Spinach-based RNA mimicking GFP in plant cells

Autour A, Westhof E, Ryckelynck M (2016) iSpinach: a fluorogenic RNA aptamer optimized for in vitro applications. Nucleic Acids Res 44:2491–2500 Aw SS, Tang MX, Teo YN, Cohen SM (2016) A conformation-induced fluorescence method for microRNA detection. Nucleic Acids Res 44:e92 Bai JY, Luo Y, Wang X, Li S, Luo M, Yin M, Zuo YL, Li GL, Yao JY, Yang H, Zhang MD, Wei W, Wang ML, Wang R, Fan CH, Zhao Y (2020) A protein-independent fluorescent RNA aptamer reporter system for plant genetic engineering. Nat Commun 11:3847 Banerjee AK, Chatterjee M, Yu Y, Suh SG, Miller WA, Hannapel DJ (2006) Dynamics of a mobile RNA of potato involved in a long-distance signaling pathway. Plant Cell 18:3443–3457 Chen X, Zhang D, Su N, Bao B, Xie X, Zuo F, Yang L, Wang H, Jiang L, Lin Q, Fang M, Li N, Hua X, Chen Z, Bao C, Xu J, Du W, Zhang L, Zhao Y, Zhu L, Loscalzo J, Yang Y (2019) Visualizing RNA dynamics in live cells with bright and stable fluorescent RNAs. Nat Biotechnol 37:1287–1293 Ding WN, Yu ZM, Tong YL, Huang W, Chen HM, Wu P (2009) A transcription factor with a bHLH domain regulates root hair development in rice. Cell Res 19:1309–1311 Dolgosheina EV, Jeng SC, Panchapakesan SS, Cojocaru R, Chen PS, Wilson PD, Hawkins N, Wiggins PA, Unrau PJ (2014) RNA mango aptamer-fluorophore: a bright, high-affinity complex for RNA labeling and tracking. ACS Chem Biol 9:2412–2420 Ehrhardt DW, Frommer WB (2012) New technologies for 21st century plant science. Plant Cell 24:374–394 Ellison EE, Nagalakshmi U, Gamo ME, Huang PJ, Dinesh-Kumar S, Voytas DF (2020) Multiplexed heritable gene editing using RNA viruses and mobile single guide RNAs. Nat Plants 6:620–624 Filonov GS, Moon JD, Svensen N, Jaffrey SR (2014) Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. J Am Chem Soc 136:16299–16308 Filonov GS, Song W, Jaffrey SR (2019) Spectral tuning by a single nucleotide controls the fluorescence properties of a fluorogenic aptamer. Biochemistry 58:1560–1564 Guet D, Burns LT, Maji S, Boulanger J, Hersen P, Wente SR, Salamero J, Dargemont C (2015) Combining Spinach-tagged RNA and gene localization to image gene expression in live yeast. Nat Commun 6:8882 Hong Y, Davies DL, Van Wezel R, Ellerker BE, Morton A, Barbara D (2001) Expression of the immunodominant membrane protein of chlorantie-aster yellows phytoplasma in Nicotiana benthamiana from a potato virus X-based vector. Acta Hort 550:409–415 Huang NC, Jane WN, Chen J, Yu TS (2012) Arabidopsis thaliana CENTRORADIALIS homologue (ATC) acts systemically to inhibit floral initiation in Arabidopsis. Plant J 72:175–184 Huang H, Suslov NB, Li NS, Shelke SA, Evans ME, Koldobskaya Y, Rice PA, Piccirilli JA (2014) A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore. Nat Chem Biol 10:686–691 Huang K, Doyle F, Wurz ZE, Tenenbaum SA, Hammond RK, Caplan JL, Meyers BC (2017) FASTmiR: an RNA-based sensor for in vitro quantification and live-cell localization of small RNAs. Nucleic Acids Res 45:e130 Jackson SD, Hong Y (2012) Systemic movement of FT mRNA and a possible role in floral induction. Front Plant Sci 3:127 Kim G, LeBlanc ML, Wafula EK, dePamphilis CW, Westwood JH (2014) Genomic-scale exchange of mRNA between a parasitic plant and its hosts. Science 345:808–811 Li C, Zhang K, Zeng X, Jackson S, Zhou Y, Hong Y (2009) A cis element within Flowering Locus T mRNA determines its mobility and facilitates trafficking of heterologous viral RNA. J Virol 