Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency
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Ajikumar, 2010, Isoprenoid pathway optimization for taxol precursor overproduction in Escherichia coli, Science, 330, 70, 10.1126/science.1191652
Allen, 2005, The cryo-EM structure of a translation initiation complex from Escherichia coli, Cell, 121, 703, 10.1016/j.cell.2005.03.023
Alper, 2005, Tuning genetic control through promoter engineering, Proc. Nat. Acad. Sci. U S A, 102, 12678, 10.1073/pnas.0504604102
Boyle, 2012, Parts plus pipes: synthetic biology approaches to metabolic engineering, Metab. Eng., 14, 223, 10.1016/j.ymben.2011.10.003
Copeland, 2012, Computational tools for metabolic engineering, Metab. Eng., 14, 270, 10.1016/j.ymben.2012.03.001
De Smit, 2003, Translational standby sites: how ribosomes may deal with the rapid folding kinetics of mRNA, J. Mol. Biol., 331, 737, 10.1016/S0022-2836(03)00809-X
Dirks, 2007, Thermodynamic analysis of interacting nucleic acid strands, SIAM Rev., 49, 65, 10.1137/060651100
Dos Reis, 2004, Solving the riddle of codon usage preferences: a test for translational selection, Nucleic. Acids. Res., 32, 5036, 10.1093/nar/gkh834
Gibson, 2010, Creation of a bacterial cell controlled by a chemically synthesized genome, Science, 329, 52, 10.1126/science.1190719
Isaacs, 2011, Precise manipulation of chromosomes in vivo enables genome-wide codon replacement, Science, 333, 348, 10.1126/science.1205822
Jensen, 1998, Artificial promoters for metabolic optimization, Biotechnol. Bioeng., 58, 191, 10.1002/(SICI)1097-0290(19980420)58:2/3<191::AID-BIT11>3.0.CO;2-G
Keasling, 2010, Manufacturing molecules through metabolic engineering, Science, 330, 1355, 10.1126/science.1193990
Keasling, 2012, Synthetic biology and the development of tools for metabolic engineering, Metab. Eng., 14, 189, 10.1016/j.ymben.2012.01.004
Komarova, 2002, Protein S1 counteracts the inhibitory effect of the extended Shine–Dalgarno sequence on translation, RNA, 8, 1137, 10.1017/S1355838202029990
Kosuri, 2010, Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips, Nat. Biotechnol., 28, 1295, 10.1038/nbt.1716
Kudla, 2009, Coding-sequence determinants of gene expression in Escherichia coli, Science, 324, 255, 10.1126/science.1170160
Lu, 2007, Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation, Nat. Biotechnol., 25, 117, 10.1038/nbt1270
Makino, 2011, Comprehensive engineering of Escherichia coli for enhanced expression of IgG antibodies, Metab. Eng., 13, 241, 10.1016/j.ymben.2010.11.002
Marzi, 2007, Structured mRNAs regulate translation initiation by binding to the platform of the ribosome, Cell, 130, 1019, 10.1016/j.cell.2007.07.008
Mijakovic, 2005, Tunable promoters in systems biology, Curr. Opin. Biotechnol., 16, 329, 10.1016/j.copbio.2005.04.003
Park, 2007, Design of 5′-untranslated region variants for tunable expression in Escherichia coli, Biochem. Biophys. Res. Commun., 356, 136, 10.1016/j.bbrc.2007.02.127
Pfleger, 2006, Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes, Nat. Biotechnol., 24, 1027, 10.1038/nbt1226
Plotkin, 2011, Synonymous but not the same: the causes and consequences of codon bias, Nat. Rev. Genet., 12, 32, 10.1038/nrg2899
Ramakrishnan, 2002, Ribosome structure and the mechanism of translation, Cell, 108, 557, 10.1016/S0092-8674(02)00619-0
Salis, 2009, Automated design of synthetic ribosome binding sites to control protein expression, Nat. Biotechnol., 27, 946, 10.1038/nbt.1568
Seo, 2012, Synthetic regulatory tools for microbial engineering, Biotechnol. Bioprocess Eng., 17, 1, 10.1007/s12257-011-0563-z
Seo, 2009, Quantitative correlation between mRNA secondary structure around the region downstream of the initiation codon and translational efficiency in Escherichia coli. Biotechnol, Bioeng., 104, 611, 10.1002/bit.22431
Sharp, 1987, The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications, Nucleic Acids Res., 15, 1281, 10.1093/nar/15.3.1281
Sinha, 2006, Probing messenger RNA conformational heterogeneity using single-molecule fluorescence anisotropy, Appl. Phys. Lett., 88
Studer, 2006, Unfolding of mRNA secondary structure by the bacterial translation initiation complex, Mol. Cell, 22, 105, 10.1016/j.molcel.2006.02.014