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Mikhaylina AO, Nikonova EY, Kostareva OS, Piendl W, Erlacher M, Tishchenko SV. Characterization of Regulatory Elements of L11 and L1 Operons in Thermophilic Bacteria and Archaea. BIOCHEMISTRY (MOSCOW) 2021; 86:397-408. [PMID: 33941062 DOI: 10.1134/s0006297921040027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ribosomal protein L1 is a conserved two-domain protein that is involved in formation of the L1 stalk of the large ribosomal subunit. When there are no free binding sites available on the ribosomal 23S RNA, the protein binds to the specific site on the mRNA of its own operon (L11 operon in bacteria and L1 operon in archaea) preventing translation. Here we show that the regulatory properties of the r-protein L1 and its domain I are conserved in the thermophilic bacteria Thermus and Thermotoga and in the halophilic archaeon Haloarcula marismortui. At the same time the revealed features of the operon regulation in thermophilic bacteria suggest presence of two regulatory regions.
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Affiliation(s)
- Alisa O Mikhaylina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Ekaterina Y Nikonova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Olga S Kostareva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Wolfgang Piendl
- Division of Medical Biochemistry, Biocenter, Medical University of Innsbruck, Innsbruck, 6020, Austria.
| | - Matthias Erlacher
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innsbruck, 6020, Austria.
| | - Svetlana V Tishchenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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2
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Abstract
The rRNA is the largest and most abundant RNA in bacterial and archaeal cells. It is also one of the best-characterized RNAs in terms of its structural motifs and sequence variation. Production of ribosome components including >50 ribosomal proteins (r-proteins) consumes significant cellular resources. Thus, RNA cis-regulatory structures that interact with r-proteins to repress further r-protein synthesis play an important role in maintaining appropriate stoichiometry between r-proteins and rRNA. Classically, such mRNA structures were thought to directly mimic the rRNA. However, more than 30 years of research has demonstrated that a variety of different recognition and regulatory paradigms are present. This review will demonstrate how structural mimicry between the rRNA and mRNA cis-regulatory structures may take many different forms. The collection of mRNA structures that interact with r-proteins to regulate r-protein operons are best characterized in Escherichia coli, but are increasingly found within species from nearly all phyla of bacteria and several archaea. Furthermore, they represent a unique opportunity to assess the plasticity of RNA structure in the context of RNA-protein interactions. The binding determinants imposed by r-proteins to allow regulation can be fulfilled in many ways. Some r-protein-interacting mRNAs are immediately obvious as rRNA mimics from primary sequence similarity, others are identifiable only after secondary or tertiary structure determination, and some show no obvious similarity. In addition, across different bacterial species a host of different mechanisms of action have been characterized, showing that there is no simple one-size-fits-all solution.
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Kostareva OS, Nevskaya NA, Tishchenko SV, Gabdulkhakov AG, Garber MB, Nikonov SV. Influence of Nonconserved Regions of L1 Protuberance of Thermus thermophilus Ribosome on the Affinity of L1 Protein to 23s rRNA. Mol Biol 2018. [DOI: 10.1134/s0026893318010090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mikhaylina AO, Kostareva OS, Nikonova EY, Garber MB, Tishchenko SV. Identification of Ribosomal Protein L1-Binding Sites in Thermus thermophilus and Thermotoga maritima mRNAs. Mol Biol 2018. [DOI: 10.1134/s0026893318010132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Meyer MM. The role of mRNA structure in bacterial translational regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27301829 DOI: 10.1002/wrna.1370] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 01/08/2023]
Abstract
The characteristics of bacterial messenger RNAs (mRNAs) that influence translation efficiency provide many convenient handles for regulation of gene expression, especially when coupled with the processes of transcription termination and mRNA degradation. An mRNA's structure, especially near the site of initiation, has profound consequences for how readily it is translated. This property allows bacterial gene expression to be altered by changes to mRNA structure induced by temperature, or interactions with a wide variety of cellular components including small molecules, other RNAs (such as sRNAs and tRNAs), and RNA-binding proteins. This review discusses the links between mRNA structure and translation efficiency, and how mRNA structure is manipulated by conditions and signals within the cell to regulate gene expression. The range of RNA regulators discussed follows a continuum from very complex tertiary structures such as riboswitch aptamers and ribosomal protein-binding sites to thermosensors and mRNA:sRNA interactions that involve only base-pairing interactions. Furthermore, the high degrees of diversity observed for both mRNA structures and the mechanisms by which inhibition of translation occur have significant consequences for understanding the evolution of bacterial translational regulation. WIREs RNA 2017, 8:e1370. doi: 10.1002/wrna.1370 For further resources related to this article, please visit the WIREs website.
