2.8-Å Cryo-EM Structure of the Large Ribosomal Subunit from the Eukaryotic Parasite Leishmania

Cell Reports

Volumn 16, Issue 2, 2016, Pages 288-294

  Shalev Benami, Moran ^a   Zhang, Yan ^b   Matzov, Donna ^a   Halfon, Yehuda ^a   Zackay, Arie ^c   Rozenberg, Haim ^a   Zimmerman, Ella ^a   Bashan, Anat ^a   Jaffe, Charles L ^c   Yonath, Ada ^a   Skiniotis, Georgios ^b  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^c HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

GUANOSINE TRIPHOSPHATASE; RIBOSOME RNA; PROTOZOAL PROTEIN; PROTOZOAL RNA; RIBOSOME PROTEIN;

ARTICLE; CELL STRUCTURE; CONTROLLED STUDY; CRYOELECTRON MICROSCOPY; DNA FRAGMENTATION; KINETOPLASTIDA; LEISHMANIA DONOVANI; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROMASTIGOTE; PROMOTER REGION; PROTEIN ASSEMBLY; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN LOCALIZATION; RIBOSOME; RNA ANALYSIS; CHEMISTRY; CONFORMATION; LARGE RIBOSOMAL SUBUNIT; MOLECULAR MODEL; PROTEIN QUATERNARY STRUCTURE; ULTRASTRUCTURE;

CRYOELECTRON MICROSCOPY; LEISHMANIA DONOVANI; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN STRUCTURE, QUATERNARY; PROTOZOAN PROTEINS; RIBOSOMAL PROTEINS; RIBOSOME SUBUNITS, LARGE; RNA, PROTOZOAN; RNA, RIBOSOMAL;

EID: 84978511982     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2016.06.014     Document Type: Article

References (27)

