Abstract
Ebp2 plays an essential role in biogenesis of 60S ribosomal subunits. We determined the genetic interactions between EBP2 and RPL36A/B, which encodes ribosomal protein L36a/b. RPL36A/B was a multicopy suppressor to ebp2 mutants, and the suppression was not common to defects in ribosome biogenesis resulting from other mutations of assembly factors. Disruption of RPL36A or RPL36B caused synthetic enhancement of the growth defect of the ebp2-14 allele at high temperatures. Disruption of RPL36B led to a more severe growth defect than that of RPL36A due to imbalances in the expression levels of the duplicated genes. Primer-extension analysis revealed that L36a/b is required for the processing of 27SA2, 27SA3, and 27SBL pre-rRNAs. Two-hybrid analysis indicated that Ebp2 interacts with ribosomal proteins L36a/b, L34a/b, and L8, which in mature ribosomes are located adjacent to each other in close proximity to the 3′ end of 5.8S rRNA. These results suggest that Ebp2 functions cooperatively with ribosomal proteins L36, L34, and L8 in biogenesis of the 60S ribosomal subunit.
Similar content being viewed by others
Abbreviations
- BD:
-
lexA binding domain
- AD:
-
Gal4 activation domain
References
Baudin-Baillieu A, Tollervey D, Cullin C, Lacroute F (1997) Functional analysis of Rrp7p, an essential yeast protein involved in pre-rRNA processing and ribosome assembly. Mol Cell Biol 17:5023–5032
Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M (2011) The structure of the eukaryotic ribosome at 3.0 Å resolution. Science 334:1524–1529
Henras AK, Soudet J, Gérus M, Lebaron S, Caizergues-Ferrer M, Mougin A, Henry Y (2008) The post-transcriptional steps of eukaryotic ribosome biogenesis. Cell Mol Life Sci 65:2334–2359
Horigome C, Okada T, Matsuki K, Mizuta K (2008) A ribosome assembly factor Ebp2p, the yeast homologue of EBNA1-binding protein 2, is involved in the secretory response. Biosci Biotechnol Biochem 72:1080–1086
Jakovljevic J, Ohmayer U, Gamalinda M, Talkish J, Alexander L, Linnemann J, Milkereit P, Woolford JL Jr (2012) Ribosomal proteins L7 and L8 function in concert with six A3 assembly factors to propagate assembly of domains I and II of 25S rRNA in yeast 60S ribosomal subunits. RNA 18:1805–1822
Kaiser C, Michaelis S, Mitchell A (1994) Methods in yeast genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
Komili S, Farny NG, Roth FP, Silver PA (2007) Functional specificity among ribosomal proteins regulates gene expression. Cell 131:557–571
Kressler D, Hurt E, Baßler J (2010) Driving ribosome assembly. Biochim Biophys Acta 1803:673–683
Lee JC, Henry B, Yeh YC (1983) Binding of proteins from the large ribosomal subunits to 5.8S rRNA of Saccharomyces cerevisiae. J Biol Chem 258:854–858
Lucioli A, Presutti C, Ciafrè S, Caffarelli E, Fragapane P, Bozzoni I (1988) Gene dosage alteration of L2 ribosomal protein genes in Saccharomyces cerevisiae: effects on ribosome synthesis. Mol Cell Biol 8:4792–4798
Mager WH, Planta RJ, Ballesta JG, Lee JC, Mizuta K, Suzuki K, Warner JR, Woolford JL Jr (1997) A new nomenclature for the cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Nucleic Acids Res 25:4872–4875
Miyoshi K, Tsujii R, Yoshida H, Maki Y, Wada A, Matsui Y, Toh-e A, Mizuta K (2002) Normal assembly of 60S ribosomal subunits is required for the signaling in response to a secretory defect in Saccharomyces cerevisiae. J Biol Chem 277:18334–18339
Miyoshi K, Shirai C, Horigome C, Takenami K, Kawasaki J, Mizuta K (2004) Rrs1p, a ribosomal protein L11-binding protein, is required for nuclear export of the 60S pre-ribosomal subunit in Saccharomyces cerevisiae. FEBS Lett 565:106–110
Mizuta K, Warner JR (1994) Continued functioning of the secretory pathway is essential for ribosome synthesis. Mol Cell Biol 14:2493–2502
Morita D, Miyoshi K, Matsui Y, Toh-e A, Shinkawa H, Miyakawa T, Mizuta K (2002) Rpf2p, an evolutionarily conserved protein, interacts with ribosomal protein L11 and is essential for the processing of 27SB pre-rRNA to 25S rRNA and the 60S ribosomal subunit assembly in Saccharomyces cerevisiae. J Biol Chem 277:28780–28786
Nariai M, Tanaka T, Okada T, Shirai C, Horigome C, Mizuta K (2005) Synergistic defect in 60S ribosomal subunit assembly caused by a mutation of Rrs1p, a ribosomal protein L11-binding protein, and 3′-extension of 5S rRNA in Saccharomyces cerevisiae. Nucleic Acids Res 33:4553–4562