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The ribosome as a missing link in prebiotic evolution II: Ribosomes encode ribosomal proteins that bind to common regions of their own mRNAs and rRNAs. J Theor Biol 2016; 397:115-27. [DOI: 10.1016/j.jtbi.2016.02.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 02/16/2016] [Accepted: 02/19/2016] [Indexed: 11/18/2022]
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Ohno H, Inoue T. Designed Regular Tetragon-Shaped RNA-Protein Complexes with Ribosomal Protein L1 for Bionanotechnology and Synthetic Biology. ACS NANO 2015; 9:4950-4956. [PMID: 25933202 DOI: 10.1021/nn5069622] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
RNA nanotechnology has been established by employing the molecular architecture of RNA structural motifs. Here, we report two designed RNA-protein complexes (RNPs) composed of ribosomal protein L1 (RPL1) and its RNA-binding motif that are square-shaped nano-objects. The formation and the shape of the objects were confirmed by gel electrophoresis analysis and atomic force microscopy, respectively. Any protein can be attached to the RNA via a fusion protein with RPL1, indicating that it can be used as a scaffold for loading a variety of functional proteins or for building higher-order structures. In summary, the RNP object will serve as a useful tool in the fields of bionanotechnology and synthetic biology. Moreover, the RNP interaction enhances the RNA stability against nucleases, rendering these complexes stable in cells.
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Affiliation(s)
- Hirohisa Ohno
- Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tan Inoue
- Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
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8
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Studying the properties of domain I of the ribosomal protein l1: incorporation into ribosome and regulation of the l1 operon expression. Protein J 2015; 34:103-10. [PMID: 25681234 DOI: 10.1007/s10930-015-9602-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
L1 is a conserved protein of the large ribosomal subunit. This protein binds strongly to the specific region of the high molecular weight rRNA of the large ribosomal subunit, thus forming a conserved flexible structural element--the L1 stalk. L1 protein also regulates translation of the operon that comprises its own gene. Crystallographic data suggest that L1 interacts with RNA mainly by means of its domain I. We show here for the first time that the isolated domain I of the bacterial protein L1 of Thermus thermophilus and Escherichia coli is able to incorporate in vivo into the E. coli ribosome. Furthermore, domain I of T. thermophilus L1 can regulate expression of the L1 gene operon of Archaea in the coupled transcription-translation system in vitro, as well as the intact protein. We have identified the structural elements of domain I of the L1 protein that may be responsible for its regulatory properties.
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Mikhaylina AO, Kostareva OS, Sarskikh AV, Fedorov RV, Piendl W, Garber MB, Tishchenko SV. Investigation of the regulatory function of archaeal ribosomal protein L4. BIOCHEMISTRY (MOSCOW) 2014; 79:69-76. [PMID: 24512666 DOI: 10.1134/s0006297914010106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ribosomal protein L4 is a regulator of protein synthesis in the Escherichia coli S10 operon, which contains genes of 11 ribosomal proteins. In this work, we have investigated regulatory functions of ribosomal protein L4 of the thermophilic archaea Methanococcus jannaschii. The S10-like operon from M. jannaschii encodes not 11, but only five ribosomal proteins (L3, L4, L23, L2, S19), and the first protein is L3 instead of S10. We have shown that MjaL4 and its mutant form lacking an elongated loop specifically inhibit expression of the first gene of the S10-like operon from the same organism in a coupled transcription-translation system in vitro. By deletion analysis, an L4-binding regulatory site has been found on MjaL3 mRNA, and a fragment of mRNA with length of 40 nucleotides has been prepared that is necessary and sufficient for the specific interaction with the MjaL4 protein.
