Fibrillarin is one of the most important nucleolar proteins that have been shown as essential for life. Fibrillarin localizes primarily at the periphery between fibrillar center and dense fibrillar component as well as in Cajal bodies. In most plants there are at least two different genes for fibrillarin. In Arabidopsis thaliana both genes show high level of expression in transcriptionally active cells. Here, we focus on two important differences between A. thaliana fibrillarins. First and most relevant is the enzymatic activity by AtFib2. The AtFib2 shows a novel ribonuclease activity that is not seen with AtFib1. Second is a difference in the ability to interact with phosphoinositides and phosphatidic acid between both proteins. We also show that the novel ribonuclease activity as well as the phospholipid binding region of fibrillarin is confine to the GAR domain. The ribonuclease activity of fibrillarin reveals in this study represents a new role for this protein in rRNA processing.

Biosystematics Group Department of Plant Sciences Wageningen University and Research Wageningen Netherlands

Department of Biology of the Cell Nucleus Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic Prague Czechia

Unidad de Bioquímica y Biología Molecular de Plantas Centro de Investigación Científica de Yucatán Mérida Mexico

Unidad de Biotecnología Centro de Investigación Científica de Yucatán Mérida Mexico

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Amin M. A., Matsunaga S., Ma N., Takata H., Yokoyama M., Uchiyama S., et al. (2007). Fibrillarin, a nucleolar protein, is required for normal nuclear morphology and cellular growth in HeLa cells. Biochem. Biophys. Res. Commun. 360 320–326. 10.1016/j.bbrc.2007.06.092 PubMed DOI

Amiri K. A. (1994). Fibrillarin-like proteins occur in the domain Archaea. J. Bacteriol. 176 2124–2127. 10.1128/jb.176.7.2124-2127.1994 PubMed DOI PMC

Barneche F., Steinmetz F., Echeverria M. (2000). Fibrillarin genes encode both a conserved nucleolar protein and a novel small nucleolar RNA involved in ribosomal RNA methylation in Arabidopsis thaliana. J. Biol. Chem. 275 27212–27220. 10.1074/jbc.M002996200 PubMed DOI

Bowers J. E., Chapman B. A., Rong J., Paterson A. H. (2003). Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422 433–438. 10.1038/nature01521 PubMed DOI

Cerdido A., Medina F. J. (1995). Subnucleolar location of fibrillarin and variation in its levels during the cell cycle and during differentiation of plant cells. Chromosoma 103 625–634. 10.1007/BF00357689 PubMed DOI

Chang C. H., Hsu F. C., Lee S. C., Lo Y. S., Wang J. D., Shaw J., et al. (2016). The nucleolar fibrillarin protein is required for helper virus-independent long-distance trafficking of a subviral satellite RNA in plants. Plant Cell 28 2586–2602. 10.1105/tpc.16.00071 PubMed DOI PMC

Cockell M. M., Gasser S. M. (1999). The nucleolus: nucleolar space for RENT. Curr. Biol. 9 R575–R576. 10.1016/S0960-9822(99)80359-5 PubMed DOI

Dassanayake M., Oh D. H., Haas J. S., Hernandez A., Hong H., Ali S., et al. (2011). The genome of the extremophile crucifer Thellungiella parvula. Nat. Genet. 43 913–918. 10.1038/ng.889 PubMed DOI PMC

Desterro J. M., Keegan L. P., Lafarga M., Berciano M. T., O’connell M., Carmo-Fonseca M. (2003). Dynamic association of RNA-editing enzymes with the nucleolus. J. Cell Sci. 116 1805–1818. 10.1242/jcs.00371 PubMed DOI

Divecha N. (2016). Phosphoinositides in the nucleus and myogenic differentiation: how a nuclear turtle with a PHD builds muscle. Biochem. Soc. Trans. 44 299–306. 10.1042/BST20150238 PubMed DOI

Dragon F., Gallagher J. E., Compagnone-Post P. A., Mitchell B. M., Porwancher K. A., Wehner K. A., et al. (2002). A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis. Nature 417 967–970. 10.1038/nature00769 PubMed DOI

Dudkina E., Ulyanova V., Shah Mahmud R., Khodzhaeva V., Dao L., Vershinina V., et al. (2016). Three-step procedure for preparation of pure Bacillus altitudinis ribonuclease. FEBS Open Bio 6 24–32. 10.1002/2211-5463.12023 PubMed DOI PMC

Feric M., Vaidya N., Harmon T. S., Mitrea D. M., Zhu L., Richardson T. M., et al. (2016). Coexisting liquid phases underlie nucleolar subcompartments. Cell 165 1686–1697. 10.1016/j.cell.2016.04.047 PubMed DOI PMC

Garcia S. N., Pillus L. (1999). Net results of nucleolar dynamics. Cell 97 825–828. 10.1016/S0092-8674(00)80794-1 PubMed DOI

