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Aseev LV, Koledinskaya LS, Boni IV. Extraribosomal Functions of Bacterial Ribosomal Proteins-An Update, 2023. Int J Mol Sci 2024; 25:2957. [PMID: 38474204 DOI: 10.3390/ijms25052957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Ribosomal proteins (r-proteins) are abundant, highly conserved, and multifaceted cellular proteins in all domains of life. Most r-proteins have RNA-binding properties and can form protein-protein contacts. Bacterial r-proteins govern the co-transcriptional rRNA folding during ribosome assembly and participate in the formation of the ribosome functional sites, such as the mRNA-binding site, tRNA-binding sites, the peptidyl transferase center, and the protein exit tunnel. In addition to their primary role in a cell as integral components of the protein synthesis machinery, many r-proteins can function beyond the ribosome (the phenomenon known as moonlighting), acting either as individual regulatory proteins or in complexes with various cellular components. The extraribosomal activities of r-proteins have been studied over the decades. In the past decade, our understanding of r-protein functions has advanced significantly due to intensive studies on ribosomes and gene expression mechanisms not only in model bacteria like Escherichia coli or Bacillus subtilis but also in little-explored bacterial species from various phyla. The aim of this review is to update information on the multiple functions of r-proteins in bacteria.
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Affiliation(s)
- Leonid V Aseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
| | | | - Irina V Boni
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
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2
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Wang D, Zhang X, Yin L, Liu Q, Yu Z, Xu C, Ma Z, Xia Y, Shi J, Gong Y, Bai F, Cheng Z, Wu W, Lin J, Jin Y. RplI interacts with 5’ UTR of exsA to repress its translation and type III secretion system in Pseudomonas aeruginosa. PLoS Pathog 2022; 18:e1010170. [PMID: 34986198 PMCID: PMC8730436 DOI: 10.1371/journal.ppat.1010170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/04/2021] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas aeruginosa is an important opportunistic pathogen capable of causing variety of infections in humans. The type III secretion system (T3SS) is a critical virulence determinant of P. aeruginosa in the host infections. Expression of the T3SS is regulated by ExsA, a master regulator that activates the expression of all known T3SS genes. Expression of the exsA gene is controlled at both transcriptional and posttranscriptional levels. Here, we screened a P. aeruginosa transposon (Tn5) insertional mutant library and found rplI, a gene coding for the ribosomal large subunit protein L9, to be a repressor for the T3SS gene expression. Combining real-time quantitative PCR (qPCR), western blotting and lacZ fusion assays, we show that RplI controls the expression of exsA at the posttranscriptional level. Further genetic experiments demonstrated that RplI mediated control of the exsA translation involves 5’ untranslated region (5’ UTR). A ribosome immunoprecipitation assay and qPCR revealed higher amounts of a 24 nt fragment from exsA mRNA being associated with ribosomes in the ΔrplI mutant. An interaction between RplI and exsA mRNA harboring its 24 nt, but not 12 nt, 5’ UTR was confirmed by RNA Gel Mobility Shift and Microscale Thermophoresis assays. Overall, this study identifies the ribosomal large subunit protein L9 as a novel T3SS repressor that inhibits ExsA translation in P. aeruginosa. Ribosomes provide all living organisms the capacity to synthesize proteins. The production of many ribosomal proteins is often controlled by an autoregulatory feedback mechanism. P. aeruginosa is an opportunistic human pathogen and its type III secretion system (T3SS) is a critical virulence determinant in host infections. In this study, by screening a Tn5 mutant library, we identified rplI, encoding ribosomal large subunit protein L9, as a novel repressor for the T3SS. Further exploring the regulatory mechanism, we found that the RplI protein interacts with the 5’ UTR (5’ untranslated region) of exsA, a gene coding for transcriptional activator of the T3SS. Such an interaction likely blocks ribosome loading on the exsA 5’ UTR, inhibiting the initiation of exsA translation. The significance of this work is in the identification of a novel repressor for the T3SS and elucidation of its molecular mechanism. Furthermore, this work provides evidence for individual ribosomal protein regulating mRNA translation beyond its autogenous feedback control.