Ni L, Snyder M (2001) A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell 12:2147–2170
Parenteau J, Durand M, Morin G, Gagnon J, Lucier JF, Wellinger RJ, Chabot B, Elela SA (2011) Introns within ribosomal protein genes regulate the production and function of yeast ribosomes. Cell 147:320–331
Pratte D, Singh U, Murat G, Kressler D (2013) Mak5 and Ebp2 act together on early pre-60S particles and their reduced functionality bypasses the requirement for the essential pre-60S factor Nsa1. PLoS One 8:e82741
Rotenberg MO, Moritz M, Woolford JL Jr (1988) Depletion of Saccharomyces cerevisiae ribosomal protein L16 causes a decrease in 60S ribosomal subunits and formation of half-mer polyribosomes. Genes Dev 2:160–172
Shimoji K, Jakovljevic J, Tsuchihashi K, Umeki Y, Wan K, Kawasaki S, Talkish J, Woolford JL Jr, Mizuta K (2012) Ebp2 and Brx1 function cooperatively in 60S ribosomal subunit assembly in Saccharomyces cerevisiae. Nucleic Acids Res 40:4574–4588
Shirai C, Mizuta K (2008) SUMO mediates interaction of Ebp2p, the yeast homolog of Epstein-Barr virus nuclear antigen 1-binding protein 2, with a RING finger protein Ris1p. Biosci Biotechnol Biochem 72:1881–1886
Shirai C, Takai T, Nariai M, Horigome C, Mizuta K (2004) Ebp2p, the yeast homolog of Epstein–Barr virus nuclear antigen1-binding protein2, interacts with factors of both the 60S and the 40S ribosomal subunit assembly. J Biol Chem 279:25353–25358
Steffen KK, MacKay VL, Kerr EO, Tsuchiya M, Hu D, Fox LA, Dang N, Johnston ED, Oakes JA, Tchao BN, Pak DN, Fields S, Kennedy BK, Kaeberlein M (2008) Yeast life span extension by depletion of 60S ribosomal subunits is mediated by Gcn4. Cell 133:292–302
Talkish J, Campbell IW, Sahasranaman A, Jakovljevic J, Woolford JL Jr (2014) Ribosome assembly factors Pwp1 and Nop12 are important for folding of 5.8S rRNA during ribosome biogenesis in Saccharomyces cerevisiae. Mol Cell Biol 34:1863–1877
Tsuchiya E, Matsuzaki G, Kurano K, Fukuchi T, Tsukao A, Miyakawa T (1996) The Saccharomyces cerevisiae SSD1 gene is involved in the tolerance to high concentration of Ca2+ with the participation of HST1/NRC1/BFR1. Gene 176:35–38
Tsujii R, Miyoshi K, Tsuno A, Matsui Y, Toh-e A, Miyakawa T, Mizuta K (2000) Ebp2p, yeast homologue of a human protein that interacts with Epstein–Barr virus Nuclear Antigen 1, is required for pre-rRNA processing and ribosomal subunit assembly. Genes Cells 5:543–553
Tsuno A, Miyoshi K, Tsujii R, Miyakawa T, Mizuta K (2000) RRS1, a conserved essential gene, encodes a novel regulatory protein required for ribosome biogenesis in Saccharomyces cerevisiae. Mol Cell Biol 20:2066–2074
Wan K, Tsuchihashi K, Kanda K, Shimoji K, Mizuta K (2013) N α-Acetyltransferase NatA is involved in ribosome synthesis in Saccharomyces cerevisiae. Biosci Biotechnol Biochem 77:631–638
Wehner KA, Baserga SJ (2002) The σ70-like motif: a eukaryotic RNA binding domain unique to a superfamily of proteins required for ribosome biogenesis. Mol Cell 9:329–339
Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708–713
Zhang W, Morris QD, Chang R, Shai O, Bakowski MA, Mitsakakis N, Mohammad N, Robinson MD, Zirngibl R, Somogyi E, Laurin N, Eftekharpour E, Sat E, Grigull J, Pan Q, Peng WT, Krogan N, Greenblatt J, Fehlings M, van der Kooy D, Aubin J, Bruneau BG, Rossant J, Blencowe BJ, Frey BJ, Hughes TR (2004) The functional landscape of mouse gene expression. J Biol 3:21
Zhang J, Harnpicharnchai P, Jakovljevic J, Tang L, Guo Y, Oeffinger M, Rout MP, Hiley SL, Hughes T, Woolford JL Jr (2007) Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes. Genes Dev 21:2580–2592
Acknowledgments
We thank K. Kanda for screening of multicopy suppressors, Dr. E. Tsuchiya for the yeast genomic library, Dr. J. L. Woolford, Jr., Dr. D. Shore, and Dr. K. Tanaka for plasmids, and Dr. K. Funato for helpful discussion. This work was supported by JSPS KAKENHI Grant Number 25450516 (to K.M.).
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by P. Sunnerhagen.
Rights and permissions
About this article
Cite this article
Wan, K., Yabuki, Y. & Mizuta, K. Roles of Ebp2 and ribosomal protein L36 in ribosome biogenesis in Saccharomyces cerevisiae . Curr Genet 61, 31–41 (2015). https://doi.org/10.1007/s00294-014-0442-1
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00294-014-0442-1