Applicability of a computational design approach for synthetic riboswitches.

作者: Gesine Domin , Sven Findeiß , Manja Wachsmuth , Sebastian Will , Peter F. Stadler

DOI: 10.1093/NAR/GKW1267

关键词: Computational biologyProtein secondary structureRNAIn silicoRiboswitchBiologySynthetic biologyAptamerMinimal free energyComputational design

摘要: Riboswitches have gained attention as tools for synthetic biology, since they enable researchers to reprogram cells sense and respond exogenous molecules. In vitro evolutionary approaches produced numerous RNA aptamers that bind such small ligands, but their conversion into functional riboswitches remains difficult. We previously developed a computational approach the design of theophylline based on secondary structure prediction. These been constructed regulate ligand-dependent transcription termination in Escherichia coli. Here, we test usability this strategy by applying tetracycline streptomycin aptamers. The resulting exhibit robust regulatory properties vivo. Tandem fusions these with represent logic gates responding two different input signals. contrast, aptamer appears be Investigations underlying revealed differences between silico prediction probing. conclude only adopting minimal free energy (MFE) are suitable targets construction equilibrium thermodynamics structures. Further improvements required implement structures not corresponding calculated MFE state.

参考文章(66)
Elizabeth E. Regulski, Ronald R. Breaker, In-line probing analysis of riboswitches. Methods of Molecular Biology. ,vol. 419, pp. 53- 67 ,(2008) , 10.1007/978-1-59745-033-1_4
Michael S. Goodson, Svetlana V. Harbaugh, Yaroslav G. Chushak, Nancy Kelley-Loughnane, Integrating and amplifying signal from riboswitch biosensors. Methods in Enzymology. ,vol. 550, pp. 73- 91 ,(2014) , 10.1016/BS.MIE.2014.10.032
Manja Wachsmuth, Gesine Domin, Ronny Lorenz, Robert Serfling, Sven Findeiß, Peter F Stadler, Mario Mörl, Design criteria for synthetic riboswitches acting on transcription. RNA Biology. ,vol. 12, pp. 221- 231 ,(2015) , 10.1080/15476286.2015.1017235
Gert Peters, Pieter Coussement, Jo Maertens, Jeroen Lammertyn, Marjan De Mey, Putting RNA to work: Translating RNA fundamentals into biotechnological engineering practice Biotechnology Advances. ,vol. 33, pp. 1829- 1844 ,(2015) , 10.1016/J.BIOTECHADV.2015.10.011
A. Donhofer, S. Franckenberg, S. Wickles, O. Berninghausen, R. Beckmann, D. N. Wilson, Structural basis for TetM-mediated tetracycline resistance. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 109, pp. 16900- 16905 ,(2012) , 10.1073/PNAS.1208037109
Ronald R. Breaker, Prospects for Riboswitch Discovery and Analysis Molecular Cell. ,vol. 43, pp. 867- 879 ,(2011) , 10.1016/J.MOLCEL.2011.08.024
Christian Berens, Beatrix Suess, Riboswitch engineering - making the all-important second and third steps. Current Opinion in Biotechnology. ,vol. 31, pp. 10- 15 ,(2015) , 10.1016/J.COPBIO.2014.07.014
Benedikt Klauser, Janina Atanasov, Lena K. Siewert, Jörg S. Hartig, Ribozyme-based aminoglycoside switches of gene expression engineered by genetic selection in S. cerevisiae. ACS Synthetic Biology. ,vol. 4, pp. 516- 525 ,(2015) , 10.1021/SB500062P
Sean A. Lynch, Shawn K. Desai, Hari Krishna Sajja, Justin P. Gallivan, A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function. Chemistry & Biology. ,vol. 14, pp. 173- 184 ,(2007) , 10.1016/J.CHEMBIOL.2006.12.008