1
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Parker MD, Karbstein K. Quality control ensures fidelity in ribosome assembly and cellular health. J Cell Biol 2023; 222:213871. [PMID: 36790396 PMCID: PMC9960125 DOI: 10.1083/jcb.202209115] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/09/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
The coordinated integration of ribosomal RNA and protein into two functional ribosomal subunits is safeguarded by quality control checkpoints that ensure ribosomes are correctly assembled and functional before they engage in translation. Quality control is critical in maintaining the integrity of ribosomes and necessary to support healthy cell growth and prevent diseases associated with mistakes in ribosome assembly. Its importance is demonstrated by the finding that bypassing quality control leads to misassembled, malfunctioning ribosomes with altered translation fidelity, which change gene expression and disrupt protein homeostasis. In this review, we outline our understanding of quality control within ribosome synthesis and how failure to enforce quality control contributes to human disease. We first provide a definition of quality control to guide our investigation, briefly present the main assembly steps, and then examine stages of assembly that test ribosome function, establish a pass-fail system to evaluate these functions, and contribute to altered ribosome performance when bypassed, and are thus considered "quality control."
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Affiliation(s)
- Melissa D. Parker
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA,University of Florida—Scripps Biomedical Research, Jupiter, FL, USA
| | - Katrin Karbstein
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA,University of Florida—Scripps Biomedical Research, Jupiter, FL, USA,Howard Hughes Medical Institute Faculty Scholar, Howard Hughes Medical Institute, Chevy Chase, MD, USA,Correspondence to Katrin Karbstein:
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2
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A Comparative Molecular Dynamics Study of Selected Point Mutations in the Shwachman–Bodian–Diamond Syndrome Protein SBDS. Int J Mol Sci 2022; 23:ijms23147938. [PMID: 35887285 PMCID: PMC9320453 DOI: 10.3390/ijms23147938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/15/2022] [Accepted: 07/17/2022] [Indexed: 01/27/2023] Open
Abstract
The Shwachman–Diamond Syndrome (SDS) is an autosomal recessive disease whose majority of patients display mutations in a ribosome assembly protein named Shwachman–Bodian–Diamond Syndrome protein (SBDS). A specific therapy for treating this rare disease is missing, due to the lack of knowledge of the molecular mechanisms responsible for its pathogenesis. Starting from the observation that SBDS single-point mutations, localized in different domains of the proteins, are responsible for an SDS phenotype, we carried out the first comparative Molecular Dynamics simulations on three SBDS mutants, namely R19Q, R126T and I212T. The obtained 450-ns long trajectories were compared with those returned by both the open and closed forms of wild type SBDS and strongly indicated that two distinct conformations (open and closed) are both necessary for the proper SBDS function, in full agreement with recent experimental observations. Our study supports the hypothesis that the SBDS function is governed by an allosteric mechanism involving domains I and III and provides new insights into SDS pathogenesis, thus offering a possible starting point for a specific therapeutic option.
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3
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Bauer JA, Pavlović J, Bauerová-Hlinková V. Normal Mode Analysis as a Routine Part of a Structural Investigation. Molecules 2019; 24:molecules24183293. [PMID: 31510014 PMCID: PMC6767145 DOI: 10.3390/molecules24183293] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Normal mode analysis (NMA) is a technique that can be used to describe the flexible states accessible to a protein about an equilibrium position. These states have been shown repeatedly to have functional significance. NMA is probably the least computationally expensive method for studying the dynamics of macromolecules, and advances in computer technology and algorithms for calculating normal modes over the last 20 years have made it nearly trivial for all but the largest systems. Despite this, it is still uncommon for NMA to be used as a component of the analysis of a structural study. In this review, we will describe NMA, outline its advantages and limitations, explain what can and cannot be learned from it, and address some criticisms and concerns that have been voiced about it. We will then review the most commonly used techniques for reducing the computational cost of this method and identify the web services making use of these methods. We will illustrate several of their possible uses with recent examples from the literature. We conclude by recommending that NMA become one of the standard tools employed in any structural study.
