1
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Peffers MJ, Chabronova A, Balaskas P, Fang Y, Dyer P, Cremers A, Emans PJ, Feczko PZ, Caron MM, Welting TJM. SnoRNA signatures in cartilage ageing and osteoarthritis. Sci Rep 2020; 10:10641. [PMID: 32606371 PMCID: PMC7326970 DOI: 10.1038/s41598-020-67446-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/08/2020] [Indexed: 01/23/2023] Open
Abstract
Osteoarthritis presents as a change in the chondrocyte phenotype and an imbalance between anabolic and catabolic processes. Age affects its onset and progression. Small nucleolar RNAs (SnoRNAs) direct chemical modification of RNA substrates to fine-tune spliceosomal and rRNA function, accommodating changing requirements for splicing and protein synthesis during health and disease. Articular cartilage from young, old and OA knees was used in a microarray study to identify alterations in snoRNA expression. Changes in snoRNAs in osteoarthritis-like conditions were studied in chondrocytes using interleukin-1 and osteoarthritic synovial fluid. SNORD26 and SNORD96A knockdown and overexpression were undertaken using antisense oligonucleotides and overexpression plasmids. We identified panels of snoRNAs differentially expressed due to ageing (including SNORD96A, SNORD44) and osteoarthritis (including SNORD26 and SNORD116). In vitro experiments using osteoarthritis-like conditions affected snoRNA expression. Knockdown or overexpression of SNORD26 or SNORD96A resulted in changes in chondrogenic, hypertrophic, rRNA and osteoarthritis related gene expression. We demonstrate that snoRNA expression changes in cartilage ageing, and osteoarthritis and in osteoarthritis-like conditions, and when the expression of these snoRNAs is altered this affects chondrogenic and hypertrophic gene expression. Thus, we propose an additional dimension in the molecular mechanisms underlying cartilage ageing and osteoarthritis through the dysregulation of snoRNAs.
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Affiliation(s)
- Mandy J Peffers
- Institute of Ageing and Chronic Disease, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - Alzbeta Chabronova
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Centre, 6202 AZ, Maastricht, The Netherlands
| | - Panagiotis Balaskas
- Institute of Ageing and Chronic Disease, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK
| | - Yongxiang Fang
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
| | - Philip Dyer
- Institute of Ageing and Chronic Disease, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK
| | - Andy Cremers
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Centre, 6202 AZ, Maastricht, The Netherlands
| | - Pieter J Emans
- Department of Orthopaedic Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Peter Z Feczko
- Department of Orthopaedic Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Marjolein M Caron
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Centre, 6202 AZ, Maastricht, The Netherlands
| | - Tim J M Welting
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Centre, 6202 AZ, Maastricht, The Netherlands.,Department of Orthopaedic Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
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2
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Petrov AS, Bernier CR, Gulen B, Waterbury CC, Hershkovits E, Hsiao C, Harvey SC, Hud NV, Fox GE, Wartell RM, Williams LD. Secondary structures of rRNAs from all three domains of life. PLoS One 2014; 9:e88222. [PMID: 24505437 PMCID: PMC3914948 DOI: 10.1371/journal.pone.0088222] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 01/03/2014] [Indexed: 12/19/2022] Open
Abstract
Accurate secondary structures are important for understanding ribosomes, which are extremely large and highly complex. Using 3D structures of ribosomes as input, we have revised and corrected traditional secondary (2°) structures of rRNAs. We identify helices by specific geometric and molecular interaction criteria, not by co-variation. The structural approach allows us to incorporate non-canonical base pairs on parity with Watson-Crick base pairs. The resulting rRNA 2° structures are up-to-date and consistent with three-dimensional structures, and are information-rich. These 2° structures are relatively simple to understand and are amenable to reproduction and modification by end-users. The 2° structures made available here broadly sample the phylogenetic tree and are mapped with a variety of data related to molecular interactions and geometry, phylogeny and evolution. We have generated 2° structures for both large subunit (LSU) 23S/28S and small subunit (SSU) 16S/18S rRNAs of Escherichia coli, Thermus thermophilus, Haloarcula marismortui (LSU rRNA only), Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We provide high-resolution editable versions of the 2° structures in several file formats. For the SSU rRNA, the 2° structures use an intuitive representation of the central pseudoknot where base triples are presented as pairs of base pairs. Both LSU and SSU secondary maps are available (http://apollo.chemistry.gatech.edu/RibosomeGallery). Mapping of data onto 2° structures was performed on the RiboVision server (http://apollo.chemistry.gatech.edu/RiboVision).
