Abstract
Nature selected certain regions of the genome for encoding proteins. Most of the sequences were used to encode only RNA. What happened to the remaining sections of the genome? It is possible that some sequences were retired and retained as non-functional entities called pseudogenes. Though several evolutionary prospects with functional endpoints exist, we looked at the possibility of hypothetical proteins correlating with the emergence of pseudogenes and potential of such genes to make novel synthetic molecules. In this commentary, we consider two key aspects: (1) does any correlation exist between hypothetical proteins and pseudogenes and (2)—can we make novel and functional proteins from pseudogenes?
Similar content being viewed by others
References
Bianchi MM, Sartori G, Vandenbol M, Kaniak A, Uccelletti D, Mazzoni C, Di Rago JP, Carignani G, Slonimski PP, Frontali L (1999) How to bring orphan genes into functional. Yeast 15(6):513–526
Branca R, Orre L, Johansson H, Granholm V, Huss M, Pérez-Bercoff Å et al (2014) HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics. Nat Methods 11(1):59–62
Dhar PK, Thwin CS, Tun K, Tsumoto Y, Maurer-Stroh S, Eisenhaber F, Surana U (2009) Synthesizing non-natural parts from natural genomic template. J Biol Eng 3(3):2
Dujon B (1996) The yeast genome project: what did we learn? Trends Genet 12:263–270
Fortugno LP (2007) Frontiers in Breast Cancer Research. Nova Publishers, New York, p 195
Galperin MY, Koonin EV (2004) Conserved hypothetical’ proteins: prioritization of targets for experimental study. Nucleic Acids Res 32(18):5452–5463
Knies K, Schuster B, Ameziane N, Rooimans M, Bettecken T, de Winter J, Schindler D (2012) Genotyping of fanconi anemia patients by whole exome sequencing: advantages and challenges. PLoS ONE 7(12):e52648
Lan L, Djuric N, Guo Y, Vucetic S (2013) MS-kNN: protein function prediction by integrating multiple data sources. BMC Bioinformatics 14(3):S8
Sivashankari S, Shanmughavel P (2006) Functional annotation of hypothetical proteins—A review. Bioinformation 1(8):335–338
Wang J, Zhang D, Li J (2013) PREAL: prediction of allergenic protein by maximum relevance minimum redundancy (mRMR) feature selection. BMC Syst Biol 7(5):S9
Zhang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9:40
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Shidhi, P.R., Nair, A.S. & Suravajhala, P. Identifying pseudogenes from hypothetical proteins for making synthetic proteins. Syst Synth Biol 8, 169–171 (2014). https://doi.org/10.1007/s11693-014-9148-4
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11693-014-9148-4