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Xu M, Chen Y, Chen L, Chen Y, Yin X, Ji N, Cai Y, Sun S, Shen X. Investigating the molecular mechanisms of Pseudalteromonas sp. LD-B1's algicidal effects on the harmful alga Heterosigma akashiwo. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 282:116690. [PMID: 38981394 DOI: 10.1016/j.ecoenv.2024.116690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 06/29/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024]
Abstract
Heterosigma akashiwo is a harmful algal bloom species that causes significant detrimental effects on marine ecosystems worldwide. The algicidal bacterium Pseudalteromonas sp. LD-B1 has demonstrated potential effectiveness in mitigating these blooms. However, the molecular mechanisms underlying LD-B1's inhibitory effects on H. akashiwo remain poorly understood. In this study, we employed the comprehensive methodology, including morphological observation, assessment of photosynthetic efficiency (Fv/Fm), and transcriptomic analysis, to investigate the response of H. akashiwo to LD-B1. Exposure to LD-B1 resulted in a rapid decline of H. akashiwo's Fv/Fm ratio, with cells transitioning to a rounded shape within 2 hours, subsequently undergoing structural collapse and cytoplasmic leakage. Transcriptomic data revealed sustained downregulation of photosynthetic genes, indicating impaired functionality of the photosynthetic system. Additionally, genes related to the respiratory electron transfer chain and antioxidant defenses were consistently downregulated, suggesting prolonged oxidative stress beyond the cellular antioxidative capacity. Notably, upregulation of autophagy-related genes was observed, indicating autophagic responses in the algal cells. This study elucidates the molecular basis of LD-B1's algicidal effects on H. akashiwo, advancing our understanding of algicidal mechanisms and contributing to the development of effective strategies for controlling harmful algal blooms.
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Affiliation(s)
- Mingyang Xu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005China
| | - Yujiao Chen
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005China
| | - Lei Chen
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005China
| | - Yifan Chen
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005China
| | - Xueyao Yin
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005China
| | - Nanjing Ji
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005China; Jiangsu Marine Resources Development Research Institute, Lianyungang 222005, China; CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Yuefeng Cai
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005China
| | - Song Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xin Shen
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005China.
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2
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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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3
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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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4
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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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5
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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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6
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Ogiwara K, Shinohara M, Takahashi T. Structure and expression of Furin mRNA in the ovary of the medaka, Oryzias latipes. ACTA ACUST UNITED AC 2004; 301:449-59. [PMID: 15114652 DOI: 10.1002/jez.a.20071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A cDNA for furin was cloned from the ovary of the medaka, Oryzias latipes, by a combination of cDNA library screening, 5'-rapid amplification of cDNA ends (RACE), and 3'- RACE. The cDNA sequence codes for a protein of 814 amino acid residues highly homologous to other vertebrate furins, Ca(2+)-dependent serine proteases belonging to the subtilysin-like proprotein convertase family. The medaka preprofurin consists of a leader sequence, a propeptide with autoactivation sites, a Kex2-like catalytic domain, a P domain, a cysteine-rich domain, a putative transmembrane domain, and a cytoplasmic domain. The catalytic triad residues (Asp-164, His-205, and Ser-379) were all conserved. Furin mRNA was expressed in many tissues of this, including the ovary. In the ovary, the greatest expression of furin mRNA occurred in oocytes of small growing follicles, as demonstrated by Northern blotting, RT-PCR, and in situ hybridization analysis. Temporary and spatial expression patterns of the medaka fish furin were similar to those of stromelysin-3 and MT5-MMP during oocyte growth and postnatal development.
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Affiliation(s)
- Katsueki Ogiwara
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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7
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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] [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.
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Affiliation(s)
- N Nevskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142292, Moscow Region, Russia
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8
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Kraft A, Lutz C, Lingenhel A, Gröbner P, Piendl W. Control of ribosomal protein L1 synthesis in mesophilic and thermophilic archaea. Genetics 1999; 152:1363-72. [PMID: 10430567 PMCID: PMC1460717 DOI: 10.1093/genetics/152.4.1363] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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.