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Affiliation(s)
- Dan Wang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xinxin Zhang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Liwen Yin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Qi Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhaoli Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Congjuan Xu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhenzhen Ma
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yushan Xia
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jing Shi
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yuehua Gong
- Cancer Institute, the First Affiliated Hospital of China Medical University, Shenyang, China
| | - Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
- * E-mail:
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Rosinski-Chupin I, Sauvage E, Fouet A, Poyart C, Glaser P. Conserved and specific features of Streptococcus pyogenes and Streptococcus agalactiae transcriptional landscapes. BMC Genomics 2019; 20:236. [PMID: 30902048 PMCID: PMC6431027 DOI: 10.1186/s12864-019-5613-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 03/14/2019] [Indexed: 12/11/2022] Open
Abstract
Background The human pathogen Streptococcus pyogenes, or group A Streptococcus, is responsible for mild infections to life-threatening diseases. To facilitate the characterization of regulatory networks involved in the adaptation of this pathogen to its different environments and their evolution, we have determined the primary transcriptome of a serotype M1 S. pyogenes strain at single-nucleotide resolution and compared it with that of Streptococcus agalactiae, also from the pyogenic group of streptococci. Results By using a combination of differential RNA-sequencing and oriented RNA-sequencing we have identified 892 transcription start sites (TSS) and 885 promoters in the S. pyogenes M1 strain S119. 8.6% of S. pyogenes mRNAs were leaderless, among which 81% were also classified as leaderless in S. agalactiae. 26% of S. pyogenes transcript 5′ untranslated regions (UTRs) were longer than 60 nt. Conservation of long 5′ UTRs with S. agalactiae allowed us to predict new potential regulatory sequences. In addition, based on the mapping of 643 transcript ends in the S. pyogenes strain S119, we constructed an operon map of 401 monocistrons and 349 operons covering 81.5% of the genome. One hundred fifty-six operons and 254 monocistrons retained the same organization, despite multiple genomic reorganizations between S. pyogenes and S. agalactiae. Genomic reorganization was found to more often go along with variable promoter sequences and 5′ UTR lengths. Finally, we identified 117 putative regulatory RNAs, among which nine were regulated in response to magnesium concentration. Conclusions Our data provide insights into transcriptome evolution in pyogenic streptococci and will facilitate the analysis of genetic polymorphisms identified by comparative genomics in S. pyogenes. Electronic supplementary material The online version of this article (10.1186/s12864-019-5613-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Isabelle Rosinski-Chupin
- Ecology and Evolution of Resistance to Antibiotics, Institut Pasteur-APHP-Université Paris Saclay, UMR3525 CNRS, Paris, France.
| | - Elisabeth Sauvage
- Ecology and Evolution of Resistance to Antibiotics, Institut Pasteur-APHP-Université Paris Saclay, UMR3525 CNRS, Paris, France
| | - Agnès Fouet
- INSERM U1016, Institut Cochin, CNRS UMR 8104, Université Paris Descartes (UMR-S1016), Paris, France.,Centre Nationale de Référence des Streptocoques, Hôpitaux Universitaires Paris Centre, Cochin, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Claire Poyart
- INSERM U1016, Institut Cochin, CNRS UMR 8104, Université Paris Descartes (UMR-S1016), Paris, France.,Centre Nationale de Référence des Streptocoques, Hôpitaux Universitaires Paris Centre, Cochin, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Philippe Glaser
- Ecology and Evolution of Resistance to Antibiotics, Institut Pasteur-APHP-Université Paris Saclay, UMR3525 CNRS, Paris, France
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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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Krepl M, Réblová K, Koča J, Sponer J. Bioinformatics and molecular dynamics simulation study of L1 stalk non-canonical rRNA elements: kink-turns, loops, and tetraloops. J Phys Chem B 2013; 117:5540-55. [PMID: 23534440 DOI: 10.1021/jp401482m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The L1 stalk is a prominent mobile element of the large ribosomal subunit. We explore the structure and dynamics of its non-canonical rRNA elements, which include two kink-turns, an internal loop, and a tetraloop. We use bioinformatics to identify the L1 stalk RNA conservation patterns and carry out over 11.5 μs of MD simulations for a set of systems ranging from isolated RNA building blocks up to complexes of L1 stalk rRNA with the L1 protein and tRNA fragment. We show that the L1 stalk tetraloop has an unusual GNNA or UNNG conservation pattern deviating from major GNRA and YNMG RNA tetraloop families. We suggest that this deviation is related to a highly conserved tertiary contact within the L1 stalk. The available X-ray structures contain only UCCG tetraloops which in addition differ in orientation (anti vs syn) of the guanine. Our analysis suggests that the anti orientation might be a mis-refinement, although even the anti interaction would be compatible with the sequence pattern and observed tertiary interaction. Alternatively, the anti conformation may be a real substate whose population could be pH-dependent, since the guanine syn orientation requires protonation of cytosine in the tertiary contact. In absence of structural data, we use molecular modeling to explore the GCCA tetraloop that is dominant in bacteria and suggest that the GCCA tetraloop is structurally similar to the YNMG tetraloop. Kink-turn Kt-77 is unusual due to its 11-nucleotide bulge. The simulations indicate that the long bulge is a stalk-specific eight-nucleotide insertion into consensual kink-turn only subtly modifying its structural dynamics. We discuss a possible evolutionary role of helix H78 and a mechanism of L1 stalk interaction with tRNA. We also assess the simulation methodology. The simulations provide a good description of the studied systems with the latest bsc0χOL3 force field showing improved performance. Still, even bsc0χOL3 is unable to fully stabilize an essential sugar-edge H-bond between the bulge and non-canonical stem of the kink-turn. Inclusion of Mg(2+) ions may deteriorate the simulations. On the other hand, monovalent ions can in simulations readily occupy experimental Mg(2+) binding sites.
