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Volumn 5, Issue 12, 2016, Pages 1441-1454

Development of Design Rules for Reliable Antisense RNA Behavior in E. coli

Author keywords

antisense RNA; gene repression; genetic circuit; RNA regulator; RNA synthetic biology

Indexed keywords

COMPLEMENTARY RNA; MESSENGER RNA; CARRIER PROTEIN; ESCHERICHIA COLI PROTEIN; HFQ PROTEIN, E COLI; HOST FACTOR 1;

EID: 85006511345     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.6b00036     Document Type: Article
Times cited : (43)

References (45)
  • 2
    • 84910594404 scopus 로고    scopus 로고
    • Synthetic biology. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations
    • Farzadfard, F. and Lu, T. K. ( 2014 ) Synthetic biology. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations Science 346, 1256272 10.1126/science.1256272
    • (2014) Science , vol.346 , pp. 1256272
    • Farzadfard, F.1    Lu, T.K.2
  • 4
    • 77951107086 scopus 로고    scopus 로고
    • Synthetic biology: applications come of age
    • Khalil, A. S. and Collins, J. J. ( 2010 ) Synthetic biology: applications come of age Nat. Rev. Genet. 11, 367-379 10.1038/nrg2775
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 367-379
    • Khalil, A.S.1    Collins, J.J.2
  • 5
    • 84898878580 scopus 로고    scopus 로고
    • A versatile framework for microbial engineering using synthetic non-coding RNAs
    • Qi, L. S. and Arkin, A. P. ( 2014 ) A versatile framework for microbial engineering using synthetic non-coding RNAs Nat. Rev. Microbiol. 12, 341-354 10.1038/nrmicro3244
    • (2014) Nat. Rev. Microbiol. , vol.12 , pp. 341-354
    • Qi, L.S.1    Arkin, A.P.2
  • 6
    • 84895962809 scopus 로고    scopus 로고
    • Application of TALEs, CRISPR/Cas and sRNAs as trans-acting regulators in prokaryotes
    • Copeland, M. F., Politz, M. C., and Pfleger, B. F. ( 2014 ) Application of TALEs, CRISPR/Cas and sRNAs as trans-acting regulators in prokaryotes Curr. Opin. Biotechnol. 29, 46-54 10.1016/j.copbio.2014.02.010
    • (2014) Curr. Opin. Biotechnol. , vol.29 , pp. 46-54
    • Copeland, M.F.1    Politz, M.C.2    Pfleger, B.F.3
  • 7
    • 84928159353 scopus 로고    scopus 로고
    • Regulating malonyl-CoA metabolism via synthetic antisense RNAs for enhanced biosynthesis of natural products
    • Yang, Y., Lin, Y., Li, L., Linhardt, R. J., and Yan, Y. ( 2015 ) Regulating malonyl-CoA metabolism via synthetic antisense RNAs for enhanced biosynthesis of natural products Metab. Eng. 29, 217-226 10.1016/j.ymben.2015.03.018
    • (2015) Metab. Eng. , vol.29 , pp. 217-226
    • Yang, Y.1    Lin, Y.2    Li, L.3    Linhardt, R.J.4    Yan, Y.5
  • 8
    • 84873596341 scopus 로고    scopus 로고
    • Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs
    • Na, D., Yoo, S. M., Chung, H., Park, H., Park, J. H., and Lee, S. Y. ( 2013 ) Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs Nat. Biotechnol. 31, 170-174 10.1038/nbt.2461
    • (2013) Nat. Biotechnol. , vol.31 , pp. 170-174
    • Na, D.1    Yoo, S.M.2    Chung, H.3    Park, H.4    Park, J.H.5    Lee, S.Y.6
  • 9
    • 84869102255 scopus 로고    scopus 로고
    • A dynamic metabolite valve for the control of central carbon metabolism
    • Solomon, K. V., Sanders, T. M., and Prather, K. L. ( 2012 ) A dynamic metabolite valve for the control of central carbon metabolism Metab. Eng. 14, 661-671 10.1016/j.ymben.2012.08.006
