Optimization of Ribosome Structure and Function by rRNA Base Modification
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{"title"=>"Optimization of ribosome structure and function by rRNA base modification", "type"=>"journal", "authors"=>[{"first_name"=>"Jennifer L.", "last_name"=>"Baxter-Roshek", "scopus_author_id"=>"15043817000"}, {"first_name"=>"Alexey N.", "last_name"=>"Petrov", "scopus_author_id"=>"7401779911"}, {"first_name"=>"Jonathan D.", "last_name"=>"Dinman", "scopus_author_id"=>"7004662921"}], "year"=>2007, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"34249868208", "doi"=>"10.1371/journal.pone.0000174", "pui"=>"352599027", "pmid"=>"17245450", "scopus"=>"2-s2.0-34249868208", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"61f56299-8874-3e2c-8fc2-fbca32941ef9", "abstract"=>"BACKGROUND: Translating mRNA sequences into functional proteins is a fundamental process necessary for the viability of organisms throughout all kingdoms of life. The ribosome carries out this process with a delicate balance between speed and accuracy. This work investigates how ribosome structure and function are affected by rRNA base modification. The prevailing view is that rRNA base modifications serve to fine tune ribosome structure and function.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: To test this hypothesis, yeast strains deficient in rRNA modifications in the ribosomal peptidyltransferase center were monitored for changes in and translational fidelity. These studies revealed allele-specific sensitivity to translational inhibitors, changes in reading frame maintenance, nonsense suppression and aa-tRNA selection. Ribosomes isolated from two mutants with the most pronounced phenotypic changes had increased affinities for aa-tRNA, and surprisingly, increased rates of peptidyltransfer as monitored by the puromycin assay. rRNA chemical analyses of one of these mutants identified structural changes in five specific bases associated with the ribosomal A-site.\\n\\nCONCLUSIONS/SIGNIFICANCE: Together, the data suggest that modification of these bases fine tune the structure of the A-site region of the large subunit so as to assure correct positioning of critical rRNA bases involved in aa-tRNA accommodation into the PTC, of the eEF-1A.aa-tRNA.GTP ternary complex with the GTPase associated center, and of the aa-tRNA in the A-site. These findings represent a direct demonstration in support of the prevailing hypothesis that rRNA modifications serve to optimize rRNA structure for production of accurate and efficient ribosomes.", "link"=>"http://www.mendeley.com/research/optimization-ribosome-structure-function-rrna-base-modification", "reader_count"=>71, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>5, "Student > Doctoral Student"=>7, "Researcher"=>18, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>2, "Student > Master"=>12, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>5, "Student > Doctoral Student"=>7, "Researcher"=>18, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>2, "Student > Master"=>12, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>13, "Agricultural and Biological Sciences"=>50, "Medicine and Dentistry"=>2, "Neuroscience"=>1, "Arts and Humanities"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Chemistry"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>50}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>13}, "Unspecified"=>{"Unspecified"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"United States"=>3, "Japan"=>1, "United Kingdom"=>1, "Portugal"=>1, "India"=>1}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/953637"], "description"=>"<p>Mutant strain <i>snr46</i><i>Δ</i> and the isogenic wild-type are shown in the top row, and mutant strain <i>spb1DA/snr52</i><i>Δ</i> and the isogenic wild-type are show in the bottom row. Error bars represent standard error for all graphs. A. [<sup>14</sup>C]Phe-tRNA binding to the A-site of the ribosome. One site binding curves of bound tRNA as analyzed using GraphPad Prism software. Data are reported as a percentage of the total tRNA bound. B. Ac-[<sup>14</sup>C]Phe-tRNA binding to the P-site of the ribosome. One site binding curves of bound tRNA as analyzed using GraphPad Prism software. Data are reported as a percentage of the total tRNA bound. C. Peptidyltransfer. Timecourse assays of peptidyltransferase activities as measured by the puromycin reaction.</p>", "links"=>[], "tags"=>["microbiology", "biochemistry/rna structure", "cell biology/gene expression", "genetics and genomics/gene expression", "molecular biology/translation mechanisms", "virology/antivirals, including modes of action and resistance"], "article_id"=>623938, "categories"=>["Genetics", "Microbiology", "Cell Biology", "Virology", "Biochemistry", "Molecular Biology"], "users"=>["Jennifer L. Baxter-Roshek", "Alexey N. Petrov", "Jonathan D. Dinman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000174.g004", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ribosome_biochemistry_/623938", "title"=>"Ribosome biochemistry.