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Joo M, Yeom JH, Choi Y, Jun H, Song W, Kim HL, Lee K, Shin E. Specialised ribosomes as versatile regulators of gene expression. RNA Biol 2022; 19:1103-1114. [PMID: 36255182 PMCID: PMC9586635 DOI: 10.1080/15476286.2022.2135299] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The ribosome has long been thought to be a homogeneous cellular machine that constitutively and globally synthesises proteins from mRNA. However, recent studies have revealed that ribosomes are highly heterogeneous, dynamic macromolecular complexes with specialised roles in translational regulation in many organisms across the kingdoms. In this review, we summarise the current understanding of ribosome heterogeneity and the specialised functions of heterogeneous ribosomes. We also discuss specialised translation systems that utilise orthogonal ribosomes.
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Affiliation(s)
- Minju Joo
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Ji-Hyun Yeom
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Younkyung Choi
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Hyeon Jun
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Wooseok Song
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Hyun-Lee Kim
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Eunkyoung Shin
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
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2
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Sediment-associated bacterial community and predictive functionalities are influenced by choice of 16S ribosomal RNA hypervariable region(s): An amplicon-based diversity study. Genomics 2020; 112:4968-4979. [PMID: 32911024 DOI: 10.1016/j.ygeno.2020.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/15/2020] [Accepted: 09/03/2020] [Indexed: 11/22/2022]
Abstract
Meta-omics approaches such as high-throughput sequencing of 16S hypervariable region(s) [HVR(s)] is extensively applied for profiling microbial community. Several studies have deciphered the influence of HVR(s) on bacterial diversity; most of these were devoted to human body habitats. Extent to which targeted HVR(s) influences the diversity estimates of environmental samples is rather unclear. Here, we evaluated the performance of five widely used universal primer pairs spanning V1-V3, V3-V4, V4, V5-V6 and V7-V9 HVRs to characterize bacterial diversity and predictive functionality of complex marine sediments. Obtained results revealed that the HVR(s) V4 and V5-V6 represented the higher species richness than others while, V1-V3 and V7-V9 were unsuccessful to detect Bacteroidetes and Planctomycetes. Further, PICRUSt analysis showed that the selected HVR(s) also had significant impact on the predictive functional profile. Conclusively, this study proved that HVR selection has a profound effect on overall results and thus should be selected with utmost caution.
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3
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Javan GT, Finley SJ, Smith T, Miller J, Wilkinson JE. Cadaver Thanatomicrobiome Signatures: The Ubiquitous Nature of Clostridium Species in Human Decomposition. Front Microbiol 2017; 8:2096. [PMID: 29163394 PMCID: PMC5670113 DOI: 10.3389/fmicb.2017.02096] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/12/2017] [Indexed: 01/21/2023] Open
Abstract
Human thanatomicrobiome studies have established that an abundant number of putrefactive bacteria within internal organs of decaying bodies are obligate anaerobes, Clostridium spp. These microorganisms have been implicated as etiological agents in potentially life-threatening infections; notwithstanding, the scale and trajectory of these microbes after death have not been elucidated. We performed phylogenetic surveys of thanatomicrobiome signatures of cadavers' internal organs to compare the microbial diversity between the 16S rRNA gene V4 hypervariable region and V3-4 conjoined regions from livers and spleens of 45 cadavers undergoing forensic microbiological studies. Phylogenetic analyses of 16S rRNA gene sequences revealed that the V4 region had a significantly higher mean Chao1 richness within the total microbiome data. Permutational multivariate analysis of variance statistical tests, based on unweighted UniFrac distances, demonstrated that taxa compositions were significantly different between V4 and V3-4 hypervariable regions (p < 0.001). Of note, we present the first study, using the largest cohort of criminal cases to date, that two hypervariable regions show discriminatory power for human postmortem microbial diversity. In conclusion, here we propose the impact of hypervariable region selection for the 16S rRNA gene in differentiating thanatomicrobiomic profiles to provide empirical data to explain a unique concept, the Postmortem Clostridium Effect.
