1
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Gabdulkhakov A, Mitroshin I, Garber M. Structure of the ribosomal P stalk base in archaean Methanococcus jannaschii. J Struct Biol 2020; 211:107559. [PMID: 32653645 DOI: 10.1016/j.jsb.2020.107559] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/18/2020] [Accepted: 06/28/2020] [Indexed: 11/29/2022]
Abstract
Complexes of archaeal ribosomal proteins uL11 and uL10/P0 (the two-domain N-terminal fragment of uL10, uL10NTF/P0NTF) with the adjacent 74 nucleotides of 23S rRNA fragment (23SrRNA(74)) from Methanococcus jannaschii (Mja) were obtained, crystallized and their structures were studied. The comparative structural analysis of the complexes of Mja uL10NTF•23SrRNA(74) and Mja uL10NTF•uL11•23SrRNA(74) shows that the insertion of uL11 in the binary complex does not change the conformation of the 23S rRNA fragment. On the other hand, the interaction with this specific RNA fragment leads to the restructuring of uL11 compared to the structure of this protein in the free state. Besides, although analysis confirmed the mobility of uL10/P0 domain II, disproved the assumption that it may be in contact with rRNA or uL11. In addition, the Mja uL10NTF•uL11•23SrRNA(74) complex was cocrystallized with the antibiotic thiostrepton, and the structure of this complex was solved. The thiostrepton binding site in this archaeal complex was found between the 23S rRNA and the N-terminal domain (NTD) of the Mja uL11 protein, similar to its binding site in the one of bacterial ribosome complex with thiostrepton. Upon binding of thiostrepton, the NTD of uL11 shifts toward rRNA by 7 Å. Such a shift may be the cause of the inhibitory effect of the antibiotic on the recruitment of translation factors to the GTPase-activating region in archaeal ribosomes, similar to its inhibitory effect on protein synthesis in bacterial ribosomes.
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Affiliation(s)
- Azat Gabdulkhakov
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Pushchino, Moscow Region 142290, Russian Federation.
| | - Ivan Mitroshin
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Pushchino, Moscow Region 142290, Russian Federation
| | - Maria Garber
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Pushchino, Moscow Region 142290, Russian Federation
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2
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Burkhart BJ, Schwalen CJ, Mann G, Naismith JH, Mitchell DA. YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function. Chem Rev 2017; 117:5389-5456. [PMID: 28256131 DOI: 10.1021/acs.chemrev.6b00623] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
With advances in sequencing technology, uncharacterized proteins and domains of unknown function (DUFs) are rapidly accumulating in sequence databases and offer an opportunity to discover new protein chemistry and reaction mechanisms. The focus of this review, the formerly enigmatic YcaO superfamily (DUF181), has been found to catalyze a unique phosphorylation of a ribosomal peptide backbone amide upon attack by different nucleophiles. Established nucleophiles are the side chains of Cys, Ser, and Thr which gives rise to azoline/azole biosynthesis in ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products. However, much remains unknown about the potential for YcaO proteins to collaborate with other nucleophiles. Recent work suggests potential in forming thioamides, macroamidines, and possibly additional post-translational modifications. This review covers all knowledge through mid-2016 regarding the biosynthetic gene clusters (BGCs), natural products, functions, mechanisms, and applications of YcaO proteins and outlines likely future research directions for this protein superfamily.
