Di Serio, F., & Flores, R. (2008). Viroids: Molecular implements for dissecting RNA trafficking in plants. RNA Biology, 5(3), 128-131. doi:10.4161/rna.5.3.6638
Flores, R., Owens, R. A., & Taylor, J. (2016). Pathogenesis by subviral agents: viroids and hepatitis delta virus. Current Opinion in Virology, 17, 87-94. doi:10.1016/j.coviro.2016.01.022
Di Serio, F., Flores, R., Verhoeven, J. T. J., Li, S.-F., Pallás, V., Randles, J. W., … Owens, R. A. (2014). Current status of viroid taxonomy. Archives of Virology, 159(12), 3467-3478. doi:10.1007/s00705-014-2200-6
[+]
Di Serio, F., & Flores, R. (2008). Viroids: Molecular implements for dissecting RNA trafficking in plants. RNA Biology, 5(3), 128-131. doi:10.4161/rna.5.3.6638
Flores, R., Owens, R. A., & Taylor, J. (2016). Pathogenesis by subviral agents: viroids and hepatitis delta virus. Current Opinion in Virology, 17, 87-94. doi:10.1016/j.coviro.2016.01.022
Di Serio, F., Flores, R., Verhoeven, J. T. J., Li, S.-F., Pallás, V., Randles, J. W., … Owens, R. A. (2014). Current status of viroid taxonomy. Archives of Virology, 159(12), 3467-3478. doi:10.1007/s00705-014-2200-6
Vogt, U., Pélissier, T., Pütz, A., Razvi, F., Fischer, R., & Wassenegger, M. (2004). Viroid-induced RNA silencing of GFP-viroid fusion transgenes does not induce extensive spreading of methylation or transitive silencing. The Plant Journal, 38(1), 107-118. doi:10.1111/j.1365-313x.2004.02029.x
Martínez de Alba, A. E., Flores, R., & Hernández, C. (2002). Two Chloroplastic Viroids Induce the Accumulation of Small RNAs Associated with Posttranscriptional Gene Silencing. Journal of Virology, 76(24), 13094-13096. doi:10.1128/jvi.76.24.13094-13096.2002
Markarian, N., Li, H. W., Ding, S. W., & Semancik, J. S. (2004). RNA silencing as related to viroid induced symptom expression. Archives of Virology, 149(2), 397-406. doi:10.1007/s00705-003-0215-5
Carbonell, A., Martínez de Alba, Á.-E., Flores, R., & Gago, S. (2008). Double-stranded RNA interferes in a sequence-specific manner with the infection of representative members of the two viroid families. Virology, 371(1), 44-53. doi:10.1016/j.virol.2007.09.031
St-Pierre, P., Hassen, I. F., Thompson, D., & Perreault, J. P. (2009). Characterization of the siRNAs associated with peach latent mosaic viroid infection. Virology, 383(2), 178-182. doi:10.1016/j.virol.2008.11.008
MARTINEZ, G., DONAIRE, L., LLAVE, C., PALLAS, V., & GOMEZ, G. (2010). High-throughput sequencing ofHop stunt viroid-derived small RNAs from cucumber leaves and phloem. Molecular Plant Pathology, 11(3), 347-359. doi:10.1111/j.1364-3703.2009.00608.x
Ivanova, D., Milev, I., Vachev, T., Baev, V., Yahubyan, G., Minkov, G., & Gozmanova, M. (2014). Small RNA analysis of Potato Spindle Tuber Viroid infected Phelipanche ramosa. Plant Physiology and Biochemistry, 74, 276-282. doi:10.1016/j.plaphy.2013.11.019
Islam, W., Noman, A., Qasim, M., & Wang, L. (2018). Plant Responses to Pathogen Attack: Small RNAs in Focus. International Journal of Molecular Sciences, 19(2), 515. doi:10.3390/ijms19020515