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Affiliation(s)
- Gulnaz T. Javan
- Forensic Science Program, Physical Sciences Department, Alabama State University, Montgomery, AL, United States
| | - Sheree J. Finley
- Physical Sciences Department, Alabama State University, Montgomery, AL, United States
| | - Tasia Smith
- Forensic Science Program, Physical Sciences Department, Alabama State University, Montgomery, AL, United States
| | - Joselyn Miller
- Forensic Science Program, Physical Sciences Department, Alabama State University, Montgomery, AL, United States
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4
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Baker KA, Lamichhane R, Lamichhane T, Rueda D, Cunningham PR. Protein-RNA Dynamics in the Central Junction Control 30S Ribosome Assembly. J Mol Biol 2016; 428:3615-31. [PMID: 27192112 DOI: 10.1016/j.jmb.2016.05.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 05/02/2016] [Accepted: 05/07/2016] [Indexed: 11/18/2022]
Abstract
Interactions between ribosomal proteins (rproteins) and ribosomal RNA (rRNA) facilitate the formation of functional ribosomes. S15 is a central domain primary binding protein that has been shown to trigger a cascade of conformational changes in 16S rRNA, forming the functional structure of the central domain. Previous biochemical and structural studies in vitro have revealed that S15 binds a three-way junction of helices 20, 21, and 22, including nucleotides 652-654 and 752-754. All junction nucleotides except 653 are highly conserved among the Bacteria. To identify functionally important motifs within the junction, we subjected nucleotides 652-654 and 752-754 to saturation mutagenesis and selected and analyzed functional mutants. Only 64 mutants with greater than 10% ribosome function in vivo were isolated. S15 overexpression complemented mutations in the junction loop in each of the partially active mutants, although mutations that produced inactive ribosomes were not complemented by overexpression of S15. Single-molecule Förster or fluorescence resonance energy transfer (smFRET) was used to study the Mg(2+)- and S15-induced conformational dynamics of selected junction mutants. Comparison of the structural dynamics of these mutants with the wild type in the presence and absence of S15 revealed specific sequence and structural motifs in the central junction that are important in ribosome function.
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MESH Headings
- DNA Mutational Analysis
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Fluorescence Resonance Energy Transfer
- Genetic Complementation Test
- Macromolecular Substances/metabolism
- Magnesium/metabolism
- Models, Biological
- Models, Molecular
- Protein Binding
- Protein Conformation
- Protein Interaction Maps
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Ribosomal Proteins/metabolism
- Ribosome Subunits, Small, Bacterial/metabolism
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Affiliation(s)
- Kris Ann Baker
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Rajan Lamichhane
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Tek Lamichhane
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA; Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - David Rueda
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA; Section of Virology, Department of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK; Single Molecule Imaging Group, MRC Clinical Sciences Centre (CSC), Du Cane Road, London W12 0NN, UK.
| | - Philip R Cunningham
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA.
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5
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Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis. BMC Bioinformatics 2016; 17:135. [PMID: 27000765 PMCID: PMC4802574 DOI: 10.1186/s12859-016-0992-y] [Citation(s) in RCA: 286] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 03/17/2016] [Indexed: 11/10/2022] Open
Abstract
Background Prokaryotic 16S ribosomal RNA (rRNA) sequences are widely used in environmental microbiology and molecular evolution as reliable markers for the taxonomic classification and phylogenetic analysis of microbes. Restricted by current sequencing techniques, the massive sequencing of 16S rRNA gene amplicons encompassing the full length of genes is not yet feasible. Thus, the selection of the most efficient hypervariable regions for phylogenetic analysis and taxonomic classification is still debated. In the present study, several bioinformatics tools were integrated to build an in silico pipeline to evaluate the phylogenetic sensitivity of the hypervariable regions compared with the corresponding full-length sequences. Results The correlation of seven sub-regions was inferred from the geodesic distance, a parameter that is applied to quantitatively compare the topology of different phylogenetic trees constructed using the sequences from different sub-regions. The relationship between different sub-regions based on the geodesic distance indicated that V4-V6 were the most reliable regions for representing the full-length 16S rRNA sequences in the phylogenetic analysis of most bacterial phyla, while V2 and V8 were the least reliable regions. Conclusions Our results suggest that V4-V6 might be optimal sub-regions for the design of universal primers with superior phylogenetic resolution for bacterial phyla. A potential relationship between function and the evolution of 16S rRNA is also discussed. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0992-y) contains supplementary material, which is available to authorized users.