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Affiliation(s)
| | | | - Greg Mann
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom
| | - James H Naismith
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom.,State Key Laboratory of Biotherapy, Sichuan University , Sichuan, China
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3
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Voronina EN, Kolokoltsova TD, Slinko NM, Nechaeva EA, Filipenko ML. Transcription factor YY1 is involved in activation of transcription of the human gene for ribosomal protein L11. Mol Biol 2011. [DOI: 10.1134/s0026893308010147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Bai Y, Wu C, Zhao J, Liu YH, Ding W, Ling WLW. Role of iron and sodium citrate in animal protein-free CHO cell culture medium on cell growth and monoclonal antibody production. Biotechnol Prog 2010; 27:209-19. [DOI: 10.1002/btpr.513] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 08/18/2010] [Indexed: 01/04/2023]
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5
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Ciufolini MA, Lefranc D. Micrococcin P1: Structure, biology and synthesis. Nat Prod Rep 2010; 27:330-42. [DOI: 10.1039/b919071f] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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Abstract
Antibiotic resistance is a fundamental aspect of microbiology, but it is also a phenomenon of vital importance in the treatment of diseases caused by pathogenic microorganisms. A resistance mechanism can involve an inherent trait or the acquisition of a new characteristic through either mutation or horizontal gene transfer. The natural susceptibilities of bacteria to a certain drug vary significantly from one species of bacteria to another and even from one strain to another. Once inside the cell, most antibiotics affect all bacteria similarly. The ribosome is a major site of antibiotic action and is targeted by a large and chemically diverse group of antibiotics. A number of these antibiotics have important applications in human and veterinary medicine in the treatment of bacterial infections. The antibiotic binding sites are clustered at functional centers of the ribosome, such as the decoding center, the peptidyl transferase center, the GTPase center, the peptide exit tunnel, and the subunit interface spanning both subunits on the ribosome. Upon binding, the drugs interfere with the positioning and movement of substrates, products, and ribosomal components that are essential for protein synthesis. Ribosomal antibiotic resistance is due to the alteration of the antibiotic binding sites through either mutation or methylation. Our knowledge of antibiotic resistance mechanisms has increased, in particular due to the elucidation of the detailed structures of antibiotic-ribosome complexes and the components of the efflux systems. A number of mutations and methyltransferases conferring antibiotic resistance have been characterized. These developments are important for understanding and approaching the problems associated with antibiotic resistance, including design of antimicrobials that are impervious to known bacterial resistance mechanisms.
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7
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Xie Q, Tian Y, Zheng L, Bu W. 18S rRNA hyper-elongation and the phylogeny of Euhemiptera (Insecta: Hemiptera). Mol Phylogenet Evol 2008; 47:463-71. [PMID: 18358745 DOI: 10.1016/j.ympev.2008.01.024] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2006] [Revised: 10/27/2007] [Accepted: 01/22/2008] [Indexed: 10/22/2022]
Abstract
The small subunit of nuclear ribosomal RNA (SSU nrRNA), whose sedimentation is mostly 18S in eukaryotes, is considered a relatively conservative marker for resolving phylogenetic relationship at the order level or higher. Length variation in SSU nrDNA is common, and can be rather large in some groups. In studies of Hexapoda phylogeny, the SSU nrDNA has been repeatedly used as a marker. Sternorrhyncha has been rarely included. The lengths of SSU nrDNAs of sternorrhynchids, the basal group of Hemiptera identified in the previous study are 0.3-0.6 kb longer than the usual ones in Hexapoda (1.8-1.9 kb). To use the entire SSU nrDNA sequences or the length-variable parts could cause alignment trouble and therefore affect phylogenetic results, as shown in this study of Euhemiptera phylogeny. Two problems are particularly noticeable. One is that two hyper-variable regions flanking a short length-conservative region could become overlapped in the alignment. This will destroy the positional homology over a larger range. The other is that, when a base pair in a stem of the secondary structure is located near the length-variable regions (LVRs), the simultaneous positional homology of these two bases in the pair is always lost in the alignment results. In this study, the secondary structure model of Hexapoda SSU nrRNA was slightly adjusted and the LVR distributions in it were finely positioned. The noise caused by the hyper LVRs was eliminated and the simultaneous homology for the paired bases was recovered based on the secondary structure model. These corrections improved the quality of the data matrix and hence improved the resolving behavior of the algorithm used. This study provided more convincing evidence for resolving the Euhemiptera suborders phylogeny as (Archaeorrhyncha+(Clypeorrhyncha+(Coleorrhyncha+Heteroptera))). This result provided a more solid background for outgroup determination according to the phylogenetic studies inside each suborder. The problems caused by LVRs have seldom been well addressed. As phylogenetic reconstruction depends more on the data matrix itself than on the algorithm, and length variation of SSU/LSU rRNA exists more or less in any group, it is necessary to closely investigate the effect of rRNA length variation on alignment and phylogenetic reconstruction in more groups.
