Babina AM, Lea NE, Meyer MM (2017) In vivo behavior of the tandem glycine riboswitch in Bacillus subtilis. mBio 8. https://doi.org/10.1128/mBio.01602-17
Banta AB, Enright AL, Siletti C, Peters JM (2020) A high-efficacy CRISPR interference system for gene function discovery in Zymomonas mobilis. Appl Environ Microbiol 86:1–16. https://doi.org/10.1128/AEM.01621-20
Barrick JE, Breaker RR (2007) The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol 8. https://doi.org/10.1186/gb-2007-8-11-r239
Boy C, Lesage J, Alfenore S, Guillouet SE, Gorret N (2022) Study of plasmid-based expression level heterogeneity under plasmid-curing like conditions in Cupriavidus necator. J Biotechnol 345:17–29. https://doi.org/10.1016/j.jbiotec.2021.12.015
Article CAS PubMed Google Scholar
Brayton CF (1986) Dimethyl sulfoxide (DMSO): a review. Cornell Vet 76(1):61–90
Breaker RR (2011) Prospects for Riboswitch Discovery and Analysis. Mol Cell 43:867–879
Article CAS PubMed PubMed Central Google Scholar
Ceres P, Garst AD, Marcano-Velázquez JG, Batey RT (2013a) Modularity of select riboswitch expression platforms enables facile engineering of novel genetic regulatory devices. ACS Synth Biol 2:463–472. https://doi.org/10.1021/sb4000096
Article CAS PubMed PubMed Central Google Scholar
Ceres P, Trausch JJ, Batey RT (2013b) Engineering modular “ON” RNA switches using biological components. Nucleic Acids Res 41:10449–10461. https://doi.org/10.1093/nar/gkt787
Article CAS PubMed PubMed Central Google Scholar
Cui W, Cheng J, Miao S, Zhou L, Liu Z, Guo J, Zhou Z (2017) Comprehensive characterization of a theophylline riboswitch reveals two pivotal features of Shine-Dalgarno influencing activated translation property. Appl Microbiol Biotechnol 101:2107–2120. https://doi.org/10.1007/s00253-016-7988-4
Article CAS PubMed Google Scholar
Cui W, Han L, Cheng J, Liu Z, Zhou L, Guo J, Zhou Z (2016) Engineering an inducible gene expression system for Bacillus subtilis from a strong constitutive promoter and a theophylline-activated synthetic riboswitch. Microb Cell Fact:15. https://doi.org/10.1186/s12934-016-0599-z
Dalia TN, Chlebek JL, Dalia AB (2020) A modular chromosomally integrated toolkit for ectopic gene expression in Vibrio cholerae. Sci Rep 10. https://doi.org/10.1038/s41598-020-72387-8
Desai SK, Gallivan JP (2004) Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. J Am Chem Soc 126:13247–13254. https://doi.org/10.1021/ja048634j
Article CAS PubMed Google Scholar
Dohno C, Kohyama I, Kimura M, Hagihara M, Nakatani K (2013) A synthetic riboswitch that operates using a rationally designed ligand-RNA pair. Angewandte Chemie - Int Edition 52:9976–9979. https://doi.org/10.1002/anie.201303370
Domin G, Findeiß S, Wachsmuth M, Will S, Stadler PF, Mörl M (2017) Applicability of a computational design approach for synthetic riboswitches. Nucleic Acids Res 45:4108–4119. https://doi.org/10.1093/nar/gkw1267
Article CAS PubMed Google Scholar
Dong X, Qi S, Khan IM, Sun Y, Zhang Y, Wang Z (2023) Advances in riboswitch-based biosensor as food samples detection tool. Compr Rev Food Sci Food Saf 22:451–472
Article CAS PubMed Google Scholar
Dwidar M, Seike Y, Kobori S, Whitaker C, Matsuura T, Yokobayashi Y (2019) Programmable artificial cells using histamine-responsive synthetic riboswitch. J Am Chem Soc 141:11103–11114. https://doi.org/10.1021/jacs.9b03300
Article CAS PubMed Google Scholar
Garst AD, Edwards AL, Batey RT (2011) Riboswitches: structures and mechanisms. Cold Spring Harb Perspect Biol 3:1–13
Gong S, Du C, Wang Y (2020) Regulation of the thiamine pyrophosphate (TPP)-sensing riboswitch in NMT1 mRNA from Neurospora crassa. FEBS Lett 594:625–635. https://doi.org/10.1002/1873-3468.13654
Article CAS PubMed Google Scholar
Groher F, Suess B (2014) Synthetic riboswitches - a tool comes of age. Biochim Biophys Acta Gene Regul Mech 1839:964–973
Hao M, He Y, Zhang H, Liao XP, Liu YH, Sun J, Du H, Kreiswirth BN, Chen L (2020) CRISPR-Cas9-mediated carbapenemase gene and plasmid curing in carbapenem-resistant enterobacteriaceae. Antimicrob Agents Chemother 64. https://doi.org/10.1128/AAC.00843-20
Higo A, Isu A, Fukaya Y, Hisabori T (2017) Designing synthetic flexible gene regulation networks using RNA devices in Cyanobacteria. ACS Synth Biol 6:55–61. https://doi.org/10.1021/acssynbio.6b00201
Article CAS PubMed Google Scholar
Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ (2004) Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotechnol 22:841–847. https://doi.org/10.1038/nbt986