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6
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Jiang J, Sakakibara Y, Chow CS. Helix 69: A Multitasking RNA Motif as a Novel Drug Target. Isr J Chem 2013. [DOI: 10.1002/ijch.201300012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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7
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Ichinose M, Iizuka M, Kusumi J, Takefu M. Models of compensatory molecular evolution: Effects of back mutation. J Theor Biol 2013; 323:1-10. [DOI: 10.1016/j.jtbi.2013.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 01/10/2013] [Accepted: 01/13/2013] [Indexed: 01/15/2023]
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8
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HUANG HSIENDA, HORNG JORNGTZONG, WU LICHENG, FANG SHUFEN. DISCOVERING COMMON STRUCTURAL MOTIFS OF RIBOSOMAL RNA SECONDARY STRUCTURES IN PROKARYOTES. INT J ARTIF INTELL T 2011. [DOI: 10.1142/s0218213005002296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Certain structural motifs, like tetra-loops, in ribosomal RNA are known to functionally implicate in virtually every aspect of protein synthesis. Ribosomal RNA molecules were also widely used as a tool in molecular evolutionary studies because of their ubiquity, size and low evolutionary rate. In this study, we adapt a data mining approach to discover common structural motifs, and then we use a machine learning approach to identify discriminating CSMs from groups of organisms. Finally, we construct phylogeneitc trees to investigate the evolution of ribosomal RNA by serving the CSMs discovered as targets, which are used to estimate the evolutionary relatedness between organisms. The aim of this study is to discover common structural motifs (CSMs), i.e., those single-strain regions shared in ribosomal RNA secondary structures by several organisms, which are related to specific domains or functions. We discover a set of common structural motifs from several data sets of Archaea and Bacteria. Significant CSMs are then induced by a decision tree. Furthermore, phylogenetic trees are constructed based on CSMs and primary sequences of SSU 16 S ribosomal RNA.
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Affiliation(s)
- HSIEN-DA HUANG
- Department of Biological Science and Technology, Institute of Bioinformatics, National Chiao Tung University, Hsin-Chu 300, Taiwan, ROC
| | - JORNG-TZONG HORNG
- Department of Life Science, Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan, ROC
| | - LI-CHENG WU
- Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan, ROC
| | - SHU-FEN FANG
- Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan, ROC
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9
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Llano-Sotelo B, Klepacki D, Mankin AS. Selection of small peptides, inhibitors of translation. J Mol Biol 2009; 391:813-9. [PMID: 19576904 DOI: 10.1016/j.jmb.2009.06.069] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 06/25/2009] [Accepted: 06/26/2009] [Indexed: 11/30/2022]
Abstract
Identification of small molecular weight compounds targeting specific sites in the ribosome can accelerate development of new antibiotics and provide new tools for ribosomal research. We demonstrate here that antibiotic-size short peptides capable of inhibiting protein synthesis can be selected by using specific elements of ribosomal RNA as a target. The 'h18' pseudoknot encompassing residues 500-545 of the small ribosomal subunit RNA was used as a target in screening a heptapeptide phage-display library. Two of the selected peptides could efficiently interfere with both bacterial and eukaryotic translation. One of these inhibitory peptides exhibited a high-affinity binding to the isolated small ribosomal subunit (K(d) of 1.1 microM). Identification of inhibitory peptides that likely target a specific rRNA structure may pave new ways for validating new antibiotic sites in the ribosome. The selected peptides can be used as a tool in search of novel site-specific inhibitors of translation.
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Affiliation(s)
- Beatriz Llano-Sotelo
- Center for Pharmaceutical Biotechnology, University of Illinois, Chicago, 60607, USA
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10
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Gagnon MG, Mukhopadhyay A, Steinberg SV. Close Packing of Helices 3 and 12 of 16 S rRNA Is Required for the Normal Ribosome Function. J Biol Chem 2006; 281:39349-57. [PMID: 17060325 DOI: 10.1074/jbc.m607725200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The along-groove packing motif is a quasi-reciprocal arrangement of two RNA double helices in which a backbone of each helix is closely packed within the minor groove of the other helix. At the center of the inter-helix contact, a GU base pair in one helix packs against a Watson-Crick base pair in the other helix. Here, based on in vivo selection from a combinatorial gene library of 16 S rRNA and on functional characterization of the selected clones, we demonstrate that the normal ribosome performance requires that helices 3 and 12 be closely packed. In some clones the Watson-Crick and GU base pairs exchange in their positions between the two helices, which affects neither the quality of the helix packing, nor the ribosome function. On the other hand, perturbations in the close packing usually lead to a substantial drop in the ribosome activity. The functionality of the clones containing such perturbations may depend on the presence of particular elements in the vicinity of the area of contact between helices 3 and 12. Such cases do not exist in natural 16 S rRNA, and their selection enriches our knowledge of the constraints imposed on the structure of ribosomal RNA in functional ribosomes.