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Affiliation(s)
- Qiang Xie
- Institute of Entomology, College of Life Sciences, Nankai University, Department of Zoology, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
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8
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García-Marcos A, Morreale A, Guarinos E, Briones E, Remacha M, Ortiz AR, Ballesta JPG. In vivo assembling of bacterial ribosomal protein L11 into yeast ribosomes makes the particles sensitive to the prokaryotic specific antibiotic thiostrepton. Nucleic Acids Res 2007; 35:7109-17. [PMID: 17940088 PMCID: PMC2175356 DOI: 10.1093/nar/gkm773] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Eukaryotic ribosomal stalk protein L12 and its bacterial orthologue L11 play a central role on ribosomal conformational changes during translocation. Deletion of the two genes encoding L12 in Saccharomyces cerevisiae resulted in a very slow-growth phenotype. Gene RPL12B, but not the RPL12A, cloned in centromeric plasmids fully restored control protein level and the growth rate when expressed in a L12-deprived strain. The same strain has been transformed to express Escherichia coli protein EcL11 under the control of yeast RPL12B promoter. The bacterial protein has been found in similar amounts in washed ribosomes from the transformed yeast strain and from control E. coli cells, however, EcL11 was unable to restore the defective acidic protein stalk composition caused by the absence of ScL12 in the yeast ribosome. Protein EcL11 induced a 10% increase in L12-defective cell growth rate, although the in vitro polymerizing capacity of the EcL11-containing ribosomes is restored in a higher proportion, and, moreover, the particles became partially sensitive to the prokaryotic specific antibiotic thiostrepton. Molecular dynamic simulations using modelled complexes support the correct assembly of bacterial L11 into the yeast ribosome and confirm its direct implication of its CTD in the binding of thiostrepton to ribosomes.
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Affiliation(s)
- Alberto García-Marcos
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid and Consejo Superior de investigaciones Científicas, Cantoblanco, Madrid 28049, Spain
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9
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Lee D, Walsh JD, Yu P, Markus MA, Choli-Papadopoulou T, Schwieters CD, Krueger S, Draper DE, Wang YX. The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes. J Mol Biol 2007; 367:1007-22. [PMID: 17292917 PMCID: PMC2045704 DOI: 10.1016/j.jmb.2007.01.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Revised: 11/21/2006] [Accepted: 01/04/2007] [Indexed: 11/22/2022]
Abstract
The L11 binding site is one of the most important functional sites in the ribosome. The N-terminal domain of L11 has been implicated as a "reversible switch" in facilitating the coordinated movements associated with EF-G-driven GTP hydrolysis. The reversible switch mechanism has been hypothesized to require conformational flexibility involving re-orientation and re-positioning of the two L11 domains, and warrants a close examination of the structure and dynamics of L11. Here we report the solution structure of free L11, and relaxation studies of free L11, L11 complexed to its 58 nt RNA recognition site, and L11 in a ternary complex with the RNA and thiostrepton antibiotic. The binding site of thiostrepton on L11 was also defined by analysis of structural and dynamics data and chemical shift mapping. The conclusions of this work are as follows: first, the binding of L11 to RNA leads to sizable conformation changes in the regions flanking the linker and in the hinge area that links a beta-sheet and a 3(10)-helix-turn-helix element in the N terminus. Concurrently, the change in the relative orientation may lead to re-positioning of the N terminus, as implied by a decrease of radius of gyration from 18.5 A to 16.2 A. Second, the regions, which undergo large conformation changes, exhibit motions on milliseconds-microseconds or nanoseconds-picoseconds time scales. Third, binding of thiostrepton results in more rigid conformations near the linker (Thr71) and near its putative binding site (Leu12). Lastly, conformational changes in the putative thiostrepton binding site are implicated by the re-emergence of cross-correlation peaks in the spectrum of the ternary complex, which were missing in that of the binary complex. Our combined analysis of both the chemical shift perturbation and dynamics data clearly indicates that thiostrepton binds to a pocket involving residues in the 3(10)-helix in L11.