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Affiliation(s)
- A O Mikhaylina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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Sarskikh AV, Gabdulkhakov AG, Kostareva OS, Shklyaeva AA, Tishchenko SV. Crystal structure of a mutant of archaeal ribosomal protein L1 from Methanococcus jannaschii. CRYSTALLOGR REP+ 2014. [DOI: 10.1134/s1063774514030158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Matelska D, Purta E, Panek S, Boniecki MJ, Bujnicki JM, Dunin-Horkawicz S. S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA. RNA (NEW YORK, N.Y.) 2013; 19:1341-8. [PMID: 23980204 PMCID: PMC3854524 DOI: 10.1261/rna.038794.113] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 07/05/2013] [Indexed: 05/24/2023]
Abstract
Prokaryotic ribosomal protein genes are typically grouped within highly conserved operons. In many cases, one or more of the encoded proteins not only bind to a specific site in the ribosomal RNA, but also to a motif localized within their own mRNA, and thereby regulate expression of the operon. In this study, we computationally predicted an RNA motif present in many bacterial phyla within the 5' untranslated region of operons encoding ribosomal proteins S6 and S18. We demonstrated that the S6:S18 complex binds to this motif, which we hereafter refer to as the S6:S18 complex-binding motif (S6S18CBM). This motif is a conserved CCG sequence presented in a bulge flanked by a stem and a hairpin structure. A similar structure containing a CCG trinucleotide forms the S6:S18 complex binding site in 16S ribosomal RNA. We have constructed a 3D structural model of a S6:S18 complex with S6S18CBM, which suggests that the CCG trinucleotide in a specific structural context may be specifically recognized by the S18 protein. This prediction was supported by site-directed mutagenesis of both RNA and protein components. These results provide a molecular basis for understanding protein-RNA recognition and suggest that the S6S18CBM is involved in an auto-regulatory mechanism.
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MESH Headings
- 5' Untranslated Regions/genetics
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Pairing
- Base Sequence
- Binding Sites
- Electrophoretic Mobility Shift Assay
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Operon/genetics
- Protein Binding
- Protein Structure, Tertiary
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Ribosomal Protein S6/chemistry
- Ribosomal Protein S6/genetics
- Ribosomal Protein S6/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
- Sequence Homology, Nucleic Acid
- Thermus thermophilus/genetics
- Thermus thermophilus/metabolism
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Affiliation(s)
- Dorota Matelska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
| | - Elzbieta Purta
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
| | - Sylwia Panek
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
| | - Michal J. Boniecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
| | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, 61-614, Poland
| | - Stanislaw Dunin-Horkawicz
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
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Fu Y, Deiorio-Haggar K, Anthony J, Meyer MM. Most RNAs regulating ribosomal protein biosynthesis in Escherichia coli are narrowly distributed to Gammaproteobacteria. Nucleic Acids Res 2013; 41:3491-503. [PMID: 23396277 PMCID: PMC3616713 DOI: 10.1093/nar/gkt055] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/02/2013] [Accepted: 01/10/2013] [Indexed: 01/30/2023] Open
Abstract
In Escherichia coli, 12 distinct RNA structures within the transcripts encoding ribosomal proteins interact with specific ribosomal proteins to allow autogenous regulation of expression from large multi-gene operons, thus coordinating ribosomal protein biosynthesis across multiple operons. However, these RNA structures are typically not represented in the RNA Families Database or annotated in genomic sequences databases, and their phylogenetic distribution is largely unknown. To investigate the extent to which these RNA structures are conserved across eubacterial phyla, we created multiple sequence alignments representing 10 of these messenger RNA (mRNA) structures in E. coli. We find that while three RNA structures are widely distributed across many phyla of bacteria, seven of the RNAs are narrowly distributed to a few orders of Gammaproteobacteria. To experimentally validate our computational predictions, we biochemically confirmed dual L1-binding sites identified in many Firmicute species. This work reveals that RNA-based regulation of ribosomal protein biosynthesis is used in nearly all eubacterial phyla, but the specific RNA structures that regulate ribosomal protein biosynthesis in E. coli are narrowly distributed. These results highlight the limits of our knowledge regarding ribosomal protein biosynthesis regulation outside of E. coli, and the potential for alternative RNA structures responsible for regulating ribosomal proteins in other eubacteria.