1. Afonine, P.V., Headd, J.J., Terwilliger, T.C., Adams, P.D., New tool: phenix.real_space_refine. Computational Crystallography Newsletter 4 (2013), 43–44.
2. Ben-Shem, A., Garreau de Loubresse, N., Melnikov, S., Jenner, L., Yusupova, G., Yusupov, M., The structure of the eukaryotic ribosome at 3.0 Å resolution. Science 334 (2011), 1524–1529.
3. Brown, A., Shao, S., Murray, J., Hegde, R.S., Ramakrishnan, V., Structural basis for stop codon recognition in eukaryotes. Nature 524 (2015), 493–496.
4. Demirci, H., Murphy, F. 4th, Belardinelli, R., Kelley, A.C., Ramakrishnan, V., Gregory, S.T., Dahlberg, A.E., Jogl, G., Modification of 16S ribosomal RNA by the KsgA methyltransferase restructures the 30S subunit to optimize ribosome function. RNA 16 (2010), 2319–2324.
5. Eliaz, D., Doniger, T., Tkacz, I.D., Biswas, V.K., Gupta, S.K., Kolev, N.G., Unger, R., Ullu, E., Tschudi, C., Michaeli, S., Genome-wide analysis of small nucleolar RNAs of Leishmania major reveals a rich repertoire of RNAs involved in modification and processing of rRNA. RNA Biol. 12 (2015), 1222–1255.
6. Emsley, P., Lohkamp, B., Scott, W.G., Cowtan, K., Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66 (2010), 486–501.
7. Fernandez-Rodrigez, J.C., Godinho, J.L., de Souza, W., Biology of human pathogenic trypanosomatids: epidemiology, lifecycle and ultrastructure. Subcell. Biochem. 74 (2014), 1–42.
8. Fischer, N., Neumann, P., Konevega, A.L., Bock, L.V., Ficner, R., Rodnina, M.V., Stark, H., Structure of the E. coli ribosome-EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM. Nature 520 (2015), 567–570.
9. Gamalinda, M., Ohmayer, U., Jakovljevic, J., Kumcuoglu, B., Woolford, J., Mbom, B., Lin, L., Woolford, J.L. Jr., A hierarchical model for assembly of eukaryotic 60S ribosomal subunit domains. Genes Dev. 28 (2014), 198–210.
10. Gao, H., Ayub, M.J., Levin, M.J., Frank, J., The structure of the 80S ribosome from Trypanosoma cruzi reveals unique rRNA components. Proc. Natl. Acad. Sci. USA 102 (2005), 10206–10211.
11. Green, R., Noller, H.F., In vitro complementation analysis localizes 23S rRNA posttranscriptional modifications that are required for Escherichia coli 50S ribosomal subunit assembly and function. RNA 2 (1996), 1011–1021.
12. Hashem, Y., des Georges, A., Fu, J., Buss, S.N., Jossinet, F., Jobe, A., Zhang, Q., Liao, H.Y., Grassucci, R.A., Bajaj, C., et al. High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Nature 494 (2013), 385–389.
13. Hernández, R., Cevallos, A.M., Ribosomal RNA gene transcription in trypanosomes. Parasitol. Res. 113 (2014), 2415–2424.
14. Khatter, H., Myasnikov, A.G., Natchiar, S.K., Klaholz, B.P., Structure of the human 80S ribosome. Nature 520 (2015), 640–645.
15. Lafontaine, D.L.J., Noncoding RNAs in eukaryotic ribosome biogenesis and function. Nat. Struct. Mol. Biol. 22 (2015), 11–19.
16. Liang, X.H., Uliel, S., Hury, A., Barth, S., Doniger, T., Unger, R., Michaeli, S., A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA modification. RNA 11 (2005), 619–645.
17. Michaeli, S., Doniger, T., Gupta, S.K., Wurtzel, O., Romano, M., Visnovezky, D., Sorek, R., Unger, R., Ullu, E., RNA-seq analysis of small RNPs in Trypanosoma brucei reveals a rich repertoire of non-coding RNAs. Nucleic Acids Res. 40 (2012), 1282–1298.
18. Piekna-Przybylska, D., Decatur, W.A., Fournier, M.J., The 3D rRNA modification maps database: with interactive tools for ribosome analysis. Nucleic Acids Res. 36 (2008), D178–D183.
19. Polikanov, Y.S., Melnikov, S.V., Söll, D., Steitz, T.A., Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly. Nat. Struct. Mol. Biol. 22 (2015), 342–344.
20. Rabl, J., Leibundgut, M., Ataide, S.F., Haag, A., Ban, N., Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1. Science 331 (2011), 730–736.
21. Scheres, S.H., RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180 (2012), 519–530.
22. Schmeing, T.M., Huang, K.S., Kitchen, D.E., Strobel, S.A., Steitz, T.A., Structural insights into the roles of water and the 2′ hydroxyl of the P site tRNA in the peptidyl transferase reaction. Mol. Cell 20 (2005), 437–448.
23. Schmidt, C., Becker, T., Heuer, A., Braunger, K., Shanmuganathan, V., Pech, M., Berninghausen, O., Wilson, D.N., Beckmann, R., Structure of the hypusinylated eukaryotic translation factor eIF-5A bound to the ribosome. Nucleic Acids Res. 44 (2016), 1944–1951.
24. Strunk, B.S., Loucks, C.R., Su, M., Vashisth, H., Cheng, S., Schilling, J., Brooks, C.L. 3rd, Karbstein, K., Skiniotis, G., Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates. Science 333 (2011), 1449–1453.
25. Wong, W., Bai, X.C., Brown, A., Fernandez, I.S., Hanssen, E., Condron, M., Tan, Y.H., Baum, J., Scheres, S.H., Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine. eLife, 3, 2014, e03080.
26. Woolford, J.L. Jr., Baserga, S.J., Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics 195 (2013), 643–681.
27. Yip, W.S., Vincent, N.G., Baserga, S.J., Ribonucleoproteins in archaeal pre-rRNA processing and modification. Archaea, 2013, 2013, 614735.