83:3540–3548 Li C, Gu M, Shi N, Zhang H, Yang X, Osman T, Liu Y, Wang H, Vatish M, Jackson S, Hong Y (2011) Mobile FT mRNA contributes to the systemic florigen signalling in floral induction. Sci Rep 1:73 Liu L, Chen X (2018) Intercellular and systemic trafficking of RNAs in plants. Nat Plants 4:869–878 Lu KJ, Huang NC, Liu YS, Lu CA, Yu TS (2012) Long-distance movement of Arabidopsis FLOWERING LOCUS T RNA participates in systemic floral regulation. RNA Biol 9:653–662 Luo KR, Huang NC, Yu TS (2018) Selective targeting of mobile mRNAs to plasmodesmata for cell-to-cell movement. Plant Physiol 177:604–614 Notaguchi M, Higashiyama T, Suzuki T (2015) Identification of mRNAs that move over long distances using an RNA-Seq analysis of Arabidopsis/Nicotiana benthamiana heterografts. Plant Cell Physiol 56:311–321 Paige JS, Wu KY, Jaffrey SR (2011) RNA mimics of green fluorescent protein. Science 333:642–646 Pothoulakis G, Ceroni F, Reeve B, Ellis T (2014) The Spinach RNA aptamer as a characterization tool for synthetic biology. ACS Synth Biol 3:182–187 Sainsbury F, Lomonossoff GP (2008) Extremely high-level and rapid transient protein production in plants without the use of viral replication. Plant Physiol 148:1212–1218 Sainsbury F, Thuenemann EC, Lomonossoff GP (2009) pEAQ: versatile expression vectors for easy and quick transient expression of heterologous proteins in plants. Plant Biotechnol J 7:682–693 Strack RL, Disney MD, Jaffrey SR (2013) A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA. Nat Methods 10:1219–1224 Thieme CJ, Rojas-Triana M, Stecyk E, Schudoma C, Zhang W, Yang L, Miñambres M, Walther D, Schulze WX, Paz-Ares J, Scheible WR, Kragler F (2015) Endogenous Arabidopsis messenger RNAs transported to distant tissues. Nat Plants 1:15025 Tutucci E, Livingston NM, Singer RH, Wu B (2018) Imaging mRNA in vivo, from birth to death. Annu Rev Biophys 47:85–106 Uddin MN, Kim JY (2013) Intercellular and systemic spread of RNA and RNAi in plants. Wiley Interdiscip Rev RNA 4:279–293 van Wezel R, Liu H, Tien P, Stanley J, Hong Y (2001) Gene C2 of the monopartite geminivirus tomato yellow leaf curl virus-China encodes a pathogenicity determinant that is localized in the nucleus. Mol Plant Microbe Interact 14:1125–1128 Warner KD, Chen MC, Song W, Strack RL, Thorn A, Jaffrey SR, Ferré-D’Amaré AR (2014) Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nat Struct Mol Biol 21:658–663 Warner KD, Sjekloća L, Song W, Filonov GS, Jaffrey SR, Ferré-D’Amaré AR (2017) A homodimer interface without base pairs in an RNA mimic of red fluorescent protein. Nat Chem Biol 13:1195–1201 You M, Jaffrey SR (2015) Structure and mechanism of RNA mimics of green fluorescent protein. Annu Rev Biophys 44:187–206 Yu Z, Cho SK, Zhang P, Hong Y, Hannapel DJ (2020a) Utilizing potato virus X to monitor RNA movement. In: Heinlein M. (eds) RNA tagging. Methods in Molecular Biology 2166: 181–194 Yu Z, Mei F, Yan H, Chen Q, Yao M, Liu S, Wang Y, Zhang X, Zhang P, Jackson S, Shi N, Liu Y, Hong Y (2020b) Reappraisal of Spinach-based RNA visualization in plants. bioRxiv 2020b.09.24.310607. https://doi.org/10.1101/2020b.09.24.310607. Zhang J, Fei J, Leslie BJ, Han KY, Kuhlman TE, Ha T (2015) Tandem Spinach array for mRNA imaging in living bacterial cells. Sci Rep 5:17295 Zhang X, Lai T, Zhang P, Zhang X, Yuan C, Jin Z, Li H, Yu Z, Qin C, Tör M, Ma P, Cheng Q, Hong Y (2019) Mini review: Revisiting mobile RNA silencing in plants. Plant Sci 278:113–117