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Affiliation(s)
| | | | | | - Michelle M. Meyer
- Department of Biology, Boston College, 140 Commonwealth Ave. Chestnut Hill, MA 02467, USA
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Nikonova EY, Tishchenko SV, Gabdulkhakov AG, Shklyaeva AA, Garber MB, Nikonov SV, Nevskaya NA. Crystal structure of ribosomal protein L1 from the bacterium Aquifex aeolicus. CRYSTALLOGR REP+ 2011. [DOI: 10.1134/s1063774511040158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Abhyankar A, Park HB, Tonolo G, Luthman H. Comparative sequence analysis of the non-protein-coding mitochondrial DNA of inbred rat strains. PLoS One 2009; 4:e8148. [PMID: 19997590 PMCID: PMC2781161 DOI: 10.1371/journal.pone.0008148] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Accepted: 11/08/2009] [Indexed: 11/19/2022] Open
Abstract
The proper function of mammalian mitochondria necessitates a coordinated expression of both nuclear and mitochondrial genes, most likely due to the co-evolution of nuclear and mitochondrial genomes. The non-protein coding regions of mitochondrial DNA (mtDNA) including the D-loop, tRNA and rRNA genes form a major component of this regulated expression unit. Here we present comparative analyses of the non-protein-coding regions from 27 Rattus norvegicus mtDNA sequences. There were two variable positions in 12S rRNA, 20 in 16S rRNA, eight within the tRNA genes and 13 in the D-loop. Only one of the three neutrality tests used demonstrated statistically significant evidence for selection in 16S rRNA and tRNA-Cys. Based on our analyses of conserved sequences, we propose that some of the variable nucleotide positions identified in 16S rRNA and tRNA-Cys, and the D-loop might be important for mitochondrial function and its regulation.
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Affiliation(s)
- Avinash Abhyankar
- Medical Genetics Unit, Department of Clinical Sciences-Malmö, Lund University, Malmö, Sweden.
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15
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Tishchenko S, Nikonova E, Kljashtorny V, Kostareva O, Nevskaya N, Piendl W, Davydova N, Streltsov V, Garber M, Nikonov S. Domain I of ribosomal protein L1 is sufficient for specific RNA binding. Nucleic Acids Res 2007; 35:7389-95. [PMID: 17962298 PMCID: PMC2175363 DOI: 10.1093/nar/gkm898] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ribosomal protein L1 has a dual function as a ribosomal protein binding 23S rRNA and as a translational repressor binding its mRNA. L1 is a two-domain protein with N- and C-termini located in domain I. Earlier it was shown that L1 interacts with the same targets on both rRNA and mRNA mainly through domain I. We have suggested that domain I is necessary and sufficient for specific RNA-binding by L1. To test this hypothesis, a truncation mutant of L1 from Thermus thermophilus, representing domain I, was constructed by deletion of the central part of the L1 sequence, which corresponds to domain II. It was shown that the isolated domain I forms stable complexes with specific fragments of both rRNA and mRNA. The crystal structure of the isolated domain I was determined and compared with the structure of this domain within the intact protein L1. This comparison revealed a close similarity of both structures. Our results confirm our suggestion that in protein L1 its domain I alone is sufficient for specific RNA binding, whereas domain II stabilizes the L1-rRNA complex.
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Affiliation(s)
- Svetlana Tishchenko
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow region, Russia
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16
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Nikonova EY, Volchkov SA, Kljashtorny VG, Tishchenko SV, Kostareva OS, Nevskaya NA, Nikonov OS, Gabdoulkhakov AG, Nikulin AD, Davydova NL, Streltsov VA, Garber MB, Nikonov SV. Crystal structures of mutant ribosomal proteins L1. Mol Biol 2007. [DOI: 10.1134/s0026893307040152] [Citation(s) in RCA: 4] [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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17
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Ameres SL, Shcherbakov D, Nikonova E, Piendl W, Schroeder R, Semrad K. RNA chaperone activity of L1 ribosomal proteins: phylogenetic conservation and splicing inhibition. Nucleic Acids Res 2007; 35:3752-63. [PMID: 17517772 PMCID: PMC1920258 DOI: 10.1093/nar/gkm318] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
RNA chaperone activity is defined as the ability of proteins to either prevent RNA from misfolding or to open up misfolded RNA conformations. One-third of all large ribosomal subunit proteins from E. coli display this activity, with L1 exhibiting one of the highest activities. Here, we demonstrate via the use of in vitro trans- and cis-splicing assays that the RNA chaperone activity of L1 is conserved in all three domains of life. However, thermophilic archaeal L1 proteins do not display RNA chaperone activity under the experimental conditions tested here. Furthermore, L1 does not exhibit RNA chaperone activity when in complexes with its cognate rRNA or mRNA substrates. The evolutionary conservation of the RNA chaperone activity among L1 proteins suggests a functional requirement during ribosome assembly, at least in bacteria, mesophilic archaea and eukarya. Surprisingly, rather than facilitating catalysis, the thermophilic archaeal L1 protein from Methanococcus jannaschii (MjaL1) completely inhibits splicing of the group I thymidylate synthase intron from phage T4. Mutational analysis of MjaL1 excludes the possibility that the inhibitory effect is due to stronger RNA binding. To our knowledge, MjaL1 is the first example of a protein that inhibits group I intron splicing.