Gu Z., Eils R., Schlesner M. (2016). Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32 2847–2849. 10.1093/bioinformatics/btw313 PubMed DOI

Hatton N., Lintz E., Mahankali M., Henkels K. M., Gomez-Cambronero J. (2015). Phosphatidic acid increases epidermal growth factor receptor expression by stabilizing mRNA decay and by inhibiting lysosomal and proteasomal degradation of the internalized receptor. Mol. Cell. Biol. 35 3131–3144. 10.1128/MCB.00286-15 PubMed DOI PMC

Henras A. K., Plisson-Chastang C., O’donohue M. F., Chakraborty A., Gleizes P. E. (2015). An overview of pre-ribosomal RNA processing in eukaryotes. Wiley Interdiscip. Rev. RNA 6 225–242. 10.1002/wrna.1269 PubMed DOI PMC

Hernandez-Verdun D., Roussel P., Thiry M., Sirri V., Lafontaine D. L. (2010). The nucleolus: structure/function relationship in RNA metabolism. Wiley Interdiscip. Rev. RNA 1 415–431. 10.1002/wrna.39 PubMed DOI

Hickey A. J., Macario A. J., Conway De Macario E. (2000). Identification of genes in the genome of the archaeon Methanosarcina mazeii that code for homologs of nuclear eukaryotic molecules involved in RNA processing. Gene 253 77–85. 10.1016/S0378-1119(00)00235-3 PubMed DOI

Huber W., Carey V. J., Gentleman R., Anders S., Carlson M., Carvalho B. S., et al. (2015). Orchestrating high-throughput genomic analysis with Bioconductor. Nat. Methods 12 115–121. 10.1038/nmeth.3252 PubMed DOI PMC

Jacobson M. R., Pederson T. (1998). Localization of signal recognition particle RNA in the nucleolus of mammalian cells. Proc. Natl. Acad. Sci. U.S.A. 95 7981–7986. 10.1073/pnas.95.14.7981 PubMed DOI PMC

Kass S., Tyc K., Steitz J. A., Sollner-Webb B. (1990). The U3 small nucleolar ribonucleoprotein functions in the first step of preribosomal RNA processing. Cell 60 897–908. 10.1016/0092-8674(90)90338-F PubMed DOI

Laboure A. M., Faik A., Mandaron P., Falconet D. (1999). RGD-dependent growth of maize calluses and immunodetection of an integrin-like protein. FEBS Lett. 442 123–128. 10.1016/S0014-5793(98)01634-2 PubMed DOI

Loza-Muller L., Rodriguez-Corona U., Sobol M., Rodriguez-Zapata L. C., Hozak P., Castano E. (2015). Fibrillarin methylates H2A in RNA polymerase I trans-active promoters in Brassica oleracea. Front. Plant Sci. 6:976. 10.3389/fpls.2015.00976 PubMed DOI PMC

Marcel V., Ghayad S. E., Belin S., Therizols G., Morel A.-P., Solano-Gonzàlez E., et al. (2013). p53 Acts as a safeguard of translational control by regulating fibrillarin and rRNA methylation in cancer. Cancer Cell 24 318–330. 10.1016/j.ccr.2013.08.013 PubMed DOI PMC

Ochs R. L., Lischwe M. A., Spohn W. H., Busch H. (1985). Fibrillarin: a new protein of the nucleolus identified by autoimmune sera. Biol. Cell 54 123–133. 10.1111/j.1768-322X.1985.tb00387.x PubMed DOI

Olson M. O., Dundr M. (2015). Nucleolus: structure and function. eLS 1–9. 10.1002/9780470015902.a0005975.pub3 DOI

Osborne S. L., Thomas C. L., Gschmeissner S., Schiavo G. (2001). Nuclear PtdIns(4,5)P2 assembles in a mitotically regulated particle involved in pre-mRNA splicing. J. Cell Sci. 114 2501–2511. PubMed

Peng Y., Yu G., Tian S., Li H. (2014). Co-expression and co-purification of archaeal and eukaryal box C/D RNPs. PLOS ONE 9:e103096. 10.1371/journal.pone.0103096 PubMed DOI PMC

Pih K. T., Yi M. J., Liang Y. S., Shin B. J., Cho M. J., Hwang I., et al. (2000). Molecular cloning and targeting of a fibrillarin homolog from Arabidopsis. Plant Physiol. 123 51–58. 10.1104/pp.123.1.51 PubMed DOI PMC

Rodriguez-Corona U., Sobol M., Rodriguez-Zapata L. C., Hozak P., Castano E. (2015). Fibrillarin from Archaea to human. Biol. Cell 107 159–174. 10.1111/boc.201400077 PubMed DOI

