메뉴 건너뛰기




Volumn 11, Issue 2, 2016, Pages

Synthetic transcription amplifier system for orthogonal control of gene expression in saccharomyces cerevisiae

Author keywords

[No Author keywords available]

Indexed keywords

LEXA PROTEIN; TRANSCRIPTION FACTOR;

EID: 84960977369     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0148320     Document Type: Article
Times cited : (31)

References (47)
  • 1
    • 84863322344 scopus 로고    scopus 로고
    • Contextualizing context for synthetic biology - Identifying causes of failure of synthetic biological systems
    • PMID: 22649052
    • Cardinale S, Arkin AP (2012) Contextualizing context for synthetic biology - identifying causes of failure of synthetic biological systems. Biotechnol J 7: 856-866. doi: 10.1002/biot.201200085 PMID: 22649052
    • (2012) Biotechnol J , vol.7 , pp. 856-866
    • Cardinale, S.1    Arkin, A.P.2
  • 2
    • 84943665243 scopus 로고    scopus 로고
    • Recent applications of synthetic biology tools for yeast metabolic engineering
    • Jensen MK, Keasling JD (2014) Recent applications of synthetic biology tools for yeast metabolic engineering. FEMS Yeast Res.
    • (2014) FEMS Yeast Res.
    • Jensen, M.K.1    Keasling, J.D.2
  • 3
    • 84864634066 scopus 로고    scopus 로고
    • A synthetic biology framework for programming eukaryotic transcription functions
    • PMID: 22863014
    • Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK, et al. (2012) A synthetic biology framework for programming eukaryotic transcription functions. Cell 150: 647-658. doi: 10.1016/j.cell.2012.05.045 PMID: 22863014
    • (2012) Cell , vol.150 , pp. 647-658
    • Khalil, A.S.1    Lu, T.K.2    Bashor, C.J.3    Ramirez, C.L.4    Pyenson, N.C.5    Joung, J.K.6
  • 4
    • 84899694320 scopus 로고    scopus 로고
    • Principles of genetic circuit design
    • PMID: 24781324
    • Brophy JA, Voigt CA (2014) Principles of genetic circuit design. Nat Methods 11: 508-520. doi: 10.1038/nmeth.2926 PMID: 24781324
    • (2014) Nat Methods , vol.11 , pp. 508-520
    • Brophy, J.A.1    Voigt, C.A.2
  • 5
    • 84890178034 scopus 로고    scopus 로고
    • Advances in genetic circuit design: Novel biochemistries, deep part mining, and precision gene expression
    • PMID: 24268307
    • Nielsen AA, Segall-Shapiro TH, Voigt CA (2013) Advances in genetic circuit design: novel biochemistries, deep part mining, and precision gene expression. CurrOpin ChemBiol 17: 878-892. doi: 10.1016/j.cbpa.2013.10.003 PMID: 24268307
    • (2013) CurrOpin ChemBiol , vol.17 , pp. 878-892
    • Nielsen, A.A.1    Segall-Shapiro, T.H.2    Voigt, C.A.3
  • 6
    • 84875230351 scopus 로고    scopus 로고
    • Synthetic circuits integrating logic and memory in living cells
    • PMID: 23396014
    • Siuti P, Yazbek J, Lu TK (2013) Synthetic circuits integrating logic and memory in living cells. Nat Bio-technol 31: 448-452. doi: 10.1038/nbt.2510 PMID: 23396014
    • (2013) Nat Bio-technol , vol.31 , pp. 448-452
    • Siuti, P.1    Yazbek, J.2    Lu, T.K.3
  • 7
    • 80055035853 scopus 로고    scopus 로고
    • Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology
    • PMID: 22009040
    • Wang B, Kitney RI, Joly N, Buck M (2011) Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology. Nat Commun 2: 508. doi: 10.1038/ncomms1516 PMID: 22009040
    • (2011) Nat Commun , vol.2 , pp. 508
    • Wang, B.1    Kitney, R.I.2    Joly, N.3    Buck, M.4
  • 8
    • 84906268034 scopus 로고    scopus 로고
