1
|
Tishchenko SV, Mikhailina AO, Lekontseva NV, Stolboushkina EA, Nikonova EY, Nikonov OS, Nikulin AD. Structural Investigations of RNA–Protein Complexes in Post-Ribosomal Era. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Structural studies of RNA–protein complexes are important for understanding many molecular mechanisms occurring in cells (e.g., regulation of protein synthesis and RNA-chaperone activity of proteins). Various objects investigated at the Institute of Protein Research of the Russian Academy of Sciences are considered. Based on the analysis of the structures of the complexes of the ribosomal protein L1 with specific regions on both mRNA and rRNA, the principles of regulation of the translation of the mRNA of its own operon are presented. The studies of the heterotrimeric translation initiation factor IF2 of archaea and eukaryotes are described, and the data on the interaction of glycyl-tRNA-synthetase with viral IRES are reported. The results of studying the interaction of RNA molecules with one of functionally important sites of the Hfq protein are presented, and the differences in the RNA-binding properties of the Hfq and archaeal Lsm proteins are revealed.
Collapse
|
2
|
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 (Mosc) 2021; 86:397-408. [PMID: 33941062 DOI: 10.1134/s0006297921040027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
3
|
|
4
|
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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
5
|
Root-bernstein R, Root-bernstein M. 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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 02/16/2016] [Accepted: 02/19/2016] [Indexed: 11/18/2022]
|
6
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
7
|
Korepanov AP, Kostareva OS, Bazhenova MV, Bubunenko MG, Garber MB, Tishchenko SV. 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] [What about the content of this article? (0)] [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.
Collapse
|
8
|
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 (Mosc) 2014; 79:69-76. [PMID: 24512666 DOI: 10.1134/s0006297914010106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
Affiliation(s)
- A O Mikhaylina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | | | | | | | | | | | | |
Collapse
|
9
|
Davydov II, Wohlgemuth I, Artamonova II, Urlaub H, Tonevitsky AG, Rodnina MV. Evolution of the protein stoichiometry in the L12 stalk of bacterial and organellar ribosomes. Nat Commun 2013; 4:1387. [DOI: 10.1038/ncomms2373] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 12/12/2012] [Indexed: 01/08/2023] Open
|
10
|
Gordiyenko Y, Videler H, Zhou M, McKay AR, Fucini P, Biegel E, Müller V, Robinson CV. Mass spectrometry defines the stoichiometry of ribosomal stalk complexes across the phylogenetic tree. Mol Cell Proteomics 2010; 9:1774-83. [PMID: 20467040 DOI: 10.1074/mcp.m000072-mcp201] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ribosomal stalk complex plays a crucial role in delivering translation factors to the catalytic site of the ribosome. It has a very similar architecture in all cells, although the protein components in bacteria are unrelated to those in archaea and eukaryotes. Here we used mass spectrometry to investigate ribosomal stalk complexes from bacteria, eukaryotes, and archaea in situ on the ribosome. Specifically we targeted ribosomes with different optimal growth temperatures. Our results showed that for the mesophilic bacterial ribosomes we investigated the stalk complexes are exclusively pentameric or entirely heptameric in the case of thermophilic bacteria, whereas we observed only pentameric stalk complexes in eukaryotic species. We also found the surprising result that for mesophilic archaea, Methanococcus vannielii, Methanococcus maripaludis, and Methanosarcina barkeri, both pentameric and heptameric stoichiometries are present simultaneously within a population of ribosomes. Moreover the ratio of pentameric to heptameric stalk complexes changed during the course of cell growth. We consider these differences in stoichiometry within ribosomal stalk complexes in the context of convergent evolution.
Collapse
Affiliation(s)
- Yuliya Gordiyenko
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|
11
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
Affiliation(s)
- Avinash Abhyankar
- Medical Genetics Unit, Department of Clinical Sciences-Malmö, Lund University, Malmö, Sweden.
| | | | | | | |
Collapse
|
12
|
Abstract
Large ribosomal subunit proteins L10 and L12 form a pentameric protein complex, L10(L12) 4, that is intimately involved in the ribosome elongation cycle. Its contacts with rRNA or other ribosomal proteins have been only partially resolved by crystallography. In Escherichia coli, L10 and L12 are encoded from a single operon for which L10(L12) 4 is a translational repressor that recognizes a secondary structure in the mRNA leader. In this study, L10(L12) 4 was expressed from the moderate thermophile Bacillus stearothermophilus to quantitatively compare strategies for binding of the complex to mRNA and ribosome targets. The minimal mRNA recognition structure is widely distributed among bacteria and has the potential to form a kink-turn structure similar to one identified in the rRNA as part of the L10(L12) 4 binding site. Mutations in equivalent positions between the two sequences have similar effects on L10(L12) 4-RNA binding affinity and identify the kink-turn motif and a loop AA sequence as important recognition elements. In contrast to the larger rRNA structure, the mRNA apparently positions the kink-turn motif and loop for protein recognition without the benefit of Mg (2+)-dependent tertiary structure. The mRNA and rRNA fragments bind L10(L12) 4 with similar affinity ( approximately 10 (8) M (-1)), but fluorescence binding studies show that a nearby protein in the ribosome, L11, enhances L10(L12) 4 binding approximately 100-fold. Thus, mRNA and ribosome targets use similar RNA features, held in different structural contexts, to recognize L10(L12) 4, and the ribosome ensures the saturation of its L10(L12) 4 binding site by means of an additional protein-protein interaction.