    • (2012) Metab. Eng. , vol.14 , pp. 661-671
    • Solomon, K.V.1    Sanders, T.M.2    Prather, K.L.3
  • 10
    • 0037337740 scopus 로고    scopus 로고
    • Design of antisense RNA constructs for downregulation of the acetone formation pathway of Clostridium acetobutylicum
    • Tummala, S. B., Welker, N. E., and Papoutsakis, E. T. ( 2003 ) Design of antisense RNA constructs for downregulation of the acetone formation pathway of Clostridium acetobutylicum J. Bacteriol. 185, 1923-1934 10.1128/JB.185.6.1923-1934.2003
    • (2003) J. Bacteriol. , vol.185 , pp. 1923-1934
    • Tummala, S.B.1    Welker, N.E.2    Papoutsakis, E.T.3
  • 11
    • 84963828879 scopus 로고    scopus 로고
    • Programmable control of bacterial gene expression with the combined CRISPR and antisense RNA system
    • Lee, Y. J., Hoynes-O’Connor, A., Leong, M., and Moon, T. S. ( 2016 ) Programmable control of bacterial gene expression with the combined CRISPR and antisense RNA system Nucleic Acids Res. 44, 2462-2473 10.1093/nar/gkw056
    • (2016) Nucleic Acids Res. , vol.44 , pp. 2462-2473
    • Lee, Y.J.1    Hoynes-O’Connor, A.2    Leong, M.3    Moon, T.S.4
  • 12
    • 84943360282 scopus 로고    scopus 로고
    • Counterselection method based on conditional silencing of antitoxin genes in Escherichia coli
    • Tsukuda, M., Nakashima, N., and Miyazaki, K. ( 2015 ) Counterselection method based on conditional silencing of antitoxin genes in Escherichia coli J. Biosci Bioeng 120, 591-595 10.1016/j.jbiosc.2015.03.008
    • (2015) J. Biosci Bioeng , vol.120 , pp. 591-595
    • Tsukuda, M.1    Nakashima, N.2    Miyazaki, K.3
  • 15
    • 84856431819 scopus 로고    scopus 로고
    • RNA therapeutics: beyond RNA interference and antisense oligonucleotides
    • Kole, R., Krainer, A. R., and Altman, S. ( 2012 ) RNA therapeutics: beyond RNA interference and antisense oligonucleotides Nat. Rev. Drug Discovery 11, 125-140 10.1038/nrd3625
    • (2012) Nat. Rev. Drug Discovery , vol.11 , pp. 125-140
    • Kole, R.1    Krainer, A.R.2    Altman, S.3
  • 16
    • 50949097496 scopus 로고    scopus 로고
    • Artificial antisense RNAs silence lacZ in E-coli by decreasing target mRNA concentration
    • Alessandra, S., Alessandro, T., Flavio, S., and Alejandro, H. ( 2008 ) Artificial antisense RNAs silence lacZ in E-coli by decreasing target mRNA concentration Bmb Reports 41, 568-574 10.5483/BMBRep.2008.41.8.568
    • (2008) Bmb Reports , vol.41 , pp. 568-574
    • Alessandra, S.1    Alessandro, T.2    Flavio, S.3    Alejandro, H.4
  • 17
    • 0022256693 scopus 로고
    • Thermal regulation of beta-galactosidase synthesis using anti-sense RNA directed against the coding portion of the messenger-RNA
    • Ellison, M. J., Kelleher, R. J., and Rich, A. ( 1985 ) Thermal regulation of beta-galactosidase synthesis using anti-sense RNA directed against the coding portion of the messenger-RNA J. Biol. Chem. 260, 9085-9087
    • (1985) J. Biol. Chem. , vol.260 , pp. 9085-9087
    • Ellison, M.J.1    Kelleher, R.J.2    Rich, A.3
  • 18
    • 0033579543 scopus 로고    scopus 로고
    • Antisense RNA regulation in prokaryotes: Rapid RNA/RNA interaction facilitated by a general U-turn loop structure