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Affiliation(s)
- A Kraft
- Institute of Medical Chemistry and Biochemistry, University of Innsbruck, A-6020 Innsbruck, Austria
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9
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Wu G, Hashimoto T. Sequence analysis of genes encoding ribosomal proteins of amitochondriate protists: L1 of Trichomonas vaginalis and L29 of Giardia lamblia. Parasitol Int 1999; 48:135-44. [PMID: 11269274 DOI: 10.1016/s1383-5769(99)00010-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Two genes encoding the ribosomal proteins were cloned and sequenced from amitochondriate protists, L1 (L10a in mammalian nomenclature) from Trichomonas vaginalis and L29 (L35 in mammalian nomenclature) from Giardia lamblia. The deduced amino acid sequences were analyzed by sequence alignments and phylogenetic reconstructions. Both the T. vaginalis L1 and the G. lamblia L29 displayed eukaryotic sequence features, when compared with all the homologs from the three primary kingdoms.
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Affiliation(s)
- G Wu
- The Rockefeller University, New York, NY 10021, USA
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10
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Nikonov SV, Nevskaya NA, Fedorov RV, Khairullina AR, Tishchenko SV, Nikulin AD, Garber MB. Structural studies of ribosomal proteins. Biol Chem 1998; 379:795-805. [PMID: 9705143 DOI: 10.1515/bchm.1998.379.7.795] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Crystal and solution structures of fourteen ribosomal proteins from thermophilic bacteria have been determined during the last decade. This paper reviews structural studies of ribosomal proteins from Thermus thermophilus carried out at the Institute of Protein Research (Pushchino, Russia) in collaboration with the University of Lund (Lund, Sweden) and the Center of Structural Biochemistry (Karolinska Institute, Huddinge, Sweden). New experimental data on the crystal structure of the ribosomal protein L30 from T. thermophilus are also included.
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Affiliation(s)
- S V Nikonov
- Institute of Protein Research, Russian Academy of Sciences, Moscow Region
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11
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Nevskaya N, Tishchenko S, Nikulin A, al-Karadaghi S, Liljas A, Ehresmann B, Ehresmann C, Garber M, Nikonov S. Crystal structure of ribosomal protein S8 from Thermus thermophilus reveals a high degree of structural conservation of a specific RNA binding site. J Mol Biol 1998; 279:233-44. [PMID: 9636713 DOI: 10.1006/jmbi.1998.1758] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
S8 is one of the core ribosomal proteins. It binds to 16 S RNA with high affinity and independently of other ribosomal proteins. It also acts as a translational repressor in Escherichia coli by binding to its own mRNA. The structure of Thermus thermophilus S8 has been determined by the method of multiple isomorphous replacement at 2.9 A resolution and refined to a crystallographic R-factor of 16.2% (Rfree 27.5%). The two domains of the structure have an alpha/beta fold and are connected by a long protruding loop. The two molecules in the asymmetric unit of the crystal interact through an extensive hydrophobic core and form a tightly associated dimer, while symmetry-related molecules form a joint beta-sheet of mixed type. This type of protein-protein interaction could be realized within the ribosomal assembly. A comparison of the structures of T. thermophilus and Bacillus stearothermophilus S8 shows that the interdomain loop is eight residues longer in the former and reveals high structural conservation of an extensive region, located in the C-terminal domain. From mutational studies this region was proposed earlier to be involved in specific interaction with RNA. On the basis of these data and on the comparison of the two structures of S8, it is proposed that the three-dimensional structure of specific RNA binding sites in ribosomal proteins is highly conserved among different species.
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Affiliation(s)
- N Nevskaya
- Institute of Protein Research, Russian Academy of Sciences, Moscow Region, Russia
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12
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Abstract
Since the late 1970s, determining the phylogenetic relationships among the contemporary domains of life, the Archaea (archaebacteria), Bacteria (eubacteria), and Eucarya (eukaryotes), has been central to the study of early cellular evolution. The two salient issues surrounding the universal tree of life are whether all three domains are monophyletic (i.e., all equivalent in taxanomic rank) and where the root of the universal tree lies. Evaluation of the status of the Archaea has become key to answering these questions. This review considers our cumulative knowledge about the Archaea in relationship to the Bacteria and Eucarya. Particular attention is paid to the recent use of molecular phylogenetic approaches to reconstructing the tree of life. In this regard, the phylogenetic analyses of more than 60 proteins are reviewed and presented in the context of their participation in major biochemical pathways. Although many gene trees are incongruent, the majority do suggest a sisterhood between Archaea and Eucarya. Altering this general pattern of gene evolution are two kinds of potential interdomain gene transferrals. One horizontal gene exchange might have involved the gram-positive Bacteria and the Archaea, while the other might have occurred between proteobacteria and eukaryotes and might have been mediated by endosymbiosis.