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Affiliation(s)
- Donghan Lee
- Protein Nucleic Acid Interaction Section, Structural Biophysics Laboratory, NCI-Frederick, NIH, Frederick, MD 21702, U.S.A
- Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, U.S.A
| | - Joseph D. Walsh
- Protein Nucleic Acid Interaction Section, Structural Biophysics Laboratory, NCI-Frederick, NIH, Frederick, MD 21702, U.S.A
| | - Ping Yu
- Protein Nucleic Acid Interaction Section, Structural Biophysics Laboratory, NCI-Frederick, NIH, Frederick, MD 21702, U.S.A
- Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, U.S.A
| | - Michelle A. Markus
- Structural Biology and Computational Chemistry, Wyeth Research, 87 CambridgePark Drive Cambridge, MA 02140
| | - Theodora Choli-Papadopoulou
- Laboratory of Biochemistry, School of Chemistry, Aristotle University of Thessaloniki, Thessaloniki 54006, Greece
| | - Charles D. Schwieters
- Computational Bioscience and Engineering Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624
| | - Susan Krueger
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8562, Bldg. 235/Room E151, Gaithersburg, MD 20899-8562, U.S.A
| | - David E. Draper
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21210, U.S.A
| | - Yun-Xing Wang
- Protein Nucleic Acid Interaction Section, Structural Biophysics Laboratory, NCI-Frederick, NIH, Frederick, MD 21702, U.S.A
- *To whom correspondence should be addressed: (e-mail) , (Phone) 301-846-5985, (Fax) 301-846-6231
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10
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Pucci MJ, Bronson JJ, Barrett JF, DenBleyker KL, Discotto LF, Fung-Tomc JC, Ueda Y. Antimicrobial evaluation of nocathiacins, a thiazole peptide class of antibiotics. Antimicrob Agents Chemother 2004; 48:3697-701. [PMID: 15388422 PMCID: PMC521901 DOI: 10.1128/aac.48.10.3697-3701.2004] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nocathiacins are cyclic thiazolyl peptides with inhibitory activity against gram-positive bacteria. BMS-249524 (nocathiacin I), identified from screening a library of compounds against a multiply antibiotic-resistant Enterococcus faecium strain, was used as a lead chemotype to obtain additional structurally related compounds. The MIC assay results of BMS-249524 and two more water-soluble derivatives, BMS-411886 and BMS-461996, revealed potent in vitro activities against a variety of gram-positive pathogens including methicillin-resistant Staphylococcus aureus, penicillin-resistant Streptococcus pneumoniae, vancomycin intermediate-resistant S. aureus, vancomycin-resistant enterococci, Mycobacterium tuberculosis and Mycobacterium avium. Analysis of killing kinetics revealed that these compounds are bactericidal for S. aureus with at least a 3-log(10) reduction of bacterial growth within 6 h of exposure to four times the MICs. Nocathiacin-resistant mutants were characterized by DNA sequence analyses. The mutations mapped to the rplK gene encoding the L11 ribosomal protein in the 50S subunit in a region previously shown to be involved in the binding of related thiazolyl peptide antibiotics. These compounds demonstrated potential for further development as a new class of antibacterial agents with activity against key antibiotic-resistant gram-positive bacterial pathogens.
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Affiliation(s)
- Michael J Pucci
- Achillion Pharmaceuticals, 300 George St., New Haven, CT 06511, USA.
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11
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Brandi L, Marzi S, Fabbretti A, Fleischer C, Hill WE, Gualerzi CO, Stephen Lodmell J. The translation initiation functions of IF2: targets for thiostrepton inhibition. J Mol Biol 2004; 335:881-94. [PMID: 14698286 DOI: 10.1016/j.jmb.2003.10.067] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bacterial translation initiation factor IF2 was localized on the ribosome by rRNA cleavage using free Cu(II):1,10-orthophenanthroline. The results indicated proximity of IF2 to helix 89, to the sarcin-ricin loop and to helices 43 and 44, which constitute the "L11/thiostrepton" stem-loops of 23S rRNA. These findings prompted an investigation of the L11 contribution to IF2 activity and a re-examination of the controversial issue of the effect on IF2 functions of thiostrepton, a peptide antibiotic known primarily as a powerful inhibitor of translocation. Ribosomes lacking L11 were found to have wild-type capacity to bind IF2 but a strongly reduced ability to elicit its GTPase activity. We found that thiostrepton caused a faster recycling of this factor on and off the 70S ribosomes and 50S subunits, which in turn resulted in an increased rate of the multiple turnover IF2-dependent GTPase. Although thiostrepton did not inhibit the P-site binding of fMet-tRNA, the A-site binding of the EF-Tu-GTP-Phe-tRNA or the activity of the ribosomal peptidyl transferase center (as measured by the formation of fMet-puromycin), it severely inhibited IF2-dependent initiation dipeptide formation. This inhibition can probably be traced back to a thiostrepton-induced distortion of the ribosomal-binding site of IF2, which leads to a non-productive interaction between the ribosome and the aminoacyl-tRNA substrates of the peptidyl transferase reaction. Overall, our data indicate that the translation initiation function of IF2 is as sensitive as the translocation function of EF-G to thiostrepton inhibition.