    • Franch, T., Petersen, M., Wagner, E. G. H., Jacobsen, J. P., and Gerdes, K. ( 1999 ) Antisense RNA regulation in prokaryotes: Rapid RNA/RNA interaction facilitated by a general U-turn loop structure J. Mol. Biol. 294, 1115-1125 10.1006/jmbi.1999.3306
    • (1999) J. Mol. Biol. , vol.294 , pp. 1115-1125
    • Franch, T.1    Petersen, M.2    Wagner, E.G.H.3    Jacobsen, J.P.4    Gerdes, K.5
  • 19
    • 0028919939 scopus 로고
    • Bulged-out nucleotides protect an antisense RNA from RNase-III cleavage
    • Hjalt, T. A. H. and Wagner, E. G. H. ( 1995 ) Bulged-out nucleotides protect an antisense RNA from RNase-III cleavage Nucleic Acids Res. 23, 571-579 10.1093/nar/23.4.571
    • (1995) Nucleic Acids Res. , vol.23 , pp. 571-579
    • Hjalt, T.A.H.1    Wagner, E.G.H.2
  • 20
    • 79955607368 scopus 로고    scopus 로고
    • Artificial trans-encoded small non-coding RNAs specifically silence the selected gene expression in bacteria
    • Man, S., Cheng, R., Miao, C., Gong, Q., Gu, Y., Lu, X., Han, F., and Yu, W. ( 2011 ) Artificial trans-encoded small non-coding RNAs specifically silence the selected gene expression in bacteria Nucleic Acids Res. 39, e50 10.1093/nar/gkr034
    • (2011) Nucleic Acids Res. , vol.39 , pp. e50
    • Man, S.1    Cheng, R.2    Miao, C.3    Gong, Q.4    Gu, Y.5    Lu, X.6    Han, F.7    Yu, W.8
  • 21
    • 84859842558 scopus 로고    scopus 로고
    • Rationally designed families of orthogonal RNA regulators of translation
    • Mutalik, V. K., Qi, L., Guimaraes, J. C., Lucks, J. B., and Arkin, A. P. ( 2012 ) Rationally designed families of orthogonal RNA regulators of translation Nat. Chem. Biol. 8, 447-454 10.1038/nchembio.919
    • (2012) Nat. Chem. Biol. , vol.8 , pp. 447-454
    • Mutalik, V.K.1    Qi, L.2    Guimaraes, J.C.3    Lucks, J.B.4    Arkin, A.P.5
  • 22
    • 84883419083 scopus 로고    scopus 로고
    • Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli
    • Yoo, S. M., Na, D., and Lee, S. Y. ( 2013 ) Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli Nat. Protoc. 8, 1694-1707 10.1038/nprot.2013.105
    • (2013) Nat. Protoc. , vol.8 , pp. 1694-1707
    • Yoo, S.M.1    Na, D.2    Lee, S.Y.3
  • 23
    • 84922730280 scopus 로고    scopus 로고
    • A computational analysis of antisense off-targets in prokaryotic organisms
    • Worley-Morse, T. O. and Gunsch, C. K. ( 2015 ) A computational analysis of antisense off-targets in prokaryotic organisms Genomics 105, 123-130 10.1016/j.ygeno.2014.11.010
    • (2015) Genomics , vol.105 , pp. 123-130
    • Worley-Morse, T.O.1    Gunsch, C.K.2
  • 25
    • 61449128339 scopus 로고    scopus 로고
    • Role of the Escherichia coli Hfq protein in GcvB regulation of oppA and dppA mRNAs
    • Pulvermacher, S. C., Stauffer, L. T., and Stauffer, G. V. ( 2009 ) Role of the Escherichia coli Hfq protein in GcvB regulation of oppA and dppA mRNAs Microbiology (London, U. K.) 155, 115-123 10.1099/mic.0.023432-0
    • (2009) Microbiology (London, U. K.) , vol.155 , pp. 115-123
    • Pulvermacher, S.C.1    Stauffer, L.T.2    Stauffer, G.V.3
  • 26
    • 84896961495 scopus 로고    scopus 로고
    • Improving the Gene-Regulation Ability of Small RNAs by Scaffold Engineering in Escherichia coli
    • Sakai, Y., Abe, K., Nakashima, S., Yoshida, W., Ferri, S., Sode, K., and Ikebukuro, K. ( 2014 ) Improving the Gene-Regulation Ability of Small RNAs by Scaffold Engineering in Escherichia coli ACS Synth. Biol. 3, 152-162 10.1021/sb4000959
    • (2014) ACS Synth. Biol. , vol.3 , pp. 152-162