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Affiliation(s)
- Miroslav Krepl
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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6
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Sato H, Ito K, Nakamura Y. Ribosomal protein L11 mutations in two functional domains equally affect release factors 1 and 2 activity. Mol Microbiol 2006; 60:108-20. [PMID: 16556224 DOI: 10.1111/j.1365-2958.2006.05094.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Bacterial release factors (RFs) 1 and 2 catalyse translation termination at UAG/UAA and UGA/UAA stop codons respectively. It has been shown that limiting the amount of ribosomal protein L11 affects translation termination at UAG and UGA differently. To understand the functional interplay between L11 and RF1/RF2, we isolated 21 distinct mutations in L11 as suppressors of either temperature-sensitive (ts) RF1/RF2 strains or read-through mutants of lacZ nonsense (UAG or UGA) strains. 10 of 21 mutants restored ts lethal growth of RF1 and/or RF2 strains. All the selected L11 mutants, including the RF1ts- and RF2ts-specific suppressors, had the same effect, either enhancing or reducing, on UAG and UGA termination efficiency in vivo. The specific properties of the selected L11 mutations remained unchanged in an RF3 deletion strain. Moreover, ribosomes absent of L11 had equally reduced activity for both RF1- and RF2-mediated peptide release in vitro. These results suggest that, unlike the previous notion, L11 has a common, cooperative role with RF1 and RF2. These L11 mutations were located on the surface of two domains of L11, and interpreted to affect the interaction between L11 and rRNA or the RFs thereby leading to the altered translation termination.
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Affiliation(s)
- Hanae Sato
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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7
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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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8
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Abstract
This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.
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Affiliation(s)
- M K Berlyn
- Department of Biology and School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut 06520-8104, USA.
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9
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Mayer C, Köhrer C, Gröbner P, Piendl W. MvaL1 autoregulates the synthesis of the three ribosomal proteins encoded on the MvaL1 operon of the archaeon Methanococcus vannielii by inhibiting its own translation before or at the formation of the first peptide bond. Mol Microbiol 1998; 27:455-68. [PMID: 9484899 DOI: 10.1046/j.1365-2958.1998.00693.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The control of ribosomal protein synthesis has been investigated extensively in Eukarya and Bacteria. In Archaea, only the regulation of the MvaL1 operon (encoding ribosomal proteins MvaL1, MvaL10 and MvaL12) of Methanococcus vannielii has been studied in some detail. As in Escherichia coil, regulation takes place at the level of translation. MvaL1, the homologue of the regulatory protein L1 encoded by the L11 operon of E. coli, was shown to be an autoregulator of the MvaL1 operon. The regulatory MvaL1 binding site on the mRNA is located about 30 nucleotides downstream of the ATG start codon, a sequence that is not in direct contact with the initiating ribosome. Here, we demonstrate that autoregulation of MvaL1 occurs at or before the formation of the first peptide bond of MvaL1. Specific interaction of purified MvaL1 with both 23S RNA and its own mRNA is confirmed by filter binding studies. In vivo expression experiments reveal that translation of the distal MvaL10 and MvaL12 cistrons is coupled to that of the MvaL1 cistron. A mRNA secondary structure resembling a canonical L10 binding site and preliminary in vitro regulation experiments had suggested a co-regulatory function of MvaL10, the homologue of the regulatory protein L10 of the beta-operon of E. coil. However, we show that MvaL10 does not have a regulatory function.
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Affiliation(s)
- C Mayer
- Institut für Medizinische Chemie und Biochemie, Universität Innsbruck, Austria
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10
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Shimmin LC, Dennis PP. Conserved sequence elements involved in regulation of ribosomal protein gene expression in halophilic archaea. J Bacteriol 1996; 178:4737-41. [PMID: 8755911 PMCID: PMC178250 DOI: 10.1128/jb.178.15.4737-4741.1996] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A region of the Haloferax volcanii genome encoding ribosomal proteins L11e, L1e, L10e, and L12e was cloned and sequenced, and the transcripts derived from the cluster were characterized. Flanking and noncoding regions of the sequence were analyzed phylogenetically by comparison with the homologous sequences from two other halophilic archaea, i.e., Halobacterium cutirubrum and Haloarcula marismortui. Motifs, identified by high-level sequence conservation, include both transcriptional and translational regulatory elements and other elements of unknown function.