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Affiliation(s)
- Jacob A Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia.
| | - Jelena Pavlović
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Vladena Bauerová-Hlinková
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
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4
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Proteins of the Nucleolus of Dictyostelium discoideum: Nucleolar Compartmentalization, Targeting Sequences, Protein Translocations and Binding Partners. Cells 2019; 8:cells8020167. [PMID: 30781559 PMCID: PMC6406644 DOI: 10.3390/cells8020167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 12/31/2022] Open
Abstract
The nucleoli of Dictyostelium discoideum have a comparatively unique, non-canonical, localization adjacent to the inner nuclear membrane. The verified nucleolar proteins of this eukaryotic microbe are detailed while other potential proteins are introduced. Heat shock protein 32 (Hsp32), eukaryotic translation initiation factor 6 (eIF6), and tumour necrosis factor receptor-associated protein 1 (TRAP1) are essential for cell survival. NumA1, a breast cancer type 1 susceptibility protein-C Terminus domain-containing protein linked to cell cycle, functions in the regulation of nuclear number. The cell cycle checkpoint kinase 2 homologue forkhead-associated kinase A (FhkA) and BRG1-associated factor 60a homologue Snf12 are also discussed. While nucleoli appear homogeneous ultrastructurally, evidence for nucleolar subcompartments exists. Nucleolar localization sequences (NoLS) have been defined that target proteins to either the general nucleolar area or to a specific intranucleolar domain. Protein translocations during mitosis are protein-specific and support the multiple functions of the Dictyostelium nucleolus. To enrich the picture, binding partners of NumA1, the most well-characterized nucleolar protein, are examined: nucleolar Ca2+-binding protein 4a (CBP4a), nuclear puromycin-sensitive aminopeptidase A (PsaA) and Snf12. The role of Dictyostelium as a model for understanding the contribution of nucleolar proteins to various diseases and cellular stress is discussed throughout the review.
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5
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Gijsbers A, Montagut DC, Méndez-Godoy A, Altamura D, Saviano M, Siliqi D, Sánchez-Puig N. Interaction of the GTPase Elongation Factor Like-1 with the Shwachman-Diamond Syndrome Protein and Its Missense Mutations. Int J Mol Sci 2018; 19:E4012. [PMID: 30545121 PMCID: PMC6321010 DOI: 10.3390/ijms19124012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 12/06/2018] [Accepted: 12/08/2018] [Indexed: 12/14/2022] Open
Abstract
The Shwachman-Diamond Syndrome (SDS) is a disorder arising from mutations in the genes encoding for the Shwachman-Bodian-Diamond Syndrome (SBDS) protein and the GTPase known as Elongation Factor Like-1 (EFL1). Together, these proteins remove the anti-association factor eIF6 from the surface of the pre-60S ribosomal subunit to promote the formation of mature ribosomes. SBDS missense mutations can either destabilize the protein fold or affect surface epitopes. The molecular alterations resulting from the latter remain largely unknown, although some evidence suggest that binding to EFL1 may be affected. We further explored the effect of these SBDS mutations on the interaction with EFL1, and showed that all tested mutations disrupted the binding to EFL1. Binding was either severely weakened or almost abolished, depending on the assessed mutation. In higher eukaryotes, SBDS is essential for development, and lack of the protein results in early lethality. The existence of patients whose only source of SBDS consists of that with surface missense mutations highlights the importance of the interaction with EFL1 for their function. Additionally, we studied the interaction mechanism of the proteins in solution and demonstrated that binding consists of two independent and cooperative events, with domains 2⁻3 of SBDS directing the initial interaction with EFL1, followed by docking of domain 1. In solution, both proteins exhibited large flexibility and consisted of an ensemble of conformations, as demonstrated by Small Angle X-ray Scattering (SAXS) experiments.
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Affiliation(s)
- Abril Gijsbers
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México 04510, Mexico.
| | - Diana Carolina Montagut
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México 04510, Mexico.
| | - Alfonso Méndez-Godoy
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México 04510, Mexico.
| | - Davide Altamura
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Michele Saviano
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Dritan Siliqi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Nuria Sánchez-Puig
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México 04510, Mexico.
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6
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Conformational Flexibility of Proteins Involved in Ribosome Biogenesis: Investigations via Small Angle X-ray Scattering (SAXS). CRYSTALS 2018. [DOI: 10.3390/cryst8030109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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7
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The Crystal Structure and Conformations of an Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages. J Mol Biol 2017; 429:3801-3813. [PMID: 29111344 DOI: 10.1016/j.jmb.2017.10.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/22/2017] [Accepted: 10/24/2017] [Indexed: 11/23/2022]
Abstract
The ability of ubiquitin to function in a wide range of cellular processes is ascribed to its capacity to cause a diverse spectrum of modifications. While a target protein can be modified with monoubiquitin, it can also be modified with ubiquitin chains. The latter include seven types of homotypic chains as well as mixed ubiquitin chains. In a mixed chain, not all the isopeptide bonds are restricted to a specific lysine of ubiquitin, resulting in a chain possessing more than one type of linkage. While structural characterization of homotypic chains has been well elucidated, less is known about mixed chains. Here we present the crystal structure of a mixed tri-ubiquitin chain at 3.1-Å resolution. In the structure, the proximal ubiquitin is connected to the middle ubiquitin via K48 and these two ubiquitins adopt a compact structure as observed in K48 di-ubiquitin. The middle ubiquitin links to the distal ubiquitin via its K63 and these ubiquitins adopt two conformations, suggesting a flexible structure. Using small-angle X-ray scattering, we unexpectedly found differences between the conformational ensembles of the above tri-ubiquitin chains and chains possessing the same linkages but in the reverse order. In addition, cleavage of the K48 linkage by DUB is faster if this linkage is at the distal end. Taken together, our results suggest that in mixed chains, not only the type of the linkages but also their sequence determine the structural and functional properties of the chain.