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Affiliation(s)
- Letizia Brandi
- Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino (MC), Italy
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12
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Triantafillidou D, Persidou E, Lazarou D, Andrikopoulos P, Leontiadou F, Choli-Papadopoulou T. Structural destabilization of the recombinant thermophilic TthL11 ribosomal protein by a single amino acid substitution. Biol Chem 2004; 385:31-9. [PMID: 14977044 DOI: 10.1515/bc.2004.005] [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: 11/15/2022]
Abstract
Thermus thermophilus L11 protein has previously been reported to be resistant against tryptic and chymotryptic proteolysis under native conditions. With a single amino acid substitution, namely Trp101Arg, conformational changes were induced that resulted in the exhibition of specific amino acids that served as targets for tryptic and chymotryptic action and rendered the protein highly unstable even during purification. This unexpected process was evidenced by the isolation with size exclusion gel chromatography of the well-structured chymotryptic N-terminal domain in a high amount and its characterization both by Edman degradation and QTOF-EMS spectroscopy. On the other hand, the substitution of Val38Cys, which did not contribute to structural changes, indicates a very possible implication of this amino acid in the protein methylation process. The data reported in this work illustrate the distinctive amino acid dynamics in a thermophilic protein, which, while serving the function common to its counterparts from mesophilic organisms, has had to adapt to the extreme environmental conditions typical of thermophilic organisms.
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Affiliation(s)
- Dimitra Triantafillidou
- Laboratory of Biochemistry, School of Chemistry, Aristotle University of Thessaloniki, GR-54006 Thessaloniki, Greece
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13
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Larsson SL, Sloma MS, Nygård O. Conformational changes in the structure of domains II and V of 28S rRNA in ribosomes treated with the translational inhibitors ricin or alpha-sarcin. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1577:53-62. [PMID: 12151095 DOI: 10.1016/s0167-4781(02)00406-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Ricin and alpha-sarcin modify neighbouring sites in the so-called sarcin/ricin (S/R) loop of 28S rRNA, thereby destroying the necessary dynamic flexibility of the ribosome, and inhibiting the elongation factor assisted steps of the elongation cycle. The effects of the two translational inhibitors on the conformation of domains II and V of 28S rRNA were investigated by chemical modification of programmed mouse ribosomes pretreated with ricin or alpha-sarcin. The results showed that the two ribosome-inactivating proteins (RIP) influenced the structure of the ribosomal RNA. Inhibitor-affected sites were located at or near sites previously proposed to be involved in functional domains. The modification patterns obtained after ricin or alpha-sarcin treatment of ribosomes were partially overlapping. However, there were several inhibitor-specific structural changes in 28S rRNA. Such changes were found at positions located at the GTPase activating centre of the ribosome and in the S/R domain, indicating that the structure in these regions of the ribosomes differed after treatment with the two inhibitors. These changes are consistent with ricin and alpha-sarcin having specific effects on eEF-2 and eEF-1 interaction with the ribosome, respectively.
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Affiliation(s)
- Sofia L Larsson
- Cell Biology Unit, Natural Science Section, Södertörns Högskola, Box 4101, S-141 04 Huddinge, Sweden
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14
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Xu W, Pagel FT, Murgola EJ. Mutations in the GTPase center of Escherichia coli 23S rRNA indicate release factor 2-interactive sites. J Bacteriol 2002; 184:1200-3. [PMID: 11807083 PMCID: PMC134791 DOI: 10.1128/jb.184.4.1200-1203.2002] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutations in the GTPase center of Escherichia coli 23S rRNA were characterized in vivo as UGA-specific nonsense suppressors. Some site-directed mutations did not exhibit suppressor activity and were interspersed among suppressor mutations. Our results demonstrate the involvement of the two adjacent loops of this conserved rRNA structure in UGA-dependent translation termination and, taken with previous in vitro analyses and with consideration of the crystal structure of the GTPase center RNA, indicate that nucleotides 1067, 1093, 1094, and 1095 are sites of interaction with release factor 2.