    • Sakai, Y.1    Abe, K.2    Nakashima, S.3    Yoshida, W.4    Ferri, S.5    Sode, K.6    Ikebukuro, K.7
  • 27
    • 84867191934 scopus 로고    scopus 로고
    • Engineering Artificial Small RNAs for Conditional Gene Silencing in Escherichia coli
    • Sharma, V., Yamamura, A., and Yokobayashi, Y. ( 2012 ) Engineering Artificial Small RNAs for Conditional Gene Silencing in Escherichia coli ACS Synth. Biol. 1, 6-13 10.1021/sb200001q
    • (2012) ACS Synth. Biol. , vol.1 , pp. 6-13
    • Sharma, V.1    Yamamura, A.2    Yokobayashi, Y.3
  • 30
    • 33847386673 scopus 로고    scopus 로고
    • Translational control and target recognition by Escherichia coli small RNAs in vivo
    • Urban, J. H. and Vogel, J. ( 2007 ) Translational control and target recognition by Escherichia coli small RNAs in vivo Nucleic Acids Res. 35, 1018-1037 10.1093/nar/gkl1040
    • (2007) Nucleic Acids Res. , vol.35 , pp. 1018-1037
    • Urban, J.H.1    Vogel, J.2
  • 31
    • 84930511038 scopus 로고    scopus 로고
    • Systematic analysis of the role of bacterial Hfq-interacting sRNAs in the response to antibiotics
    • Kim, T., Bak, G., Lee, J., and Kim, K. S. ( 2015 ) Systematic analysis of the role of bacterial Hfq-interacting sRNAs in the response to antibiotics J. Antimicrob. Chemother. 70, 1659-1668 10.1093/jac/dkv042
    • (2015) J. Antimicrob. Chemother. , vol.70 , pp. 1659-1668
    • Kim, T.1    Bak, G.2    Lee, J.3    Kim, K.S.4
  • 32
    • 79960433506 scopus 로고    scopus 로고
    • Hfq and its constellation of RNA
    • Vogel, J. and Luisi, B. F. ( 2011 ) Hfq and its constellation of RNA Nat. Rev. Microbiol. 9, 578-589 10.1038/nrmicro2615
    • (2011) Nat. Rev. Microbiol. , vol.9 , pp. 578-589
    • Vogel, J.1    Luisi, B.F.2
  • 33
    • 0021167601 scopus 로고
    • The use of RNAs complementary to specific messenger RNAs to regulats the expression of individual bacterial genes
    • Coleman, J., Green, P. J., and Inouye, M. ( 1984 ) The use of RNAs complementary to specific messenger RNAs to regulats the expression of individual bacterial genes Cell 37, 429-436 10.1016/0092-8674(84)90373-8
    • (1984) Cell , vol.37 , pp. 429-436
    • Coleman, J.1    Green, P.J.2    Inouye, M.3
  • 34
    • 84914809939 scopus 로고    scopus 로고
    • Effects of different target sites on antisense RNA-mediated regulation of gene expression
    • Park, H., Yoon, Y., Suk, S., Lee, J. Y., and Lee, Y. ( 2014 ) Effects of different target sites on antisense RNA-mediated regulation of gene expression BMB Rep. 47, 619-624 10.5483/BMBRep.2014.47.11.257
    • (2014) BMB Rep. , vol.47 , pp. 619-624
    • Park, H.1    Yoon, Y.2    Suk, S.3    Lee, J.Y.4    Lee, Y.5
  • 35
    • 20644462362 scopus 로고    scopus 로고
    • Micros for microbes: non-coding regulatory RNAs in bacteria
    • Gottesman, S. ( 2005 ) Micros for microbes: non-coding regulatory RNAs in bacteria Trends Genet. 21, 399-404 10.1016/j.tig.2005.05.008
    • (2005) Trends Genet. , vol.21 , pp. 399-404
    • Gottesman, S.1
  • 36
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker, M. ( 2003 ) Mfold web server for nucleic acid folding and hybridization prediction Nucleic Acids Res. 31, 3406-3415 10.1093/nar/gkg595
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 37
    • 0037494980 scopus 로고    scopus 로고