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8
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Warren AJ. Molecular basis of the human ribosomopathy Shwachman-Diamond syndrome. Adv Biol Regul 2017; 67:109-127. [PMID: 28942353 PMCID: PMC6710477 DOI: 10.1016/j.jbior.2017.09.002] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 01/05/2023]
Abstract
Mutations that target the ubiquitous process of ribosome assembly paradoxically cause diverse tissue-specific disorders (ribosomopathies) that are often associated with an increased risk of cancer. Ribosomes are the essential macromolecular machines that read the genetic code in all cells in all kingdoms of life. Following pre-assembly in the nucleus, precursors of the large 60S and small 40S ribosomal subunits are exported to the cytoplasm where the final steps in maturation are completed. Here, I review the recent insights into the conserved mechanisms of ribosome assembly that have come from functional characterisation of the genes mutated in human ribosomopathies. In particular, recent advances in cryo-electron microscopy, coupled with genetic, biochemical and prior structural data, have revealed that the SBDS protein that is deficient in the inherited leukaemia predisposition disorder Shwachman-Diamond syndrome couples the final step in cytoplasmic 60S ribosomal subunit maturation to a quality control assessment of the structural and functional integrity of the nascent particle. Thus, study of this fascinating disorder is providing remarkable insights into how the large ribosomal subunit is functionally activated in the cytoplasm to enter the actively translating pool of ribosomes.
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MESH Headings
- Bone Marrow Diseases/metabolism
- Bone Marrow Diseases/pathology
- Cryoelectron Microscopy
- Exocrine Pancreatic Insufficiency/metabolism
- Exocrine Pancreatic Insufficiency/pathology
- Humans
- Lipomatosis/metabolism
- Lipomatosis/pathology
- Mutation
- Proteins/genetics
- Proteins/metabolism
- Ribosome Subunits, Large, Eukaryotic/genetics
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Ribosome Subunits, Large, Eukaryotic/ultrastructure
- Ribosome Subunits, Small, Eukaryotic/genetics
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Ribosome Subunits, Small, Eukaryotic/ultrastructure
- Shwachman-Diamond Syndrome
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Affiliation(s)
- Alan J Warren
- Cambridge Institute for Medical Research, Cambridge, UK; The Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK.
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9
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Perkins RJ, Kukharchuk A, Delcroix P, Shoemaker RK, Roeselová M, Cwiklik L, Vaida V. The Partitioning of Small Aromatic Molecules to Air–Water and Phospholipid Interfaces Mediated by Non-Hydrophobic Interactions. J Phys Chem B 2016; 120:7408-22. [DOI: 10.1021/acs.jpcb.6b05084] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Russell J. Perkins
- Department
of Chemistry and Biochemistry, University of Colorado at Boulder, UCB 215, Boulder, Colorado 80309, United States
- Cooperative
Institute for Research In Environmental Sciences, University of Colorado Boulder, UCV 215, Boulder, Colorado 80309, United States
| | - Alexandra Kukharchuk
- J. Heyrovský
Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Pauline Delcroix
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Richard K. Shoemaker
- Department
of Chemistry and Biochemistry, University of Colorado at Boulder, UCB 215, Boulder, Colorado 80309, United States
| | - Martina Roeselová
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Lukasz Cwiklik
- J. Heyrovský
Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Veronica Vaida
- Department
of Chemistry and Biochemistry, University of Colorado at Boulder, UCB 215, Boulder, Colorado 80309, United States
- Cooperative
Institute for Research In Environmental Sciences, University of Colorado Boulder, UCV 215, Boulder, Colorado 80309, United States
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10
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Ma C, Yan K, Tan D, Li N, Zhang Y, Yuan Y, Li Z, Dong MQ, Lei J, Gao N. Structural dynamics of the yeast Shwachman-Diamond syndrome protein (Sdo1) on the ribosome and its implication in the 60S subunit maturation. Protein Cell 2016; 7:187-200. [PMID: 26850260 PMCID: PMC4791427 DOI: 10.1007/s13238-015-0242-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 12/14/2015] [Indexed: 12/16/2022] Open
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.
