Efficient and inducible use of artificial MicroRNAs in Marchantia polymorpha

Plant and Cell Physiology

Volumn 57, Issue 2, 2016, Pages 281-290

  Flores Sandoval, Eduardo ^a   Dierschke, Tom ^a   Fisher, Tom J ^a   Bowman, John L ^a,b  

^a MONASH UNIVERSITY   (Australia)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Artificial microRNA; AUXIN RESPONSE FACTOR; ENHANCER OF ZESTE; Marchantia; MicroRNA; RESPONSE REGULATOR; Reverse genetics

Indexed keywords

INDOLEACETIC ACID DERIVATIVE; MICRORNA;

DRUG EFFECTS; GENE SILENCING; GENE VECTOR; GENETIC TRANSFORMATION; GENETICS; MARCHANTIA; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHENOTYPE; TRANSGENIC PLANT;

BASE SEQUENCE; GENE KNOCKDOWN TECHNIQUES; GENETIC VECTORS; INDOLEACETIC ACIDS; MARCHANTIA; MICRORNAS; MOLECULAR SEQUENCE DATA; PHENOTYPE; PLANTS, GENETICALLY MODIFIED; TRANSFORMATION, GENETIC;

EID: 84964852740     PISSN: 00320781     EISSN: 14719053     Source Type: Journal    
DOI: 10.1093/pcp/pcv068     Document Type: Article

References (54)

