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Napper N, Culver GM. Analysis of r-protein and RNA conformation of 30S subunit intermediates in bacteria. RNA (NEW YORK, N.Y.) 2015; 21:1323-34. [PMID: 25999315 PMCID: PMC4478351 DOI: 10.1261/rna.048918.114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 04/10/2015] [Indexed: 05/15/2023]
Abstract
The ribosome is a large macromolecular complex that must be assembled efficiently and accurately for the viability of all organisms. In bacteria, this process must be robust and tunable to support life in diverse conditions from the ice of arctic glaciers to thermal hot springs. Assembly of the Small ribosomal SUbunit (SSU) of Escherichia coli has been extensively studied and is highly temperature-dependent. However, a lack of data on SSU assembly for other bacteria is problematic given the importance of the ribosome in bacterial physiology. To broaden the understanding of how optimal growth temperature may affect SSU assembly, in vitro SSU assembly of two thermophilic bacteria, Geobacillus kaustophilus and Thermus thermophilus, was compared with that of E. coli. Using these phylogenetically, morphologically, and environmentally diverse bacteria, we show that SSU assembly is highly temperature-dependent and efficient SSU assembly occurs at different temperatures for each organism. Surprisingly, the assembly landscape is characterized by at least two distinct intermediate populations in the organisms tested. This novel, second intermediate, is formed in the presence of the full complement of r-proteins, unlike the previously observed RI* particle formed in the absence of late-binding r-proteins in E. coli. This work reveals multiple distinct intermediate populations are present during SSU assembly in vitro for several bacteria, yielding insights into RNP formation and possible antimicrobial development toward this common SSU target.
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Affiliation(s)
- Nathan Napper
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Gloria M Culver
- Department of Biology, University of Rochester, Rochester, New York 14627, USA Center for RNA Biology: from Genome to Therapeutics, University of Rochester Medical Center, Rochester, New York 14627, USA
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2
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Gupta N, Culver GM. Multiple in vivo pathways for Escherichia coli small ribosomal subunit assembly occur on one pre-rRNA. Nat Struct Mol Biol 2014; 21:937-43. [PMID: 25195050 PMCID: PMC4355579 DOI: 10.1038/nsmb.2887] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/07/2014] [Indexed: 01/01/2023]
Abstract
Processing of transcribed precursor ribosomal RNA (pre-rRNA) to a mature state is a conserved aspect of ribosome biogenesis in vivo. We developed an affinity-purification system to isolate and analyze in vivo-formed pre-rRNA-containing ribonucleoprotein (RNP) particles (rRNPs) from wild-type E. coli. We observed that the first processing intermediate of pre-small subunit (pre-SSU) rRNA is a platform for biogenesis. These pre-SSU-containing RNPs have differing ribosomal-protein and auxiliary factor association and rRNA folding. Each RNP lacks the proper architecture in functional regions, thus suggesting that checkpoints preclude immature subunits from entering the translational cycle. This work offers in vivo snapshots of SSU biogenesis and reveals that multiple pathways exist for the entire SSU biogenesis process in wild-type E. coli. These findings have implications for understanding SSU biogenesis in vivo and offer a general strategy for analysis of RNP biogenesis.
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Affiliation(s)
- Neha Gupta
- Department of Biology, University of Rochester, Rochester, New York, USA
| | - Gloria M Culver
- 1] Department of Biology, University of Rochester, Rochester, New York, USA. [2] Center for RNA Biology, University of Rochester, Rochester, New York, USA
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3
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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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Wang K, Schmied WH, Chin JW. Reprogramming the genetic code: from triplet to quadruplet codes. Angew Chem Int Ed Engl 2012; 51:2288-97. [PMID: 22262408 DOI: 10.1002/anie.201105016] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Indexed: 11/10/2022]
Abstract
The genetic code of cells is near-universally triplet, and since many ribosomal mutations are lethal, changing the cellular ribosome to read nontriplet codes is challenging. Herein we review work on the incorporation of unnatural amino acids into proteins in response to quadruplet codons, and the creation of an orthogonal translation system in the cell that uses an evolved orthogonal ribosome to efficiently direct the incorporation of unnatural amino acids in response to quadruplet codons. Using this system multiple distinct unnatural amino acids have been incorporated and used to genetically program emergent properties into recombinant proteins. Extension of approaches to incorporate multiple unnatural amino acids may allow the combinatorial biosynthesis of materials and therapeutics, and drive investigations into whether life with additional genetically encoded polymers can evolve to perform functions that natural biological systems cannot.