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Affiliation(s)
- Anton S Petrov
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Chad R Bernier
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Burak Gulen
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Chris C Waterbury
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Eli Hershkovits
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Chiaolong Hsiao
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Stephen C Harvey
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Nicholas V Hud
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - George E Fox
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Roger M Wartell
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Loren Dean Williams
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
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3
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Spano MN, Walter NG. Solution structure of an alternate conformation of helix27 from Escherichia coli16S rRNA. Biopolymers 2011; 95:653-68. [PMID: 21442607 DOI: 10.1002/bip.21626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 03/08/2011] [Accepted: 03/09/2011] [Indexed: 11/09/2022]
Abstract
Helix (H)27 of 16S ribosomal (r)RNA from Escherichia coli was dubbed the "switch helix" when mutagenesis suggested that two alternative base pair registers may have distinct functional roles in the bacterial ribosome. Although more recent genetic analyses suggest that H27 conformational switching is not required for translation, previous solution studies demonstrated that the isolated E. coli H27 can dynamically convert between the 885 and 888 conformations. Here, we have solved the nuclear magnetic resonance solution structure of a locked 888 conformation. NOE and residual dipolar coupling restraints reveal an architecture that markedly differs from that of the 885 conformation found in crystal structures of the bacterial ribosome. In place of the loop E motif that characterizes the 885 conformer and that the 888 conformer cannot adopt, we find evidence for an asymmetrical A-rich internal loop stabilized by stacking interactions among the unpaired A's. Comparison of the isolated H27 888 solution structure with the 885 crystal structure within the context of the ribosome suggests a difference in overall length of H27 that presents one plausible reason for the absence of H27 conformational switching within the sterically confining ribosome.
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4
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Zhigaĭlov AV, Graĭfer DM, Babaĭlova ES, Polimbetova NS, Karpova GG, Iskakov BK. [Region 1112-1123 in the central domain of 18S rRNA in 40S subunits of plant ribosomes: accessibility for complementary interactions and the functional role]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:366-74. [PMID: 20644591 DOI: 10.1134/s1068162010030088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The binding of the 18S RNA of the 40S subunits of wheat germ ribosomes to an oligodeoxyribonucleotide complementary to the 1112-1123 region of the central domain of this RNA molecule has been studied. The selective binding of this oligomer to the complementary RNA fragment and the inhibition of the translation of uncapped chimeric RNA containing enhancer sequences in the 5'-untranslated region upstream of the reporter sequence coding for beta-glucuronidase has been shown in a cell-free protein-synthesizing system. The use of a derivative of the aforementioned oligomer containing an alkylating group at the 5' end allowed for the demonstration that the 1112-1123 region of 18S RNA can form a heteroduplex with the complementary sequence of the oligomer. The data obtained show that the 1112-1123 region in loop 27 of the central domain of 18S RNA of 40S ribosomal subunits is exposed on the subunit surface and probably participates in the cap-independent binding of the subunits to mRNA due to the complementary interaction with the enhancer sequences.