Collapse
Affiliation(s)
- James R Iben
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | | |
Collapse
|
13
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
Affiliation(s)
- Svetlana Tishchenko
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow region, Russia
| | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
15
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
Affiliation(s)
- D Shcherbakov
- Biocenter, Division of Medical Biochemistry, Innsbruck Medical University, Fritz-Pregl-Strasse 3, 6020, Innsbruck, Austria.
| | | | | | | | | |
Collapse
|
16
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
17
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
Affiliation(s)
- Thomas Gruber
- Institute of Medical Chemistry and Biochemistry, University of Innsbruck, Fritz-Pregl-Str 3, A-6020 Innsbruck, Austria
| | | | | | | | | |
Collapse
|
18
|
|
19
|
Abstract
In common with many bacterial virulence genes, the fimbrillin (fimA) gene of Porphyromonas gingivalis is modulated in response to environmental fluctuation. The trans-acting components that comprise the regulatory system for transcriptional activity of the fimA gene in P. gingivalis were investigated. Three major proteins were found to bind to the upstream region of the fimA promoter. One of these proteins was fimbrillin itself, and the other two were a major arginine protease (Rgp) and lysine protease (Kgp). Production of these proteins was necessary for maximal fimA transcription. An exogenous fimA promoter-lacZ reporter was inactive when introduced into a strain of P. gingivalis carrying a mutation in the indigenous fimA gene. Furthermore, fimA mRNA levels were significantly decreased in rgp and kgp mutant strains. These data indicate that P. gingivalis has evolved multiple levels of control of fimbrial gene expression to enhance its survival in hostile environments.
Collapse
Affiliation(s)
- H Xie
- School of Dentistry, Meharry Medical College, Nashville, Tennessee 37208, USA.
| | | | | | | |
Collapse
|
20
|
Nevskaya N, Tischenko S, Fedorov R, Al-Karadaghi S, Liljas A, Kraft A, Piendl W, Garber M, Nikonov S. Archaeal ribosomal protein L1: the structure provides new insights into RNA binding of the L1 protein family. Structure 2000; 8:363-71. [PMID: 10801481 DOI: 10.1016/s0969-2126(00)00116-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND L1 is an important primary rRNA-binding protein, as well as a translational repressor that binds mRNA. It was shown that L1 proteins from some bacteria and archaea are functionally interchangeable within the ribosome and in the repression of translation. The crystal structure of bacterial L1 from Thermus thermophilus (TthL1) has previously been determined. RESULTS We report here the first structure of a ribosomal protein from archaea, L1 from Methanococcus jannaschii (MjaL1). The overall shape of the two-domain molecule differs dramatically from that of its bacterial counterpart (TthL1) because of the different relative orientations of the domains. Two strictly conserved regions of the amino acid sequence, each belonging to one of the domains and positioned close to each other in the interdomain cavity of TthL1, are separated by about 25 A in MjaL1 owing to a significant opening of the structure. These regions are structurally highly conserved and are proposed to be the specific RNA-binding sites. CONCLUSIONS The unusually high RNA-binding affinity of MjaL1 might be explained by the exposure of its highly conserved regions. The open conformation of MjaL1 is strongly stabilized by nonconserved interdomain interactions and suggests that the closed conformations of L1 (as in TthL1) open upon RNA binding. Comparison of the two L1 protein structures reveals a high conformational variability of this ribosomal protein. Determination of the MjaL1 structure offers an additional variant for fitting the L1 protein into electron-density maps of the 50S ribosomal subunit.
Collapse
Affiliation(s)
- N Nevskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142292, Moscow Region, Russia
| | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Abstract
The mechanisms for the control of ribosomal protein synthesis have been characterized in detail in Eukarya and in Bacteria. In Archaea, only the regulation of the MvaL1 operon (encoding ribosomal proteins MvaL1, MvaL10, and MvaL12) of the mesophilic Methanococcus vannielii has been extensively investigated. As in Bacteria, regulation takes place at the level of translation. The regulator protein MvaL1 binds preferentially to its binding site on the 23S rRNA, and, when in excess, binds to the regulatory target site on its mRNA and thus inhibits translation of all three cistrons of the operon. The regulatory binding site on the mRNA, a structural mimic of the respective binding site on the 23S rRNA, is located within the structural gene about 30 nucleotides downstream of the ATG start codon. MvaL1 blocks a step before or at the formation of the first peptide bond of MvaL1. Here we demonstrate that a similar regulatory mechanism exists in the thermophilic M. thermolithotrophicus and M. jannaschii. The L1 gene is cotranscribed together with the L10 and L11 gene, in all genera of the Euryarchaeota branch of the Archaea studied so far. A potential regulatory L1 binding site located within the structural gene, as in Methanococcus, was found in Methanobacterium thermoautotrophicum and in Pyrococcus horikoshii. In contrast, in Archaeoglobus fulgidus a typical L1 binding site is located in the untranslated leader of the L1 gene as described for the halophilic Archaea. In Sulfolobus, a member of the Crenarchaeota, the L1 gene is part of a long transcript (encoding SecE, NusG, L11, L1, L10, L12). A previously suggested regulatory L1 target site located within the L11 structural gene could not be confirmed as an L1 binding site.
Collapse
Affiliation(s)
- A Kraft
- Institute of Medical Chemistry and Biochemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| | | | | | | | | |
Collapse
|