    • Engineering modular and tunable genetic amplifiers for scaling transcriptional signals in cascaded gene networks
    • PMID: 25030903
    • Wang B, Barahona M, Buck M (2014) Engineering modular and tunable genetic amplifiers for scaling transcriptional signals in cascaded gene networks. Nucleic Acids Res 42: 9484-9492. doi: 10.1093/nar/gku593 PMID: 25030903
    • (2014) Nucleic Acids Res , vol.42 , pp. 9484-9492
    • Wang, B.1    Barahona, M.2    Buck, M.3
  • 10
    • 84858609338 scopus 로고    scopus 로고
    • Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology
    • PMID: 22442681
    • Blount BA, Weenink T, Vasylechko S, Ellis T (2012) Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology. PLoS One 7: e33279. doi: 10.1371/journal.pone.0033279 PMID: 22442681
    • (2012) PLoS One , vol.7
    • Blount, B.A.1    Weenink, T.2    Vasylechko, S.3    Ellis, T.4
  • 11
    • 33747376106 scopus 로고    scopus 로고
    • Engineering of promoter replacement cassettes for fine-tuning of gene expression in saccharomyces cerevisiae
    • PMID: 16885275
    • Nevoigt E, Kohnke J, Fischer CR, Alper H, Stahl U, Stephanopoulos G (2006) Engineering of promoter replacement cassettes for fine-tuning of gene expression in Saccharomyces cerevisiae. Appl Environ Microbiol 72: 5266-5273. PMID: 16885275
    • (2006) Appl Environ Microbiol , vol.72 , pp. 5266-5273
    • Nevoigt, E.1    Kohnke, J.2    Fischer, C.R.3    Alper, H.4    Stahl, U.5    Stephanopoulos, G.6
  • 12
    • 84901388705 scopus 로고    scopus 로고
    • Design of synthetic yeast promoters via tuning of nucleosome architecture
    • PMID: 24862902
    • Curran KA, Crook NC, Karim AS, Gupta A, Wagman AM, Alper HS (2014) Design of synthetic yeast promoters via tuning of nucleosome architecture. Nat Commun 5: 4002. doi: 10.1038/ncomms5002 PMID: 24862902
    • (2014) Nat Commun , vol.5 , pp. 4002
    • Curran, K.A.1    Crook, N.C.2    Karim, A.S.3    Gupta, A.4    Wagman, A.M.5    Alper, H.S.6
  • 13
    • 84881004490 scopus 로고    scopus 로고
    • Use of expression-enhancing terminators in saccharomyces cerevisiae to increase mRNA half-life and improve gene expression control for metabolic engineering applications
    • PMID: 23856240
    • Curran KA, Karim AS, Gupta A, Alper HS (2013) Use of expression-enhancing terminators in Saccharomyces cerevisiae to increase mRNA half-life and improve gene expression control for metabolic engineering applications. Metab Eng 19: 88-97. doi: 10.1016/j.ymben.2013.07.001 PMID: 23856240
    • (2013) Metab Eng , vol.19 , pp. 88-97
    • Curran, K.A.1    Karim, A.S.2    Gupta, A.3    Alper, H.S.4
  • 14
    • 79952348850 scopus 로고    scopus 로고
    • A synthetic library of RNA control modules for predictable tuning of gene expression in yeast
    • PMID: 21364573
    • Babiskin AH, Smolke CD (2011) A synthetic library of RNA control modules for predictable tuning of gene expression in yeast. Mol Syst Biol 7: 471. doi: 10.1038/msb.2011.4 PMID: 21364573
    • (2011) Mol Syst Biol , vol.7 , pp. 471
    • Babiskin, A.H.1    Smolke, C.D.2
  • 15
    • 84876355027 scopus 로고    scopus 로고
    • Coordinated induction of multi-gene pathways in saccharomyces cerevisiae
    • PMID: 23262224
    • Liang J, Ning JC, Zhao H (2013) Coordinated induction of multi-gene pathways in Saccharomyces cerevisiae. Nucleic Acids Res 41: e54. doi: 10.1093/nar/gks1293 PMID: 23262224
    • (2013) Nucleic Acids Res , vol.41 , pp. e54
    • Liang, J.1    Ning, J.C.2    Zhao, H.3
  • 16