Article CAS PubMed Google Scholar
Kamiura R, Toya Y, Matsuda F, Shimizu H (2019) Theophylline-inducible riboswitch accurately regulates protein expression at low level in Escherichia coli. Biotechnol Lett 41:743–751. https://doi.org/10.1007/s10529-019-02672-8
Article CAS PubMed Google Scholar
Kerr AL, Jeon YJ, Svenson CJ, Rogers PL, Neilan BA (2011) DNA restriction-modification systems in the ethanologen, Zymomonas mobilis ZM4. Appl Microbiol Biotechnol 89:761–769. https://doi.org/10.1007/s00253-010-2936-1
Article CAS PubMed Google Scholar
Lal PB, Wells F, Myers KS, Banerjee R, Guss AM, Kiley PJ (2021) Improving mobilization of foreign DNA into Zymomonas mobilis strain ZM4 by removal of multiple restriction systems. Appl Environ Microbiol 87:1–16. https://doi.org/10.1128/AEM.00808-21
Li Q, Sun B, Chen J, Zhang Y, Jiang Y, Yang S (2021) A modified pCas/pTargetF system for CRISPR-Cas9-assisted genome editing in Escherichia coli. Acta Biochim Biophys Sin (Shanghai) 53:620–627. https://doi.org/10.1093/abbs/gmab036
Article CAS PubMed Google Scholar
Lin J, Liu Y, Lai P, Ye H, Xu L (2020) Conditional guide RNA through two intermediate hairpins for programmable CRISPR/Cas9 function: building regulatory connections between endogenous RNA expressions. Nucleic Acids Res 48:11773–11784. https://doi.org/10.1093/nar/gkaa842
Article CAS PubMed PubMed Central Google Scholar
Liu D, Huang C, Guo J, Zhang P, Chen T, Wang Z, Zhao X (2019) Development and characterization of a CRISPR/Cas9n-based multiplex genome editing system for Bacillus subtilis. Biotechnol Biofuels 12. https://doi.org/10.1186/s13068-019-1537-1
Liu X, Wang D, Wang H, Feng E, Zhu L, Wang H (2012) Curing of plasmid pXO1 from Bacillus anthracis using plasmid incompatibility. PLoS One 7. https://doi.org/10.1371/journal.pone.0029875
Luchansky JB, Benson AK, Atherly AG (1989) Construction, transfer and properties of a novel temperature-sensitive integrable plasmid for genomic analysis of Staphyiococcus aureus. Mol Microbiol 3:65–78. https://doi.org/10.1111/j.1365-2958.1989.tb00105.x
Article CAS PubMed Google Scholar
Mccown PJ, Corbino KA, Stav S, Sherlock ME, Breaker RR (2017) Riboswitch diversity and distribution. RNA 23:995–1011. https://doi.org/10.1261/rna.061234.117
Article CAS PubMed PubMed Central Google Scholar
Michel-briand Y, Uccelli V, Laporte JM, Plesiat P (1986) Elimination of plasmids from enterobacteriaceae by 4-quinolone derivatives. J Antimicrob Chemother 18:667–674. https://doi.org/10.1093/jac/18.6.667
Article CAS PubMed Google Scholar
Muranaka N, Yokobayashi Y (2010) A synthetic riboswitch with chemical band-pass response. Chem Comm 46:6825–6827. https://doi.org/10.1039/c0cc01438a
Article CAS PubMed Google Scholar
Okibe N, Suzuki N, Inui M, Yukawa H (2011) Efficient markerless gene replacement in Corynebacterium glutamicum using a new temperature-sensitive plasmid. J Microbiol Methods 85:155–163. https://doi.org/10.1016/j.mimet.2011.02.012
Article CAS PubMed Google Scholar
Peters JM, Colavin A, Shi H, Czarny TL, Larson MH, Wong S, Hawkins JS, Lu CHS, Koo BM, Marta E, Shiver AL, Whitehead EH, Weissman JS, Brown ED, Qi LS, Huang KC, Gross CA (2016) A comprehensive, CRISPR-based functional analysis of essential genes in bacteria. Cell 165:1493–1506. https://doi.org/10.1016/j.cell.2016.05.003
Article CAS PubMed PubMed Central Google Scholar
Pickar-Oliver A, Gersbach CA (2019) The next generation of CRISPR–Cas technologies and applications. Nat Rev Mol Cell Biol 20:490–507
Article CAS PubMed PubMed Central Google Scholar
Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA (2021) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 184:844
Article CAS PubMed Google Scholar
Reuss AJ, Vogel M, Weigand JE, Suess B, Wachtveitl J (2014) Tetracycline determines the conformation of its aptamer at physiological magnesium concentrations. Biophys J 107:2962–2971. https://doi.org/10.1016/j.bpj.2014.11.001
Article CAS PubMed PubMed Central Google Scholar
Rudolph MM, Vockenhuber MP, Suess B (2015) Conditional control of gene expression by synthetic riboswitches in Streptomyces coelicolor. Methods Enzymol 550:283–299. https://doi.org/10.1016/bs.mie.2014.10.036
Article CAS PubMed Google Scholar
Shen W, Zhang J, Geng B, Qiu M, Hu M, Yang Q, Bao W, Xiao Y, Zheng Y, Peng W, Zhang G, Ma L, Yang S (2019) Establishment and application of a CRISPR-Cas12a assisted genome-editing system in Zymomona
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