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Affiliation(s)
- Stefan L. Ameres
- Max F. Perutz Laboratories, Department of Biochemistry, University of Vienna, Dr Bohrgasse 9/5, A-1030 Vienna, Austria, Biocenter, Division of Medical Biochemistry, Innsbruck Medical University, Fritz-Pregl-Str. 3, A-6020 Innsbruck, Austria and Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Dmitry Shcherbakov
- Max F. Perutz Laboratories, Department of Biochemistry, University of Vienna, Dr Bohrgasse 9/5, A-1030 Vienna, Austria, Biocenter, Division of Medical Biochemistry, Innsbruck Medical University, Fritz-Pregl-Str. 3, A-6020 Innsbruck, Austria and Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Ekaterina Nikonova
- Max F. Perutz Laboratories, Department of Biochemistry, University of Vienna, Dr Bohrgasse 9/5, A-1030 Vienna, Austria, Biocenter, Division of Medical Biochemistry, Innsbruck Medical University, Fritz-Pregl-Str. 3, A-6020 Innsbruck, Austria and Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Wolfgang Piendl
- Max F. Perutz Laboratories, Department of Biochemistry, University of Vienna, Dr Bohrgasse 9/5, A-1030 Vienna, Austria, Biocenter, Division of Medical Biochemistry, Innsbruck Medical University, Fritz-Pregl-Str. 3, A-6020 Innsbruck, Austria and Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Renée Schroeder
- Max F. Perutz Laboratories, Department of Biochemistry, University of Vienna, Dr Bohrgasse 9/5, A-1030 Vienna, Austria, Biocenter, Division of Medical Biochemistry, Innsbruck Medical University, Fritz-Pregl-Str. 3, A-6020 Innsbruck, Austria and Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Katharina Semrad
- Max F. Perutz Laboratories, Department of Biochemistry, University of Vienna, Dr Bohrgasse 9/5, A-1030 Vienna, Austria, Biocenter, Division of Medical Biochemistry, Innsbruck Medical University, Fritz-Pregl-Str. 3, A-6020 Innsbruck, Austria and Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- *To whom correspondence should be addressed. +43-1-4277-54694+43-1-4277-9522
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Shcherbakov D, Dontsova M, Tribus M, Garber M, Piendl W. Stability of the 'L12 stalk' in ribosomes from mesophilic and (hyper)thermophilic Archaea and Bacteria. Nucleic Acids Res 2006; 34:5800-14. [PMID: 17053098 PMCID: PMC1635324 DOI: 10.1093/nar/gkl751] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The ribosomal stalk complex, consisting of one molecule of L10 and four or six molecules of L12, is attached to 23S rRNA via protein L10. This complex forms the so-called ‘L12 stalk’ on the 50S ribosomal subunit. Ribosomal protein L11 binds to the same region of 23S rRNA and is located at the base of the ‘L12 stalk’. The ‘L12 stalk’ plays a key role in the interaction of the ribosome with translation factors. In this study stalk complexes from mesophilic and (hyper)thermophilic species of the archaeal genus Methanococcus and from the Archaeon Sulfolobus solfataricus, as well as from the Bacteria Escherichia coli, Geobacillus stearothermophilus and Thermus thermophilus, were overproduced in E.coli and purified under non-denaturing conditions. Using filter-binding assays the affinities of the archaeal and bacterial complexes to their specific 23S rRNA target site were analyzed at different pH, ionic strength and temperature. Affinities of both archaeal and bacterial complexes for 23S rRNA vary by more than two orders of magnitude, correlating very well with the growth temperatures of the organisms. A cooperative effect of binding to 23S rRNA of protein L11 and the L10/L124 complex from mesophilic and thermophilic Archaea was shown to be temperature-dependent.
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Affiliation(s)
- D Shcherbakov
- Biocenter, Division of Medical Biochemistry, Innsbruck Medical University, Fritz-Pregl-Strasse 3, 6020, Innsbruck, Austria.