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Affiliation(s)
- Chengying Ma
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Kaige Yan
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Dan Tan
- National Institute of Biological Sciences, Beijing, 102206, China.,Graduate Program in Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Ningning Li
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yixiao Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yi Yuan
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhifei Li
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, 102206, China.,Graduate Program in Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Jianlin Lei
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ning Gao
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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11
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Weis F, Giudice E, Churcher M, Jin L, Hilcenko C, Wong CC, Traynor D, Kay RR, Warren AJ. Mechanism of eIF6 release from the nascent 60S ribosomal subunit. Nat Struct Mol Biol 2015; 22:914-9. [PMID: 26479198 PMCID: PMC4871238 DOI: 10.1038/nsmb.3112] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/17/2015] [Indexed: 12/20/2022]
Abstract
SBDS protein (deficient in the inherited leukemia-predisposition disorder Shwachman-Diamond syndrome) and the GTPase EFL1 (an EF-G homolog) activate nascent 60S ribosomal subunits for translation by catalyzing eviction of the antiassociation factor eIF6 from nascent 60S ribosomal subunits. However, the mechanism is completely unknown. Here, we present cryo-EM structures of human SBDS and SBDS-EFL1 bound to Dictyostelium discoideum 60S ribosomal subunits with and without endogenous eIF6. SBDS assesses the integrity of the peptidyl (P) site, bridging uL16 (mutated in T-cell acute lymphoblastic leukemia) with uL11 at the P-stalk base and the sarcin-ricin loop. Upon EFL1 binding, SBDS is repositioned around helix 69, thus facilitating a conformational switch in EFL1 that displaces eIF6 by competing for an overlapping binding site on the 60S ribosomal subunit. Our data reveal the conserved mechanism of eIF6 release, which is corrupted in both inherited and sporadic leukemias.
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Affiliation(s)
- Félix Weis
- Cambridge Institute for Medical Research, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge Research Unit, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Emmanuel Giudice
- Université de Rennes 1, Centre Nationale de la Recherche Scientifique, Unité Mixte de Recherche 6290, Institut de Génétique et Développement de Rennes, Rennes, France
| | - Mark Churcher
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge Research Unit, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Li Jin
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge Research Unit, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Christine Hilcenko
- Cambridge Institute for Medical Research, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge Research Unit, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Chi C Wong
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
| | - David Traynor
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Robert R Kay
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Alan J Warren
- Cambridge Institute for Medical Research, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge Research Unit, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
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12
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Zhang Y, Mandava CS, Cao W, Li X, Zhang D, Li N, Zhang Y, Zhang X, Qin Y, Mi K, Lei J, Sanyal S, Gao N. HflX is a ribosome-splitting factor rescuing stalled ribosomes under stress conditions. Nat Struct Mol Biol 2015; 22:906-13. [PMID: 26458047 DOI: 10.1038/nsmb.3103] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 09/04/2015] [Indexed: 12/16/2022]
Abstract
Adverse cellular conditions often lead to nonproductive translational stalling and arrest of ribosomes on mRNAs. Here, we used fast kinetics and cryo-EM to characterize Escherichia coli HflX, a GTPase with unknown function. Our data reveal that HflX is a heat shock-induced ribosome-splitting factor capable of dissociating vacant as well as mRNA-associated ribosomes with deacylated tRNA in the peptidyl site. Structural data demonstrate that the N-terminal effector domain of HflX binds to the peptidyl transferase center in a strikingly similar manner as that of the class I release factors and induces dramatic conformational changes in central intersubunit bridges, thus promoting subunit dissociation. Accordingly, loss of HflX results in an increase in stalled ribosomes upon heat shock. These results suggest a primary role of HflX in rescuing translationally arrested ribosomes under stress conditions.
