: Pawan K
authors.initials: PK
authors.lastname: Dhar
mesh_terms: D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D011487:Protein Conformation; D011544:Pseudogenes / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D029701:Saccharomyces cerevisiae Proteins