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Affiliation(s)
- J R Brown
- Canadian Institute for Advanced Research, Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada.
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13
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Geiger M, Gröbner P, Piendl W. Nucleotide sequence of a gene cluster encoding NusG and the L11-L1-L10-L12 ribosomal proteins from the thermophilic archaeon Sulfolobus solfataricus. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1340:170-7. [PMID: 9252104 DOI: 10.1016/s0167-4838(97)00073-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The complete nucleotide sequence of a gene cluster encoding the NusG and the L 11-L1-L10-L12 ribosomal proteins from the thermophilic crenarchaeon Sulfolobus solfataricus has been determined. The genes are arranged in the same order as the equivalent genes in the rif region of Escherichia coli. The ribosomal proteins exhibit between 66% (L10) and 80% (L12) identity with their respective equivalents from Sulfolobus acidocaldarius. The short distance (5 nucleotides) between the nusG stop codon and the L11 start codon suggests that nusG and the genes for the ribosomal proteins are transcribed as a single unit.
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Affiliation(s)
- M Geiger
- Institut für Medizinische Chemie und Biochemie, Universität Innsbruck, Austria
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14
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Nikonov S, Nevskaya N, Eliseikina I, Fomenkova N, Nikulin A, Ossina N, Garber M, Jonsson BH, Briand C, Al-Karadaghi S, Svensson A, Aevarsson A, Liljas A. Crystal structure of the RNA binding ribosomal protein L1 from Thermus thermophilus. EMBO J 1996; 15:1350-9. [PMID: 8635468 PMCID: PMC450039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
L1 has a dual function as a ribosomal protein binding rRNA and as a translational repressor binding mRNA. The crystal structure of L1 from Thermus thermophilus has been determined at 1.85 angstroms resolution. The protein is composed of two domains with the N- and C-termini in domain I. The eight N-terminal residues are very flexible, as the quality of electron density map shows. Proteolysis experiments have shown that the N-terminal tail is accessible and important for 23S rRNA binding. Most of the conserved amino acids are situated at the interface between the two domains. They probably form the specific RNA binding site of L1. Limited non-covalent contacts between the domains indicate an unstable domain interaction in the present conformation. Domain flexibility and RNA binding by induced fit seems plausible.
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Affiliation(s)
- S Nikonov
- Department of Structure and Function of Ribosomes, Russian Academy of Sciences, Russia
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15
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Köhrer C, Mayer C, Gröbner P, Piendl W. Use of T7 RNA polymerase in an optimized Escherichia coli coupled in vitro transcription-translation system. Application in regulatory studies and expression of long transcription units. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 236:234-9. [PMID: 8617270 DOI: 10.1111/j.1432-1033.1996.00234.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
An Escherichia coli coupled in vitro transcription-translation system has been modified to allow efficient expression of genes under the control of a T7 promoter. We describe both the characterization and use of two S30 crude extracts prepared from E. coli, namely S30 BL21(DE3) (containing endogenous T7 RNA polymerase) and S30 BL21 (supplemented with exogenous T7 RNA polymerase). Since transcription by the highly active T7 RNA polymerase is known to overload the translational machinery of E. coli, the ratio between mRNA and ribosomes has to be regulated in the coupled in vitro system. For this purpose, the level of mRNA is controlled by varying the amount of DNA template (S30 extract with endogenous T7 RNA polymerase) or by limited amounts of exogenously added T7 RNA polymerase. The coupled in vitro system described in this paper provides two especially useful applications. First, it is most suitable for studying the regulation of gene expression in vitro, second, it can be used to express DNA templates carrying up to 10 genes. We show that genes which are not well expressed in E. coli in vivo because of unfavourable codon usage or plasmid instability are synthesized efficiently in the coupled in vitro system.
