51
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Dieci G, Bottarelli L, Ballabeni A, Ottonello S. tRNA-assisted overproduction of eukaryotic ribosomal proteins. Protein Expr Purif 2000; 18:346-54. [PMID: 10733889 DOI: 10.1006/prep.2000.1203] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Structural studies of eukaryotic ribosomes are complicated by the tendency of their constituent proteins to be expressed at very low levels in Escherichia coli. We find that this is mainly due to their exceptionally high content of AGA/AGG arginine codons, which are poorly utilized by the bacterial translational machinery. In fact, we could overcome this limitation by the combined use of a T7 RNA polymerase expression vector and a plasmid carrying the E. coli gene argU, which encodes the minor tRNA(Arg) species that reads AGA/AGG codons. In this system, five cytoplasmic ribosomal proteins from three different eukaryotic lineages (Saccharomyces cerevisiae S8, L13, and L14; Arabidopsis thaliana L13; and Homo sapiens L7) could be overexpressed to up to 50% of total bacterial protein and were purified to homogeneity in tens of milligrams amounts. The purification procedure simply involved metal affinity chromatography followed, in some cases, by an additional heparin chromatography step. Recombinant polypeptides bound RNA with high affinity (K(d) between 50 and 300 nM). This novel overexpression/purification strategy will allow the production of high amounts of most eukaryotic ribosomal proteins in a form suitable for structural and functional studies. Coupled with recently completed and ongoing whole-genome sequencing projects, it will facilitate the molecular characterization of the eukaryotic ribosome.
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Affiliation(s)
- G Dieci
- Institute of Biochemical Sciences, University of Parma, Parma, I-43100, Italy
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52
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Malygin AA, Dobrikov MI, Repkova MN, Shishkin GV, Ven'yaminova AG, Karpova GG. Proteins neighboring 18S rRNA conserved sequences 609-618 and 1047-1061 within the 40S human ribosomal subunit. RNA (NEW YORK, N.Y.) 1999; 5:1656-1664. [PMID: 10606275 PMCID: PMC1369886 DOI: 10.1017/s1355838299990908] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The structure of human 40S ribosomal subunits has been probed by a cross-linking strategy based on the use of oligonucleotide derivatives that modify proteins in the vicinity of specific 18S rRNA sequences. The oligonucleotide derivatives carried a p-azidoperfluorobenzamide group at the 5' ends and were complementary to 18S rRNA sequences 609-618 and 1047-1061, homologous to the highly conserved regions designated as the "530 stem-loop" and "790 stem-loop", respectively, in Escherichia coli 16S rRNA. Ribosomal proteins surrounding these sequences were the main targets of the cross-linking. Proteins S3 and S5 were cross-linked to the derivative complementary to the sequence 609-618, and proteins S2 and S3 were modified by the derivative complementary to the sequence 1047-1061. Cross-linking was not affected by binding of 40S subunits to either poly(U) or poly(U) and Phe-tRNA(Phe).