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Affiliation(s)
- L C Shimmin
- Department of Biochemistry & Molecular Biology, The University of British Columbia, Vancouver, Canada
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11
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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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12
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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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Saito K, Nomura M. Post-transcriptional regulation of the str operon in Escherichia coli. Structural and mutational analysis of the target site for translational repressor S7. J Mol Biol 1994; 235:125-39. [PMID: 8289236 DOI: 10.1016/s0022-2836(05)80021-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In the Escherichia coli str operon, translation of the S12 and S7 genes is largely coupled, and the translational repressor S7 inhibits S7 translation, which is coupled to that of S12, but does not inhibit independent translation of S7 by free ribosomes in the intracellular pool. We have studied the S12-S7 intercistronic region of mRNA by analyzing RNA synthesized in vitro using structure-specific nucleases and a chemical probe, dimethyl sulfate. Based on the results obtained, we have deduced a secondary structure model of the S12-S7 intercistronic region and identified nucleotide residues "protected" by S7. We then carried out site-directed mutagenesis to identify nucleotide residues important for S7 translation as well as for repression by S7. The results showed that two distinct regions are important for S7-mediated repression; one is the S7 binding region identified by the protection analysis and the second is the stem structure that sequesters the Shine-Dalgarno sequence for the S7 gene. Some of the base alterations in the first region abolished S7 binding and, as a consequence, abolished S7-mediated repression, without affecting the efficiency of S7 translation. Other mutations disrupting the stem structure in the second region abolished S7-mediated repression without significantly affecting the S7-mRNA interaction. We also found that certain mutations drastically decrease S7 translation achieved by translational coupling without affecting S7 translation achieved by independent initiation. These mutations are in base-paired regions and evidence was obtained to suggest that these base-paired structures are important for translational coupling. We suggest that some specific RNA structures in the intercistronic region play an active role in achieving translational coupling in this system, and that repression of S7 translation by S7 protein is due to disruption of such structures induced by binding of S7 protein to the target site, rendering translational coupling very inefficient, but leaving independent translation initiation unaffected.
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Affiliation(s)
- K Saito
- Department of Biological Chemistry, University of California, Irvine 92717-1700
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14
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Zengel JM, Lindahl L. Diverse mechanisms for regulating ribosomal protein synthesis in Escherichia coli. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1994; 47:331-70. [PMID: 7517053 DOI: 10.1016/s0079-6603(08)60256-1] [Citation(s) in RCA: 201] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- J M Zengel
- Department of Biology, University of Rochester, New York 14627
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15
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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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16
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Rasmussen MD, Sørensen MA, Pedersen S. Isolation and characterization of mutants with impaired regulation of rpsA, the gene encoding ribosomal protein S1 of Escherichia coli. MOLECULAR & GENERAL GENETICS : MGG 1993; 240:23-8. [PMID: 8341261 DOI: 10.1007/bf00276879] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In order to select mutants that would help to characterize the post-transcriptional regulation of rpsA, we constructed a strain in which the growth rate on lactose minimal medium is determined by the amount of an rpsA-lacZ' alpha-fragment fusion protein produced, even when this is encoded by a high-copy-number plasmid. In the parental strain, synthesis of the fusion protein is repressed by a wild-type rpsA gene, present on a compatible plasmid. Twenty-eight spontaneous and independent mutants, all of them mapping in the rpsA leader region, were isolated as strains that showed higher growth rates, on lactose medium, due to increased synthesis of the rpsA-lacZ' fusion protein. Among these mutants only three sequence changes were found, mapping 9, 10 and 27 bases upstream of the rpsA start codon. At both the -9 and -10 positions an A to G transition and at -27 a C to G transversion all resulted in a sequence with better complementarity to the 3' end of 16S rRNA. We also isolated two mutations mapping in the plasmid-encoded rpsA structural gene: an ochre nonsense mutation in codon 15 of the rpsA gene and a frameshift mutation, deleting the T residue at position +1186. To facilitate the in vitro assay of alpha-fragment activity we also constructed a strain that overproduces the alpha-acceptor fragment four-fold relative to a strain that is diploid for this lacZ delta M15 allele.
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Affiliation(s)
- M D Rasmussen
- Institute of Microbiology, University of Copenhagen, Denmark
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17
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Liao D, Dennis P. The organization and expression of essential transcription translation component genes in the extremely thermophilic eubacterium Thermotoga maritima. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)50016-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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18
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Identification of the sequences responsible for the splicing phenotype of the regulatory intron of the L1 ribosomal protein gene of Xenopus laevis. Mol Cell Biol 1992. [PMID: 1545793 DOI: 10.1128/mcb.12.3.1117] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Splicing of the regulated third intron of the L1 ribosomal protein gene of Xenopus laevis has been studied in vivo by oocyte microinjection of wild-type and mutant SP6 precursor RNAs and in vitro in the heterologous HeLa nuclear extract. We show that two different phenomena combine to produce the peculiar splicing phenotype of this intron. One, which can be defined constitutive, shows the same features in the two systems and leads to the accumulation of spliced mRNA, but in very small amounts. The low efficiency of splicing is due to the presence of a noncanonical 5' splice site which acts in conjunction with sequences present in the 3' portion of the intron. The second leads to the massive conversion of the pre-mRNA into site specific truncated molecules. This has the effect of decreasing the concentration of the pre-mRNA available for splicing. We show that this aberrant cleavage activity occurs only in the in vivo oocyte system and depends on the presence of an intact U1 RNA.