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Affiliation(s)
- Matthieu G Gagnon
- Département de Biochimie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
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11
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Haag ES. Compensatory vs. pseudocompensatory evolution in molecular and developmental interactions. Genetica 2006; 129:45-55. [PMID: 17109184 DOI: 10.1007/s10709-006-0032-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2004] [Accepted: 06/17/2005] [Indexed: 11/25/2022]
Abstract
The evolution of molecules, developmental circuits, and new species are all characterized by the accumulation of incompatibilities between ancestors and descendants. When specific interactions between components are necessary at any of these levels, this requires compensatory coevolution. Theoretical treatments of compensatory evolution that only consider the endpoints predict that it should be rare because intermediate states are deleterious. However, empirical data suggest that compensatory evolution is common at all levels of molecular interaction. A general solution to this paradox is provided by plausible neutral or nearly neutral intermediates that possess informational redundancy. These intermediates provide an evolutionary path between coadapted allelic combinations. Although they allow incompatible end points to evolve, at no point was a deleterious mutation ever in need of compensation. As a result, what appears to be compensatory evolution may often actually be "pseudocompensatory." Both theoretical and empirical studies indicate that pseudocompensation can speed the evolution of intergenic incompatibility, especially when driven by adaptation. However, under strong stabilizing selection the rate of pseudocompensatory evolution is still significant. Important examples of this process at work discussed here include the evolution of rRNA secondary structures, intra- and inter-protein interactions, and developmental genetic pathways. Future empirical work in this area should focus on comparing the details of intra- and intergenic interactions in closely related organisms.
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Affiliation(s)
- Eric S Haag
- Department of Biology, University of Maryland, College Park, MD 20742, USA.
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12
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Sato NS, Hirabayashi N, Agmon I, Yonath A, Suzuki T. Comprehensive genetic selection revealed essential bases in the peptidyl-transferase center. Proc Natl Acad Sci U S A 2006; 103:15386-91. [PMID: 17032763 PMCID: PMC1592644 DOI: 10.1073/pnas.0605970103] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During protein synthesis, the ribosome catalyzes peptide-bond formation. Biochemical and structural studies revealed that conserved nucleotides in the peptidyl-transferase center (PTC) and its proximity may play a key role in peptide-bond formation; the exact mechanism involved remains unclear. To more precisely define the functional importance of the highly conserved residues, we used a systematic genetic method, which we named SSER (systematic selection of functional sequences by enforced replacement), that allowed us to identify essential nucleotides for ribosomal function from randomized rRNA libraries in Escherichia coli cells. These libraries were constructed by complete randomization of the critical regions in and around the PTC. The selected variants contained natural rRNA sequences from other organisms and organelles as well as unnatural functional sequences; hence providing insights into the functional roles played by these essential bases and suggesting how the universal catalytic mechanism of peptide-bond formation could evolve in all living organisms. Our results highlight essential bases and interactions, which are shaping the PTC architecture and guiding the motions of the tRNA terminus from the A to the P site, found to be crucial not only for the formation of the peptide bond but also for nascent chain elongation.