Saez-Vasquez J., Caparros-Ruiz D., Barneche F., Echeverria M. (2004). A plant snoRNP complex containing snoRNAs, fibrillarin, and nucleolin-like proteins is competent for both rRNA gene binding and pre-rRNA processing in vitro. Mol. Cell. Biol. 24 7284–7297. 10.1128/MCB.24.16.7284-7297.2004 PubMed DOI PMC

Scheer U., Benavente R. (1990). Functional and dynamic aspects of the mammalian nucleolus. Bioessays 12 14–21. 10.1002/bies.950120104 PubMed DOI

Schmid M., Davison T. S., Henz S. R., Pape U. J., Demar M., Vingron M., et al. (2005). A gene expression map of Arabidopsis thaliana development. Nat. Genet. 37 501–506. 10.1038/ng1543 PubMed DOI

Schranz M. E., Mohammadin S., Edger P. P. (2012). Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model. Curr. Opin. Plant Biol. 15 147–153. 10.1016/j.pbi.2012.03.011 PubMed DOI

Schwarz D. S., Blower M. D. (2014). The calcium-dependent ribonuclease XendoU promotes ER network formation through local RNA degradation. J. Cell Biol. 207 41–57. 10.1083/jcb.201406037 PubMed DOI PMC

Shubina M. Y., Musinova Y. R., Sheval E. V. (2016). Nucleolar methyltransferase fibrillarin: evolution of structure and functions. Biochemistry 81 941–950. 10.1134/S0006297916090030 PubMed DOI

Snaar S., Wiesmeijer K., Jochemsen A. G., Tanke H. J., Dirks R. W. (2000). Mutational analysis of fibrillarin and its mobility in living human cells. J. Cell Biol. 151 653–662. 10.1083/jcb.151.3.653 PubMed DOI PMC

Sobol M., Yildirim S., Philimonenko V. V., Marasek P., Castano E., Hozak P. (2013). UBF complexes with phosphatidylinositol 4,5-bisphosphate in nucleolar organizer regions regardless of ongoing RNA polymerase I activity. Nucleus 4 478–486. 10.4161/nucl.27154 PubMed DOI PMC

Stijf-Bultsma Y., Sommer L., Tauber M., Baalbaki M., Giardoglou P., Jones D. R., et al. (2015). The basal transcription complex component TAF3 transduces changes in nuclear phosphoinositides into transcriptional output. Mol. Cell 58 453–467. 10.1016/j.molcel.2015.03.009 PubMed DOI PMC

Sugimoto K., Meyerowitz E. M. (2013). Regeneration in Arabidopsis tissue culture. Methods Mol. Biol. 959 265–275. 10.1007/978-1-62703-221-6_18 PubMed DOI

Tessarz P., Santos-Rosa H., Robson S. C., Sylvestersen K. B., Nelson C. J., Nielsen M. L., et al. (2014). Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated modification. Nature 505 564–568. 10.1038/nature12819 PubMed DOI PMC

Tiku V., Jain C., Raz Y., Nakamura S., Heestand B., Liu W., et al. (2016). Small nucleoli are a cellular hallmark of longevity. Nat. Commun. 8:16083. 10.1038/ncomms16083 PubMed DOI PMC

Tollervey D., Lehtonen H., Jansen R., Kern H., Hurt E. C. (1993). Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly. Cell 72 443–457. 10.1016/0092-8674(93)90120-F PubMed DOI

van den Bergh E., Hofberger J. A., Schranz M. E. (2016). Flower power and the mustard bomb: comparative analysis of gene and genome duplications in glucosinolate biosynthetic pathway evolution in Cleomaceae and Brassicaceae. Am. J. Bot. 103 1212–1222. 10.3732/ajb.1500445 PubMed DOI

Wang H., Boisvert D., Kim K. K., Kim R., Kim S. H. (2000). Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 A resolution. EMBO J. 19 317–323. 10.1093/emboj/19.3.317 PubMed DOI PMC

Yanagida M., Hayano T., Yamauchi Y., Shinkawa T., Natsume T., Isobe T., et al. (2004). Human fibrillarin forms a sub-complex with splicing factor 2-associated p32, protein arginine methyltransferases, and tubulins alpha 3 and beta 1 that is independent of its association with preribosomal ribonucleoprotein complexes. J. Biol. Chem. 279 1607–1614. 10.1074/jbc.M305604200 PubMed DOI

Yildirim S., Castano E., Sobol M., Philimonenko V. V., Dzijak R., Venit T., et al. (2013). Involvement of phosphatidylinositol 4,5-bisphosphate in RNA polymerase I transcription. J. Cell Sci. 126 2730–2739. 10.1242/jcs.123661 PubMed DOI

Yoo S. D., Cho Y. H., Sheen J. (2007). Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat. Protoc. 2 1565–1572. 10.1038/nprot.2007.199 PubMed DOI

Fibrillarin Ribonuclease Activity is Dependent on the GAR Domain and Modulated by Phospholipids