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19
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Fragapane P, Caffarelli E, Lener M, Prislei S, Santoro B, Bozzoni I. Identification of the sequences responsible for the splicing phenotype of the regulatory intron of the L1 ribosomal protein gene of Xenopus laevis. Mol Cell Biol 1992; 12:1117-25. [PMID: 1545793 PMCID: PMC369543 DOI: 10.1128/mcb.12.3.1117-1125.1992] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Splicing of the regulated third intron of the L1 ribosomal protein gene of Xenopus laevis has been studied in vivo by oocyte microinjection of wild-type and mutant SP6 precursor RNAs and in vitro in the heterologous HeLa nuclear extract. We show that two different phenomena combine to produce the peculiar splicing phenotype of this intron. One, which can be defined constitutive, shows the same features in the two systems and leads to the accumulation of spliced mRNA, but in very small amounts. The low efficiency of splicing is due to the presence of a noncanonical 5' splice site which acts in conjunction with sequences present in the 3' portion of the intron. The second leads to the massive conversion of the pre-mRNA into site specific truncated molecules. This has the effect of decreasing the concentration of the pre-mRNA available for splicing. We show that this aberrant cleavage activity occurs only in the in vivo oocyte system and depends on the presence of an intact U1 RNA.
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Affiliation(s)
- P Fragapane
- Centro Acidi Nucleici, Consiglio Nazionale delle Ricerche, Rome, Italy
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20
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Egebjerg J, Christiansen J, Garrett RA. Attachment sites of primary binding proteins L1, L2 and L23 on 23 S ribosomal RNA of Escherichia coli. J Mol Biol 1991; 222:251-64. [PMID: 1960726 DOI: 10.1016/0022-2836(91)90210-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The attachment sites of the primary binding proteins L1, L2 and L23 on 23 S ribosomal RNA of Escherichia coli were examined by a chemical and ribonuclease footprinting method using several probes with different specificities. The results show that the sites are confined to localized RNA regions within the large ribonuclease-protected ribonucleoprotein fragments that were characterized earlier. They are as follows: (1) L1 recognizes a tertiary structural motif in domain V centred on two interacting internal loops; the main protein interaction sites occur at the internal loop/helix junctions. (2) The L2 site constitutes a single irregular stem/loop structure in the centre of domain IV where non-Watson-Crick pairing is likely to occur. (3) L23 recognizes a tertiary structural motif involving a single terminal loop structure and part of an adjacent internal loop at the centre of domain III. Each of the three primary binding proteins, whose presence is essential for ribosomal assembly, has been associated with important ribosomal functions: L1 lies in the E-site for deacylated tRNA binding while L2 and L23 have been implicated in the P and A substrate sites, respectively, of the peptidyl transferase centre. Moreover, each of the protein sites, but particularly those of L2 and L23, lies at the centre of RNA domains where they can maximally influence both the assembly of secondary binding proteins and the function of the RNA region.
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Affiliation(s)
- J Egebjerg
- Biostrukturkemi, Aarhus Universitet, Denmark
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21
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Zengel JM, Lindahl L. Ribosomal protein L4 of Escherichia coli: in vitro analysis of L4-mediated attenuation control. Biochimie 1991; 73:719-27. [PMID: 1764518 DOI: 10.1016/0300-9084(91)90052-3] [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: 12/28/2022]
Abstract
Ribosomal protein L4 of Escherichia coli functions not only as a component of the ribosome but also as a regulatory factor inhibiting both transcription and translation of its own operon, the 11 gene S10 operon. L4-mediated transcription control results in premature termination of transcription within the 172 base S10 operon leader. This attenuation control can be reproduced in a purified transcription system containing RNA polymerase, but depends on the addition of transcription factor NusA. The NusA stimulation saturates at about 2-4 copies per RNA polymerase. The L4 effect plateaus at about 4 copies per RNA polymerase. The specific recognition sites on 23S rRNA and in the S10 leader for L4 binding are not yet known. However, we can demonstrate that a fragment of 23S rRNA containing the proximal 840 bases can eliminate in vitro L4-stimulated attenuation, and hence, contains the information sufficient for L4 binding to 23S rRNA.
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Affiliation(s)
- J M Zengel
- Department of Biology, University of Rochester, NY 14627
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22
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Craigen WJ, Lee CC, Caskey CT. Recent advances in peptide chain termination. Mol Microbiol 1990; 4:861-5. [PMID: 2215213 PMCID: PMC7168415 DOI: 10.1111/j.1365-2958.1990.tb00658.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/1989] [Revised: 02/05/1990] [Indexed: 12/30/2022]
Abstract
Peptide chain termination occurs when a stop codon is decoded by a release factor. In Escherichia coli two codon-specific release factors (RF1 and RF2) direct the termination of protein synthesis, while in eukaryotes a single factor is required. The E. coli factors have been purified and their genes isolated. A combination of protein and DNA sequence data reveal that the RFs are structurally similar and that RF2 is encoded in two reading frames. Frame-shifting from one reading frame to the next occurs at a rate of 50%, is regulated by the RF2-specific stop codon UGA, and involves the direct interaction of the RF2 mRNA with the 3' end of the 16S rRNA. The RF genes are located in two separate operons, with the RF1 gene located at 26.7 min and the RF2 gene at 62.3 min on the chromosome map. Ribosomal binding studies place the RF-binding region at the interface between the ribosomal subunits. A possible mechanism of stop-codon recognition is reviewed.