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MESH Headings
- Base Sequence
- Conserved Sequence
- Escherichia coli/genetics
- Female
- Humans
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Placenta/chemistry
- Pregnancy
- RNA, Bacterial/chemistry
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/isolation & purification
- Ribonuclease H
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/isolation & purification
- Ribosomes/chemistry
- Ribosomes/genetics
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Affiliation(s)
- A A Malygin
- Novosibirsk Institute of Bioorganic Chemistry, Siberian Branch of the Russian Academy of Sciences
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53
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Harms J, Tocilj A, Levin I, Agmon I, Stark H, Kölln I, van Heel M, Cuff M, Schlünzen F, Bashan A, Franceschi F, Yonath A. Elucidating the medium-resolution structure of ribosomal particles: an interplay between electron cryo-microscopy and X-ray crystallograhy. Structure 1999; 7:931-41. [PMID: 10467138 DOI: 10.1016/s0969-2126(99)80120-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Ribosomes are the universal cellular organelles that accomplish the translation of the genetic code into proteins. Electron cryo-microscopy (cryo-EM) has yielded fairly detailed three-dimensional reconstructions of ribosomes. These were used to assist in the determination of higher resolution structures by X-ray crystallography. RESULTS Molecular replacement studies using cryo-EM reconstructions provided feasible packing schemes for crystals of ribosomes and their two subunits from Thermus thermophilus, and of the large subunits from Haloarcula marismortui. For the large subunits, these studies also confirmed the major heavy-atom sites obtained by single isomorphous replacement combined with anomalous diffraction (SIRAS) and by multiple isomorphous replacement combined with anomalous diffraction (MIRAS) at approximately 10 A. Although adequate starting phases could not be obtained for the small subunits, the crystals of which diffract to 3.0 A, cryo-EM reconstructions were indispensable for analyzing their 7.2 A multiple isomorphous replacement (MIR) map. This work indicated that the conformation of the crystallized small subunits resembles that seen within the 70S ribosomes. Subsequently, crystals of particles trapped in their functionally active state were grown. CONCLUSIONS Single-particle cryo-EM can contribute to the progress of crystallography of non-symmetrical, large and flexible macromolecular assemblies. Besides confirming heavy-atom sites, obtained from flat or overcrowded difference Patterson maps, the cryo-EM reconstructions assisted in elucidating packing arrangements. They also provided tools for the identification of the conformation within the crystals and for the estimation of the level of inherent non-isomorphism.
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Affiliation(s)
- J Harms
- Max-Planck Research Unit for Ribosomal Structure, Hamburg, Germany
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54
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Moy TI, Silver PA. Nuclear export of the small ribosomal subunit requires the ran-GTPase cycle and certain nucleoporins. Genes Dev 1999; 13:2118-33. [PMID: 10465789 PMCID: PMC316945 DOI: 10.1101/gad.13.16.2118] [Citation(s) in RCA: 147] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
After their assembly in the nucleolus, ribosomal subunits are exported from the nucleus to the cytoplasm. After export, the 20S rRNA in the small ribosomal subunit is cleaved to yield 18S rRNA and the small 5' ITS1 fragment. The 5' ITS1 RNA is normally degraded by the cytoplasmic Xrn1 exonuclease, but in strains lacking XRN1, the 5' ITS1 fragment accumulates in the cytoplasm. Using the cytoplasmic localization of the 5' ITS1 fragment as an indicator for the export of the small ribosomal subunit, we have identified genes that are required for ribosome export. Ribosome export is dependent on the Ran-GTPase as mutations in Ran or its regulators caused 5' ITS1 to accumulate in the nucleoplasm. Mutations in the genes encoding the nucleoporin Nup82 and in the NES exporter Xpo1/Crm1 also caused the nucleoplasmic accumulation of 5' ITS1. Mutants in a subset of nucleoporins and in the nuclear transport factors Srp1, Kap95, Pse1, Cse1, and Mtr10 accumulate the 5' ITS1 in the nucleolus and affect ribosome assembly. In contrast, we did not detect nuclear accumulation of 5' ITS1 in 28 yeast strains that have mutations in other genes affecting nuclear trafficking.
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Affiliation(s)
- T I Moy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and The Dana-Farber Cancer Institute, Boston, Massachusetts 02115 USA
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55
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Abstract
BACKGROUND The vault is a ubiquitous and highly conserved ribonucleoprotein particle of approximately 13 MDa. This particle has been shown to be upregulated in certain multidrug-resistant cancer cell lines and to share a protein component with the telomerase complex. Determination of the structure of the vault was undertaken to provide a first step towards understanding the role of this cellular component in normal metabolism and perhaps to shed some light on its role in mediating drug resistance. RESULTS Over 1300 particle images were combined to calculate an approximately 31 A resolution structure of the vault. Rotational power spectra did not yield a clear symmetry peak, either because of the thin, smooth walls or inherent flexibility of the vault. Although cyclic eightfold (C8) symmetry was imposed, the resulting reconstruction may be partially cylindrically averaged about the eightfold axis. Our results reveal the vault to be a hollow, barrel-like structure with two protruding caps and an invaginated waist. CONCLUSIONS Although the normal cellular function of the vault is as yet undetermined, the structure of the vault is consistent with either a role in subcellular transport, as previously suggested, or in sequestering macromolecular assemblies.
