Structural dynamics of the yeast Shwachman-Diamond syndrome protein (Sdo1) on the ribosome and its implication in the 60S subunit maturation

Abstract

The human Shwachman-Diamond syndrome (SDS) is an autosomal recessive disease caused by mutations in a highly conserved ribosome assembly factor SBDS. The functional role of SBDS is to cooperate with another assembly factor, elongation factor 1-like (Efl1), to promote the release of eukaryotic initiation factor 6 (eIF6) from the late-stage cytoplasmic 60S precursors. In the present work, we characterized, both biochemically and structurally, the interaction between the 60S subunit and SBDS protein (Sdo1p) from yeast. Our data show that Sdo1p interacts tightly with the mature 60S subunit in vitro through its domain I and II, and is capable of bridging two 60S subunits to form a stable 2:2 dimer. Structural analysis indicates that Sdo1p bind to the ribosomal P-site, in the proximity of uL16 and uL5, and with direct contact to H69 and H38. The dynamic nature of Sdo1p on the 60S subunit, together with its strategic binding position, suggests a surveillance role of Sdo1p in monitoring the conformational maturation of the ribosomal P-site. Altogether, our data support a conformational signal-relay cascade during late-stage 60S maturation, involving uL16, Sdo1p, and Efl1p, which interrogates the functional P-site to control the departure of the anti-association factor eIF6.

Key words： ribosome biogenesis; SBDS; SDS; Sdo1; cryo-electron microscopy (cryo-EM)

References

1 Asano N, Atsuumi H, Nakamura A, Tanaka Y, Tanaka I, Yao M (2014) Direct interaction between EFL1 and SBDS is mediated by an intrinsically disordered insertion domain. Biochem Biophys Res Commun 443:1251–1256

2 Austin KM, Leary RJ, Shimamura A (2005) The shwachmandiamond SBDS protein localizes to the nucleolus. Blood 106:1253–1258

3 Ball HL, Zhang B, Riches JJ, Gandhi R, Li J, Rommens JM, Myers JS (2009) Shwachman-Bodian diamond syndrome is a multi-functional protein implicated in cellular stress responses. Hum Mol Genet 18:3684–3695

4 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 a resolution. Science 334:1524–1529

5 Bernstein KA, Bleichert F, Bean JM, Cross FR, Baserga SJ (2007) Ribosome biogenesisis sensed at the start cell cycle checkpoint. Mol Biol Cell 18:953–964

6 Boocock GR, Morrison JA, Popovic M, Richards N, Ellis L, Durie PR, Rommens JM (2003) Mutations in SBDS are associated with Shwachman-Diamond syndrome. Nat Genet 33:97–101

7 Boocock GR, Marit MR, Rommens JM(2006) Phylogeny, sequence conservation, and functional complementation of the SBDS protein family. Genomics 87:758–771

8 Boulon S, Westman BJ, Hutten S, Boisvert FM, Lamond AI (2010) The nucleolus under stress. Mol Cell 40:216–227

9 Bradatsch B, Leidig C, Granneman S, Gnadig M, Tollervey D, Bottcher B, Beckmann R, Hurt E(2012) Structureof the pre-60S ribosomal subunit with nuclear export factor Arx1 bound at the exit tunnel. Nat Struct Mol Biol 19:1234–1241

10 Burwick N, Coats SA, Nakamura T, Shimamura A (2012) Impaired ribosomal subunit association in Shwachman-Diamond syndrome. Blood 120:5143–5152

11 Bussiere C, Hashem Y, Arora S, Frank J, Johnson AW (2012) Integrity of the P-site is probed during maturation of the 60S ribosomal subunit. J Cell Biol 197:747–759

12 Chakraborty A, Uechi T, Kenmochi N (2011) Guarding the ‘translation apparatus’: defective ribosome biogenesis and the p53 signaling pathway. Wiley interdiscip Rev RNA 2:507–522

13 de JFOliveira ML, Sforca TM, Blumenschein MB, Goldfeder BG, Guimaraes CC, Oliveira NI, Zanchin AC, Zeri (2010) Structure, dynamics, and RNA interaction analysis of the human SBDS protein. J Mol Biol 396:1053–1069