1. Althoff, F., Kopischke, S., Zobell, O., Ide, K., Ishizaki, K., Kohchi, T., et al. (2013) Comparison of the MpEF1a and CaMV35 promoters for application in Marchantia polymorpha overexpression studies. Transgenic Res. 23: 1-10.
2. Alvarez, J.P., Pekker, I., Goldshmidt, A., Blum, E., Amsellem, Z. and Eshed, Y. (2006) Endogenous and synthetic microRNAs stimulate simultaneous, efficient, and localized regulation of multiple targets in diverse species. Plant Cell 18: 1134-1151.
3. Argyros, R.D., Mathews, D.E., Chiang, Y.-H., Palmer, C.M., Thibault, D.M., Etheridge, N., et al. (2008) Type B response regulators of Arabidopsis play key roles in cytokinin signaling and plant development. Plant Cell 20: 2102-2116.
4. Aukerman, M.J. and Sakai, H. (2003) Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell 15: 2730-2741.
5. Auyeung, V.C., Ulitsky, I., McGeary, S.E. and Bartel, D.P. (2013) Beyond secondary structure: primary-sequence determinants license PrimiRNA hairpins for processing. Cell 152: 844-858.
6. Axtell, M.J., Snyder, J.A. and Bartel, D.P. (2007) Common functions for diverse small RNAs of land plants. Plant Cell 19: 1750-1769.
7. Bartel, D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233.
8. Bowman, J.L., Floyd, S.K. and Sakakibara, K. (2007) Green genes - comparative genomics of the green branch of life. Cell 129: 229-234.
9. Brand, L., Horler, M., Nuesch, E., Vassalli, S., Barrell, P., Yang, W., et al. (2006) A versatile and reliable two-component system for tissue-specific gene induction in Arabidopsis. Plant Physiol. 141: 1194-1204.
10. Carlsbecker, A., Lee, J.Y., Roberts, C.J., Dettmer, J., Lehesranta, S., Zhou, J., et al. (2010) Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate. Nature 465: 316-321.
11. Chanvivattana, Y., Bishopp, A., Schubert, D., Stock, C., Moon, Y.-H., Sung, Z.R., et al. (2004) Interaction of Polycomb-group proteins controlling flowering in Arabidopsis. Development 131: 5263-5276.
12. Chen, X. (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303: 2022-2025.
13. Coruh, C., Shahid, S. and Axtell, M.J. (2014) Seeing the forest for the trees: annotating small RNA producing genes in plants. Curr. Opin. Plant Biol. 18: 87-95.
14. Deveaux, Y., Peaucelle, A., Roberts, G.R., Coen, E., Simon, R., Mizukami, Y., et al. (2003) The ethanol switch: a tool for tissue-specific gene induction during plant development. Plant J. 36: 918-930.
15. Dugas, D.V. and Bartel, B. (2004) MicroRNA regulation of gene expression in plants. Curr. Opin. Plant Biol. 7: 512-520.
16. Eklund, D.M., Ishizaki, I., Flores-Sandoval, E., Kikuchi, S., Takebayashi, Y., Tsukamoto, S., et al. (2015) Auxin produced by the indole-3-pyruvate pathway regulates development and gemmae dormancy in the liverwort Marchantia polymorpha. Plant Cell, doi: 10.1105/tpc.15.00065.
17. Felippes, F.F. De, Ott, F. and Weigel, D. (2011) Comparative analysis of nonautonomous effects of tasiRNAs and miRNAs in Arabidopsis thaliana. Nucleic Acids Res. 39: 2880-2889.
18. Flores-Sandoval, E., Eklund, D.M. and Bowman J.L. (2015) A simple auxin transcriptional response system regulates multiple morphogenetic processes in the liverwort Marchantia polymorpha. PLoS Genet. 11: 1005207.
19. Floyd, S.K. and Bowman, J.L. (2004) Gene regulation: ancient microRNA target sequences in plants. Nature 428: 485-486.
20. Gleave, A.P. (1992) A versatile binary vector system with a T-DNA organisational structure conducive to efficient integration of cloned DNA into the plant genome. Plant Mol. Biol. 20: 1203-1207.
21. Ishida, K., Yamashino, T., Yokoyama, A. and Mizuno, T. (2008) Three type- B response regulators, ARR1, ARR10 and ARR12, play essential but redundant roles in cytokinin signal transduction throughout the life cycle of Arabidopsis thaliana. Plant Cell Physiol. 49: 47-57.
22. Ishizaki, K., Chiyoda, S., Yamato, K.T. and Kohchi, T. (2008) Agrobacteriummediated transformation of the haploid liverwort Marchantia polymorpha L., an emerging model for plant biology. Plant Cell Physiol. 49: 1084-1091.
23. Ishizaki, K., Johzuka-Hisatomi, Y., Ishida, S., Iida, S. and Kohchi, T. (2013) Homologous recombination-mediated gene targeting in the liverwort Marchantia polymorpha L. Sci. Rep. 3: 1532.
24. Ishizaki, K., Nonomura, M., Kato, H., Yamato, K.T. and Kohchi, T. (2012) Visualization of auxin-mediated transcriptional activation using a common auxin-responsive reporter system in the liverwort Marchantia polymorpha. J. Plant Res. 125: 643-651.
25. Jeong, D.-H., Thatcher, S.R., Brown, R.S.H., Zhai, J., Park, S., Rymarquis, L.A., et al. (2013) Comprehensive investigation of microRNAs enhanced by analysis of sequence variants, expression patterns, ARGONAUTE loading, and target cleavage. Plant Physiol. 162: 1225-1245.
26. Jones-Rhoades, M.W., Bartel, D.P. and Bartel, B. (2006) MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant Biol. 57: 19-53.