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Affiliation(s)
- W J Craigen
- Institute for Molecular Genetics, Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030
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23
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Baier G, Piendl W, Redl B, Stöffler G. Structure, organization and evolution of the L1 equivalent ribosomal protein gene of the archaebacterium Methanococcus vannielii. Nucleic Acids Res 1990; 18:719-24. [PMID: 2107529 PMCID: PMC330318 DOI: 10.1093/nar/18.4.719] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The gene for ribosomal protein MvaL1 from the arachaebacterium Methanococcus vannielii was cloned and characterized. It is clustered together with the genes for MvaL10 and MvaL12, thus is organized in the same order as in E.coli and other archaebacteria. Unexpectedly, analysis of the sequence in front of the MvaL1 gene revealed an ORF of unknown identity, whereas in E.coli, Halobacterium and Sulfolobus solfataricus the gene for the L11 equivalent protein is located in this position. Northern blot analysis revealed a single tricistronic transcript encoding proteins MvaL1, MvaL10 and MvaL12. The 5'-end of the MvaL1-L10-L12 transcript contains a region that has a sequence and structure almost identical to a region on the 23S rRNA which is the putative binding domain for MvaL1, and is highly similar to the E.coli L11-L1 mRNA leader sequence that has been implicated in autogenous translational regulation. Amino acid sequence comparison revealed that MvaL1 shares 30.5% identity with ribosomal protein L1 from E.coli and 41.5% and 33.3% identity with the L1-equivalent proteins from the archaebacteria H.cutirubrum and S.solfataricus respectively.
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Affiliation(s)
- G Baier
- Institut für Mikrobiologie, Medizinischen Fakultät, Universität Innsbruck, Austria
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24
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Portier C, Dondon L, Grunberg-Manago M. Translational autocontrol of the Escherichia coli ribosomal protein S15. J Mol Biol 1990; 211:407-14. [PMID: 2407854 DOI: 10.1016/0022-2836(90)90361-o] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
When rpsO, the gene encoding the ribosomal protein S15 in Escherichia coli, is carried by a multicopy plasmid, the mRNA synthesis rate of S15 increases with the gene dosage but the rate of synthesis of S15 does not rise. A translational fusion between S15 and beta-galactosidase was introduced on the chromosome in a delta lac strain and the expression of beta-galactosidase studied under different conditions. The presence of S15 in trans represses the beta-galactosidase level five- to sixfold, while the synthesis rate of the S15-beta-galactosidase mRNA decreases by only 30 to 50%. These data indicate that S15 is subject to autogenous translational control. Derepressed mutants were isolated and sequenced. All the point mutations map in the second codon of S15, suggesting a location for the operator site that is very near to the translation initiation codon. However, the creation of deletion mutations shows that the operator extends into the 5' non-coding part of the message, thus overlapping the ribosome loading site.
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Affiliation(s)
- C Portier
- Institut de Biologie Physico-Chimique, Paris, France
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25
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Fragapane P, Caffarelli E, Santoro B, Sperandio S, Lener M, Bozzoni I. Splicing control of the L1 ribosomal protein gene of X.laevis: structural similarities between sequences present in the regulatory intron and in the 28S ribosomal RNA. Mol Biol Rep 1990; 14:111-2. [PMID: 2362566 DOI: 10.1007/bf00360436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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26
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Draper DE. How do proteins recognize specific RNA sites? New clues from autogenously regulated ribosomal proteins. Trends Biochem Sci 1989; 14:335-8. [PMID: 2678632 DOI: 10.1016/0968-0004(89)90167-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Some ribosomal proteins which bind specifically to ribosomal RNA also act as translational repressors and recognize their encoding messenger RNAs. The messenger- and ribosomal-RNA binding sites for four of these proteins are now well defined, and striking similarities in primary and secondary structure are apparent in most cases. These 'consensus' structures are useful clues to the features proteins use to recognize specific RNAs.
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27
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Margalit H, Shapiro BA, Oppenheim AB, Maizel JV. Detection of common motifs in RNA secondary structures. Nucleic Acids Res 1989; 17:4829-45. [PMID: 2473442 PMCID: PMC318035 DOI: 10.1093/nar/17.12.4829] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We describe a novel computerized system for comparison of RNA secondary structures and demonstrate its use for experimental studies. The system is able to screen a very large number of structures, to cluster similar structures and to detect specific structural motifs. In particular, the system is useful for detecting mutations with specific structural effects among all possible point mutations, and for predicting compensatory mutations that will restore the wild type structure. The algorithms are independent of the folding rules that are used to generate the secondary structures.