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Affiliation(s)
- Kaihang Wang
- Medical Research Council Laboratory of Molecular Biology, Hills Rd, Cambridge, CB2 0QH UK
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Wang K, Schmied WH, Chin JW. Die Umprogrammierung des genetischen Codes: vom Triplett- zum Quadruplettcode. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201105016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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6
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Rudenko MI, Holmes MR, Ermolenko DN, Lunt EJ, Gerhardt S, Noller HF, Deamer DW, Hawkins A, Schmidt H. Controlled gating and electrical detection of single 50S ribosomal subunits through a solid-state nanopore in a microfluidic chip. Biosens Bioelectron 2011; 29:34-9. [DOI: 10.1016/j.bios.2011.07.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2011] [Revised: 07/17/2011] [Accepted: 07/19/2011] [Indexed: 10/17/2022]
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7
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Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nat Struct Mol Biol 2009; 16:528-33. [PMID: 19363482 PMCID: PMC2679717 DOI: 10.1038/nsmb.1577] [Citation(s) in RCA: 277] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Accepted: 02/19/2009] [Indexed: 11/09/2022]
Abstract
Protein synthesis is catalyzed in the peptidyl transferase center (PTC), located in the large (50S) subunit of the ribosome. No high-resolution structure of the intact ribosome has contained a complete active site including both A- and P-site tRNAs. Additionally, though structures of the 50S subunit found no ordered proteins at the PTC, biochemical evidence suggests specific proteins are capable of interacting with the 3′ ends of the tRNA ligands. Here we present structures at 3.5 Å and 3.55 Å resolution of the 70S ribosome in complex with A- and P-site tRNAs that mimic pre- and post-peptidyl transfer states. These structures demonstrate that the PTC is very similar between the 50S subunit and the intact ribosome. Additionally they reveal interactions between ribosomal proteins L16 and L27 and the tRNA substrates, helping to elucidate the role of these proteins in peptidyl transfer.
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Kiparisov SV, Sergiev PV, Bogdanov AA, Dontsova OA. Structural changes in the ribosome during the elongation cycle. Mol Biol 2006. [DOI: 10.1134/s0026893306050013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Dale T, Uhlenbeck OC. Binding of misacylated tRNAs to the ribosomal A site. RNA (NEW YORK, N.Y.) 2005; 11:1610-5. [PMID: 16244128 PMCID: PMC1370846 DOI: 10.1261/rna.2130505] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Accepted: 08/15/2005] [Indexed: 05/05/2023]
Abstract
To test whether the ribosome displays specificity for the esterified amino acid and the tRNA body of an aminoacyl-tRNA (aa-tRNA), the stabilities of 4 correctly acylated and 12 misacylated tRNAs in the ribosomal A site were determined. By introducing the GAC (valine) anticodon into each tRNA, a constant anticodon.codon interaction was maintained, thus removing concern that different anticodon.codon strengths might affect the binding of the different aa-tRNAs to the A site. Surprisingly, all 16 aa-tRNAs displayed similar dissociation rate constants from the A site. These results suggest that either the ribosome is not specific for different amino acids and tRNA bodies when intact aa-tRNAs are used or the specificity for the amino acid side chain and tRNA body is masked by a conformational change upon aa-tRNA release.
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Affiliation(s)
- Taraka Dale
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, IL 60208, USA
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Kiparisov S, Petrov A, Meskauskas A, Sergiev PV, Dontsova OA, Dinman JD. Structural and functional analysis of 5S rRNA in Saccharomyces cerevisiae. Mol Genet Genomics 2005; 274:235-47. [PMID: 16047201 PMCID: PMC1276653 DOI: 10.1007/s00438-005-0020-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2005] [Accepted: 05/27/2005] [Indexed: 11/26/2022]
Abstract
5S rRNA extends from the central protuberance of the large ribosomal subunit, through the A-site finger, and down to the GTPase-associated center. Here, we present a structure-function analysis of seven 5S rRNA alleles which are sufficient for viability in the yeast Saccharomyces cerevisiae when expressed in the absence of wild-type 5S rRNAs, and extend this analysis using a large bank of mutant alleles that show semi-dominant phenotypes in the presence of wild-type 5S rRNA. This analysis supports the hypothesis that 5S rRNA serves to link together several different functional centers of the ribosome. Data are also presented which suggest that in eukaryotic genomes selection has favored the maintenance of multiple alleles of 5S rRNA, and that these may provide cells with a mechanism to post-transcriptionally regulate gene expression.
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Howard MT, Gesteland RF, Atkins JF. Efficient stimulation of site-specific ribosome frameshifting by antisense oligonucleotides. RNA (NEW YORK, N.Y.) 2004; 10:1653-61. [PMID: 15383681 PMCID: PMC1370650 DOI: 10.1261/rna.7810204] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2004] [Accepted: 07/20/2004] [Indexed: 05/21/2023]
Abstract
Evidence is presented that morpholino, 2'-O-methyl, phosphorothioate, and RNA antisense oligonucleotides can direct site-specific -1 translational frameshifting when annealed to mRNA downstream from sequences where the P- and A-site tRNAs are both capable of repairing with -1 frame codons. The efficiency of ribosomes shifting into the new frame can be as high as 40%, determined by the sequence of the frameshift site, as well as the location, sequence composition, and modification of the antisense oligonucleotide. These results demonstrate that a perfect duplex formed by complementary oligonucleotides is sufficient to induce high level -1 frameshifting. The implications for the mechanism of action of natural programmed translational frameshift stimulators are discussed.
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Affiliation(s)
- Michael T Howard
- Department of Human Genetics, University of Utah, 15 N. 2030 E., Rm. 7410, Salt Lake City, UT 84112-5330, USA.
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Morioka K. Degeneration of Ribosomes in Keratinizing Cells: Possible Participation of RNase A in the Skin and Hair of Rat. Acta Histochem Cytochem 2004. [DOI: 10.1267/ahc.37.399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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13
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Abstract
Structures of the ribosomal large and small subunits have been solved to atomic resolution by X-ray crystallography. These structures provide a new foundation to address the complex process of protein biosynthesis by the ribosome. Translocation of the tRNA-mRNA complex is one of the most fascinating tasks performed by the ribosome. The impact of the crystal structures in understanding the molecular mechanism of translocation is highlighted in this review.
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Affiliation(s)
- Simpson Joseph
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0314, USA.
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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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