Spanning high-dimensional expression space using ribosome-binding site combinatorics

Nucleic Acids Research

Volumn 41, Issue 9, 2013, Pages

  Zelcbuch, Lior ^a   Antonovsky, Niv ^a   Bar Even, Arren ^a   Levin Karp, Ayelet ^a   Barenholz, Uri ^a   Dayagi, Michal ^a   Liebermeister, Wolfram ^a,b   Flamholz, Avi ^a   Noor, Elad ^a   Amram, Shira ^a   Brandis, Alexander ^a   Bareia, Tasneem ^a   Yofe, Ido ^a   Jubran, Halim ^c   Milo, Ron ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^c HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

CAROTENOID; FLUORESCENT DYE;

ARTICLE; BACTERIAL STRAIN; BINDING SITE; BIOSYNTHESIS; CONTROLLED STUDY; ESCHERICHIA COLI; FLUORESCENCE IMAGING; GENETIC VARIABILITY; MICROSCOPY; NONHUMAN; OPERON; PHENOTYPE; PRIORITY JOURNAL; PROTEIN EXPRESSION; RIBOSOME BINDING SITE;

BINDING SITES; CAROTENOIDS; ESCHERICHIA COLI; FLUORESCENT DYES; GENE EXPRESSION REGULATION; LUMINESCENT PROTEINS; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; OPERON; PROTEIN BIOSYNTHESIS; PROTEINS; RIBOSOMES;

EID: 84877292750     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt151     Document Type: Article

References (31)