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Affiliation(s)
- Wenbing Xu
- Department of Molecular Genetics, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA
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15
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Abstract
Ribosomes have been visualized in electron micrographs in 1943 but 5S rRNA was discovered 20 years later. The next four decades witnessed big advances in our understanding of the ribosome using biochemical, genetic and low resolution structural approaches. During those times many experimental data accumulates also on 5S rRNA, but its precise function remains unknown. To understand the role of this RNA in ribosome a high-resolution structure is urgently needed. Because the ribosome is a dynamic machine, details on the interaction of 5S rRNA with proteins within entire ribosome are required. Big progress in the structural analysis of ribosome will stimulate further understanding of 5S rRNA.
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Affiliation(s)
- M Z Barciszewska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12, 61704 Poznan, Poland.
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16
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Schäferkordt J, Wagner R. Effects of base change mutations within an Escherichia coli ribosomal RNA leader region on rRNA maturation and ribosome formation. Nucleic Acids Res 2001; 29:3394-403. [PMID: 11504877 PMCID: PMC55841 DOI: 10.1093/nar/29.16.3394] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The effects of base change mutations in a highly conserved sequence (boxC) within the leader of bacterial ribosomal RNAs (rRNAs) was studied. The boxC sequence preceding the 16S rRNA structural gene constitutes part of the RNase III processing site, one of the first cleavage sites on the pathway to mature 16S rRNA. Moreover, rRNA leader sequences facilitate correct 16S rRNA folding, thereby assisting ribosomal subunit formation. Mutations in boxC cause cold sensitivity and result in 16S rRNA and 30S subunit deficiency. Strains in which all rRNA operons are replaced by mutant transcription units are viable. Thermodynamic studies by temperature gradient gel electrophoresis reveal that mutant transcripts have a different, less ordered structure. In addition, RNA secondary structure differences between mutant and wild-type transcripts were determined by chemical and enzymatic probing. Differences are found in the leader RNA sequence itself but also in structurally important regions of the mature 16S rRNA. A minor fraction of the rRNA transcripts from mutant operons is not processed by RNase III, resulting in a significantly extended precursor half-life compared to the wild-type. The boxC mutations also give rise to a new aberrant degradation product of 16S rRNA. This intermediate cannot be detected in strains lacking RNase III. Together the results indicate that the boxC sequence, although important for RNase III processing, is likely to serve additional functions by facilitating correct formation of the mature 16S rRNA structure. They also suggest that quality control steps are acting during ribosome biogenesis.
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MESH Headings
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- Cold Temperature
- Conserved Sequence/genetics
- Endoribonucleases/metabolism
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Escherichia coli/metabolism
- Escherichia coli Proteins
- Half-Life
- Molecular Sequence Data
- Mutation/genetics
- Nuclease Protection Assays
- Nucleic Acid Conformation
- Operon/genetics
- Phenotype
- Protein Subunits
- RNA Processing, Post-Transcriptional
- RNA Stability
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Ribonuclease III
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
- Sequence Deletion/genetics
- Temperature
- Thermodynamics
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Affiliation(s)
- J Schäferkordt
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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17
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Abstract
Structural analyses of the large and small ribosomal subunits have allowed us to think about how they work in more detail than ever before. The mechanisms that underlie ribosomal synthesis, translocation and catalysis are now being unravelled, with practical implications for the design of antibiotics.
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Affiliation(s)
- D L Lafontaine
- FNRS, Université Libre de Bruxelles, Département de Biologie Moléculaire, IRMW - Campus CERIA, Avenue Emile Gryson 1, B-1070 Brussels, Belgium.
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18
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Abstract
Most box C/D small nucleolar RNAs (snoRNAs) direct the formation of 2'-O-methylated nucleotides in ribosomal RNA and, apparently, other RNAs present in the nucleolar complex. Sites to be modified are selected by a long (>10-nt) antisense guide sequence in the snoRNA and a distance measurement from a box D or D' element that follows the snoRNA guide sequence. Modification of the substrate occurs in the region of complementarity, at a position five nucleotides upstream from box D/D'. Methylation can be targeted to novel sites by expressing a snoRNA with a new guide sequence. In some cases methylation impairs the growth rate of the cell, indicating that a functionally important nucleotide has been altered. With a view to harnessing snoRNA-directed methylation for functional mapping, we have developed a method for constructing libraries of snoRNA genes that, in principle, can introduce methylation point mutations into any rRNA segment of interest. The strategy and procedures are described here, and preliminary results are presented that show the feasibility of using this technology to probe a region of the yeast large subunit rRNA that includes the core of the peptidyltransferase center.