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Affiliation(s)
- C Köhrer
- Institute of Medical Chemistry and Biochemistry, University of Innsbruck, Austria
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16
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Evers U, Franceschi F, Böddeker N, Yonath A. Crystallography of halophilic ribosome: the isolation of an internal ribonucleoprotein complex. Biophys Chem 1994; 50:3-16. [PMID: 8011938 DOI: 10.1016/0301-4622(94)85015-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Crystals of 50S ribosomal subunits from Haloarcula marismortui diffracting to 2.9 A resolution were grown. Because of their large unit cells and the extremely weak diffracting power, almost all X-ray crystallographic analysis of these crystals must be performed with intense synchrotron radiation. At ambient temperature, all ribosomal crystals decay upon the first instance of X-irradiation. To overcome this severe sensitivity, procedures for data collection at cryo temperature were developed. Under these conditions the crystals can be irradiated for periods sufficient for the collection of more than one data set from an individual crystal (days or weeks) with no observable damage. They also can be stored for months, to resume interrupted measurements. To assist the interpretation of the anticipated electron density map, a specific internal nucleoprotein complex of protein HmaL1 and a stretch of H23S rRNA was isolated from the halophilic ribosome. The fragments of the 23S rRNA protected by the protein from nuclease digestion were sequenced. Alignment of the sequences of some archaebacterial L1-specific RNA fragments to the corresponding parts of eubacterial and eukaryotic rDNAs, localized the sequence identities to two distinct regions. Chimeric complexes were reconstituted with the corresponding E. coli ribosomal components, indicating a rather high homology, despite the evolution distance. A feasible secondary structure of the rRNA stretch participating in this complex was found to be compatible with the one proposed for the corresponding part in the E. coli ribosomal RNA.
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Affiliation(s)
- U Evers
- Max-Planck-Laboratory for Ribosomal Structure, Hamburg, Germany
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17
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Liao D, Dennis PP. Molecular phylogenies based on ribosomal protein L11, L1, L10, and L12 sequences. J Mol Evol 1994; 38:405-19. [PMID: 8007008 DOI: 10.1007/bf00163157] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Available sequences that correspond to the E. coli ribosomal proteins L11, L1, L10, and L12 from eubacteria, archaebacteria, and eukaryotes have been aligned. The alignments were analyzed qualitatively for shared structural features and for conservation of deletions or insertions. The alignments were further subjected to quantitative phylogenetic analysis, and the amino acid identity between selected pairs of sequences was calculated. In general, eubacteria, archaebacteria, and eukaryotes each form coherent and well-resolved nonoverlapping phylogenetic domains. The degree of diversity of the four proteins between the three groups is not uniform. For L11, the eubacterial and archaebacterial proteins are very similar whereas the eukaryotic L11 is clearly less similar. In contrast, in the case of the L12 proteins and to a lesser extent the L10 proteins, the archaebacterial and eukaryotic proteins are similar whereas the eubacterial proteins are different. The eukaryotic L1 equivalent protein has yet to be identified. If the root of the universal tree is near or within the eubacterial domain, our ribosomal protein-based phylogenies indicate that archaebacteria are monophyletic. The eukaryotic lineage appears to originate either near or within the archaebacterial domain.
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Affiliation(s)
- D Liao
- Canadian Institute for Advanced Research, University of British Columbia, Vancouver
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18
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Hennigan AN, Reeve JN. mRNAs in the methanogenic archaeon Methanococcus vannielii: numbers, half-lives and processing. Mol Microbiol 1994; 11:655-70. [PMID: 7515144 DOI: 10.1111/j.1365-2958.1994.tb00344.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Cells from the early exponential growth phase of cultures of the methanogenic archaeon Methanococcus vannielii have been shown to contain c. 180 transcripts of the mcrBDCGA (mcr) operon, c. 100 transcripts of the MvaL1,L10,L12 (Mva) operon, c. 8 transcripts of the argG gene and c. 1 transcript of the secY gene. These values decreased to c. 50 mcr transcripts, c. 30 Mva transcripts, c. 3 argG transcripts and < 1 secY transcript per cell as the cultures entered the stationary phase of growth. Addition of bromo-ethanesulphonate (BES) or removal of H2 inhibited growth and RNA synthesis in vivo and, at 37 degrees C in the presence of BES, the half-lives of the mcr, Mva, argG and secY transcripts were found to be 15 min, 30 min, 57 min and 7 min, respectively. Addition of puromycin, pseudomonic acid or virginiamycin also inhibited growth but did not inhibit transcription. In the presence of puromycin the half-lives of the mcr and Mva transcripts increased c. 4.6-fold and c. 3.5-fold, respectively, and there was a net accumulation of the Mva transcript. Addition of pseudomonic acid or virginiamycin also increased the half-life of the Mva transcript and also resulted in the accumulation of a second, shorter Mva transcript but did not increase the half-life of the mcr transcript. Transcription of the mcr operon was not stimulated by partial inhibition of methanogenesis.