Minoia, S., Carbonell, A., Di Serio, F., Gisel, A., Carrington, J. C., Navarro, B., & Flores, R. (2014). Specific Argonautes Selectively Bind Small RNAs Derived from Potato Spindle Tuber Viroid and Attenuate Viroid Accumulation In Vivo. Journal of Virology, 88(20), 11933-11945. doi:10.1128/jvi.01404-14
Katsarou, K., Mavrothalassiti, E., Dermauw, W., Van Leeuwen, T., & Kalantidis, K. (2016). Combined Activity of DCL2 and DCL3 Is Crucial in the Defense against Potato Spindle Tuber Viroid. PLOS Pathogens, 12(10), e1005936. doi:10.1371/journal.ppat.1005936
Dadami, E., Boutla, A., Vrettos, N., Tzortzakaki, S., Karakasilioti, I., & Kalantidis, K. (2013). DICER-LIKE 4 But Not DICER-LIKE 2 May Have a Positive Effect on Potato Spindle Tuber Viroid Accumulation in Nicotiana benthamiana. Molecular Plant, 6(1), 232-234. doi:10.1093/mp/sss118
Navarro, B., Gisel, A., Rodio, M. E., Delgado, S., Flores, R., & Di Serio, F. (2012). Small RNAs containing the pathogenic determinant of a chloroplast-replicating viroid guide the degradation of a host mRNA as predicted by RNA silencing. The Plant Journal, 70(6), 991-1003. doi:10.1111/j.1365-313x.2012.04940.x
Eamens, A. L., Smith, N. A., Dennis, E. S., Wassenegger, M., & Wang, M.-B. (2014). In Nicotiana species, an artificial microRNA corresponding to the virulence modulating region of Potato spindle tuber viroid directs RNA silencing of a soluble inorganic pyrophosphatase gene and the development of abnormal phenotypes. Virology, 450-451, 266-277. doi:10.1016/j.virol.2013.12.019
Adkar-Purushothama, C. R., Brosseau, C., Giguère, T., Sano, T., Moffett, P., & Perreault, J.-P. (2015). Small RNA Derived from the Virulence Modulating Region of the Potato spindle tuber viroid Silences callose synthase Genes of Tomato Plants. The Plant Cell, 27(8), 2178-2194. doi:10.1105/tpc.15.00523
Adkar-Purushothama, C. R., Iyer, P. S., & Perreault, J.-P. (2017). Potato spindle tuber viroid infection triggers degradation of chloride channel protein CLC-b-like and Ribosomal protein S3a-like mRNAs in tomato plants. Scientific Reports, 7(1). doi:10.1038/s41598-017-08823-z
Carbonell, A., & Daròs, J.-A. (2017). Artificial microRNAs and synthetictrans-acting small interfering RNAs interfere with viroid infection. Molecular Plant Pathology, 18(5), 746-753. doi:10.1111/mpp.12529
Lisón, P., Tárraga, S., López-Gresa, P., Saurí, A., Torres, C., Campos, L., … Rodrigo, I. (2013). A noncoding plant pathogen provokes both transcriptional and posttranscriptional alterations in tomato. PROTEOMICS, 13(5), 833-844. doi:10.1002/pmic.201200286
Dubé, A., Bisaillon, M., & Perreault, J.-P. (2009). Identification of Proteins from
Prunus persica
That Interact with Peach Latent Mosaic Viroid. Journal of Virology, 83(23), 12057-12067. doi:10.1128/jvi.01151-09
Eiras, M., Nohales, M. A., Kitajima, E. W., Flores, R., & Daròs, J. A. (2010). Ribosomal protein L5 and transcription factor IIIA from Arabidopsis thaliana bind in vitro specifically Potato spindle tuber viroid RNA. Archives of Virology, 156(3), 529-533. doi:10.1007/s00705-010-0867-x