1. Lu, P., Vogel, C., Wang, R., Yao, X. and Marcotte, E.M. (2006) Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol., 25, 117-124.
2. Scott, M., Gunderson, C.W., Mateescu, E.M., Zhang, Z. and Hwa, T. (2010) Interdependence of cell growth and gene expression: origins and consequences. Science, 330, 1099-1102.
3. Na, D., Kim, T.Y. and Lee, S.Y. (2010) Construction and optimization of synthetic pathways in metabolic engineering. Curr. Opin. Microbiol., 13, 363-370.
4. Dekel, E. and Alon, U. (2005) Optimality and evolutionary tuning of the expression level of a protein. Nature, 436, 588-592.
5. Koffas, M.A.G., Jung, G.Y. and Stephanopoulos, G. (2003) Engineering metabolism and product formation in Corynebacterium glutamicum by coordinated gene overexpression. Metab. Eng., 5, 32-41.
6. Pitera, D.J., Paddon, C.J., Newman, J.D. and Keasling, J.D. (2007) Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli. Metab. Eng., 9, 193-207.
7. Glick, B.R. (1995) Metabolic load and heterologous gene expression. Biotechnol. Adv., 13, 247-261.
8. Hammer, K., Mijakovic, I. and Jensen, P.R. (2006) Synthetic promoter libraries-tuning of gene expression. Trends Biotechnol., 24, 53-55.
9. Salis, H.M., Mirsky, E.A. and Voigt, C.A. (2009) Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol., 27, 946-950.
10. Wang, H.H., Isaacs, F.J., Carr, P.A., Sun, Z.Z., Xu, G., Forest, C.R. and Church, G.M. (2009) Programming cells by multiplex genome engineering and accelerated evolution. Nature, 460, 894-898.
11. Pfleger, B.F., Pitera, D.J., Smolke, C.D. and Keasling, J.D. (2006) Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat. Biotechnol., 24, 1027-1032.
12. Babiskin, A.H. and Smolke, C.D. (2011) A synthetic library of RNA control modules for predictable tuning of gene expression in yeast. Mol. Syst. Biol., 7, 471.
13. McGinness, K.E., Baker, T.A. and Sauer, R.T. (2006) Engineering controllable protein degradation. Mol. Cell, 22, 701-707.
14. Shetty, R.P., Endy, D. and Knight, T.F. (2008) Engineering BioBrick vectors from BioBrick parts. J. Biol. Eng., 2, 5.
15. Britton, G., Liaaen-Jensen, S. and Pfander, H. (2004) Birkhauser. Carotenoids handbook, Basel; Boston.
16. Chu, F.L., Pirastru, L., Popovic, R. and Sleno, L. (2011) Carotenogenesis up-regulation in Scenedesmus sp. using a targeted metabolomics approach by liquid chromatography-high-resolution mass spectrometry. J. Agric. Food Chem., 59, 3004-3013.
17. Løvdok, L., Bentele, K., Vladimirov, N., Muller, A., Pop, F.S., Lebiedz, D., Kollmann, M. and Sourjik, V. (2009) Role of translational coupling in robustness of bacterial chemotaxis pathway. PLoS Biol., 7, e1000171.
18. Wang, C., Oh, M.K. and Liao, J.C. (2000) Directed evolution of metabolically engineered Escherichia coli for carotenoid production. Biotechnol. Prog., 16, 922-926.
19. Farmer, W.R. and Liao, J.C. (2000) Improving lycopene production in Escherichia coli by engineering metabolic control. Nat. Biotechnol., 18, 533-537.
20. Kim, S.W. and Keasling, J.D. (2001) Metabolic engineering of the nonmevalonate isopentenyl diphosphate synthesis pathway in Escherichia coli enhances lycopene production. Biotechnol. Bioeng., 72, 408-415.
21. Cunningham, F.X. Jr and Gantt, E. (2011) Elucidation of the pathway to astaxanthin in the flowers of Adonis aestivalis. Plant Cell, 23, 3055-3069.
22. Lemuth, K., Steuer, K. and Albermann, C. (2011) Engineering of a plasmid-free Escherichia coli strain for improved in vivo biosynthesis of astaxanthin. Microb. Cell Fact., 10, 29.
23. Zhu, X.-G., de Sturler, E. and Long, S.P. (2007) Optimizing the distribution of resources between enzymes of carbon metabolism can dramatically increase photosynthetic rate: a numerical simulation using an evolutionary algorithm. Plant Physiol., 145, 513-526.
24. Holatko, J., Elisakova, V., Prouza, M., Sobotka, M., Nesvera, J. and Patek, M. (2009) Metabolic engineering of the L-valine biosynthesis pathway in Corynebacterium glutamicum using promoter activity modulation. J. Biotechnol., 139, 203-210.
25. Horton, R.M., Hunt, H.D., Ho, S.N., Pullen, J.K. and Pease, L.R. (1989) Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene, 77, 61-68.
26. Davis, J.H., Rubin, A.J. and Sauer, R.T. (2010) Design, construction and characterization of a set of insulated bacterial promoters. Nucleic Acids Res., 39, 1131-1141.
27. Shaner, N.C., Steinbach, P.A. and Tsien, R.Y. (2005) A guide to choosing fluorescent proteins. Nat. Methods, 2, 905-909.
28. Rydzanicz, R., Zhao, X.S. and Johnson, P.E. (2005) Assembly PCR oligo maker: a tool for designing oligodeoxynucleotides for constructing long DNA molecules for RNA production. Nucleic Acids Res., 33, W521-W525.
29. Baughman, G. and Nomura, M. (1983) Localization of the target site for translational regulation of the L11 operon and direct evidence for translational coupling in Escherichia coli. Cell, 34, 979-988.
30. Schumperli, D., McKenney, K., Sobieski, D.A. and Rosenberg, M. (1982) Translational coupling at an intercistronic boundary of the Escherichia coli galactose operon. Cell, 30, 865-871.
31. Rex, G., Surin, B., Besse, G., Schneppe, B. and McCarthy, J.E. (1994) The mechanism of translational coupling in Escherichia coli. Higher order structure in the atpHA mRNA acts as a conformational switch regulating the access of de novo initiating ribosomes. J. Biol. Chem., 269, 18118-18127.