    • Silencing of the gene coding for the epsilon subunit of DNA polymerase III slows down the growth rate of Escherichia coli populations
    • Stefan, A., Reggiani, L., Cianchetta, S., Radeghieri, A., Gonzalez Vara y Rodriguez, A., and Hochkoeppler, A. ( 2003 ) Silencing of the gene coding for the epsilon subunit of DNA polymerase III slows down the growth rate of Escherichia coli populations FEBS Lett. 546, 295-299 10.1016/S0014-5793(03)00604-5
    • (2003) FEBS Lett. , vol.546 , pp. 295-299
    • Stefan, A.1    Reggiani, L.2    Cianchetta, S.3    Radeghieri, A.4    Gonzalez Vara Y Rodriguez, A.5    Hochkoeppler, A.6
  • 38
    • 84966440987 scopus 로고    scopus 로고
    • Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq
    • Watters, K. E., Abbott, T. R., and Lucks, J. B. ( 2016 ) Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq Nucleic Acids Res. 44, e12 10.1093/nar/gkv879
    • (2016) Nucleic Acids Res. , vol.44 , pp. e12
    • Watters, K.E.1    Abbott, T.R.2    Lucks, J.B.3
  • 39
    • 84925225043 scopus 로고    scopus 로고
    • SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing
    • Loughrey, D., Watters, K. E., Settle, A. H., and Lucks, J. B. ( 2014 ) SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing Nucleic Acids Res. 42, e165 10.1093/nar/gku909
    • (2014) Nucleic Acids Res. , vol.42 , pp. e165
    • Loughrey, D.1    Watters, K.E.2    Settle, A.H.3    Lucks, J.B.4
  • 41
    • 84963832616 scopus 로고    scopus 로고
    • Robust, tunable genetic memory from protein sequestration combined with positive feedback
    • Shopera, T., Henson, W. R., Ng, A., Lee, Y. J., Ng, K., and Moon, T. S. ( 2015 ) Robust, tunable genetic memory from protein sequestration combined with positive feedback Nucleic Acids Res. 43, 9086-9094 10.1093/nar/gkv936
    • (2015) Nucleic Acids Res. , vol.43 , pp. 9086-9094
    • Shopera, T.1    Henson, W.R.2    Ng, A.3    Lee, Y.J.4    Ng, K.5    Moon, T.S.6
  • 42
    • 84868619337 scopus 로고    scopus 로고
    • Genetic programs constructed from layered logic gates in single cells
    • Moon, T. S., Lou, C., Tamsir, A., Stanton, B. C., and Voigt, C. A. ( 2012 ) Genetic programs constructed from layered logic gates in single cells Nature 491, 249-253 10.1038/nature11516
    • (2012) Nature , vol.491 , pp. 249-253
    • Moon, T.S.1    Lou, C.2    Tamsir, A.3    Stanton, B.C.4    Voigt, C.A.5
  • 43
    • 67650133652 scopus 로고    scopus 로고
    • Anti-activator ExsD forms a 1:1 complex with ExsA to inhibit transcription of type III secretion operons
    • Thibault, J., Faudry, E., Ebel, C., Attree, I., and Elsen, S. ( 2009 ) Anti-activator ExsD forms a 1:1 complex with ExsA to inhibit transcription of type III secretion operons J. Biol. Chem. 284, 15762-15770 10.1074/jbc.M109.003533
    • (2009) J. Biol. Chem. , vol.284 , pp. 15762-15770
    • Thibault, J.1    Faudry, E.2    Ebel, C.3    Attree, I.4    Elsen, S.5
  • 44
  • 45
    • 56649114274 scopus 로고    scopus 로고
    • A One Pot, One Step, Precision Cloning Method with High Throughput Capability
    • Engler, C., Kandzia, R., and Marillonnet, S. ( 2008 ) A One Pot, One Step, Precision Cloning Method with High Throughput Capability PLoS One 3, e3647 10.1371/journal.pone.0003647
    • (2008) PLoS One , vol.3 , pp. e3647
    • Engler, C.1    Kandzia, R.2    Marillonnet, S.3


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