De novodesign of heat-repressible RNA thermosensors in E. Coli

Nucleic Acids Research

Volumn 43, Issue 12, 2015, Pages 6166-6179

  Hoynes O'Connor, Allison ^a   Hinman, Kristina ^a   Kirchner, Lukas ^a   Moon, Tae Seok ^a  

^a WASHINGTON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RIBONUCLEASE E; RNA; RNA THERMOSENSOR; UNCLASSIFIED DRUG; RIBONUCLEASE;

5' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; ESCHERICHIA COLI; GENE EXPRESSION; HEAT; HIGH TEMPERATURE; LOW TEMPERATURE; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROCESSING; RNA CLEAVAGE; RNA DEGRADATION; RNA STRUCTURE; TRANSCRIPTION REGULATION; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; PROTEIN SYNTHESIS;

ENDORIBONUCLEASES; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; HOT TEMPERATURE; PROTEIN BIOSYNTHESIS; TRANSCRIPTION, GENETIC;

EID: 84941299991     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv499     Document Type: Article

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84. Narberhaus, F., Waldminghaus, T. and Chowdhury, S. (2006) RNA thermometers. FEMS Microbiol. Rev., 30, 3-16.
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109. 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.
110. Carpousis, A.J., Luisi, B.F. and McDowall, K.J. (2009) Endonucleolytic initiation of mRNA decay in Escherichia coli. Progr. Mol. Biol. Transl. Sci., 85, 91-135.
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112. Kuznetsov, S.V., Ren, C.C., Woodson, S.A. and Ansari, A. (2008) Loop dependence of the stability and dynamics of nucleic acid hairpins. Nucleic Acids Res., 36, 1098-1112.
113. Ansari, A., Kuznetsov, S.V. and Shen, Y. (2001) Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins. Proc. Natl. Acad. Sci. U.S.A., 98, 7771-7776.
114. Jung, J. and Van Orden, A. (2006) A three-state mechanism for DNA hairpin folding characterized by multiparameter fluorescence fluctuation spectroscopy. J. Am. Chem. Soc., 128, 1240-1249.
115. Bowman, G.R., Huang, X., Yao, Y., Sun, J., Carlsson, G., Guibas, L.J. and Pande, V.S. (2008) Structural insight into RNA hairpin folding intermediates. J. Am. Chem. Soc., 130, 9676-9678.
116. Zhang, W.B. and Chen, S.J. (2006) Exploring the complex folding kinetics of RNA hairpins. I. General folding kinetics analysis. Biophys. J., 90, 765-777.
117. Melnykov, A.V., Nayak, R.K., Hall, K.B. and Van Orden, A. (2015) Effect of loop composition on the stability and folding kinetics of RNA hairpins with large loops. Biochemistry, 54, 1886-1896.
118. Nocker, A., Hausherr, T., Balsiger, S., Krstulovic, N.P., Hennecke, H. and Narberhaus, F. (2001) A mRNA-based thermosensor controls expression of rhizobial heat shock genes. Nucleic Acids Res., 29, 4800-4807.
119. Rinnenthal, J., Klinkert, B., Narberhaus, F. and Schwalbe, H. (2011) Modulation of the stability of the Salmonella fourU-type RNA thermometer. Nucleic Acids Res., 39, 8258-8270.
120. Chowdhury, S., Maris, C., Allain, F.H. and Narberhaus, F. (2006) Molecular basis for temperature sensing by an RNA thermometer. EMBO J., 25, 2487-2497.
121. Draper, D.E. (2004) A guide to ions and RNA structure. RNA, 10, 335-343.
122. Cole, P.E., Yang, S.K. and Crothers, D.M. (1972) Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams. Biochemistry, 11, 4358-4368.
123. Oivanen, M., Kuusela, S. and Lonnberg, H. (1998) Kinetics and mechanisms for the cleavage and isomerization of the phosphodiester bonds of RNA by Bronsted acids and bases. Chem. Rev., 98, 961-990.
124. Foster, J.W. (2004) Escherichia coli acid resistance: tales of an amateur acidophile. Nat. Rev. Microbiol., 2, 898-907.
125. Richard, H. and Foster, J.W. (2004) Escherichia coli glutamate- and arginine-dependent acid resistance systems increase internal pH and reverse transmembrane potential. J. Bacteriol., 186, 6032-6041.
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