Martinez, G., Castellano, M., Tortosa, M., Pallas, V., & Gomez, G. (2013). A pathogenic non-coding RNA induces changes in dynamic DNA methylation of ribosomal RNA genes in host plants. Nucleic Acids Research, 42(3), 1553-1562. doi:10.1093/nar/gkt968
Castellano, M., Martinez, G., Marques, M. C., Moreno-Romero, J., Köhler, C., Pallas, V., & Gomez, G. (2016). Changes in the DNA methylation pattern of the host male gametophyte of viroid-infected cucumber plants. Journal of Experimental Botany, 67(19), 5857-5868. doi:10.1093/jxb/erw353
Mills, E. W., & Green, R. (2017). Ribosomopathies: There’s strength in numbers. Science, 358(6363), eaan2755. doi:10.1126/science.aan2755
Mayer, C., & Grummt, I. (2005). Cellular Stress and Nucleolar Function. Cell Cycle, 4(8), 1036-1038. doi:10.4161/cc.4.8.1925
Boulon, S., Westman, B. J., Hutten, S., Boisvert, F.-M., & Lamond, A. I. (2010). The Nucleolus under Stress. Molecular Cell, 40(2), 216-227. doi:10.1016/j.molcel.2010.09.024
Ohbayashi, I., & Sugiyama, M. (2018). Plant Nucleolar Stress Response, a New Face in the NAC-Dependent Cellular Stress Responses. Frontiers in Plant Science, 8. doi:10.3389/fpls.2017.02247
Weis, B. L., Kovacevic, J., Missbach, S., & Schleiff, E. (2015). Plant-Specific Features of Ribosome Biogenesis. Trends in Plant Science, 20(11), 729-740. doi:10.1016/j.tplants.2015.07.003
Waltz, F., Nguyen, T.-T., Arrivé, M., Bochler, A., Chicher, J., Hammann, P., … Giegé, P. (2019). Small is big in Arabidopsis mitochondrial ribosome. Nature Plants, 5(1), 106-117. doi:10.1038/s41477-018-0339-y
Ohbayashi, I., Lin, C.-Y., Shinohara, N., Matsumura, Y., Machida, Y., Horiguchi, G., … Sugiyama, M. (2017). Evidence for a Role of ANAC082 as a Ribosomal Stress Response Mediator Leading to Growth Defects and Developmental Alterations in Arabidopsis. The Plant Cell, 29(10), 2644-2660. doi:10.1105/tpc.17.00255
Kressler, D., Hurt, E., & Baßler, J. (2017). A Puzzle of Life: Crafting Ribosomal Subunits. Trends in Biochemical Sciences, 42(8), 640-654. doi:10.1016/j.tibs.2017.05.005
Rorbach, J., Aibara, S., & Amunts, A. (2017). Ribosome origami. Nature Structural & Molecular Biology, 24(11), 879-881. doi:10.1038/nsmb.3497
Ahmed, T., Yin, Z., & Bhushan, S. (2016). Cryo-EM structure of the large subunit of the spinach chloroplast ribosome. Scientific Reports, 6(1). doi:10.1038/srep35793
Henras, A. K., Soudet, J., Gérus, M., Lebaron, S., Caizergues-Ferrer, M., Mougin, A., & Henry, Y. (2008). The post-transcriptional steps of eukaryotic ribosome biogenesis. Cellular and Molecular Life Sciences, 65(15), 2334-2359. doi:10.1007/s00018-008-8027-0
Baßler, J., & Hurt, E. (2019). Eukaryotic Ribosome Assembly. Annual Review of Biochemistry, 88(1), 281-306. doi:10.1146/annurev-biochem-013118-110817
Hang, R., Wang, Z., Deng, X., Liu, C., Yan, B., Yang, C., … Cao, X. (2018). Ribosomal RNA Biogenesis and Its Response to Chilling Stress in Oryza sativa. Plant Physiology, 177(1), 381-397. doi:10.1104/pp.17.01714