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Affiliation(s)
- Neuza Satomi Sato
- *Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; and
| | - Naomi Hirabayashi
- *Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; and
| | - Ilana Agmon
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ada Yonath
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tsutomu Suzuki
- *Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; and
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13
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Bélanger F, Théberge-Julien G, Cunningham PR, Brakier-Gingras L. A functional relationship between helix 1 and the 900 tetraloop of 16S ribosomal RNA within the bacterial ribosome. RNA (NEW YORK, N.Y.) 2005; 11:906-13. [PMID: 15872184 PMCID: PMC1370775 DOI: 10.1261/rna.2160405] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The conserved 900 tetraloop that caps helix 27 of 16S ribosomal RNA (rRNA) interacts with helix 24 of 16S rRNA and also with helix 67 of 23S rRNA, forming the intersubunit bridge B2c, proximal to the decoding center. In previous studies, we investigated how the interaction between the 900 tetraloop and helix 24 participates in subunit association and translational fidelity. In the present study, we investigated whether the 900 tetraloop is involved in other undetected interactions with different regions of the Escherichia coli 16S rRNA. Using a genetic complementation approach, we selected mutations in 16S rRNA that compensate for a 900 tetraloop mutation, A900G, which severely impairs subunit association and translational fidelity. Mutations were randomly introduced in 16S rRNA, using either a mutagenic XL1-Red E. coli strain or an error-prone PCR strategy. Gain-offunction mutations were selected in vivo with a specialized ribosome system. Two mutations, the deletion of U12 and the U12C substitution, were thus independently selected in helix 1 of 16S rRNA. This helix is located in the vicinity of helix 27, but does not directly contact the 900 tetraloop in the crystal structures of the ribosome. Both mutations correct the subunit association and translational fidelity defects caused by the A900G mutation, revealing an unanticipated functional interaction between these two regions of 16S rRNA.
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MESH Headings
- Base Sequence
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Peptide Chain Initiation, Translational/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Ribosomes/metabolism
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14
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Laios E, Waddington M, Saraiya AA, Baker KA, O'Connor E, Pamarathy D, Cunningham PR. Combinatorial Genetic Technology for the Development of New Anti-infectives. Arch Pathol Lab Med 2004; 128:1351-9. [PMID: 15578878 DOI: 10.5858/2004-128-1351-cgtftd] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Context.—We previously developed a novel technology known as instant evolution for high-throughput analysis of mutations in Escherichia coli ribosomal RNA.
Objective.—To develop a genetic platform for the isolation of new classes of antiinfectives that are not susceptible to drug resistance based on the instant evolution system.
Design.—Mutation libraries were constructed in the 16S rRNA gene of E coli and analyzed. In addition, the rRNA genes from a number of pathogenic bacteria were cloned and expressed in E coli. The 16S rRNA genes were incorporated into the instant-evolution system in E coli.
Setting.—The Department of Biological Sciences, Wayne State University, Detroit, Mich.
Main Outcome Measures.—Ribosome function was assayed by measuring the amount of green fluorescent protein produced by ribosomes containing mutant or foreign RNA in vivo.
Results.—We have developed a new combinatorial genetic technology (CGT) platform that allows high-throughput in vivo isolation and analysis of rRNA mutations that might lead to drug resistance. This information is being used to develop anti-infectives that recognize the wild type and all viable mutants of the drug target. CGT also provides a novel mechanism for identifying new drug targets.
Conclusions.—Antimicrobials produced using CGT will provide new therapies for the treatment of infections caused by human pathogens that are resistant to current antibiotics. The new therapeutics will be less susceptible to de novo resistance because CGT identifies all mutations of the target that might lead to resistance during the earliest stages of the drug discovery process.
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Affiliation(s)
- Eleftheria Laios
- First Department of Pediatrics, University of Athens, St Sophia Children's Hospital, Athens, Greece
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15
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Léger M, Sidani S, Brakier-Gingras L. A reassessment of the response of the bacterial ribosome to the frameshift stimulatory signal of the human immunodeficiency virus type 1. RNA (NEW YORK, N.Y.) 2004; 10:1225-35. [PMID: 15247429 PMCID: PMC1370612 DOI: 10.1261/rna.7670704] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2004] [Accepted: 05/12/2004] [Indexed: 05/18/2023]
Abstract
HIV-1 uses a programmed -1 ribosomal frameshift to produce the precursor of its enzymes. This frameshift occurs at a specific slippery sequence followed by a stimulatory signal, which was recently shown to be a two-stem helix, for which a three-purine bulge separates the upper and lower stems. In the present study, we investigated the response of the bacterial ribosome to this signal, using a translation system specialized for the expression of a firefly luciferase reporter. The HIV-1 frameshift region was inserted at the beginning of the coding sequence of the luciferase gene, such that its expression requires a -1 frameshift. Mutations that disrupt the upper or the lower stem of the frameshift stimulatory signal or replace the purine bulge with pyrimidines decreased the frameshift efficiency, whereas compensatory mutations that re-form both stems restored the frame-shift efficiency to near wild-type level. These mutations had the same effect in a eukaryotic translation system, which shows that the bacterial ribosome responds like the eukaryote ribosome to the HIV-1 frameshift stimulatory signal. Also, we observed, in contrast to a previous report, that a stop codon immediately 3' to the slippery sequence does not decrease the frameshift efficiency, ruling out a proposal that the frameshift involves the deacylated-tRNA and the peptidyl-tRNA in the E and P sites of the ribosome, rather than the peptidyl-tRNA and the aminoacyl-tRNA in the P and A sites, as commonly assumed. Finally, mutations in 16S ribosomal RNA that facilitate the accommodation of the incoming aminoacyl-tRNA in the A site decreased the frameshift efficiency, which supports a previous suggestion that the frameshift occurs when the aminoacyl-tRNA occupies the A/T entry site.