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Affiliation(s)
- A N Hennigan
- Department of Microbiology, Ohio State University, Columbus 43210
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19
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Hanner M, Mayer C, Köhrer C, Golderer G, Gröbner P, Piendl W. Autogenous translational regulation of the ribosomal MvaL1 operon in the archaebacterium Methanococcus vannielii. J Bacteriol 1994; 176:409-18. [PMID: 8288536 PMCID: PMC205064 DOI: 10.1128/jb.176.2.409-418.1994] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The mechanisms for regulation of ribosomal gene expression have been characterized in eukaryotes and eubacteria, but not yet in archaebacteria. We have studied the regulation of the synthesis of ribosomal proteins MvaL1, MvaL10, and MvaL12, encoded by the MvaL1 operon of Methanococcus vannielii, a methanogenic archaebacterium. MvaL1, the homolog of the regulatory protein L1 encoded by the L11 operon of Escherichia coli, was shown to be an autoregulator of the MvaL1 operon. As in E. coli, regulation takes place at the level of translation. The target site for repression by MvaL1 was localized by site-directed mutagenesis to a region within the coding sequence of the MvaL1 gene commencing about 30 bases downstream of the ATG initiation codon. The MvaL1 binding site on the mRNA exhibits similarity in both primary sequence and secondary structure to the L1 regulatory target site of E. coli and to the putative binding site for MvaL1 on the 23S rRNA. In contrast to other regulatory systems, the putative MvaL1 binding site is located in a sequence of the mRNA which is not in direct contact with the ribosome as part of the initiation complex. Furthermore, the untranslated leader sequence is not involved in the regulation. Therefore, we suggest that a novel mechanism of translational feedback regulation exists in M. vannielii.
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Affiliation(s)
- M Hanner
- Institute of Medical Microbiology, University of Innsbruck, Austria
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20
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Amons R, Muranova TA, Rykunova AI, Eliseikina IA, Sedelnikova SE. The complete primary structure of ribosomal protein L1 from Thermus thermophilus. JOURNAL OF PROTEIN CHEMISTRY 1993; 12:725-34. [PMID: 8136022 DOI: 10.1007/bf01024930] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The primary structure of the 23S rRNA binding ribosomal protein L1 from the 50S ribosomal subunit of Thermus thermophilus ribosomes has been elucidated by direct protein sequencing of selected peptides prepared by enzymatic and chemical cleavage of the intact purified protein. The polypeptide chain contains 228 amino acids and has a calculated molecular mass of 24,694 D. A comparison with the primary structures of the corresponding proteins from Escherichia coli and Bacillus stearothermophilus reveals a sequence homology of 49% and 58%, respectively. With respect to both proteins, L1 from T. thermophilus contains particularly less Ala, Lys, Gln, and Val, whereas its content of Glu, Gly, His, Ile, and Arg is higher. In addition, two fragments obtained by limited proteolysis of the intact, unmodified protein were characterized.