    • 84876379604 scopus 로고    scopus 로고
    • Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast
    • PMID: 23275543
    • McIsaac RS, Oakes BL, Wang X, Dummit KA, Botstein D, Noyes MB (2013) Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast. Nucleic Acids Res 41:e57. doi: 10.1093/nar/gks1313 PMID: 23275543
    • (2013) Nucleic Acids Res , vol.41 , pp. e57
    • McIsaac, R.S.1    Oakes, B.L.2    Wang, X.3    Dummit, K.A.4    Botstein, D.5    Noyes, M.B.6
  • 17
    • 84899021567 scopus 로고    scopus 로고
    • Synthetic biology tools for programming gene expression without nutritional perturbations in saccharomyces cerevisiae
    • PMID: 24445804
    • McIsaac RS, Gibney PA, Chandran SS, Benjamin KR, Botstein D (2014) Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae. Nucleic Acids Res 42: e48. doi: 10.1093/nar/gkt1402 PMID: 24445804
    • (2014) Nucleic Acids Res , vol.42 , pp. e48
    • McIsaac, R.S.1    Gibney, P.A.2    Chandran, S.S.3    Benjamin, K.R.4    Botstein, D.5
  • 18
    • 84964314276 scopus 로고    scopus 로고
    • Inducible, tightly regulated and growth condition-independent transcription factor in saccharomyces cerevisiae
    • PMID: 25034689
    • Ottoz DS, Rudolf F, Stelling J (2014) Inducible, tightly regulated and growth condition-independent transcription factor in Saccharomyces cerevisiae. Nucleic Acids Res 42: e130. doi: 10.1093/nar/gku616 PMID: 25034689
    • (2014) Nucleic Acids Res , vol.42 , pp. e130
    • Ottoz, D.S.1    Rudolf, F.2    Stelling, J.3
  • 19
    • 84906253781 scopus 로고    scopus 로고
    • Design and characterization of a dual-mode promoter with activation and repression capability for tuning gene expression in yeast
    • PMID: 25056312
    • Mazumder M, McMillen DR (2014) Design and characterization of a dual-mode promoter with activation and repression capability for tuning gene expression in yeast. Nucleic Acids Res 42: 9514-9522. doi: 10.1093/nar/gku651 PMID: 25056312
    • (2014) Nucleic Acids Res , vol.42 , pp. 9514-9522
    • Mazumder, M.1    McMillen, D.R.2
  • 20
    • 84921415416 scopus 로고    scopus 로고
    • A highly tunable system for the simultaneous expression of multiple enzymes in saccharomyces cerevisiae
    • PMID: 24927017
    • Ito Y, Yamanishi M, Ikeuchi A, Matsuyama T (2015) A highly tunable system for the simultaneous expression of multiple enzymes in Saccharomyces cerevisiae. ACS Synth Biol 4: 12-16. doi: 10.1021/sb500096y PMID: 24927017
    • (2015) ACS Synth Biol , vol.4 , pp. 12-16
    • Ito, Y.1    Yamanishi, M.2    Ikeuchi, A.3    Matsuyama, T.4
  • 21
    • 0032519306 scopus 로고    scopus 로고
    • An activator/repressor dual system allows tight tetracycline-regulated gene expression in budding yeast
    • PMID: 9461451
    • Belli G, Gari E, Piedrafita L, Aldea M, Herrero E (1998) An activator/repressor dual system allows tight tetracycline-regulated gene expression in budding yeast. Nucleic Acids Res 26: 942-947. PMID: 9461451
    • (1998) Nucleic Acids Res , vol.26 , pp. 942-947
    • Belli, G.1    Gari, E.2    Piedrafita, L.3    Aldea, M.4    Herrero, E.5
  • 22
    • 85062115342 scopus 로고    scopus 로고
    • A general EMSA (Gel-shift) protocol
    • (2011) A General EMSA (Gel-shift) Protocol. Bio-protocol Bio 101: e24 www.bio-protocol.org/e24
    • (2011) Bio-protocol Bio , vol.101 , pp. e24
  • 26
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • PMID: 17813860
    • Kirkpatrick S, Gelatt CD Jr, Vecchi MP (1983) Optimization by simulated annealing. Science 220: 671-680. PMID: 17813860