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MESH Headings
- Enhancer Elements, Genetic
- Genes, Reporter
- Glucuronidase/biosynthesis
- Glucuronidase/genetics
- Nucleic Acid Conformation
- Nucleic Acid Heteroduplexes/biosynthesis
- Nucleic Acid Heteroduplexes/genetics
- Oligodeoxyribonucleotides/chemistry
- Potyvirus/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/chemistry
- RNA, Plant/physiology
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/physiology
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Seeds/metabolism
- Triticum/metabolism
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5
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Appropriate maturation and folding of 16S rRNA during 30S subunit biogenesis are critical for translational fidelity. Proc Natl Acad Sci U S A 2010; 107:4567-72. [PMID: 20176963 DOI: 10.1073/pnas.0912305107] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ribosomal protein S5 is critical for small ribosomal subunit (SSU) assembly and is indispensable for SSU function. Previously, we identified a point mutation in S5, (G28D) that alters both SSU formation and translational fidelity in vivo, which is unprecedented for other characterized S5 mutations. Surprisingly, additional copies of an extraribosomal assembly factor, RimJ, rescued all the phenotypes associated with S5(G28D), including fidelity defects, suggesting that the effect of RimJ on rescuing the miscoding of S5(G28D) is indirect. To understand the underlying mechanism, we focused on the biogenesis cascade and observed defects in processing of precursor 16S (p16S) rRNA in the S5(G28D) strain, which were rescued by RimJ. Analyses of p16S rRNA-containing ribosomes from other strains further supported a correspondence between the extent of 5(') end maturation of 16S rRNA and translational miscoding. Chemical probing of mutant ribosomes with additional leader sequences at the 5(') end of 16S rRNA compared to WT ribosomes revealed structural differences in the region of helix 1. Thus, the presence of additional nucleotides at the 5(') end of 16S rRNA could alter fidelity by changing the architecture of 16S rRNA in translating ribosomes and suggests that fidelity is governed by accuracy and completeness of the SSU biogenesis cascade.
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6
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Functional study of the residue C899 in the 900 tetraloop of Escherichia coli small subunit ribosomal RNA. Biosci Biotechnol Biochem 2009; 73:2544-6. [PMID: 19897894 DOI: 10.1271/bbb.90460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A mutant ribosome bearing C899G in the 900 tetraloop of Escherichia coli 16S rRNA, one implicated in a conformational switch in the dynamic movements of the ribosome, showed defects in subunit association and 30S initiation complex formation. Our results explain the basis of the loss of protein synthesis ability caused by a perturbation of the 900 tetraloop.
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7
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Critical evaluation of random mutagenesis by error-prone polymerase chain reaction protocols, Escherichia coli mutator strain, and hydroxylamine treatment. Anal Biochem 2009; 388:71-80. [PMID: 19454214 DOI: 10.1016/j.ab.2009.02.008] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 02/05/2009] [Accepted: 02/05/2009] [Indexed: 11/21/2022]
Abstract
Random mutagenesis methods constitute a valuable protein modification toolbox with applications ranging from protein engineering to directed protein evolution studies. Although a variety of techniques are currently available, the field is lacking studies that would directly compare the performance parameters and operational range of different methods. In this study, we have scrutinized several of the most commonly used random mutagenesis techniques by critically evaluating popular error-prone polymerase chain reaction (PCR) protocols as well as hydroxylamine and a mutator Escherichia coli strain mutagenesis methods. Relative mutation frequencies were analyzed using a reporter plasmid that allowed direct comparison of the methods. Error-prone PCR methods yielded the highest mutation rates and the widest operational ranges, whereas the chemical and biological methods generated a low level of mutations and exhibited a narrow range of operation. The repertoire of transitions versus transversions varied among the methods, suggesting the use of a combination of methods for high-diversity full-scale mutagenesis. Using the parameters defined in this study, the evaluated mutagenesis methods can be used for controlled mutagenesis, where the intended average frequency of induced mutations can be adjusted to a desirable level.