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Affiliation(s)
- Yanqing Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | | | - Wei Cao
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaojing Li
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dejiu Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ningning Li
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yixiao Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaoxiao Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yan Qin
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Kaixia Mi
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianlin Lei
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Ning Gao
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
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13
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Abstract
PURPOSE OF REVIEW Shwachman-Diamond syndrome (SDS) is an inherited bone marrow failure and cancer predisposition syndrome that affects multiple organ systems. Mutations in the Shwachman-Bodian-Diamond syndrome (SBDS) gene are found in the majority of patients, but the molecular function of the SBDS protein product remains unclear. In this article, we review recent progress in the clinical and molecular characterization of SDS. RECENT FINDINGS Emerging data support a multifunctional role for the SBDS protein. Current studies indicate that SBDS functions in 60S large ribosomal subunit maturation and in mitotic spindle stabilization. Recent data suggest that it may also affect actin polymerization, vacuolar pH regulation, and DNA metabolism. SBDS loss results in both hematopoietic cell-intrinsic defects as well as marrow stromal abnormalities. SUMMARY SDS is a multisystemic disease arising from defects in a protein that participates in several essential cellular processes. Elucidating the molecular function of SBDS will provide important insights into how defects in ribosome biogenesis and mitotic spindle stabilization result in hematopoietic failure, cancer predisposition, and abnormalities.
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14
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Bypass of the pre-60S ribosomal quality control as a pathway to oncogenesis. Proc Natl Acad Sci U S A 2014; 111:5640-5. [PMID: 24706786 DOI: 10.1073/pnas.1400247111] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribosomopathies are a class of diseases caused by mutations that affect the biosynthesis and/or functionality of the ribosome. Although they initially present as hypoproliferative disorders, such as anemia, patients have elevated risk of hyperproliferative disease (cancer) by midlife. Here, this paradox is explored using the rpL10-R98S (uL16-R98S) mutant yeast model of the most commonly identified ribosomal mutation in acute lymphoblastic T-cell leukemia. This mutation causes a late-stage 60S subunit maturation failure that targets mutant ribosomes for degradation. The resulting deficit in ribosomes causes the hypoproliferative phenotype. This 60S subunit shortage, in turn, exerts pressure on cells to select for suppressors of the ribosome biogenesis defect, allowing them to reestablish normal levels of ribosome production and cell proliferation. However, suppression at this step releases structurally and functionally defective ribosomes into the translationally active pool, and the translational fidelity defects of these mutants culminate in destabilization of selected mRNAs and shortened telomeres. We suggest that in exchange for resolving their short-term ribosome deficits through compensatory trans-acting suppressors, cells are penalized in the long term by changes in gene expression that ultimately undermine cellular homeostasis.
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Sulima SO, Gülay SP, Anjos M, Patchett S, Meskauskas A, Johnson AW, Dinman JD. Eukaryotic rpL10 drives ribosomal rotation. Nucleic Acids Res 2013; 42:2049-63. [PMID: 24214990 PMCID: PMC3919601 DOI: 10.1093/nar/gkt1107] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Ribosomes transit between two conformational states, non-rotated and rotated, through the elongation cycle. Here, we present evidence that an internal loop in the essential yeast ribosomal protein rpL10 is a central controller of this process. Mutations in this loop promote opposing effects on the natural equilibrium between these two extreme conformational states. rRNA chemical modification analyses reveals allosteric interactions involved in coordinating intersubunit rotation originating from rpL10 in the core of the large subunit (LSU) through both subunits, linking all the functional centers of the ribosome. Mutations promoting rotational disequilibria showed catalytic, biochemical and translational fidelity defects. An rpL3 mutation promoting opposing structural and biochemical effects, suppressed an rpL10 mutant, re-establishing rotational equilibrium. The rpL10 loop is also involved in Sdo1p recruitment, suggesting that rotational status is important for ensuring late-stage maturation of the LSU, supporting a model in which pre-60S subunits undergo a ‘test drive’ before final maturation.
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Affiliation(s)
- Sergey O Sulima
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA, Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA and Department of Biotechnology and Microbiology, Vilnius University, Vilnius LT-03101, Lithuania
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Essential ribosome assembly factor Fap7 regulates a hierarchy of RNA-protein interactions during small ribosomal subunit biogenesis. Proc Natl Acad Sci U S A 2013; 110:15253-8. [PMID: 24003121 DOI: 10.1073/pnas.1306389110] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Factor activating Pos9 (Fap7) is an essential ribosome biogenesis factor important for the assembly of the small ribosomal subunit with an uncommon dual ATPase and adenylate kinase activity. Depletion of Fap7 or mutations in its ATPase motifs lead to defects in small ribosomal subunit rRNA maturation, the absence of ribosomal protein Rps14 from the assembled subunit, and retention of the nascent small subunit in a quality control complex with the large ribosomal subunit. The molecular basis for the role of Fap7 in ribosome biogenesis is, however, not yet understood. Here we show that Fap7 regulates multiple interactions between the precursor rRNA, ribosomal proteins, and ribosome assembly factors in a hierarchical manner. Fap7 binds to Rps14 with a very high affinity. Fap7 binding blocks both rRNA-binding elements of Rps14, suggesting that Fap7 inhibits premature interactions of Rps14 with RNA. The Fap7/Rps14 interaction is modulated by nucleotide binding to Fap7. Rps14 strongly activates the ATPase activity but not the adenylate kinase activity of Fap7, identifying Rps14 as an example of a ribosomal protein functioning as an ATPase-activating factor. In addition, Fap7 inhibits the RNA cleavage activity of Nob1, the endonuclease responsible for the final maturation step of the small subunit rRNA, in a nucleotide independent manner. Thus, Fap7 may regulate small subunit biogenesis at multiple stages.