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:53:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/469641", "https://ndownloader.figshare.com/files/469729", "https://ndownloader.figshare.com/files/469759", "https://ndownloader.figshare.com/files/469779"], "description"=>"<div><h3>Background</h3><p>Translating mRNA sequences into functional proteins is a fundamental process necessary for the viability of organisms throughout all kingdoms of life. The ribosome carries out this process with a delicate balance between speed and accuracy. This work investigates how ribosome structure and function are affected by rRNA base modification. The prevailing view is that rRNA base modifications serve to fine tune ribosome structure and function.</p> <h3>Methodology/Principal Findings</h3><p>To test this hypothesis, yeast strains deficient in rRNA modifications in the ribosomal peptidyltransferase center were monitored for changes in and translational fidelity. These studies revealed allele-specific sensitivity to translational inhibitors, changes in reading frame maintenance, nonsense suppression and aa-tRNA selection. Ribosomes isolated from two mutants with the most pronounced phenotypic changes had increased affinities for aa-tRNA, and surprisingly, increased rates of peptidyltransfer as monitored by the puromycin assay. rRNA chemical analyses of one of these mutants identified structural changes in five specific bases associated with the ribosomal A-site.</p> <h3>Conclusions/Significance</h3><p>Together, the data suggest that modification of these bases fine tune the structure of the A-site region of the large subunit so as to assure correct positioning of critical rRNA bases involved in aa-tRNA accommodation into the PTC, of the eEF-1A•aa-tRNA•GTP ternary complex with the GTPase associated center, and of the aa-tRNA in the A-site. These findings represent a direct demonstration in support of the prevailing hypothesis that rRNA modifications serve to optimize rRNA structure for production of accurate and efficient ribosomes.</p> </div>", "links"=>[], "tags"=>["optimization", "ribosome", "rrna", "modification"], "article_id"=>152580, "categories"=>["Genetics", "Microbiology", "Cell Biology", "Cancer", "Biochemistry", "Molecular Biology"], "users"=>["Jennifer L. Baxter-Roshek", "Alexey N. Petrov", "Jonathan D. Dinman"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0000174.s001", "https://dx.doi.org/10.1371/journal.pone.0000174.s002", "https://dx.doi.org/10.1371/journal.pone.0000174.s003", "https://dx.doi.org/10.1371/journal.pone.0000174.s004"], "stats"=>{"downloads"=>30, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Optimization_of_Ribosome_Structure_and_Function_by_rRNA_Base_Modification/152580", "title"=>"Optimization of Ribosome Structure and Function by rRNA Base Modification", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2007-01-24 00:43:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/953474"], "description"=>"<p>Mutant and isogenic wild-type yeast strains were spotted as ten fold dilutions from 10<sup>5</sup> to 10<sup>1</sup> CFU onto YPAD media containing 20 µg/ml anisomycin or sparsomycin. Cells were incubated for 3 days at 30°C, and growth was monitored as compared to growth on plates in the absence of drug. Each strain and drug was assayed at least twice.</p>", "links"=>[], "tags"=>["rrna", "modification", "mutants", "translational"], "article_id"=>623781, "categories"=>["Genetics", "Microbiology", "Cell Biology", "Virology", "Biochemistry", "Molecular Biology"], "users"=>["Jennifer L. Baxter-Roshek", "Alexey N. Petrov", "Jonathan D. Dinman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000174.g002", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sensitivity_of_rRNA_base_modification_mutants_to_Translational_Inhibitors_/623781", "title"=>"Sensitivity of rRNA base modification mutants to Translational Inhibitors.