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Affiliation(s)
- H Margalit
- Laboratory of Mathematical Biology, National Cancer Institute, Bethesda, MD 20892
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28
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Vasserot AP, Schaufele FJ, Birnstiel ML. Conserved terminal hairpin sequences of histone mRNA precursors are not involved in duplex formation with the U7 RNA but act as a target site for a distinct processing factor. Proc Natl Acad Sci U S A 1989; 86:4345-9. [PMID: 2734288 PMCID: PMC287265 DOI: 10.1073/pnas.86.12.4345] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The hairpin loop structure and the downstream spacer element of histone mRNA precursors are both needed for efficient 3' end formation in vivo and in vitro. Though generally considered as a single processing signal, these two motifs are involved in different types of interaction with the processing machinery. Whereas RNA duplex formation between the downstream spacer element and the U7 small nuclear RNA is essential for processing, we show here that base pairing between the histone stem-loop structure and the U7 RNA is not relevant. Our experiments demonstrate that a processing factor other than the U7 RNA makes contact with the highly conserved hairpin structure of the histone precursor. The recognition of the target site by the processing factor is structure and sequence specific. Prevention of this interaction results in an 80% decrease of 3' cleavage efficiency in vitro. The hairpin binding factor is Sm-precipitable and can be partially separated from the U7 small nuclear ribonucleoprotein particle on a Mono Q column.
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Affiliation(s)
- A P Vasserot
- Research Institute of Molecular Pathology, Vienna, Austria
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29
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Said B, Cole JR, Nomura M. Mutational analysis of the L1 binding site of 23S rRNA in Escherichia coli. Nucleic Acids Res 1988; 16:10529-45. [PMID: 3060846 PMCID: PMC338922 DOI: 10.1093/nar/16.22.10529] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The L11 ribosomal protein operon of Escherichia coli contains the genes for L11 and L1 and is feedback regulated by the translational repressor L1. Both the L1 binding site on 23S rRNA and the L1 repressor target site on L11 operon mRNA share similar proposed secondary structures and contain some primary sequence identity. Several site-directed mutations in the binding region of 23S rRNA were constructed and their effects on binding were examined. For in vitro analysis, a filter binding method was used. For in vivo analysis, a conditional expression system was used to overproduce a 23S rRNA fragment containing the L1 binding region, which leads to specific derepression of the synthesis of L11 and L1. Changes in the shared region of the 23S rRNA L1 binding site produced effects on L1 binding similar to those found previously in analysis of corresponding changes in the L11 operon mRNA target site. The results support the hypothesis that r-protein L1 interacts with both 23S rRNA and L11 operon mRNA by recognizing similar features on both RNAs.
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Affiliation(s)
- B Said
- Department of Biological Chemistry, University of California, Irvine 92717
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30
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Gregory RJ, Cahill PB, Thurlow DL, Zimmermann RA. Interaction of Escherichia coli ribosomal protein S8 with its binding sites in ribosomal RNA and messenger RNA. J Mol Biol 1988; 204:295-307. [PMID: 2464691 DOI: 10.1016/0022-2836(88)90577-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The ability of ribosomal protein S8 from Escherichia coli to interact with 12 variants of its 16 S rRNA binding site, as well as with a regulatory sequence within spc operon mRNA, has been assessed. Single-site alterations were introduced into the appropriate segment of the E. coli 16 S rRNA gene by mutagenesis in vitro. Their effects on S8-rRNA interaction were measured via a filter-binding assay, utilizing S8 binding sites transcribed in vitro from the altered 16 S rRNA gene fragments. Of the 12 rRNA mutants, six were unable to bind S8. Significantly, five of these occur within a small, phylogenetically conserved internal loop, defined by nucleotides 596-597 and 641-643, suggesting that this structure plays a major role in S8-16 S rRNA recognition. The reduced affinity of S8 for its binding site in these cases was closely correlated with growth defects that resulted from expression of the same mutations in vivo. Alterations at other positions in the S8 binding site had little influence on complex formation or cell growth, as long as they did not disrupt rRNA secondary structure. The specific interaction of S8 with a segment of the spc operon mRNA containing a putative site of translational feedback regulation was demonstrated using appropriate in vitro transcripts in conjunction with the filter-binding assay. The apparent association constant for the S8-mRNA interaction was determined to be approximately 5 x 10(6) M-1, about five times lower than for the interaction of S8 with wild-type 16 S rRNA. The structure of the regulatory binding site, determined by sequence analysis of spc operon mRNA protected by S8 from RNase digestion, was found to contain all of the characteristic features of the 16 S rRNA binding site, demonstrating that the protein associates with structurally similar domains in both RNAs.