Palm, D., Streit, D., Shanmugam, T., Weis, B. L., Ruprecht, M., Simm, S., & Schleiff, E. (2018). Plant-specific ribosome biogenesis factors in Arabidopsis thaliana with essential function in rRNA processing. Nucleic Acids Research, 47(4), 1880-1895. doi:10.1093/nar/gky1261
Tomecki, R., Sikorski, P. J., & Zakrzewska-Placzek, M. (2017). Comparison of preribosomal RNA processing pathways in yeast, plant and human cells - focus on coordinated action of endo- and exoribonucleases. FEBS Letters, 591(13), 1801-1850. doi:10.1002/1873-3468.12682
Perry, K. L., & Palukaitis, P. (1990). Transcription of tomato ribosomal DNA and the organization of the intergenic spacer. Molecular and General Genetics MGG, 221(1), 102-112. doi:10.1007/bf00280374
Echevarría-Zomeño, S., Yángüez, E., Fernández-Bautista, N., Castro-Sanz, A., Ferrando, A., & Castellano, M. (2013). Regulation of Translation Initiation under Biotic and Abiotic Stresses. International Journal of Molecular Sciences, 14(3), 4670-4683. doi:10.3390/ijms14034670
Wang, Z., Ying, T., Bao, B., & Huang, X. (2005). Characteristics of fruit ripening in tomato mutantepi. Journal of Zhejiang University SCIENCE, 6B(6), 502-507. doi:10.1631/jzus.2005.b0502
Bellés, J. M., Carbonell, J., & Conejero, V. (1991). Polyamines in Plants Infected by Citrus Exocortis Viroid or Treated with Silver Ions and Ethephon. Plant Physiology, 96(4), 1053-1059. doi:10.1104/pp.96.4.1053
Adkar-Purushothama, C. R., & Perreault, J.-P. (2018). Alterations of the viroid regions that interact with the host defense genes attenuate viroid infection in host plant. RNA Biology, 15(7), 955-966. doi:10.1080/15476286.2018.1462653
Rivera, M. C., Maguire, B., & Lake, J. A. (2015). Isolation of Ribosomes and Polysomes. Cold Spring Harbor Protocols, 2015(3), pdb.prot081331. doi:10.1101/pdb.prot081331
Hsu, P. Y., Calviello, L., Wu, H.-Y. L., Li, F.-W., Rothfels, C. J., Ohler, U., & Benfey, P. N. (2016). Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis. Proceedings of the National Academy of Sciences, 113(45), E7126-E7135. doi:10.1073/pnas.1614788113
Mustroph, A., Juntawong, P., & Bailey-Serres, J. (2009). Isolation of Plant Polysomal mRNA by Differential Centrifugation and Ribosome Immunopurification Methods. Methods in Molecular Biology™, 109-126. doi:10.1007/978-1-60327-563-7_6
López-Gresa, M. P., Lisón, P., Yenush, L., Conejero, V., Rodrigo, I., & Bellés, J. M. (2016). Salicylic Acid Is Involved in the Basal Resistance of Tomato Plants to Citrus Exocortis Viroid and Tomato Spotted Wilt Virus. PLOS ONE, 11(11), e0166938. doi:10.1371/journal.pone.0166938
Missbach, S., Weis, B. L., Martin, R., Simm, S., Bohnsack, M. T., & Schleiff, E. (2013). 40S Ribosome Biogenesis Co-Factors Are Essential for Gametophyte and Embryo Development. PLoS ONE, 8(1), e54084. doi:10.1371/journal.pone.0054084
Verhoeven, J. th. j., Jansen, C. C. C., Willemen, T. M., Kox, L. F. F., Owens, R. A., & Roenhorst, J. W. (2004). Natural infections of tomato by Citrus exocortis viroid, Columnea latent viroid, Potato spindle tuber viroid and Tomato chlorotic dwarf viroid. European Journal of Plant Pathology, 110(8), 823-831. doi:10.1007/s10658-004-2493-5
