551
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Abstract
In recent years, noncoding RNAs (ncRNAs) have been shown to constitute key elements implicated in a number of regulatory mechanisms in the cell. They are present in bacteria and eukaryotes. The ncRNAs are involved in regulation of expression at both transcriptional and posttranscriptional levels, by mediating chromatin modifications, modulating transcription factor activity, and influencing mRNA stability, processing, and translation. Noncoding RNAs play a key role in genetic imprinting, dosage compensation of X-chromosome-linked genes, and many processes of differentiation and development.
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Affiliation(s)
- Maciej Szymański
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
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552
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Lecompte O, Ripp R, Thierry JC, Moras D, Poch O. Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. Nucleic Acids Res 2002; 30:5382-90. [PMID: 12490706 PMCID: PMC140077 DOI: 10.1093/nar/gkf693] [Citation(s) in RCA: 252] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2002] [Revised: 10/24/2002] [Accepted: 10/24/2002] [Indexed: 11/14/2022] Open
Abstract
A comprehensive investigation of ribosomal genes in complete genomes from 66 different species allows us to address the distribution of r-proteins between and within the three primary domains. Thirty-four r-protein families are represented in all domains but 33 families are specific to Archaea and Eucarya, providing evidence for specialisation at an early stage of evolution between the bacterial lineage and the lineage leading to Archaea and Eukaryotes. With only one specific r-protein, the archaeal ribosome appears to be a small-scale model of the eukaryotic one in terms of protein composition. However, the mechanism of evolution of the protein component of the ribosome appears dramatically different in Archaea. In Bacteria and Eucarya, a restricted number of ribosomal genes can be lost with a bias toward losses in intracellular pathogens. In Archaea, losses implicate 15% of the ribosomal genes revealing an unexpected plasticity of the translation apparatus and the pattern of gene losses indicates a progressive elimination of ribosomal genes in the course of archaeal evolution. This first documented case of reductive evolution at the domain scale provides a new framework for discussing the shape of the universal tree of life and the selective forces directing the evolution of prokaryotes.
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Affiliation(s)
- Odile Lecompte
- Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS, INSERM, ULP), BP163, 67404 Illkirch Cedex, France
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553
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Morgan DG, Ménétret JF, Neuhof A, Rapoport TA, Akey CW. Structure of the mammalian ribosome-channel complex at 17A resolution. J Mol Biol 2002; 324:871-86. [PMID: 12460584 DOI: 10.1016/s0022-2836(02)01111-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The co-translational translocation of proteins into the endoplasmic reticulum (ER) lumen and the biogenesis of membrane proteins require ribosome binding to a membrane channel formed by the Sec61p complex. We now report the 17A structure of a mammalian ribosome-channel complex derived from ER membranes. Atomic models of the ribosomal subunits were aligned to the programmed ribosome from Thermus thermophilus, to provide a common reference frame. The T.thermophilus ribosome, and by extension all known high resolution subunit models, were then docked within our map of the ribosome-channel complex. The structure shows that the ribosome contains a putative tRNA in the exit site, and a comparison with a non-programmed, yeast ribosome suggests that the L1 stalk may function as a gate in the tRNA exit path. We have localized six major expansion segments in the large subunit of the vertebrate ribosome including ES27, and suggest a function for ES30. The large ribosomal subunit is linked to the channel by four connections. We identified regions in the large subunit rRNA and four proteins that may help form the connections. These regions of the ribosome probably serve as a template to guide the assembly of the asymmetric translocation channel. Three of the connections form a picket fence that separates the putative translocation pore from the attachment site of an additional membrane component. The ribosome-channel connections also create an open junction that would allow egress of a nascent chain into the cytosol. At a threshold that is appropriate for the entire complex, the channel is rather solid and the lumenal half of the putative translocation pore is closed. These data suggest that the flow of small molecules across the membrane may be impeded by the channel itself, rather than the ribosome-channel junction.
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Affiliation(s)
- David Gene Morgan
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany St., Boston, MA 02118-2526, USA
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554
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Vourloumis D, Takahashi M, Winters GC, Simonsen KB, Ayida BK, Barluenga S, Qamar S, Shandrick S, Zhao Q, Hermann T. Novel 2,5-dideoxystreptamine derivatives targeting the ribosomal decoding site RNA. Bioorg Med Chem Lett 2002; 12:3367-72. [PMID: 12419363 DOI: 10.1016/s0960-894x(02)00759-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The ribosomal decoding site is the target of aminoglycoside antibiotics that specifically recognize an internal loop RNA structure. We synthesized RNA-targeted 2,5-dideoxystreptamine-4-amides in which a sugar moiety in natural aminoglycosides is replaced by heterocycles.
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Affiliation(s)
- Dionisios Vourloumis
- Department of Medicinal Chemistry, Anadys Pharmaceuticals, Inc., San Diego, CA 92121, USA.
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555
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Simonsen KB, Ayida BK, Vourloumis D, Takahashi M, Winters GC, Barluenga S, Qamar S, Shandrick S, Zhao Q, Hermann T. Novel paromamine derivatives exploring shallow-groove recognition of ribosomal-decoding-site RNA. Chembiochem 2002; 3:1223-8. [PMID: 12465030 DOI: 10.1002/1439-7633(20021202)3:12<1223::aid-cbic1223>3.0.co;2-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Natural aminoglycoside antibiotics recognize an internal loop of bacterial ribosomal-decoding-site RNA by binding to the deep groove of the RNA structure. We have designed, synthesized, and tested RNA-targeted paromamine derivatives that exploit additional interactions on the shallow groove face of the decoding-site RNA. An in vitro transcription-translation assay of a series of 6'-derivatives showed the 6'-position to be very sensitive to substitution. This result suggests that the group at the 6'-position plays a pivotal role in RNA target recognition.