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Affiliation(s)
- R Amons
- Department of Medical Biochemistry, University of Leiden, The Netherlands
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21
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Schmidt J, Bubunenko M, Subramanian AR. A novel operon organization involving the genes for chorismate synthase (aromatic biosynthesis pathway) and ribosomal GTPase center proteins (L11, L1, L10, L12: rplKAJL) in cyanobacterium Synechocystis PCC 6803. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(19)74268-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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22
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Chapter 16 Structure and function of methanogen genes. ACTA ACUST UNITED AC 1993. [DOI: 10.1016/s0167-7306(08)60265-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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23
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Chapter 15 Halobacterial genes and genomes. ACTA ACUST UNITED AC 1993. [DOI: 10.1016/s0167-7306(08)60264-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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24
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Palmer JR, Reeve JN. Methanogen Genes and the Molecular Biology of Methane Biosynthesis. BROCK/SPRINGER SERIES IN CONTEMPORARY BIOSCIENCE 1993. [DOI: 10.1007/978-1-4615-7087-5_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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25
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Chapter 14 The structure, function and evolution of archaeal ribosomes. ACTA ACUST UNITED AC 1993. [DOI: 10.1016/s0167-7306(08)60263-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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26
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Hausner W, Frey G, Thomm M. Control regions of an archaeal gene. A TATA box and an initiator element promote cell-free transcription of the tRNA(Val) gene of Methanococcus vannielii. J Mol Biol 1991; 222:495-508. [PMID: 1748992 DOI: 10.1016/0022-2836(91)90492-o] [Citation(s) in RCA: 104] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To identify the DNA sequences required for initiation of transcription in archaea, the 5'-flanking region of the tRNA(Val) gene of Methanococcus vannielii was modified by deletions, restructuring and site-directed mutagenesis, and the tRNA encoding sequence was replaced by a fortuitous Escherichia coli sequence. The effects of these mutations on promoter function were tested in an homologous cell-free transcription system. The DNA region from position -35 to +9 relative to the transcription start site was sufficient for maximal initiation of cell-free transcription. Removal of the DNA region between -35 and -30 reduced initiation by a factor of 2. Deletions extending to position -24 almost completely abolished specific transcription. Analysis of 16 site-specific mutations in the region from -33 to +2 provided evidence that a conserved A + T-rich sequence (TATA box), centered at -25, is essential for initiation of transcription. Single point mutations in six positions of the TATA box reduced initiation of transcription from 0.2 to 0.01 of wild-type levels. A second conserved motif at the transcription start site (consensus ATGC) could be replaced by some sequences containing a pyrimidine-purine dinucleotide but appeared necessary for a maximal rate of gene transcription. Mutations altering the spacing between the two conserved elements demonstrated that initiation occurs at a strictly defined distance of 22 to 27 base-pairs downstream from the TATA box. Our results support the conclusion that the TATA box is the major DNA region mediating promoter recognition, influencing the efficiency of transcription and specifying the site of transcription initiation. This Methanococcus promoter element closely resembles in structure and function the TATA box of promoters of eukaryotic protein-encoding genes transcribed by RNA polymerase II.
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Affiliation(s)
- W Hausner
- Lehrstuhl für Mikrobiologie, Universität Regensburg, Germany
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27
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Kalmokoff ML, Jarrell KF. Cloning and sequencing of a multigene family encoding the flagellins of Methanococcus voltae. J Bacteriol 1991; 173:7113-25. [PMID: 1718944 PMCID: PMC209217 DOI: 10.1128/jb.173.22.7113-7125.1991] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The flagellins of Methanococcus voltae are encoded by a multigene family of four related genes (flaA, flaB1, flaB2, and flaB3). All four genes map within the same region of the genome, with the last three arranged in a direct tandem. Northern (RNA) blot and primer extension analyses of total cellular RNA indicate that all four genes are transcribed. The flaB1, flaB2, and flaB3 flagellins are transcribed as part of a large polycistronic message which encodes at least one more protein which is not a flagellin. An intercistronic stem-loop followed by a poly(T) tract located between the flaB2 and flaB3 genes appears to increase the resistance of the flaB1/flaB2 portion of this polycistronic message to digestion by endogenous RNases. The flaA gene, located approximately 600 bp upstream from the tandem, is transcribed as a separate message at very low levels. The four open reading frames encode proteins of molecular weights 23,900, 22,400, 22,800, and 25,500, much less than the Mr values of 33,000 and 31,000 for the flagellins calculated from sodium dodecyl sulfate-polyacrylamide gel electrophoresis of isolated flagellar filaments. Each flagellin contains multiple eukaryotic glycosylation signals (Arg-X-Ser/Thr), although they do not appear to be glycoproteins, and each has an 11- or 12-amino-acid leader peptide. The N termini of all four flagellins (amino acids 1 through 47 of the mature protein) are very hydrophobic, and this region shows a high degree of homology with the flagellins from Halobacterium halobium.
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Affiliation(s)
- M L Kalmokoff
- Department of Microbiology and Immunology, Queen's University, Kingston, Ontario, Canada
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28
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Auer J, Spicker G, Mayerhofer L, Pühler G, Böck A. Organisation and Nucleotide Sequence of a Gene Cluster Comprising the Translation Elongation Factor 1α from Sulfolobus acidocaldarius. Syst Appl Microbiol 1991. [DOI: 10.1016/s0723-2020(11)80356-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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29
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30
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New nucleotide sequence data on the EMBL File Server. Nucleic Acids Res 1990; 18:2839-49. [PMID: 2339078 PMCID: PMC330803 DOI: 10.1093/nar/18.9.2839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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