    • (1983) Science , vol.220 , pp. 671-680
    • Kirkpatrick, S.1    Gelatt, C.D.2    Vecchi, M.P.3
  • 28
    • 84888258175 scopus 로고    scopus 로고
    • Non-invasive high-throughput single-cell analysis of the intracellular pH of yeast by ratiometric flow cytometry
    • Valkonen M, Mojzita D, Penttila M, Bencina M (2013) Non-invasive High-Throughput Single-Cell Analysis of the Intracellular pH of Yeast by Ratiometric Flow Cytometry. Appl Environ Microbiol.
    • (2013) Appl Environ Microbiol.
    • Valkonen, M.1    Mojzita, D.2    Penttila, M.3    Bencina, M.4
  • 29
    • 0027437850 scopus 로고
    • Cdi1, a human G1 and S phase protein phosphatase that associates with cdk2
    • PMID: 8242750
    • Gyuris J, Golemis E, Chertkov H, Brent R (1993) Cdi1, a human G1 and S phase protein phosphatase that associates with Cdk2. Cell 75: 791-803. PMID: 8242750
    • (1993) Cell , vol.75 , pp. 791-803
    • Gyuris, J.1    Golemis, E.2    Chertkov, H.3    Brent, R.4
  • 30
    • 0023805801 scopus 로고
    • No strict alignment is required between a transcriptional activator binding site and the "TATA box" of a yeast gene
    • PMID: 3132708
    • Ruden DM, Ma J, Ptashne M (1988) No strict alignment is required between a transcriptional activator binding site and the "TATA box" of a yeast gene. Proc Natl Acad Sci U S A 85: 4262-4266. PMID: 3132708
    • (1988) Proc Natl Acad Sci USA , vol.85 , pp. 4262-4266
    • Ruden, D.M.1    Ma, J.2    Ptashne, M.3
  • 31
    • 0021924399 scopus 로고
    • Specific DNA binding of GAL4, a positive regulatory protein of yeast
    • PMID: 3886158
    • Giniger E, Varnum SM, Ptashne M (1985) Specific DNA binding of GAL4, a positive regulatory protein of yeast. Cell 40: 767-774. PMID: 3886158
    • (1985) Cell , vol.40 , pp. 767-774
    • Giniger, E.1    Varnum, S.M.2    Ptashne, M.3
  • 32
    • 0021826957 scopus 로고
    • Nucleotide sequence binding specificity of the LexA repressor of Escherichia coli K-12
    • PMID: 3891738
    • Wertman KF, Mount DW (1985) Nucleotide sequence binding specificity of the LexA repressor of Escherichia coli K-12. J Bacteriol 163: 376-384. PMID: 3891738
    • (1985) J Bacteriol , vol.163 , pp. 376-384
    • Wertman, K.F.1    Mount, D.W.2
  • 33
    • 0029092610 scopus 로고
    • Correlation of two-hybrid affinity data with in vitro measurements
    • PMID: 7565735
    • Estojak J, Brent R, Golemis EA (1995) Correlation of two-hybrid affinity data with in vitro measurements. Mol Cell Biol 15: 5820-5829. PMID: 7565735
    • (1995) Mol Cell Biol , vol.15 , pp. 5820-5829
    • Estojak, J.1    Brent, R.2    Golemis, E.A.3
  • 34
    • 84908376732 scopus 로고    scopus 로고
    • Transcriptome of saccharomyces cerevisiae during production of D-xylonate
    • PMID: 25192596
    • Mojzita D, Oja M, Rintala E, Wiebe M, Penttila M, Ruohonen L (2014) Transcriptome of Saccharomyces cerevisiae during production of D-xylonate. BMC Genomics 15: 763. doi: 10.1186/1471-2164-15-763 PMID: 25192596
    • (2014) BMC Genomics , vol.15 , pp. 763
    • Mojzita, D.1    Oja, M.2    Rintala, E.3    Wiebe, M.4    Penttila, M.5    Ruohonen, L.6
  • 35
    • 84977991300 scopus 로고    scopus 로고
    • Introduction and expression of genes for metabolic engineering applications in saccharomyces cerevisiae
    • Da Silva NA, Srikrishnan S (2011) Introduction and expression of genes for metabolic engineering applications in Saccharomyces cerevisiae. FEMS Yeast Res.