14 Deisenroth C, Zhang Y (2010) Ribosome biogenesis surveillance: probing the ribosomal protein-Mdm2-p53 pathway. Oncogene 29:4253–4260

15 Dez C, Tollervey D(2004) Ribosome synthesis meets the cell cycle. Curr Opin Microbiol 7:631–637

16 Finch AJ, Hilcenko C, Basse N, Drynan LF, Goyenechea B, Menne TF, Gonzalez Fernandez A, Simpson P, D’Santos CS, Arends MJ (2011) Uncoupling of GTP hydrolysis from eIF6 release on the ribosome causes Shwachman-Diamond syndrome. Genes Dev 25:917–929

17 Freed EF, Bleichert F, Dutca LM, Baserga SJ (2010) When ribosomes go bad: diseases of ribosome biogenesis. Mol BioSyst 6:481–493

18 Gamalinda M, Ohmayer U, Jakovljevic J, Kumcuoglu B, Woolford J, Mbom B, Lin L, Woolford JL Jr (2014) A hierarchical model for assembly of eukaryotic 60S ribosomal subunit domains. Genes Dev 28:198–210

19 Ganapathi KA, Austin KM, Lee CS, Dias A, Malsch MM, Reed R, Shimamura A (2007) The human Shwachman-Diamond syndrome protein, SBDS, associates with ribosomal RNA. Blood 110:1458–1465

20 Gartmann M, Blau M, Armache JP, Mielke T, Topf M, Beckmann R (2010) Mechanism of eIF6-mediated inhibition of ribosomal subunit joining. J Biol Chem 285:14848–14851

21 Gijsbers A, Garcia-Marquez A, Luviano A, Sanchez-Puig N (2013) Guanine nucleotide exchange in the ribosomal GTPase EFL1 is modulated by the protein mutated in the Shwachman-Diamond syndrome. Biochem Biophys Res Commun 437:349–354

22 Greber BJ, Boehringer D, Montellese C, Ban N (2012) Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit. Nat Struct Mol Biol 19:1228–1233

23 Hedges J, West M, Johnson AW (2005) Release of the export adapter, Nmd3p, from the 60S ribosomal subunit requires Rpl10p and the cytoplasmic GTPase Lsg1p. EmboJ 24:567–579

24 Holmberg KOlausson M, Nister MS, Lindstrom(2012)p53-dependent and-independent nucleolar stress responses. Cells 1:774–798

25 Jomaa A, Jain N, Davis JH, Williamson JR, Britton RA, Ortega J (2014) Functional domains of the 50S subunit mature late in the assembly process. Nucl Acids Res 42:3419–3435

26 Jorgensen P, Nishikawa JL, Breitkreutz BJ, Tyers M (2002) Systematic identification of pathways that couple cell growth and division in yeast. Science 297:395–400

27 Karbstein K (2013) Quality control mechanisms during ribosome maturation. Trends Cell Biol 23:242–250

28 Klinge S, Voigts-Hoffmann F, Leibundgut M, Arpagaus S, Ban N (2011) Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6. Science 334:941–948

29 Krokowski D, Gaccioli F, Majumder M, Mullins MR, Yuan CL, Papadopoulou B, Merrick WC, Komar AA, Taylor D, Hatzoglou M (2011) Characterization of hibernating ribosomes in mammalian cells. Cell Cycle 10:2691–2702

30 Lebaron S, Schneider C, van RWNues A, Swiatkowska D, Walsh B, Bottcher S, Granneman NJ, Watkins D, Tollervey (2012) Proofreading of pre-40S ribosome maturation by a translation initiation factor and 60S subunits. Nat Struct Mol Biol 19:744–753

31 Lei J, Frank J (2005) Automated acquisition of cryo-electron micrographs for single particle reconstruction on an FEI Tecnai electron microscope. J Struct Biol 150:69–80

32 Leidig C, Thoms M, Holdermann I, Bradatsch B, Berninghausen O, Bange G, Sinning I, Hurt E, Beckmann R (2014) 60S ribosome biogenesis requires rotation of the 5S ribonucleoprotein particle. Nat Commun 5:3491