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Myers KC, Davies SM, Shimamura A. Clinical and molecular pathophysiology of Shwachman-Diamond syndrome: an update. Hematol Oncol Clin North Am 2012; 27:117-28, ix. [PMID: 23351992 DOI: 10.1016/j.hoc.2012.10.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Shwachman-Diamond syndrome (SDS) is an inherited neutropenia syndrome associated with a significant risk of aplastic anemia and malignant transformation. Multiple additional organ systems, including the pancreas, liver, and skeletal and central nervous systems, are affected. Mutations in the Shwachman-Bodian-Diamond syndrome (SBDS) gene are present in most patients. There is growing evidence that SBDS functions in ribosomal biogenesis and other cellular processes. This article summarizes the clinical phenotype of SDS, diagnostic and treatment approaches, and novel advances in our understanding of the molecular pathophysiology of this disease.
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Affiliation(s)
- Kasiani C Myers
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, University of Cincinnati, 3333 Burnet Avenue, MLC 7015, Cincinnati, OH 45229, USA.
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Bussiere C, Hashem Y, Arora S, Frank J, Johnson AW. Integrity of the P-site is probed during maturation of the 60S ribosomal subunit. ACTA ACUST UNITED AC 2012; 197:747-59. [PMID: 22689654 PMCID: PMC3373404 DOI: 10.1083/jcb.201112131] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The P-site of the 60S ribosomal subunit signals to Tif6 via Elf1 during ribosomal maturation, suggesting a quasifunctional check of the integrity of the 60S subunit before the first round of translation. Eukaryotic ribosomes are preassembled in the nucleus and mature in the cytoplasm. Release of the antiassociation factor Tif6 by the translocase-like guanosine triphosphatase Efl1 is a critical late maturation step. In this paper, we show that a loop of Rpl10 that embraces the P-site transfer ribonucleic acid was required for release of Tif6, 90 Å away. Mutations in this P-site loop blocked 60S maturation but were suppressed by mutations in Tif6 or Efl1. Molecular dynamics simulations of the mutant Efl1 proteins suggest that they promote a conformation change in Efl1 equivalent to changes that elongation factor G and eEF2 undergo during translocation. These results identify molecular signaling from the P-site to Tif6 via Efl1, suggesting that the integrity of the P-site is interrogated during maturation. We propose that Efl1 promotes a functional check of the integrity of the 60S subunit before its first round of translation.
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Affiliation(s)
- Cyril Bussiere
- Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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Veith T, Martin R, Wurm JP, Weis BL, Duchardt-Ferner E, Safferthal C, Hennig R, Mirus O, Bohnsack MT, Wöhnert J, Schleiff E. Structural and functional analysis of the archaeal endonuclease Nob1. Nucleic Acids Res 2012; 40:3259-74. [PMID: 22156373 PMCID: PMC3326319 DOI: 10.1093/nar/gkr1186] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 11/11/2011] [Accepted: 11/14/2011] [Indexed: 01/01/2023] Open
Abstract
Eukaryotic ribosome biogenesis requires the concerted action of numerous ribosome assembly factors, for most of which structural and functional information is currently lacking. Nob1, which can be identified in eukaryotes and archaea, is required for the final maturation of the small subunit ribosomal RNA in yeast by catalyzing cleavage at site D after export of the preribosomal subunit into the cytoplasm. Here, we show that this also holds true for Nob1 from the archaeon Pyrococcus horikoshii, which efficiently cleaves RNA-substrates containing the D-site of the preribosomal RNA in a manganese-dependent manner. The structure of PhNob1 solved by nuclear magnetic resonance spectroscopy revealed a PIN domain common with many nucleases and a zinc ribbon domain, which are structurally connected by a flexible linker. We show that amino acid residues required for substrate binding reside in the PIN domain whereas the zinc ribbon domain alone is sufficient to bind helix 40 of the small subunit rRNA. This suggests that the zinc ribbon domain acts as an anchor point for the protein on the nascent subunit positioning it in the proximity of the cleavage site.