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Affiliation(s)
- B Liu
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA
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19
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Briones C, Ballesta JP. Conformational changes induced in the Saccharomyces cerevisiae GTPase-associated rRNA by ribosomal stalk components and a translocation inhibitor. Nucleic Acids Res 2000; 28:4497-505. [PMID: 11071938 PMCID: PMC113874 DOI: 10.1093/nar/28.22.4497] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The yeast ribosomal GTPase associated center is made of parts of the 26S rRNA domains II and VI, and a number of proteins including P0, P1alpha, P1beta, P2alpha, P2beta and L12. Mapping of the rRNA neighborhood of the proteins was performed by footprinting in ribosomes from yeast strains lacking different GTPase components. The absence of protein P0 dramatically increases the sensitivity of the defective ribosome to degradation hampering the RNA footprinting. In ribosomes lacking the P1/P2 complex, protection of a number of nucleotides is detected around positions 840, 880, 1100, 1220-1280 and 1350 in domain II as well as in several positions in the domain VI alpha-sarcin region. The protection pattern resembles the one reported for the interaction of elongation factors in bacterial systems. The results exclude a direct interaction of these proteins with the rRNA and are compatible with an increase in the ribosome affinity for EF-2 in the absence of the acidic P proteins. Interestingly, a sordarin derivative inhibitor of EF-2 causes an opposite effect, increasing the reactivity in positions protected by the absence of P1/P2. Similarly, a deficiency in protein L12 exposes nucleotides G1235, G1242, A1262, A1269, A1270 and A1272 to chemical modification, thus situating the protein binding site in the most conserved part of the 26S rRNA, equivalent to the bacterial protein L11 binding site.
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Affiliation(s)
- C Briones
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas y Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
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20
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Abstract
Previous studies led to the development of a model of contact-induced enhanced gonococcal invasion of human reproductive cells that utilizes the lutropin receptor (LHr) as both the induction signal for conversion to this enhanced-gonococcal-invasion phenotype (Inv(+) GC) and as the specific Inv(+) GC uptake mechanism. This model proposes that gonococci express a surface feature that mimics human chorionic gonadotropin (hCG), the cognate ligand for LHr, and that this structure is responsible for the specific and productive interaction of GC with LHr. In this report, we identify a 13-kDa gonococcal protein with immunological similarities to hCG. The antiserum reactivity is specific since interaction with the 13-kDa gonococcal protein can be blocked by the addition of highly purified hCG. This gonococcal "hCG-like" protein, purified from two-dimensional gels and by immunoprecipitation, was determined by N-terminal sequencing to be the ribosomal protein L12. We present evidence that gonococcal L12 is membrane associated and surface exposed in gonococci, as shown by immunoblot analysis of soluble and insoluble gonococcal protein and antibody adsorption studies with fixed GC. Using highly purified recombinant gonococcal L12, we show that preincubation of Inv(-) GC with micromolar amounts of rL12 leads to a subsequent five- to eightfold increase in invasion of the human endometrial cell line, Hec1B. In addition, nanomolar concentrations of exogenous L12 inhibits gonococcal invasion to approximately 70% of the level in controls. Thus, we propose a novel cellular location for the gonococcal ribosomal protein L12 and concomitant function in LHr-mediated gonococcal invasion of human reproductive cells.
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Affiliation(s)
- J M Spence
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
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21
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Szymański M, Barciszewska MZ, Erdmann VA, Barciszewski J. An analysis of G-U base pair occurrence in eukaryotic 5S rRNAs. Mol Biol Evol 2000; 17:1194-8. [PMID: 10908639 DOI: 10.1093/oxfordjournals.molbev.a026402] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The structure-function relationship in RNA molecules is a key to understanding of the expression of genetic information. Various types of RNA play crucial roles at almost every step of protein biosynthesis. In recent years, it has been shown that one of the most important structural elements in RNA is a wobble pair G-U. In this paper, we present for the first time an analysis of the distribution of G-U pairs in eukaryotic 5S ribosomal RNAs. Interestingly, the G-U pair in 5S rRNA species is predominantly found in two intrahelical regions of the stems I and V and at the junction of helix IV and loop A. The distribution of G-U pairs and the nature of adjacent bases suggests their possible role as a recognition site in interactions with other components of protein biosynthesis machinery.