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Affiliation(s)
- L B Kong
- Department of Molecular and Medical Pharmacology, Crump Institute for Biological Imaging, UCLA School of Medicine, A-324 CIBI, Box 951770, Los Angeles, CA 90095-1770, USA
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56
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Abstract
Significant progress is occurring at an accelerated rate in structural studies of ribosomes. A 3D cryoelectron microscopy map of the 70S ribosome from Escherichia coli is available at 15 A resolution and a combination of cryoelectron microscopy with X-ray crystallography has yielded a 9 A resolution map of the 50S subunit from Haloarcula marismortui, an archaebacterium. For eukaryotes, 3D cryomaps of the 80S ribosomes from yeast and from mammals have now been produced at resolutions in the range 20 to 30 A. The most ground-breaking results have been obtained from the 3D mapping of ligands in functional studies of prokaryotic ribosomes. These studies, which directly visualize the protein synthesis machine in action, have brought new excitement to a field that was relatively dormant during the past decade.
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Affiliation(s)
- R K Agrawal
- Wadsworth Center, Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA.
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57
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Justice MC, Ku T, Hsu MJ, Carniol K, Schmatz D, Nielsen J. Mutations in ribosomal protein L10e confer resistance to the fungal-specific eukaryotic elongation factor 2 inhibitor sordarin. J Biol Chem 1999; 274:4869-75. [PMID: 9988728 DOI: 10.1074/jbc.274.8.4869] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The natural product sordarin, a tetracyclic diterpene glycoside, selectively inhibits fungal protein synthesis by impairing the function of eukaryotic elongation factor 2 (eEF2). Sordarin and its derivatives bind to the eEF2-ribosome-nucleotide complex in sensitive fungi, stabilizing the post-translocational GDP form. We have previously described a class of Saccharomyces cerevisiae mutants that exhibit resistance to varying levels of sordarin and have identified amino acid substitutions in yeast eEF2 that confer sordarin resistance. We now report on a second class of sordarin-resistant mutants. Biochemical and molecular genetic analysis of these mutants demonstrates that sordarin resistance is dependent on the essential large ribosomal subunit protein L10e in S. cerevisiae. Five unique L10e alleles were characterized and sequenced, and several nucleotide changes that differ from the wild-type sequence were identified. Changes that result in the resistance phenotype map to 4 amino acid substitutions and 1 amino acid deletion clustered in a conserved 10-amino acid region of L10e. Like the previously identified eEF2 mutations, the mutant ribosomes show reduced sordarin-conferred stabilization of the eEF2-nucleotide-ribosome complex. To our knowledge, this report provides the first description of ribosomal protein mutations affecting translocation. These results and our previous observations with eEF2 suggest a functional linkage between L10e and eEF2.
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Affiliation(s)
- M C Justice
- Department of Basic Animal Science Research, Merck Research Laboratories, Rahway, New Jersey 07065, USA
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58
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Frank J. The ribosome-structure and functional ligand-binding experiments using cryo-electron microscopy. J Struct Biol 1998; 124:142-50. [PMID: 10049802 DOI: 10.1006/jsbi.1998.4071] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cryo-electron microscopy has greatly advanced our understanding of the basic steps of protein synthesis in the bacterial ribosome. This article gives an overview of what has been achieved so far. Through three-dimensional visualization of complexes that represent the ribosome in defined binding states, locations were derived for the tRNA in A, P, and E sites, as well as the elongation factors. In addition, the pathways of messenger RNA and the exiting polypeptide chain could be inferred.