Campos, L., Granell, P., Tárraga, S., López-Gresa, P., Conejero, V., Bellés, J. M., … Lisón, P. (2014). Salicylic acid and gentisic acid induce RNA silencing-related genes and plant resistance to RNA pathogens. Plant Physiology and Biochemistry, 77, 35-43. doi:10.1016/j.plaphy.2014.01.016
Kalantidis, K., Denti, M. A., Tzortzakaki, S., Marinou, E., Tabler, M., & Tsagris, M. (2007). Virp1 Is a Host Protein with a Major Role in
Potato Spindle Tuber Viroid
Infection in
Nicotiana
Plants. Journal of Virology, 81(23), 12872-12880. doi:10.1128/jvi.00974-07
Barry, C. S., Fox, E. A., Yen, H., Lee, S., Ying, T., Grierson, D., & Giovannoni, J. J. (2001). Analysis of the Ethylene Response in theepinastic Mutant of Tomato. Plant Physiology, 127(1), 58-66. doi:10.1104/pp.127.1.58
Diener, T. O. (2003). Discovering viroids — a personal perspective. Nature Reviews Microbiology, 1(1), 75-80. doi:10.1038/nrmicro736
Ding, B., & Itaya, A. (2007). Viroid: A Useful Model for Studying the Basic Principles of Infection and RNA Biology. Molecular Plant-Microbe Interactions®, 20(1), 7-20. doi:10.1094/mpmi-20-0007
Jakab, G., Kiss, T., & Solymosy, F. (1986). Viroid pathogenicity and pre-rRNA processing: A model amenable to experimental testing. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, 868(4), 190-197. doi:10.1016/0167-4781(86)90054-0
Meduski, C. J., & Velten, J. (1990). PSTV sequence similarity to large rRNA. Plant Molecular Biology, 14(4), 625-627. doi:10.1007/bf00027509
Kiss, T., Pósfai, J., & Solymosy, F. (1983). Sequence homology between potato spindle tuber viroid and U3B snRNA. FEBS Letters, 163(2), 217-220. doi:10.1016/0014-5793(83)80822-9
Hughes, J. M., & Ares, M. (1991). Depletion of U3 small nucleolar RNA inhibits cleavage in the 5′ external transcribed spacer of yeast pre-ribosomal RNA and impairs formation of 18S ribosomal RNA. The EMBO Journal, 10(13), 4231-4239. doi:10.1002/j.1460-2075.1991.tb05001.x
Sharma, K., & Tollervey, D. (1999). Base Pairing between U3 Small Nucleolar RNA and the 5′ End of 18S rRNA Is Required for Pre-rRNA Processing. Molecular and Cellular Biology, 19(9), 6012-6019. doi:10.1128/mcb.19.9.6012
Dragon, F., Gallagher, J. E. G., Compagnone-Post, P. A., Mitchell, B. M., Porwancher, K. A., Wehner, K. A., … Baserga, S. J. (2002). A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis. Nature, 417(6892), 967-970. doi:10.1038/nature00769
Dutca, L. M., Gallagher, J. E. G., & Baserga, S. J. (2011). The initial U3 snoRNA:pre-rRNA base pairing interaction required for pre-18S rRNA folding revealed by in vivo chemical probing. Nucleic Acids Research, 39(12), 5164-5180. doi:10.1093/nar/gkr044
Qi, Y., & Ding, B. (2003). Differential Subnuclear Localization of RNA Strands of Opposite Polarity Derived from an Autonomously Replicating Viroid[W]. The Plant Cell, 15(11), 2566-2577. doi:10.1105/tpc.016576
Idol, R. A., Robledo, S., Du, H.-Y., Crimmins, D. L., Wilson, D. B., Ladenson, J. H., … Mason, P. J. (2007). Cells depleted for RPS19, a protein associated with Diamond Blackfan Anemia, show defects in 18S ribosomal RNA synthesis and small ribosomal subunit production. Blood Cells, Molecules, and Diseases, 39(1), 35-43. doi:10.1016/j.bcmd.2007.02.001