33 Li N, Chen Y, Guo Q, Zhang Y, Yuan Y, Ma C, Deng H, Lei J, Gao N (2013) Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit . Nucl Acids Res 41:7073–7083

34 Lo KY, Li Z, Bussiere C, Bresson S, Marcotte EM, Johnson AW (2010) Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit. Mol Cell 39:196–208

35 Luz JS, Georg RC, Gomes CH, Machado-Santelli GM, Oliveira CC (2009) Sdo1p, the yeast orthologue of Shwachman-Bodian-Diamond syndrome protein, binds RNA and interacts with nuclear rRNA-processing factors. Yeast 26:287–298

36 Matsuo Y, Granneman S, Thoms M, Manikas RG, Tollervey D, Hurt E (2014) Coupled GTPase and remodelling ATPase activities form a checkpoint for ribosome export. Nature 505:112–116

37 Menne TF, Goyenechea B, Sanchez-Puig N, Wong CC, Tonkin LM, Ancliff PJ, Brost RL, Costanzo M, Boone C, Warren AJ(2007)The Shwachman-Bodian-Diamond syndrome protein mediates translational activation of ribosomesinyeast. NatGenet 39:486–495

38 Miluzio A, Beugnet A, Volta V, Biffo S (2009) Eukaryotic initiation factor6mediatesa continuum between 60S ribosome biogenesis and translation. EMBO Rep 10:459–465

39 Montanaro L, Trere D, Derenzini M (2008) Nucleolus, ribosomes, and cancer. Am J Pathol 173:301–310

40 Moore JBT, Farrar JE, Arceci RJ, Liu JM, Ellis SR (2010) Distinct ribosome maturation defects in yeast models of Diamond-Blackfan anemia and Shwachman-Diamond syndrome. Haematologica 95:57–64

41 Nakhoul H, Ke J, Zhou X, Liao W, Zeng SX, Lu H (2014) Ribosomopathies: mechanisms of disease. Clin Med Insights Blood Disorders 7:7–16

42 Narla A, Ebert BL (2010) Ribosomopathies: human disorders of ribosome dysfunction. Blood1 15:3196–3205

43 Ng CL, Waterman DG, Koonin EV, Walters AD, Chong JP, Isupov MN, Lebedev AA, Bunka DH, Stockley PG, Ortiz-Lombardia M (2009) Conformational flexibility and molecular interactions of an archaeal homologue of the Shwachman-Bodian-Diamond syndrome protein. BMC Struct Biol 9:32

44 Panse VG, Johnson AW(2010) Maturation of eukaryotic ribosomes: acquisition of functionality. Trends Biochem Sci 35:260–266

45 Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612

46 Rath BK, Frank J (2004) Fast automatic particle picking from cryoelectron micrographs using a locally normalized cross-correlation function:a case study. J Struct Biol 145:84–90

47 Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5:725–738

48 Ruggero D, Pandolfi PP (2003) Does the ribosome translate cancer ? Nat Rev Cancer 3:179–192

49 Savchenko A, Krogan N, Cort JR, Evdokimova E, Lew JM, Yee AA, Sanchez-Pulido L, Andrade MA, Bochkarev A, Watson JD (2005) The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism. J Biol Chem 280:19213–19220

50 Scheres SHW (2012) RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol 180:519–530

51 Scheres SHW, Nunez-Ramirez R, Sorzano COS, Carazo JM, Marabini R (2008) Image processing for electron microscopy single-particle analysis using XMIPP. Nat Protoc 3:977–990

52 Shaikh TR, Gao H, Baxter WT, Asturias FJ, Boisset N, Leith A, Frank J (2008) SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micro-graphs. Nat Protoc 3:1941–1974

53 Shammas C, Menne TF, Hilcenko C, Michell SR, Goyenechea B, Boocock GR, Durie PR, Rommens JM, Warren AJ (2005) Structural and mutational analysis of the SBDS protein family. Insight into the leukemia-associated Shwachman-Diamond Syndrome. J Biol Chem 280:19221–19229

54 Singh P, Panchaud A, Goodlett DR (2010) Chemical cross-linking and mass spectrometry as a low-resolution protein structure determination technique. Anal Chem 82:2636–2642