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Affiliation(s)
- J Frank
- Department of Biomedical Sciences, Wadsworth Center, Albany, New York, 12201-0509, USA
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59
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Malhotra A, Penczek P, Agrawal RK, Gabashvili IS, Grassucci RA, Jünemann R, Burkhardt N, Nierhaus KH, Frank J. Escherichia coli 70 S ribosome at 15 A resolution by cryo-electron microscopy: localization of fMet-tRNAfMet and fitting of L1 protein. J Mol Biol 1998; 280:103-16. [PMID: 9653034 DOI: 10.1006/jmbi.1998.1859] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cryo-electron microscopy of the ribosome in different binding states with mRNA and tRNA helps unravel the different steps of protein synthesis. Using over 29,000 projections of a ribosome complex in single-particle form, a three-dimensional map of the Escherichia coli 70 S ribosome was obtained in which a single site, the P site, is occupied by fMet-tRNAfMet as directed by an AUG codon containing mRNA. The superior resolution of this three-dimensional map, 14.9 A, has made it possible to fit the tRNA X-ray crystal structure directly and unambiguously into the electron density, thus determining the locations of anticodon-codon interaction and peptidyltransferase center of the ribosome. Furthermore, at this resolution, one of the distinctly visible domains corresponding to a ribosomal protein, L1, closely matches with its X-ray structure.
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MESH Headings
- Bacterial Proteins/chemistry
- Bacterial Proteins/metabolism
- Binding Sites
- Cryoultramicrotomy
- Crystallography, X-Ray
- Escherichia coli/genetics
- Image Processing, Computer-Assisted
- Microscopy, Electron
- Models, Molecular
- Nucleic Acid Conformation
- Peptides
- Protein Conformation
- RNA, Transfer/metabolism
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/metabolism
- RNA, Transfer, Met/ultrastructure
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/metabolism
- Ribosomes/metabolism
- Ribosomes/ultrastructure
- Spectroscopy, Fourier Transform Infrared/methods
- Thermus thermophilus/metabolism
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Affiliation(s)
- A Malhotra
- Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, 12201-0509, USA
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60
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Ban N, Freeborn B, Nissen P, Penczek P, Grassucci RA, Sweet R, Frank J, Moore PB, Steitz TA. A 9 A resolution X-ray crystallographic map of the large ribosomal subunit. Cell 1998; 93:1105-15. [PMID: 9657144 DOI: 10.1016/s0092-8674(00)81455-5] [Citation(s) in RCA: 166] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The 50S subunit of the ribosome catalyzes the peptidyl-transferase reaction of protein synthesis. We have generated X-ray crystallographic electron density maps of the large ribosomal subunit from Haloarcula marismortui at various resolutions up to 9 A using data from crystals that diffract to 3 A. Positioning a 20 A resolution EM image of these particles in the crystal lattice produced phases accurate enough to locate the bound heavy atoms in three derivatives using difference Fourier maps, thus demonstrating the correctness of the EM model and its placement in the unit cell. At 20 A resolution, the X-ray map is similar to the EM map; however, at 9 A it reveals long, continuous, but branched features whose shape, diameter, and right-handed twist are consistent with segments of double-helical RNA that crisscross the subunit.
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Affiliation(s)
- N Ban
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA
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61
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Rodnina MV, Wintermeyer W. Form follows function: structure of an elongation factor G-ribosome complex. Proc Natl Acad Sci U S A 1998; 95:7237-9. [PMID: 9636131 PMCID: PMC33864 DOI: 10.1073/pnas.95.13.7237] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- M V Rodnina
- Institute of Molecular Biology, University of Witten/Herdecke, 58448 Witten, Germany
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62
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Yonath A, Franceschi F. Functional universality and evolutionary diversity: insights from the structure of the ribosome. Structure 1998; 6:679-84. [PMID: 9655833 DOI: 10.1016/s0969-2126(98)00069-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The structure of the mammalian ribosome, reconstructed at 25 A resolution, has added a new dimension to our current knowledge, as it manifests the conservation and universality of the ribosome in respect to its primary tasks in protein biosynthesis. A combined approach to study of the ribosome, using X-ray crystallography and electron microscopy, may further improve our understanding of ribosome function in the future.
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Affiliation(s)
- A Yonath
- Max-Planck Unit for Structural Molecular Biology 22603, Hamburg, Germany Department of Structural Biology Weizmann Institute Rehovot, 76100, Israel
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