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Affiliation(s)
- Thomas Veith
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Roman Martin
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Jan P. Wurm
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Benjamin L. Weis
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Charlotta Safferthal
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Raoul Hennig
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Oliver Mirus
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Markus T. Bohnsack
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
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Burwick N, Shimamura A, Liu JM. Non-Diamond Blackfan anemia disorders of ribosome function: Shwachman Diamond syndrome and 5q- syndrome. Semin Hematol 2011; 48:136-43. [PMID: 21435510 DOI: 10.1053/j.seminhematol.2011.01.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A number of human disorders, dubbed ribosomopathies, are linked to impaired ribosome biogenesis or function. These include but are not limited to Diamond Blackfan anemia (DBA), Shwachman Diamond syndrome (SDS), and the 5q- myelodysplastic syndrome (MDS). This review focuses on the latter two non-DBA disorders of ribosome function. Both SDS and 5q- syndrome lead to impaired hematopoiesis and a predisposition to leukemia. SDS, due to bi-allelic mutations of the SBDS gene, is a multi-system disorder that also includes bony abnormalities, and pancreatic and neurocognitive dysfunction. SBDS associates with the 60S subunit in human cells and has a role in subunit joining and translational activation in yeast models. In contrast, 5q- syndrome is associated with acquired haplo-insufficiency of RPS14, a component of the small 40S subunit. RPS14 is critical for 40S assembly in yeast models, and depletion of RPS14 in human CD34(+) cells is sufficient to recapitulate the 5q- erythroid defect. Both SDS and the 5q- syndrome represent important models of ribosome function and may inform future treatment strategies for the ribosomopathies.
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Affiliation(s)
- Nicholas Burwick
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Abstract
Shwachman-Diamond syndrome (SDS), a recessive leukemia predisposition disorder characterized by bone marrow failure, exocrine pancreatic insufficiency, skeletal abnormalities and poor growth, is caused by mutations in the highly conserved SBDS gene. Here, we test the hypothesis that defective ribosome biogenesis underlies the pathogenesis of SDS. We create conditional mutants in the essential SBDS ortholog of the ancient eukaryote Dictyostelium discoideum using temperature-sensitive, self-splicing inteins, showing that mutant cells fail to grow at the restrictive temperature because ribosomal subunit joining is markedly impaired. Remarkably, wild type human SBDS complements the growth and ribosome assembly defects in mutant Dictyostelium cells, but disease-associated human SBDS variants are defective. SBDS directly interacts with the GTPase elongation factor-like 1 (EFL1) on nascent 60S subunits in vivo and together they catalyze eviction of the ribosome antiassociation factor eukaryotic initiation factor 6 (eIF6), a prerequisite for the translational activation of ribosomes. Importantly, lymphoblasts from SDS patients harbor a striking defect in ribosomal subunit joining whose magnitude is inversely proportional to the level of SBDS protein. These findings in Dictyostelium and SDS patient cells provide compelling support for the hypothesis that SDS is a ribosomopathy caused by corruption of an essential cytoplasmic step in 60S subunit maturation.
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Orelio C, van der Sluis RM, Verkuijlen P, Nethe M, Hordijk PL, van den Berg TK, Kuijpers TW. Altered intracellular localization and mobility of SBDS protein upon mutation in Shwachman-Diamond syndrome. PLoS One 2011; 6:e20727. [PMID: 21695142 PMCID: PMC3113850 DOI: 10.1371/journal.pone.0020727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2010] [Accepted: 05/09/2011] [Indexed: 11/18/2022] Open
Abstract
Shwachman-Diamond Syndrome (SDS) is a rare inherited disease caused by mutations in the SBDS gene. Hematopoietic defects, exocrine pancreas dysfunction and short stature are the most prominent clinical features. To gain understanding of the molecular properties of the ubiquitously expressed SBDS protein, we examined its intracellular localization and mobility by live cell imaging techniques. We observed that SBDS full-length protein was localized in both the nucleus and cytoplasm, whereas patient-related truncated SBDS protein isoforms localize predominantly to the nucleus. Also the nucleo-cytoplasmic trafficking of these patient-related SBDS proteins was disturbed. Further studies with a series of SBDS mutant proteins revealed that three distinct motifs determine the intracellular mobility of SBDS protein. A sumoylation motif in the C-terminal domain, that is lacking in patient SBDS proteins, was found to play a pivotal role in intracellular motility. Our structure-function analyses provide new insight into localization and motility of the SBDS protein, and show that patient-related mutant proteins are altered in their molecular properties, which may contribute to the clinical features observed in SDS patients.