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:52:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/953817"], "description"=>"<p>(A) Puromycin treated ribosomes isolated from isogenic wild-type and <i>spb1DA/snr52</i><i>Δ</i> mutant strains were used for <i>in vitro</i> chemical probing of the structure around the peptidyltransferase center of the ribosome, specifically helices 89-93. Reactions were performed in triplicate, representative autoradiographs are shown. U - untreated; C - CMCT; D – DMS; K – Kethoxal. Residues with changes in banding pattern labeled. Strongly modified bases at positions U2923, C2843, and C2851 are indicated, as are the more weakly deprotected A2932 and A2933. The increased intensity corresponding to U2845 (marked by *) is not DMS-specific. (B–D). Locations of residues demonstrating strong changes in protection patterns mapped to LSU rRNA structures. Um2920 and Gm2921 are indicated and color coded. Bases with altered protection patterns are circled in orange. aa-tRNA accommodation ‘gate’ bases <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000174#pone.0000174-Sanbonmatsu1\" target=\"_blank\">[36]</a> are indicated with purple (gate 1) and green (gate 2). The “catalytic” A base (equivalent to <i>E. coli</i> 23S rRNA A2451) is incicated with red. Individual LSU helices are numbered and color coded. (B) Secondary structure of yeast 25S rRNA around the PTC. (C) Three dimensional representation of rRNA bases of interest mapped onto the <i>E. coli</i> PTC <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000174#pone.0000174-Schuwirth1\" target=\"_blank\">[34]</a>. Arrow represents the path the 3′ end of the aa-tRNA travels when entering the A-site. (D) Rotation and zoom in of Panel C. Shows the path into the A-site from the aa-tRNA perspective. Residues demonstrating changes in protection patterns are labeled in orange. Locations of modified bases and A-site ‘gate’ residues are labeled.</p>", "links"=>[], "tags"=>["rrna", "probing", "mutant"], "article_id"=>624121, "categories"=>["Genetics", "Microbiology", "Cell Biology", "Virology", "Biochemistry", "Molecular Biology"], "users"=>["Jennifer L. Baxter-Roshek", "Alexey N. Petrov", "Jonathan D. Dinman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000174.g005", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_25S_rRNA_structure_probing_analysis_in_spb1DA_snr52_916_mutant_ribosomes_/624121", "title"=>"25S rRNA structure probing analysis in <i>spb1DA/snr52</i><i>Δ</i> mutant ribosomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:54:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/953402"], "description"=>"<p>(A) Secondary structure of yeast 25S rRNA in the PTC. snoRNAs targeted for this study are indicated along with the residues they modify. <i>Ψ</i> – pseudouridylated residue; Nm – 2′-<i>O</i>-ribose methylated residue. Helices are numbered in black. (B) Three dimensional representation of the <i>E. coli</i> PTC <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000174#pone.0000174-Schuwirth1\" target=\"_blank\">[34]</a>. Modified residues are labeled by the colors indicated in panel A. <i>Left</i>: view into the PTC from the top of the LSU, <i>righ</i>t: 90° rotation of <i>Left</i>. Helices and tRNAs are labeled.</p>", "links"=>[], "tags"=>["rrna", "peptiptidyl", "transferase"], "article_id"=>623707, "categories"=>["Genetics", "Microbiology", "Cell Biology", "Virology", "Biochemistry", "Molecular Biology"], "users"=>["Jennifer L. Baxter-Roshek", "Alexey N. Petrov", "Jonathan D. Dinman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000174.g001", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_25S_rRNA_in_the_peptiptidyl_transferase_center_of_yeast_/623707", "title"=>"25S rRNA in the peptiptidyl transferase center of yeast.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:51:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/953562"], "description"=>"<p>Yeast rRNA modification mutants were tested for their ability to maintain the L-A and M<sub>1</sub> viruses. (A) Mutant and isogenic wild-type yeast strains were spotted onto YPAD plates, and allowed to grow at 30°C, and then replica plated to a seeded lawn of 5X47 indicator cells. Plates were incubated at room temperature for 3–5 days until a zone of inhibition was clearly visible for wild-type cells. (B) Total RNAs were extracted from mutant and isogenic wild-type yeast strains and digested with RNase A under high salt conditions. The resulting double-stranded RNA was separated on a 1% agarose gel and visualized with ethidium bromide. L-A and M<sub>1</sub> dsRNAs are indicated. The image was inverted for clarity.</p>", "links"=>[], "tags"=>["rrna", "modification", "mutants", "propagation"], "article_id"=>623871, "categories"=>["Genetics", "Microbiology", "Cell Biology", "Virology", "Biochemistry", "Molecular Biology"], "users"=>["Jennifer L. Baxter-Roshek", "Alexey N. Petrov", "Jonathan D. Dinman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000174.g003", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Many_of_the_rRNA_base_modification_mutants_have_M_1_virus_propagation_defects_/623871", "title"=>"Many of the rRNA base modification mutants have M<sub>1</sub> virus propagation defects.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:53:01"}

PMC Usage Stats | Further Information

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Relative Metric

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