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8
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Tsunewaki K, Matsuoka Y, Yamazaki Y, Ogihara Y. Evolutionary dynamics of wheat mitochondrial gene structure with special remarks on the origin and effects of RNA editing in cereals. Genes Genet Syst 2008; 83:301-20. [PMID: 18931456 DOI: 10.1266/ggs.83.301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We investigated the evolutionary dynamics of wheat mitochondrial genes with respect to their structural differentiation during organellar evolution, and to mutations that occurred during cereal evolution. First, we compared the nucleotide sequences of three wheat mitochondrial genes to those of wheat chloroplast, alpha-proteobacterium and cyanobacterium orthologs. As a result, we were able to (1) differentiate the conserved and variable segments of the orthologs, (2) reveal the functional importance of the conserved segments, and (3) provide a corroborative support for the alpha-proteobacterial and cyanobacterial origins of those mitochondrial and chloroplast genes, respectively. Second, we compared the nucleotide sequences of wheat mitochondrial genes to those of rice and maize to determine the types and frequencies of base changes and indels occurred in cereal evolution. Our analyses showed that both the evolutionary speed, in terms of number of base substitutions per site, and the transition/transversion ratio of the cereal mitochondrial genes were less than two-fifths of those of the chloroplast genes. Eight mitochondrial gene groups differed in their evolutionary variability, RNA and Complex I (nad) genes being most stable whereas Complex V (atp) and ribosomal protein genes most variable. C-to-T transition was the most frequent type of base change; C-to-G and G-to-C transversions occurred at lower rates than all other changes. The excess of C-to-T transitions was attributed to C-to-U RNA editing that developed in early stage of vascular plant evolution. On the contrary, the editing of C residues at cereal T-to-C transition sites developed mostly during cereal divergence. Most indels were associated with short direct repeats, suggesting intra- and intermolecular recombination as an important mechanism for their origin. Most of the repeats associated with indels were di- or trinucleotides, although no preference was noticed for their sequences. The maize mt genome was characterized by a high incidence of indels, comparing to the wheat and rice mt genomes.
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9
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Léger M, Dulude D, Steinberg SV, Brakier-Gingras L. The three transfer RNAs occupying the A, P and E sites on the ribosome are involved in viral programmed -1 ribosomal frameshift. Nucleic Acids Res 2007; 35:5581-92. [PMID: 17704133 PMCID: PMC2018615 DOI: 10.1093/nar/gkm578] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 06/28/2007] [Accepted: 07/13/2007] [Indexed: 11/17/2022] Open
Abstract
The -1 programmed ribosomal frameshifts (PRF), which are used by many viruses, occur at a heptanucleotide slippery sequence and are currently thought to involve the tRNAs interacting with the ribosomal P- and A-site codons. We investigated here whether the tRNA occupying the ribosomal E site that precedes a slippery site influences -1 PRF. Using the human immunodeficiency virus type 1 (HIV-1) frameshift region, we found that mutating the E-site codon altered the -1 PRF efficiency. When the HIV-1 slippery sequence was replaced with other viral slippery sequences, mutating the E-site codon also altered the -1 PRF efficiency. Because HIV-1 -1 PRF can be recapitulated in bacteria, we used a bacterial ribosome system to select, by random mutagenesis, 16S ribosomal RNA (rRNA) mutations that modify the expression of a reporter requiring HIV-1 -1 PRF. Three mutants were isolated, which are located in helices 21 and 22 of 16S rRNA, a region involved in translocation and E-site tRNA binding. We propose a novel model where -1 PRF is triggered by an incomplete translocation and depends not only on the tRNAs interacting with the P- and A-site codons, but also on the tRNA occupying the E site.
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Affiliation(s)
| | | | | | - Léa Brakier-Gingras
- Département de Biochimie, Université de Montréal, Montréal, Québec, Canada, H3T 1J4
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10
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Abstract
The ribosome is responsible for protein synthesis, the translation of the genetic code, in all living organisms. Ribosomes are composed of RNA (ribosomal RNA) and protein (ribosomal protein). Soluble protein factors bind to the ribosome and facilitate different phases of translation. Genetic approaches have proved useful for the identification and characterization of the structural and functional roles of specific nucleotides in ribosomal RNA and of specific amino acids in ribosomal proteins and in ribosomal factors. This chapter summarizes examples of mutations identified in ribosomal RNA, ribosomal proteins, and ribosomal factors.