27. Kasschau, K.D., Xie, Z., Allen, E., Llave, C., Chapman, E.J., Krizan, K.A., et al. (2003) P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function. Dev. Cell 4: 205-217.
28. Kato, H., Ishizaki, K., Kouno, M., Shirakawa, M., Bowman, J.L., Nishihama, R., et al. (2015) Auxin-mediated transcriptional system with a minimal set of components is critical for morphogenesis through the life cycle in Marchantia polymorpha. PLoS Genet. 11: 1005084.
29. Khraiwesh, B., Ossowski, S., Weigel, D., Reski, R. and Frank, W. (2008) Specific gene silencing by artificial MicroRNAs in Physcomitrella patens: an alternative to targeted gene knockouts. Plant Physiol. 148: 684-693.
30. Kieber, J.J. and Schaller, G.E. (2014) Cytokinins. Arabidopsis Book 12: e0168.
31. LaRue, C.D. and Narayanaswami, S. (1957) Auxin inhibition in the liverwort Lunularia. New Phytol. 56: 61-70.
32. Lingel, A., Simon, B., Izaurralde, E. and Sattler, M. (2003) Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature 426: 465-469.
33. Llave, C., Xie, Z., Kasschau, K.D. and Carrington, J.C. (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297: 2053-2056.
34. Maravolo, N.C. and Voth, P.D. (1966) Morphogenic effects of three growth substances on Marchantia gemmalings. Bot. Gaz. 127: 79-86.
35. Mason, M.G., Mathews, D.E., Argyros, D.A., Maxwell, B.B., Kieber, J.J., Alonso, J.M., et al. (2005) Multiple type-B response regulators mediate cytokinin signal transduction in Arabidopsis. Plant Cell 17: 3007-3018.
36. Molnar, A., Bassett, A., Thuenemann, E., Schwach, F., Karkare, S., Ossowski, S., et al. (2009). Highly specific gene silencing by artificial microRNAs in the unicellular alga Chlamydomonas reinhardtii. Plant J. 58: 165-74.
37. Ossowski, S., Schwab, R. and Weigel, D. (2008) Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J. 53: 674-690.
38. Palatnik, J.F., Allen, E., Wu, X., Schommer, C., Schwab, R., Carrington, J.C., et al. (2003) Control of leaf morphogenesis by microRNAs. Nature 425: 257-263.
39. Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B. and Bartel, D.P. (2002) MicroRNAs in plants. Genes Dev. 16: 1616-1626.
40. Roslan, H.A., Salter, M.G., Wood, C.D., White, M.R.H., Croft, K.P., Robson, F., et al. (2001) Characterization of the ethanol-inducible alc gene-expression system in Arabidopsis thaliana. Plant J. 28: 225-235.
41. Saidi, Y., Finka, A., Chakhporanian, M., Zrÿd, J.P., Schaefer, D.G. and Goloubinoff, P. (2005) Controlled expression of recombinant proteins in Physcomitrella patens by a conditional heat-shock promoter: a tool for plant research and biotechnology. Plant Mol. Biol. 59: 697-711.
42. Schwab, R., Ossowski, S., Riester, M., Warthmann, N. and Weigel, D. (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18: 1121-1133.
43. Schwab, R., Palatnik, J.F., Riester, M., Schommer, C., Schmid, M. and Weigel, D. (2005) Specific effects of microRNAs on the plant transcriptome. Dev. Cell 8: 517-527.
44. Song, J.-J., Smith, S.K., Hannon, G.J. and Joshua-Tor, L. (2004) Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305: 1434-1437.
45. Sugano, S.S., Shirakawa, M., Takagi, J., Matsuda, Y., Shimada, T., Hara- Nishimura, I., et al. (2014) CRISPR/Cas9-mediated targeted mutagenesis in the liverwort Marchantia polymorpha L. Plant Cell Physiol. 55: 475- 481.
46. Tarén, N. (1958). Factors regulating the initial development of gemmae in Marchantia polymorpha. Bryologist 61: 191-204.
47. To, J.P.C., Haberer, G., Ferreira, F.J., Deruère, J., Mason, M.G., Schaller, G.E., et al. (2004) Type-A Arabidopsis response regulators are partially redundant negative regulators of cytokinin signaling. Plant Cell 16: 658-671.
48. Tretter, E.M., Alvarez, J.P., Eshed, Y. and Bowman, J.L. (2008) Activity range of Arabidopsis small RNAs derived from different biogenesis pathways. Plant Physiol. 147: 58-62.
49. Wachsman, G. and Heidstra, R. (2010) The CRE/lox system as a tool for developmental studies at the cell and tissue level. Methods Mol. Biol. 655: 47-64.
50. Warthmann, N., Chen, H., Ossowski, S., Weigel, D. and Herve, P. (2008) Highly specific gene silencing by artificial miRNAs in rice. PLoS One 3: e1829.
51. Yokoyama, A., Yamashino, T., Amano, Y.I., Tajima, Y., Imamura, A., Sakakibara, H., et al. (2007) Type-B ARR transcription factors, ARR10 and ARR12, are implicated in cytokinin-mediated regulation of protoxylem differentiation in roots of Arabidopsis thaliana. Plant Cell Physiol. 48: 84-96.
52. Zhang, X., Zhao, H., Gao, S., Wang, W.C., Katiyar-Agarwal, S., Huang, H.D., et al. (2011) Arabidopsis Argonaute 2 regulates innate immunity via miRNA393∗-mediated silencing of a Golgi-localized SNARE gene, MEMB12. Mol. Cell 42: 356-366.
53. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415.
54. Zuo, J.R., Niu, Q.W. and Chua, N.H. (2000) An estrogen receptor-based transactivator XVE mediates highly inducible gene expression in transgenic plants. Plant J. 24: 265-273.