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Affiliation(s)
- Claudia Orelio
- Sanquin Research and Landsteiner Laboratory of the Academic Medical Center (AMC), Department of Blood Cell Research, University of Amsterdam, Amsterdam, The Netherlands
| | - Renée M. van der Sluis
- Sanquin Research and Landsteiner Laboratory of the Academic Medical Center (AMC), Department of Blood Cell Research, University of Amsterdam, Amsterdam, The Netherlands
| | - Paul Verkuijlen
- Sanquin Research and Landsteiner Laboratory of the Academic Medical Center (AMC), Department of Blood Cell Research, University of Amsterdam, Amsterdam, The Netherlands
| | - Micha Nethe
- Sanquin Research and Landsteiner Laboratory of the Academic Medical Center (AMC), Department of Molecular Cell Biology, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter L. Hordijk
- Sanquin Research and Landsteiner Laboratory of the Academic Medical Center (AMC), Department of Molecular Cell Biology, University of Amsterdam, Amsterdam, The Netherlands
| | - Timo K. van den Berg
- Sanquin Research and Landsteiner Laboratory of the Academic Medical Center (AMC), Department of Blood Cell Research, University of Amsterdam, Amsterdam, The Netherlands
| | - Taco W. Kuijpers
- Sanquin Research and Landsteiner Laboratory of the Academic Medical Center (AMC), Department of Blood Cell Research, University of Amsterdam, Amsterdam, The Netherlands
- Emma Children's Hospital, Academic Medical Center (AMC), Amsterdam, The Netherlands
- * E-mail:
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Abstract
The inherited marrow failure syndromes are a diverse set of genetic disorders characterized by hematopoietic aplasia and cancer predisposition. The clinical phenotypes are highly variable and much broader than previously recognized. The medical management of the inherited marrow failure syndromes differs from that of acquired aplastic anemia or malignancies arising in the general population. Diagnostic workup, molecular pathogenesis, and clinical treatment are reviewed.
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de Oliveira JF, Sforça ML, Blumenschein TMA, Goldfeder MB, Guimarães BG, Oliveira CC, Zanchin NIT, Zeri AC. Structure, dynamics, and RNA interaction analysis of the human SBDS protein. J Mol Biol 2010; 396:1053-69. [PMID: 20053358 DOI: 10.1016/j.jmb.2009.12.039] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 12/06/2009] [Accepted: 12/18/2009] [Indexed: 12/18/2022]
Abstract
Shwachman-Bodian-Diamond syndrome is an autosomal recessive genetic syndrome with pleiotropic phenotypes, including pancreatic deficiencies, bone marrow dysfunctions with increased risk of myelodysplasia or leukemia, and skeletal abnormalities. This syndrome has been associated with mutations in the SBDS gene, which encodes a conserved protein showing orthologs in Archaea and eukaryotes. The Shwachman-Bodian-Diamond syndrome pleiotropic phenotypes may be an indication of different cell type requirements for a fully functional SBDS protein. RNA-binding activity has been predicted for archaeal and yeast SBDS orthologs, with the latter also being implicated in ribosome biogenesis. However, full-length SBDS orthologs function in a species-specific manner, indicating that the knowledge obtained from model systems may be of limited use in understanding major unresolved issues regarding SBDS function, namely, the effect of mutations in human SBDS on its biochemical function and the specificity of RNA interaction. We determined the solution structure and backbone dynamics of the human SBDS protein and describe its RNA binding site using NMR spectroscopy. Similarly to the crystal structures of Archaea, the overall structure of human SBDS comprises three well-folded domains. However, significant conformational exchange was observed in NMR dynamics experiments for the flexible linker between the N-terminal domain and the central domain, and these experiments also reflect the relative motions of the domains. RNA titrations monitored by heteronuclear correlation experiments and chemical shift mapping analysis identified a classic RNA binding site at the N-terminal FYSH (fungal, Yhr087wp, Shwachman) domain that concentrates most of the mutations described for the human SBDS.
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Affiliation(s)
- Juliana Ferreira de Oliveira
- Center for Structural Molecular Biology, Brazilian Synchrotron Light Laboratory, LNLS Rua Giuseppe Maximo Scolfaro 10000, PO Box 6192, CEP 13083-970 Campinas, SP, Brazil
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