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MESH Headings
- Animals
- Base Sequence
- DNA Mutational Analysis
- Humans
- Mutation
- Nucleic Acid Conformation
- Peptide Elongation Factors/genetics
- Peptide Initiation Factors/genetics
- Peptide Termination Factors/genetics
- Protein Subunits/genetics
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/physiology
- RNA, Ribosomal, 23S/analysis
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/physiology
- Ribosomal Proteins/genetics
- Ribosomes/genetics
- Sequence Analysis, RNA
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Affiliation(s)
- Kathleen L Triman
- Department of Biology, Franklin and Marshall College, Lancaster, PA 17604, USA
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11
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Holmes KL, Culver GM. Analysis of Conformational Changes in 16S rRNA During the Course of 30S Subunit Assembly. J Mol Biol 2005; 354:340-57. [PMID: 16246364 DOI: 10.1016/j.jmb.2005.09.056] [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: 06/06/2005] [Revised: 09/16/2005] [Accepted: 09/16/2005] [Indexed: 11/19/2022]
Abstract
Ribosome biogenesis involves an integrated series of binding events coupled with conformational changes that ultimately result in the formation of a functional macromolecular complex. In vitro, Escherichia coli 30 S subunit assembly occurs in a cooperative manner with the ordered addition of 20 ribosomal proteins (r-proteins) with 16 S rRNA. The assembly pathway for 30 S subunits has been dissected in vitro into three steps, where specific r-proteins associate with 16 S rRNA early in 30 S subunit assembly, followed by a mid-assembly conformational rearrangement of the complex that then enables the remaining r-proteins to associate in the final step. Although the three steps of 30 S subunit assembly have been known for some time, few details have been elucidated about changes that occur as a result of these three specific stages. Here, we present a detailed analysis of the concerted early and late stages of small ribosomal subunit assembly. Conformational changes, roles for base-pairing and r-proteins at specific stages of assembly, and a polar nature to the assembly process have been revealed. This work has allowed a more comprehensive and global view of E.coli 30 S ribosomal subunit assembly to be obtained.
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Affiliation(s)
- Kristi L Holmes
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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12
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Huggins W, Ghosh SK, Nanda K, Wollenzien P. Internucleotide movements during formation of 16 S rRNA-rRNA photocrosslinks and their connection to the 30 S subunit conformational dynamics. J Mol Biol 2005; 354:358-74. [PMID: 16242153 DOI: 10.1016/j.jmb.2005.09.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2005] [Revised: 09/14/2005] [Accepted: 09/19/2005] [Indexed: 10/25/2022]
Abstract
UV light-induced RNA photocrosslinks are formed at a limited number of specific sites in the Escherichia coli and in other eubacterial 16 S rRNAs. To determine if unusually favorable internucleotide geometries could explain the restricted crosslinking patterns, parameters describing the internucleotide geometries were calculated from the Thermus thermophilus 30 S subunit X-ray structure and compared to crosslinking frequencies. Significant structural adjustments between the nucleotide pairs usually are needed for crosslinking. Correlations between the crosslinking frequencies and the geometrical parameters indicate that nucleotide pairs closer to the orientation needed for photoreaction have higher crosslinking frequencies. These data are consistent with transient conformational changes during crosslink formation in which the arrangements needed for photochemical reaction are attained during the electronic excitation times. The average structural rearrangement for UVA-4-thiouridine (s4U)-induced crosslinking is larger than that for UVB or UVC-induced crosslinking; this is associated with the longer excitation time for s4U and is also consistent with transient conformational changes. The geometrical parameters do not completely predict the crosslinking frequencies, implicating other aspects of the tertiary structure or conformational flexibility in determining the frequencies and the locations of the crosslinking sites. The majority of the UVB/C and UVA-s4U-induced crosslinks are located in four regions in the 30 S subunit, within or at the ends of RNA helix 34, in the tRNA P-site, in the distal end of helix 28 and in the helix 19/helix 27 region. These regions are implicated in different aspects of tRNA accommodation, translocation and in the termination reaction. These results show that photocrosslinking is an indicator for sites where there is internucleotide conformational flexibility and these sites are largely restricted to parts of the 30 S subunit associated with ribosome function.
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MESH Headings
- Base Pairing
- Base Sequence
- Binding Sites
- Cross-Linking Reagents
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/radiation effects
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation/radiation effects
- Nucleotides/chemistry
- Nucleotides/metabolism
- Nucleotides/radiation effects
- Photochemistry
- Protein Conformation/radiation effects
- Protein Subunits
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/radiation effects
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 16S/radiation effects
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomes/chemistry
- Ribosomes/metabolism
- Ribosomes/radiation effects
- Ultraviolet Rays
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Affiliation(s)
- Wayne Huggins
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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