You're one in a googol: optimizing genes for protein expression
- 11 March 2009
- journal article
- review article
- Published by The Royal Society in Journal of The Royal Society Interface
- Vol. 6 (suppl_4) , S467-76
- https://doi.org/10.1098/rsif.2008.0520.focus
Abstract
A vast number of different nucleic acid sequences can all be translated by the genetic code into the same amino acid sequence. These sequences are not all equally useful however; the exact sequence chosen can have profound effects on the expression of the encoded protein. Despite the importance of protein-coding sequences, there has been little systematic study to identify parameters that affect expression. This is probably because protein expression has largely been tackled on an ad hoc basis in many independent projects: once a sequence has been obtained that yields adequate expression for that project, there is little incentive to continue work on the problem. Synthetic biology may now provide the impetus to transform protein expression folklore into design principles, so that DNA sequences may easily be designed to express any protein in any system. In this review, we offer a brief survey of the literature, outline the major challenges in interpreting existing data and constructing robust design algorithms, and propose a way to proceed towards the goal of rational sequence engineering.Keywords
This publication has 95 references indexed in Scilit:
- Natural computation meta-heuristics for the in silico optimization of microbial strainsBMC Bioinformatics, 2008
- Engineering prokaryotic gene circuitsFEMS Microbiology Reviews, 2008
- Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in BacteriaDNA Research, 2008
- Synonymous Mutations and Ribosome Stalling Can Lead to Altered Folding Pathways and Distinct MinimaJournal of Molecular Biology, 2008
- Following translation by single ribosomes one codon at a timeNature, 2008
- OptCircuit: An optimization based method for computational design of genetic circuitsBMC Systems Biology, 2008
- SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC FrameworkPLoS Computational Biology, 2007
- Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshiftingProceedings of the National Academy of Sciences, 2007
- Optimal encoding rules for synthetic genes: the need for a community effortMolecular Systems Biology, 2007
- Synthetic biology: new engineering rules for an emerging disciplineMolecular Systems Biology, 2006