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Affiliation(s)
- Klaus B Simonsen
- Department of Medicinal Chemistry, Anadys Pharmaceuticals, Inc, 9050 Camino Santa Fe, San Diego, CA 92121, USA.
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556
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Rupert PB, Massey AP, Sigurdsson ST, Ferré-D'Amaré AR. Transition state stabilization by a catalytic RNA. Science 2002; 298:1421-4. [PMID: 12376595 DOI: 10.1126/science.1076093] [Citation(s) in RCA: 233] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The hairpin ribozyme catalyzes sequence-specific cleavage of RNA through transesterification of the scissile phosphate. Vanadate has previously been used as a transition state mimic of protein enzymes that catalyze the same reaction. Comparison of the 2.2 angstrom resolution structure of a vanadate-hairpin ribozyme complex with structures of precursor and product complexes reveals a rigid active site that makes more hydrogen bonds to the transition state than to the precursor or product. Because of the paucity of RNA functional groups capable of general acid-base or electrostatic catalysis, transition state stabilization is likely to be an important catalytic strategy for ribozymes.
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Affiliation(s)
- Peter B Rupert
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA
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557
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Abstract
At its most basic level, pre-mRNA splicing can be described as two coordinated nuclease reactions that cleave an intron at either end and result in ligation of the flanking exons. The fact that these reactions are catalyzed by a approximately 3-MDa behemoth of protein and RNA (the spliceosome) challenges most biochemical and structural approaches currently used to characterize lesser-sized enzymes. In addition to this molecular complexity, the highly dynamic nature of splicing complexes provides additional hurdles for mechanistic studies or three-dimensional structure determination. Thus, the methods used to study the spliceosome often probe individual properties of the machine, but no complete, high-resolution picture of splicing catalysis has yet emerged. To facilitate biochemical and structural studies of native splicing complexes, we recently described purification of the catalytic form of the spliceosome (known as C complex). This native complex is suitable for electron microscopic structure determination by single-particle methods. In this paper, we describe the purification in detail and discuss additional methods for trapping and analyzing other splicing complexes.
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Affiliation(s)
- Melissa S Jurica
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02454, USA
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558
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Lancaster L, Kiel MC, Kaji A, Noller HF. Orientation of ribosome recycling factor in the ribosome from directed hydroxyl radical probing. Cell 2002; 111:129-40. [PMID: 12372306 DOI: 10.1016/s0092-8674(02)00938-8] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Ribosome recycling factor (RRF) disassembles posttermination complexes in conjunction with elongation factor EF-G, liberating ribosomes for further rounds of translation. The striking resemblance of its L-shaped structure to that of tRNA has suggested that the mode of action of RRF may be based on mimicry of tRNA. Directed hydroxyl radical probing of 16S and 23S rRNA from Fe(II) tethered to ten positions on the surface of E. coli RRF constrains it to a well-defined location in the subunit interface cavity. Surprisingly, the orientation of RRF in the ribosome differs markedly from any of those previously observed for tRNA, suggesting that structural mimicry does not necessarily reflect functional mimicry.
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Affiliation(s)
- Laura Lancaster
- Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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559
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MESH Headings
- Bacterial Proteins/biosynthesis
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Chloramphenicol/pharmacology
- Erythromycin/pharmacology
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins
- Gene Expression Regulation, Bacterial
- Peptide Chain Termination, Translational
- Peptidyl Transferases/antagonists & inhibitors
- Peptidyl Transferases/metabolism
- Protein Biosynthesis
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/metabolism
- RNA, Transfer/metabolism
- RNA, Transfer, Amino Acyl/metabolism
- Ribosomes/metabolism
- Tryptophan/metabolism
- Tryptophanase/biosynthesis
- Tryptophanase/genetics
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Affiliation(s)
- Matthew S Sachs
- Department of Biochemistry and Molecular Biology, OGI School of Science and Engineering, Oregon Health and Science University, Beaverton, OR 97006, USA.
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560
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Abstract
As the catalytic and regulatory centers of protein synthesis in cells, ribosomes are central to many aspects of cell and structural biology. Recent work highlights the unique properties and complexity of eukaryotic ribosomes and their component rRNAs and proteins.
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Affiliation(s)
- Jennifer A Doudna
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.
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561
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Abstract
Accumulating evidence for nascent-peptide-mediated regulation of translation suggests that all nascent peptides do not necessarily interact with the ribosome in a similar manner. Recent studies have helped to elucidate the exit route of the nascent chain and its interactions with the ribosome.
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Affiliation(s)
- Tanel Tenson
- Institute of Molecular and Cell Biology, Tartu University, Riia 23, Tartu, Estonia.
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562
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Abstract
The human genome has been called "the blueprint for life." This master plan is realized through the process of gene expression. Recent progress has revealed that many of the steps in the pathway from gene sequence to active protein are connected, suggesting a unified theory of gene expression.
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Affiliation(s)
- George Orphanides
- Syngenta Central Toxicology Laboratory, Alderley Park, Cheshire SK10 4TJ, United Kingdom
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