55 Soudet J, Gelugne JP, Belhabich-Baumas K, Caizergues-Ferrer M, Mougin A(2010) Immature small ribosomal subunits can engagein translation initiationin Saccharomycescerevisiae. EMBOJ 29:80–92

56 Strunk BS, Novak MN, Young CL, Karbstein K (2012)Atranslationlike cycle is a quality control checkpoint for maturing 40S ribosome subunits. Cell 150:111–121

57 Sulima SO, Gulay SP, Anjos M, Patchett S, Meskauskas A, Johnson AW, Dinman JD (2014a) Eukaryotic rpL10 drives ribosomal rotation. Nucl Acids Res 42:2049–2063

58 Sulima SO, Patchett S, Advani VM, De KKeersmaecker AW, Johnson JD, Dinman (2014b) Bypass of the pre-60S ribosomal quality control as a pathway to oncogenesis. Proc Natl Acad Sci USA 111:5640–5645

59 Tang G, Peng L, Baldwin PR, Mann DS, Jiang W, Rees I, Ludtke SJ (2007) EMAN2: An extensible image processing suite for electron microscopy. J Struct Biol 157:38–46

60 Teng T, Thomas G, Mercer CA (2013) Growth control and ribosomopathies. Curr Opin Genet Dev 23:63–71

61 Ueta M, Yoshida H, Wada C, Baba T, Mori H, Wada A (2005) Ribosome binding proteins YhbH and YfiA have opposite functions during 100S formation in the stationary phase of Escherichia coli. Genes Cells 10:1103–1112

62 Vitiello SP, Benedict JW, Padilla-Lopez S, Pearce DA (2010) Interaction between Sdo1p and Btn1p in the Saccharomyces cerevisiae model for Batten disease. Hum Mol Genet 19:931–942

63 Wada A, Igarashi K, Yoshimura S, Aimoto S, Ishihama A (1995) Ribosome modulation factor: stationary growth phase-specific inhibitor of ribosome functions from Escherichia coli. Biochem Biophys Res Commun 214:410–417

64 Watanabe KI, Dror Y (2005) Characterization of siRNA-mediated SBDS-knockdown cells: Specific hypersensitivity to Fas stimulation. Blood 106:116a

65 Watanabe K, Ambekar C, Wang H, Ciccolini A, Schimmer AD, Dror Y (2009) SBDS-deficiency results in specific hypersensitivity to Fas stimulation and accumulation of Fas at the plasma membrane. Apoptosis 14:77–89

66 Weis F, Giudice E, Churcher M, Jin L, Hilcenko C, Wong CC, Traynor D, Kay RR, Warren AJ (2015) Mechanism of eIF6 release from the nascent 60S ribosomal subunit. Nat Struct Mol Biol 22:914–919

67 West M, Hedges JB, Chen A, Johnson AW(2005)Defining the order in which Nmd3p and Rpl10p load onto nascent 60S ribosomal subunits. Mol Cell Biol 25:3802–3813

68 Wong CC, Traynor D, Basse N, Kay RR, Warren AJ(2011) Defective ribosome assembly in Shwachman-Diamond syndrome. Blood 118:4305–4312

69 Woolford JL Jr, Baserga SJ (2013) Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics 195:643–681

70 Yang B, Wu YJ, Zhu M, Fan SB, Lin J, Zhang K, Li S, Chi H, Li YX, Chen HF (2012) Identification of cross-linked peptides from complex samples. Nat Methods 9:904–906

71 Yoshida H, Wada A (2014) The 100S ribosome: ribosomal hibernation induced by stress. Wiley Interdiscip Rev RNA 5:723–732

72 Zhang X, Yan K, Zhang Y, Li N, Ma C, Li Z, Zhang Y, Feng B, Liu J, Sun Y (2014a) Structural insights into the function of a unique tandem GTPase EngA in bacterial ribosome assembly. Nucl Acids Res 42:13430–13439

73 Zhang Y, Ma C, Yuan Y, Zhu J, Li N, Chen C, Wu S, Yu L, Lei J, Gao N (2014b) Structural basis for interaction of a cotranslational chaperone with the eukaryotic ribosome. Nat struct Mol Biol 21:1042–1046