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Affiliation(s)
- M Szymański
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poland
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22
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Nadano D, Sato TA. Caspase-3-dependent and -independent degradation of 28 S ribosomal RNA may be involved in the inhibition of protein synthesis during apoptosis initiated by death receptor engagement. J Biol Chem 2000; 275:13967-73. [PMID: 10788523 DOI: 10.1074/jbc.275.18.13967] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Activation of death receptors initiates intrinsic apoptosis programs in various parts of the cell. To explore the possibility that ribosomal RNA (rRNA), essential for translation in ribosomes, is a target of pro-apoptotic proteins, rRNA was analyzed by electrophoresis in two apoptosis systems: human Jurkat cells treated with anti-Fas antibody and human U937 cells treated with tumor necrosis factor-alpha. In both systems, bands in addition to those of unmodified rRNA were detected a few hours after death receptor engagement. In both systems, the primary additional band was identical and comprised the 3'-terminal region of 28 S rRNA. The degradation of 28 S rRNA was simultaneous with protein synthesis inhibition in both systems. The caspase-3 inhibitor Z-DEVD-FMK suppressed rRNA degradation and protein synthesis inhibition in Jurkat cells but not in U937 cells. Together, our data suggest that different pathways are activated in the two systems we studied, and the final steps in these pathways use very similar or identical ribonucleases to cleave 28 S rRNA. These data suggest a physiological link between rRNA degradation and inhibition of protein synthesis. In general, apoptosis execution initiated by death receptor engagement is promoted by protein synthesis inhibition. Triggered by rRNA degradation, malfunction of the protein synthesis machinery may prompt death execution.
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Affiliation(s)
- D Nadano
- Molecular Oncology Laboratory, Tsukuba Life Science Center, RIKEN (Institute of Physical and Chemical Research), Tsukuba, Ibaraki 305-0074, Japan
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23
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Szymanski M, Barciszewska MZ, Barciszewski J, Erdmann VA. 5S ribosomal RNA database Y2K. Nucleic Acids Res 2000; 28:166-7. [PMID: 10592212 PMCID: PMC102473 DOI: 10.1093/nar/28.1.166] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This paper presents the updated version (Y2K) of the database of ribosomal 5S ribonucleic acids (5S rRNA) and their genes (5S rDNA), http://rose.man/poznan.pl/5SData/index.html. This edition of the database contains 1985primary structures of 5S rRNA and 5S rDNA. They include 60 archaebacterial, 470 eubacterial, 63 plastid, nine mitochondrial and 1383 eukaryotic sequences. The nucleotide sequences of the 5S rRNAs or 5S rDNAs are divided according to the taxonomic position of the source organisms.
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Affiliation(s)
- M Szymanski
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12, 61704 Poznan, Poland
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24
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Sayed A, Matsuyama SI, Inouye M. Era, an essential Escherichia coli small G-protein, binds to the 30S ribosomal subunit. Biochem Biophys Res Commun 1999; 264:51-4. [PMID: 10527840 DOI: 10.1006/bbrc.1999.1471] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Era is an essential G-protein in Escherichia coli identified originally as a homologue protein to Ras (E. coli Ras-like protein). It binds to GTP/GDP and contains a low intrinsic GTPase activity. Its function remains elusive, although it has been suggested that Era is associated with the cytoplasmic membrane, cell division, energy metabolism, and cell-cycle check point. Recently, a cold-sensitive phenotype was found to be suppressed by the overexpression of 16S rRNA methyltransferase, suggesting Era association with the ribosome. Here we demonstrate that Era specifically binds to 16S rRNA and the 30S ribosomal subunit. Both GTP and GDP, but not GMP, inhibit Era binding to ribosomal component. Involvement of Era in protein synthesis is suggested by the fact that Era depletion results in the translation defect both in vitro and in vivo.
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Affiliation(s)
- A Sayed
- Department of Biochemistry, Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, New Jersey, 08854, USA
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