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Affiliation(s)
- Mélissa Léger
- Département de Biochimie, Université de Montréal, 2900, boul. Edouard-Montpetit, D-353, Québec, H3T 1J4, Canada
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16
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Bélanger F, Gagnon MG, Steinberg SV, Cunningham PR, Brakier-Gingras L. Study of the Functional Interaction of the 900 Tetraloop of 16S Ribosomal RNA with Helix 24 within the Bacterial Ribosome. J Mol Biol 2004; 338:683-93. [PMID: 15099737 DOI: 10.1016/j.jmb.2004.03.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2003] [Revised: 03/08/2004] [Accepted: 03/10/2004] [Indexed: 10/26/2022]
Abstract
The 900 tetraloop that caps helix 27 of 16S ribosomal RNA (rRNA) is amongst the most conserved regions of rRNA. This tetraloop forms a GNRA motif that docks into the minor groove of three base-pairs at the bottom of helix 24 of 16S rRNA in the 30S subunit. Both the tetraloop and its receptor in helix 24 contact the 23S rRNA, forming the intersubunit bridge B2c. Here, we investigated the interaction between the 900 tetraloop and its receptor by genetic complementation. We used a specialized ribosome system in combination with an in vivo instant evolution approach to select mutations in helix 24 compensating for a mutation in the 900 tetraloop (A900G) that severely decreases ribosomal activity, impairing subunit association and translational fidelity. We selected two mutants where the G769-C810 base-pair of helix 24 was substituted with either U-A or C x A. When these mutations in helix 24 were investigated in the context of a wild-type 900 tetraloop, the C x A but not the U-A mutation severely impaired ribosome activity, interfering with subunit association and decreasing translational fidelity. In the presence of the A900G mutation, both mutations in helix 24 increased the ribosome activity to the same extent. Subunit association and translational fidelity were increased to the same level. Computer modeling was used to analyze the effect of the mutations in helix 24 on the interaction between the tetraloop and its receptor. This study demonstrates the functional importance of the interaction between the 900 tetraloop and helix 24.
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Affiliation(s)
- François Bélanger
- Département de Biochimie, Université de Montréal, Montréal, Qué., Canada H3T 1J4
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Bélanger F, Léger M, Saraiya AA, Cunningham PR, Brakier-Gingras L. Functional studies of the 900 tetraloop capping helix 27 of 16S ribosomal RNA. J Mol Biol 2002; 320:979-89. [PMID: 12126619 DOI: 10.1016/s0022-2836(02)00550-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 900 tetraloop (positions 898-901) of Escherichia coli 16S rRNA caps helix 27, which is involved in a conformational switch crucial for the decoding function of the ribosome. This tetraloop forms a GNRA motif involved in intramolecular RNA-RNA interactions with its receptor in helix 24 of 16S rRNA. It is involved also in an intersubunit bridge, via an interaction with helix 67 in domain IV of 23S rRNA. Using a specialized ribosome system and an instant-evolution procedure, the four nucleotides of this loop were randomized and 15 functional mutants were selected in vivo. Positions 899 and 900, responsible for most of the tetraloop/receptor interactions, were found to be the most critical for ribosome activity. Functional studies showed that mutations in the 900 tetraloop impair subunit association and decrease translational fidelity. Computer modeling of the mutations allows correlation of the effect of mutations with perturbations of the tetraloop/receptor interactions.