Cho, H. K., Ahn, C. S., Lee, H.-S., Kim, J.-K., & Pai, H.-S. (2013). Pescadillo plays an essential role in plant cell growth and survival by modulating ribosome biogenesis. The Plant Journal, 76(3), 393-405. doi:10.1111/tpj.12302
Weis, B. L., Missbach, S., Marzi, J., Bohnsack, M. T., & Schleiff, E. (2014). The 60S associated ribosome biogenesis factor LSG1-2 is required for 40S maturation inArabidopsis thaliana. The Plant Journal, 80(6), 1043-1056. doi:10.1111/tpj.12703
Kojima, K., Tamura, J., Chiba, H., Fukada, K., Tsukaya, H., & Horiguchi, G. (2018). Two Nucleolar Proteins, GDP1 and OLI2, Function As Ribosome Biogenesis Factors and Are Preferentially Involved in Promotion of Leaf Cell Proliferation without Strongly Affecting Leaf Adaxial–Abaxial Patterning in Arabidopsis thaliana. Frontiers in Plant Science, 8. doi:10.3389/fpls.2017.02240
Maekawa, S., Ishida, T., & Yanagisawa, S. (2017). Reduced Expression of APUM24, Encoding a Novel rRNA Processing Factor, Induces Sugar-Dependent Nucleolar Stress and Altered Sugar Responses in Arabidopsis thaliana. The Plant Cell, 30(1), 209-227. doi:10.1105/tpc.17.00778
Bonfiglioli, R. G., McFadden, G. I., & Symons, R. H. (1994). In situ hybridization localizes avocado sunblotch viroid on chloroplast thylakoid membranes and coconut cadang cadang viroid in the nucleus. The Plant Journal, 6(1), 99-103. doi:10.1046/j.1365-313x.1994.6010099.x
Hill, J. M., Zhao, Y., Bhattacharjee, S., & Lukiw, W. J. (2014). miRNAs and viroids utilize common strategies in genetic signal transfer. Frontiers in Molecular Neuroscience, 7. doi:10.3389/fnmol.2014.00010
Li, S., Liu, L., Zhuang, X., Yu, Y., Liu, X., Cui, X., … Chen, X. (2013). MicroRNAs Inhibit the Translation of Target mRNAs on the Endoplasmic Reticulum in Arabidopsis. Cell, 153(3), 562-574. doi:10.1016/j.cell.2013.04.005
Fukaya, T., Iwakawa, H., & Tomari, Y. (2014). MicroRNAs Block Assembly of eIF4F Translation Initiation Complex in Drosophila. Molecular Cell, 56(1), 67-78. doi:10.1016/j.molcel.2014.09.004
Lanet, E., Delannoy, E., Sormani, R., Floris, M., Brodersen, P., Crété, P., … Robaglia, C. (2009). Biochemical Evidence for Translational Repression by Arabidopsis MicroRNAs. The Plant Cell, 21(6), 1762-1768. doi:10.1105/tpc.108.063412
Iwakawa, H., & Tomari, Y. (2013). Molecular Insights into microRNA-Mediated Translational Repression in Plants. Molecular Cell, 52(4), 591-601. doi:10.1016/j.molcel.2013.10.033
Reis, R. S., Hart-Smith, G., Eamens, A. L., Wilkins, M. R., & Waterhouse, P. M. (2015). Gene regulation by translational inhibition is determined by Dicer partnering proteins. Nature Plants, 1(3). doi:10.1038/nplants.2014.27
Flores, R., Navarro, B., Kovalskaya, N., Hammond, R. W., & Di Serio, F. (2017). Engineering resistance against viroids. Current Opinion in Virology, 26, 1-7. doi:10.1016/j.coviro.2017.07.003
[-]
Belda-Palazón, Borja
Adkar-Purushothama, Charith Raj
Perreault, Jean-Pierre
Schleiff, Enrico