    • (2011) FEMS Yeast Res.
    • Da Silva, N.A.1    Srikrishnan, S.2
  • 36
    • 0031054098 scopus 로고    scopus 로고
    • Preferential interactions of the Escherichia coli LexA repressor with anions and protons are coupled to binding the recA operator
    • PMID: 9033397
    • Relan NK, Jenuwine ES, Gumbs OH, Shaner SL (1997) Preferential interactions of the Escherichia coli LexA repressor with anions and protons are coupled to binding the recA operator. Biochemistry 36: 1077-1084. PMID: 9033397
    • (1997) Biochemistry , vol.36 , pp. 1077-1084
    • Relan, N.K.1    Jenuwine, E.S.2    Gumbs, O.H.3    Shaner, S.L.4
  • 37
    • 78149328427 scopus 로고    scopus 로고
    • Characterization of different promoters for designing a new expression vector in saccharomyces cerevisiae
    • PMID: 20625983
    • Partow S, Siewers V, Bjorn S, Nielsen J, Maury J (2010) Characterization of different promoters for designing a new expression vector in Saccharomyces cerevisiae. Yeast 27: 955-964. doi: 10.1002/yea.1806 PMID: 20625983
    • (2010) Yeast , vol.27 , pp. 955-964
    • Partow, S.1    Siewers, V.2    Bjorn, S.3    Nielsen, J.4    Maury, J.5
  • 38
    • 0028953840 scopus 로고
    • Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds
    • PMID: 7737504
    • Mumberg D, Muller R, Funk M (1995) Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds. Gene 156: 119-122. PMID: 7737504
    • (1995) Gene , vol.156 , pp. 119-122
    • Mumberg, D.1    Muller, R.2    Funk, M.3
  • 39
    • 0026650525 scopus 로고
    • Characterization of the DNA-binding activity of GCR1: In vivo evidence for two GCR1-binding sites in the upstream activating sequence of TPI of saccharomyces cerevisiae
    • PMID: 1588965
    • Huie MA, Scott EW, Drazinic CM, Lopez MC, Hornstra IK, Yang TP, et al. (1992) Characterization of the DNA-binding activity of GCR1: in vivo evidence for two GCR1-binding sites in the upstream activating sequence of TPI of Saccharomyces cerevisiae. Mol Cell Biol 12: 2690-2700. PMID: 1588965
    • (1992) Mol Cell Biol , vol.12 , pp. 2690-2700
    • Huie, M.A.1    Scott, E.W.2    Drazinic, C.M.3    Lopez, M.C.4    Hornstra, I.K.5    Yang, T.P.6
  • 40
    • 0026355230 scopus 로고
    • A multi-component upstream activation sequence of the saccharomyces cerevisiae glyceraldehyde-3-phosphate dehydrogenase gene promoter
    • PMID: 1753943
    • Bitter GA, Chang KK, Egan KM (1991) A multi-component upstream activation sequence of the Saccharomyces cerevisiae glyceraldehyde-3-phosphate dehydrogenase gene promoter. Mol Gen Genet 231: 22-32. PMID: 1753943
    • (1991) Mol Gen Genet , vol.231 , pp. 22-32
    • Bitter, G.A.1    Chang, K.K.2    Egan, K.M.3
  • 41
    • 0034934774 scopus 로고    scopus 로고
    • Promoter-specific binding of rap1 revealed by genome-wide maps of protein-DNA association
    • PMID: 11455386