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19
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Tishchenko SV, Nikonova EY, Nevskaya NA, Nikonov OS, Garber MB, Nikonov SV. Interactions of ribosomal protein L1 with ribosomal and messenger RNAs. Mol Biol 2006. [DOI: 10.1134/s0026893306040108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Nevskaya N, Tishchenko S, Volchkov S, Kljashtorny V, Nikonova E, Nikonov O, Nikulin A, Köhrer C, Piendl W, Zimmermann R, Stockley P, Garber M, Nikonov S. New insights into the interaction of ribosomal protein L1 with RNA. J Mol Biol 2005; 355:747-59. [PMID: 16330048 DOI: 10.1016/j.jmb.2005.10.084] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2005] [Revised: 10/31/2005] [Accepted: 10/31/2005] [Indexed: 11/19/2022]
Abstract
The RNA-binding ability of ribosomal protein L1 is of profound interest, since L1 has a dual function as a ribosomal structural protein that binds rRNA and as a translational repressor that binds its own mRNA. Here, we report the crystal structure at 2.6 A resolution of ribosomal protein L1 from the bacterium Thermus thermophilus in complex with a 38 nt fragment of L1 mRNA from Methanoccocus vannielii. The conformation of RNA-bound T.thermophilus L1 differs dramatically from that of the isolated protein. Analysis of four copies of the L1-mRNA complex in the crystal has shown that domain II of the protein does not contribute to mRNA-specific binding. A detailed comparison of the protein-RNA interactions in the L1-mRNA and L1-rRNA complexes identified amino acid residues of L1 crucial for recognition of its specific targets on the both RNAs. Incorporation of the structure of bacterial L1 into a model of the Escherichia coli ribosome revealed two additional contact regions for L1 on the 23S rRNA that were not identified in previous ribosome models.
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MESH Headings
- Amino Acid Sequence
- Hydrogen Bonding
- Kinetics
- Methanococcus/genetics
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Binding
- Protein Structure, Tertiary
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/metabolism
- Sequence Alignment
- Surface Plasmon Resonance
- Thermus thermophilus
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Affiliation(s)
- Natalia Nevskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow region, Russian Federation
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21
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Ryckelynck M, Masquida B, Giegé R, Frugier M. An intricate RNA structure with two tRNA-derived motifs directs complex formation between yeast aspartyl-tRNA synthetase and its mRNA. J Mol Biol 2005; 354:614-29. [PMID: 16257416 DOI: 10.1016/j.jmb.2005.09.063] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 09/19/2005] [Accepted: 09/20/2005] [Indexed: 11/17/2022]
Abstract
Accurate translation of genetic information necessitates the tuned expression of a large group of genes. Amongst them, controlled expression of the enzymes catalyzing the aminoacylation of tRNAs, the aminoacyl-tRNA synthetases, is essential to insure translational fidelity. In the yeast Saccharomyces cerevisiae, expression of aspartyl-tRNA synthetase (AspRS) is regulated in a process necessitating recognition of the 5' extremity of AspRS messenger RNA (mRNA(AspRS)) by its translation product and adaptation to the cellular tRNA(Asp) concentration. Here, we have established the folding of the approximately 300 nucleotides long 5' end of mRNA(AspRS) and identified the structural signals involved in the regulation process. We show that the regulatory region in mRNA(AspRS) folds in two independent and symmetrically structured domains spaced by two single-stranded connectors. Domain I displays a tRNA(Asp) anticodon-like stem-loop structure with mimics of the aspartate identity determinants, that is restricted in domain II to a short double-stranded helix. The overall mRNA structure, based on enzymatic and chemical probing, supports a three-dimensional model where each monomer of yeast AspRS binds one individual domain and recognizes the mRNA structure as it recognizes its cognate tRNA(Asp). Sequence comparison of yeast genomes shows that the features within the mRNA recognized by AspRS are conserved in different Saccharomyces species. In the recognition process, the N-terminal extension of each AspRS subunit plays a crucial role in anchoring the tRNA-like motifs of the mRNA on the synthetase.
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Affiliation(s)
- Michaël Ryckelynck
- Département Machineries Traductionnelles, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS and Université Louis Pasteur, 15, rue René Descartes, F-67084 Strasbourg Cedex, France
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22
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Pohlschröder M, Hartmann E, Hand NJ, Dilks K, Haddad A. DIVERSITY AND EVOLUTION OF PROTEIN TRANSLOCATION. Annu Rev Microbiol 2005; 59:91-111. [PMID: 16153164 DOI: 10.1146/annurev.micro.59.030804.121353] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cells need to translocate proteins into and across hydrophobic membranes in order to interact with the extracellular environment. Although a subset of proteins are thought to spontaneously insert into lipid bilayers, translocation of most transported proteins requires additional cellular components. Such components catalyze efficient lateral transport into or across cellular membranes in prokaryotes and eukaryotes. These include, among others, the conserved YidC/Oxa1/Alb3 proteins as well as components of the Sec and the Tat pathways. Our current knowledge of the function and distribution of these components and their corresponding pathways in organisms of the three domains of life is reviewed. On the basis of this information, the evolution of protein translocation is discussed.