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Affiliation(s)
- François Bélanger
- Département de Biochimie, Université de Montréal, Montréal, Québec, Canada
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Moine H, Ehresmann B, Ehresmann C. In vivo selection of functional variations in essential sites of ribosomal RNA. Methods 2001; 25:358-64. [PMID: 11860290 DOI: 10.1006/meth.2001.1248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The technique of "in vivo selection of functional ribosomes" is a genetic approach to dissecting the link between the structure and function of critical sites of rRNA. This method proceeds through selection of functional variants among cells that express ribosomes from a pool of rRNA-containing randomized sites. The selection of bacterial clones with functional ribosomes is based on the use of a plasmid carrying a rRNA operon in which a site of interest has been randomized and a point mutation conferring an antibiotic resistance has been introduced. Cells expressing functional ribosomes are then selected on medium containing the antibiotic. With this approach one can isolate at once all the possible variations at a given rRNA site that are able to sustain normal ribosome function. The identification of covariations in between several nucleotides that maintain wild-type ribosome activity can thus help demonstrate the function of specific interactions in rRNA.
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Affiliation(s)
- H Moine
- UPR 9002 du CNRS, 67084 Strasbourg, France.
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Morosyuk SV, SantaLucia J, Cunningham PR. Structure and function of the conserved 690 hairpin in Escherichia coli 16 S ribosomal RNA. III. Functional analysis of the 690 loop. J Mol Biol 2001; 307:213-28. [PMID: 11243815 DOI: 10.1006/jmbi.2000.4432] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An instant-evolution experiment was performed on the eight nucleotides comprising the loop region of the 690 hairpin in Escherichia coli 16 S ribosomal RNA. Positions 690 to 697 were randomly mutated and 101 unique functional mutants were isolated, sequenced and analyzed for function in vivo. Non-random nucleotide distributions were observed at each of the mutated positions except 693 and 694. Nucleotide identity significantly affected ribosome function at positions 690, 695, 696 and 697. Pyrimidines were absent at position 696 in the instant-evolution pool as were C at position 691 and G at position 697. A highly significant covariation was observed between nucleotides 690 and 697. No functional double mutants at positions 691 and 696 were obtained from the instant-evolution pool. In our NMR structure of the 690 loop, both the G690.U697 and G691.A696 form sheared hydrogen-bonded mismatches. To further examine the functional constraints between these paired nucleotides, one set of site-directed mutations was constructed at positions 690:697 and another set was constructed at positions 691:696. Functional analysis of the site-directed mutants is consistent with our instant-evolution findings and revealed constraints on the placement of specific functional groups observed in the NMR structure. Ten instant-evolution mutants were isolated that are more functional than the wild-type. Hyperactivity in these mutants correlates with a single mutation at position 693.
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MESH Headings
- Base Pair Mismatch/physiology
- Conserved Sequence
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/physiology
- Evolution, Molecular
- Magnetic Resonance Spectroscopy
- Models, Molecular
- Mutagenesis, Site-Directed
- Nucleic Acid Conformation
- Phylogeny
- Protons
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/classification
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/physiology
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Affiliation(s)
- S V Morosyuk
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
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Morosyuk SV, Cunningham PR, SantaLucia J. Structure and function of the conserved 690 hairpin in Escherichia coli 16 S ribosomal RNA. II. NMR solution structure. J Mol Biol 2001; 307:197-211. [PMID: 11243814 DOI: 10.1006/jmbi.2000.4431] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The solution structure of the conserved 690 hairpin from Escherichia coli 16 S rRNA was determined by NMR spectroscopy. The 690 loop is located at the surface of the 30 S subunit in the platform region and has been implicated in interactions with P-site bound tRNA, E-site mRNA, S11 binding, IF3 binding, and in RNA-RNA interactions with the 790 loop of 16 S rRNA and domain IV of 23 S rRNA. The structure reveals a novel sheared type G690.U697 base-pair with a single hydrogen bond from the G690 amino to U697-04. G691 and A696 also form a sheared pair and U692 forms a U-turn with an H-bond to the A695 non-bridging phosphate oxygen. The sheared pairs and U-turn result in the continuous single-stranded stacking of five residues from 6693 to U697 with their Watson-Crick functional groups exposed in the minor groove. The overall fold of the 690 hairpin is similar to the anticodon loop of tRNA. The structure provides an explanation for chemical protection patterns in the loop upon interaction with tRNA, the 50 S subunit, and S11. In vivo genetic studies demonstrate the functional importance of the motifs observed in the solution structure of the 690 hairpin.
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Affiliation(s)
- S V Morosyuk
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
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