    • Lieb JD, Liu X, Botstein D, Brown PO (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 28: 327-334. PMID: 11455386
    • (2001) Nat Genet , vol.28 , pp. 327-334
    • Lieb, J.D.1    Liu, X.2    Botstein, D.3    Brown, P.O.4
  • 42
    • 0033104140 scopus 로고    scopus 로고
    • Binding of the glucose-dependent mig1p repressor to the GAL1 and GAL4 promoters in vivo: Regulationby glucose and chromatin structure
    • PMID: 9973625
    • Frolova E, Johnston M, Majors J (1999) Binding of the glucose-dependent Mig1p repressor to the GAL1 and GAL4 promoters in vivo: regulationby glucose and chromatin structure. Nucleic Acids Res 27: 1350-1358. PMID: 9973625
    • (1999) Nucleic Acids Res , vol.27 , pp. 1350-1358
    • Frolova, E.1    Johnston, M.2    Majors, J.3
  • 43
    • 70549086797 scopus 로고    scopus 로고
    • Validation of reference genes for quantitative expression analysis by real-time RT-PCR in saccharomyces cerevisiae
    • PMID: 19874630
    • Teste MA, Duquenne M, Francois JM, Parrou JL (2009) Validation of reference genes for quantitative expression analysis by real-time RT-PCR in Saccharomyces cerevisiae. BMC Mol Biol 10: 99. doi: 10.1186/1471-2199-10-99 PMID: 19874630
    • (2009) BMC Mol Biol , vol.10 , pp. 99
    • Teste, M.A.1    Duquenne, M.2    Francois, J.M.3    Parrou, J.L.4
  • 44
    • 0027472731 scopus 로고
    • Estradiol-inducible squelching and cell growth arrest by a chimeric VP16-estrogen receptor expressed in saccharomyces cerevisiae: Suppression by an allele of PDR1
    • PMID: 8417344
    • Gilbert DM, Heery DM, Losson R, Chambon P, Lemoine Y (1993) Estradiol-inducible squelching and cell growth arrest by a chimeric VP16-estrogen receptor expressed in Saccharomyces cerevisiae: suppression by an allele of PDR1. Mol Cell Biol 13: 462-472. PMID: 8417344
    • (1993) Mol Cell Biol , vol.13 , pp. 462-472
    • Gilbert, D.M.1    Heery, D.M.2    Losson, R.3    Chambon, P.4    Lemoine, Y.5
  • 45
    • 58549083142 scopus 로고    scopus 로고
    • Input-output behavior of ERBB signaling pathways as revealed by a mass action model trained against dynamic data
    • PMID: 19156131
    • Chen WW, Schoeberl B, Jasper PJ, Niepel M, Nielsen UB, Lauffenburger DA, et al. (2009) Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data. Mol Syst Biol 5: 239. doi: 10.1038/msb.2008.74 PMID: 19156131
    • (2009) Mol Syst Biol , vol.5 , pp. 239
    • Chen, W.W.1    Schoeberl, B.2    Jasper, P.J.3    Niepel, M.4    Nielsen, U.B.5    Lauffenburger, D.A.6
  • 46
    • 77952527470 scopus 로고    scopus 로고
    • Parameter identifiability and redundancy: Theoretical considerations
    • PMID: 20111720
    • Little MP, Heidenreich WF, Li G (2010) Parameter identifiability and redundancy: theoretical considerations. PLoS One 5: e8915. doi: 10.1371/journal.pone.0008915 PMID: 20111720
    • (2010) PLoS One , vol.5
    • Little, M.P.1    Heidenreich, W.F.2    Li, G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.