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Affiliation(s)
- Mechthild Pohlschröder
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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23
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Tu D, Blaha G, Moore PB, Steitz TA. Gene replacement in Haloarcula marismortui: construction of a strain with two of its three chromosomal rRNA operons deleted. Extremophiles 2005; 9:427-35. [PMID: 15970993 DOI: 10.1007/s00792-005-0459-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2005] [Accepted: 05/13/2005] [Indexed: 10/25/2022]
Abstract
Site-directed mutagenesis were done in Haloarcula marismortui using the strategy that Khorana and coworkers devised for deleting the bacteriorhodopsin gene from Halobacterium halobium [Krebs et al. Proc Natl Acad Sci USA 90:1987-1991 (1993)]. Strains have been prepared from H. marsimortui, which normally has three rRNA operons, that are missing either its rrnB operon or both its rrnB and rrnC operons. In rich media, both strains grow at about the same rate as wild type. The G2099 in the 23S rRNA gene of the single operon strain was changed to A, and a three amino acid deletion was introduced into the gene for ribosomal protein L22 of the wild-type organism. The structural consequences of these and other such mutations can be determined with unusual accuracy because crystals of the large ribosomal subunit of H. marismortui diffract to atomic resolution.
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MESH Headings
- Base Sequence
- Blotting, Southern
- Chromosome Mapping
- Crystallography, X-Ray
- DNA/metabolism
- DNA Primers/chemistry
- DNA Primers/metabolism
- Electrons
- Escherichia coli Proteins/metabolism
- Gene Deletion
- Genetic Techniques
- Haloarcula marismortui/genetics
- Models, Chemical
- Models, Genetic
- Models, Molecular
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Mutation
- Operon
- Plasmids/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 23S/metabolism
- RNA-Binding Proteins/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/metabolism
- Sucrose/pharmacology
- rRNA Operon
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Affiliation(s)
- Daqi Tu
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, P.O. Box 208114, New Haven, CT 06520-8114, USA
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24
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25
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Nevskaya N, Tishchenko S, Gabdoulkhakov A, Nikonova E, Nikonov O, Nikulin A, Platonova O, Garber M, Nikonov S, Piendl W. Ribosomal protein L1 recognizes the same specific structural motif in its target sites on the autoregulatory mRNA and 23S rRNA. Nucleic Acids Res 2005; 33:478-85. [PMID: 15659579 PMCID: PMC548342 DOI: 10.1093/nar/gki194] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2004] [Revised: 12/24/2004] [Accepted: 12/24/2004] [Indexed: 11/15/2022] Open
Abstract
The RNA-binding ability of ribosomal protein L1 is of profound interest since the protein has a dual function as a ribosomal protein binding rRNA and as a translational repressor binding its mRNA. Here, we report the crystal structure of ribosomal protein L1 in complex with a specific fragment of its mRNA and compare it with the structure of L1 in complex with a specific fragment of 23S rRNA determined earlier. In both complexes, a strongly conserved RNA structural motif is involved in L1 binding through a conserved network of RNA-protein H-bonds inaccessible to the solvent. These interactions should be responsible for specific recognition between the protein and RNA. A large number of additional non-conserved RNA-protein H-bonds stabilizes both complexes. The added contribution of these non-conserved H-bonds makes the ribosomal complex much more stable than the regulatory one.
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Affiliation(s)
- Natalia Nevskaya
- Institute of Protein Research, Russian Academy of Sciences142290 Pushchino, Moscow region, Russia
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
| | - Svetlana Tishchenko
- Institute of Protein Research, Russian Academy of Sciences142290 Pushchino, Moscow region, Russia
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
| | - Azat Gabdoulkhakov
- Institute of Protein Research, Russian Academy of Sciences142290 Pushchino, Moscow region, Russia
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
| | - Ekaterina Nikonova
- Institute of Protein Research, Russian Academy of Sciences142290 Pushchino, Moscow region, Russia
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
| | - Oleg Nikonov
- Institute of Protein Research, Russian Academy of Sciences142290 Pushchino, Moscow region, Russia
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
| | - Alexei Nikulin
- Institute of Protein Research, Russian Academy of Sciences142290 Pushchino, Moscow region, Russia
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
| | - Olga Platonova
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
| | - Maria Garber
- Institute of Protein Research, Russian Academy of Sciences142290 Pushchino, Moscow region, Russia
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
| | - Stanislav Nikonov
- Institute of Protein Research, Russian Academy of Sciences142290 Pushchino, Moscow region, Russia
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
| | - Wolfgang Piendl
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
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26
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Gruber T, Köhrer C, Lung B, Shcherbakov D, Piendl W. Affinity of ribosomal protein S8 from mesophilic and (hyper)thermophilic archaea and bacteria for 16S rRNA correlates with the growth temperatures of the organisms. FEBS Lett 2003; 549:123-8. [PMID: 12914937 DOI: 10.1016/s0014-5793(03)00760-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The ribosomal protein S8 plays a pivotal role in the assembly of the 30S ribosomal subunit. Using filter binding assays, S8 proteins from mesophilic, and (hyper)thermophilic species of the archaeal genus Methanococcus and from the bacteria Escherichia coli and Thermus thermophilus were tested for their affinity to their specific 16S rRNA target site. S8 proteins from hyperthermophiles exhibit a 100-fold and S8 from thermophiles exhibit a 10-fold higher affinity than their mesophilic counterparts. Thus, there is a striking correlation of affinity of S8 proteins for their specific RNA binding site and the optimal growth temperatures of the respective organisms. The stability of individual rRNA-protein complexes might modulate the stability of the ribosome, providing a maximum of thermostability and flexibility at the growth temperature of the organism.
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Affiliation(s)
- Thomas Gruber
- Institute of Medical Chemistry and Biochemistry, University of Innsbruck, Fritz-Pregl-Str 3, A-6020 Innsbruck, Austria
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27
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Serganov A, Polonskaia A, Ehresmann B, Ehresmann C, Patel DJ. Ribosomal protein S15 represses its own translation via adaptation of an rRNA-like fold within its mRNA. EMBO J 2003; 22:1898-908. [PMID: 12682022 PMCID: PMC154462 DOI: 10.1093/emboj/cdg170] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The 16S rRNA-binding ribosomal protein S15 is a key component in the assembly of the small ribosomal subunit in bacteria. We have shown that S15 from the extreme thermophile Thermus thermophilus represses the translation of its own mRNA in vitro, by interacting with the leader segment of its mRNA. The S15 mRNA-binding site was characterized by footprinting experiments, deletion analysis and site-directed mutagenesis. S15 binding triggers a conformational rearrangement of its mRNA into a fold that mimics the conserved three-way junction of the S15 rRNA-binding site. This conformational change masks the ribosome entry site, as demonstrated by direct competition between the ribosomal subunit and S15 for mRNA binding. A comparison of the T.thermophilus and Escherichia coli regulation systems reveals that the two regulatory mRNA targets do not share any similarity and that the mechanisms of translational inhibition are different. Our results highlight an astonishing plasticity of mRNA in its ability to adapt to evolutionary constraints, that contrasts with the extreme conservation of the rRNA-binding site.
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Affiliation(s)
- Alexander Serganov
- Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
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28
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Dontsova M, Frolova L, Vassilieva J, Piendl W, Kisselev L, Garber M. Translation termination factor aRF1 from the archaeon Methanococcus jannaschii is active with eukaryotic ribosomes. FEBS Lett 2000; 472:213-6. [PMID: 10788613 DOI: 10.1016/s0014-5793(00)01466-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Class-1 translation termination factors (release factors (RFs)) from Eukarya (eRF1) and Archaea (aRF1) exhibit a high degree of amino acid sequence homology and share many common motifs. In contrast to eRF1, function(s) of aRF1 have not yet been studied in vitro. Here, we describe for the first time the cloning and expression in Escherichia coli of the gene encoding the peptide chain RF from the hyperthermophilic archaeon Methanococcus jannaschii (MjaRF1). In an in vitro assay with mammalian ribosomes, MjaRF1, which was overproduced in E. coli, was active as a RF with all three termination codon-containing tetraplets, demonstrating the functional resemblance of aRF1 and eRF1. This observation confirms the earlier prediction that eRF1 and aRF1 form a common structural-functional eRF1/aRF1 protein family, originating from a common ancient ancestor.
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Affiliation(s)
- M Dontsova
- Institute of Protein Research, Russian Academy of Sciences, 142292, Pushchino, Russia
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