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Affiliation(s)
- R J Gregory
- Department of Biochemistry, University of Massachusetts, Amherst 01003
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31
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Cerretti DP, Mattheakis LC, Kearney KR, Vu L, Nomura M. Translational regulation of the spc operon in Escherichia coli. Identification and structural analysis of the target site for S8 repressor protein. J Mol Biol 1988; 204:309-29. [PMID: 2464692 DOI: 10.1016/0022-2836(88)90578-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The spc ribosomal protein operon of Escherichia coli is feedback-regulated by ribosomal protein S8, a translational repressor. We have analyzed the region of the spc mRNA that is responsible for this regulation. First, we have established that the S8 target site on the mRNA is near the translation start site of the third gene encoding ribosomal protein L5 in the operon. This was done by constructing hybrid plasmids carrying spc operon ribosomal protein genes under lac transcriptional control, as well as their deletion derivatives, and carrying out both in vivo and in vitro protein synthesis experiments. Next, the secondary structure of this region was studied by analyzing 5' end-labeled RNA synthesized from the phage SP6 promoter using structure-specific nucleases. A secondary structure model consistent with the results was deduced with the aid of a computer prediction of RNA folding. In addition, we cloned and sequenced the corresponding region from Salmonella typhimurium, Proteus vulgaris and Serratia marcescens and found five "compensating" substitutions that support some of the deduced helical structures of mRNA. None of the base changes was inconsistent with the deduced secondary structure model. Finally, site-directed mutagenesis experiments have identified bases important for regulation, including two base-paired sites representing each of two helical regions. This has led to the conclusion that some specific nucleotide residues located between these two helical regions are directly involved in S8 recognition, and that the function of the two helical regions is to maintain the proper orientation of these nucleotide residues. Comparison of the structure of the S8 target site on the spc mRNA with the known S8 binding site on rRNA has revealed a striking similarity in both primary and secondary structures. In particular, primary sequences of rRNA conserved among distantly related bacterial species in this region is found to be identical with the sequences at the corresponding positions in mRNA. These results suggest that the same structural features of the S8 repressor protein are involved in the interaction with both 16 S rRNA and the mRNA target site.
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Affiliation(s)
- D P Cerretti
- Department of Biological Chemistry, University of California-Irvine 92717
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32
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Moine H, Romby P, Springer M, Grunberg-Manago M, Ebel JP, Ehresmann C, Ehresmann B. Messenger RNA structure and gene regulation at the translational level in Escherichia coli: the case of threonine:tRNAThr ligase. Proc Natl Acad Sci U S A 1988; 85:7892-6. [PMID: 3054873 PMCID: PMC282304 DOI: 10.1073/pnas.85.21.7892] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Previous work showed that the expression of the Escherichia coli threonine:tRNAThr ligase (EC 6.1.1.3)-encoding gene (thrS) is negatively autoregulated at the translational level and that a region called the operator that is located between 10 and 50 base pairs upstream of the translation initiation codon of the thrS gene is directly involved in that control. The conformation of an in vitro synthesized RNA fragment extending over the thrS regulatory region has been investigated using chemical and enzymatic probes. This study shows that the RNA folds into four well-defined secondary-structure domains, one of them displaying structural similarities to the anticodon arm of tRNAThr. The conformation of three constitutive mutants containing single base changes in the operator region leading to the loss of the regulatory control was also investigated. The replacement of a base in the anticodon-like loop does not induce any conformational change, suggesting that the residue concerned is directly involved in the regulatory process. However, single mutations in or close to the anticodon-like stem result in a partial or complete reorganization of the structure of the operator region. These rearrangements should affect the binding of the ligase to the operator, leading to loss of the regulatory process.
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Affiliation(s)
- H Moine
- Laboratoire de Biochimie, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, Strasbourg, France
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Turner DR, Joyce LE, Butler PJ. The tobacco mosaic virus assembly origin RNA. Functional characteristics defined by directed mutagenesis. J Mol Biol 1988; 203:531-47. [PMID: 3210225 DOI: 10.1016/0022-2836(88)90190-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The in vitro reassembly of tobacco mosaic virus (TMV) begins with the specific recognition by the viral coat protein disk aggregate of an internal TMV RNA sequence, known as the assembly origin (Oa). This RNA sequence contains a putative stem-loop structure (loop 1), believed to be the target for disk binding in assembly initiation, which has the characteristic sequence AAGAAGUCG exposed as a single strand at its apex. We show that a 75-base RNA sequence encompassing loop 1 is sufficient to direct the encapsidation by TMV coat protein disks of a heterologous RNA fragment. This RNA sequence and structure, which is sufficient to elicit TMV assembly in vitro, was explored by site-directed mutagenesis. Structure analysis of the RNA identified mutations that appear to effect assembly via a perturbation in RNA structure, rather than by a direct effect on coat protein binding. The binding of the loop 1 apex RNA sequence to coat protein disks was shown to be due primarily to its regularly repeated G residues. Sequences such as (UUG)3 and (GUG)3 are equally effective at initiating assembly, indicating that the other bases are less functionally constrained. However, substitution of the sequences (CCG)3, (CUG)3 or (UCG)3 reduced the assembly initiation rate, indicating that C residues are unfavourable for assembly. Two additional RNA sequences within the 75-base Oa sequence, both of the form (NNG)3, may play subsidiary roles in disk binding. RNA structure plays an important part in permitting selective protein-RNA recognition, since altering the RNA folding close to the apex of the loop 1 stem reduces the rate of disk binding, as does shortening the stem itself. Whereas the RNA sequence making up the hairpin does not in general affect the specificity of the protein-RNA interaction, it is required to present the apex signal sequence in a special conformation. Mechanisms for this are discussed.
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Affiliation(s)
- D R Turner
- MRC Laboratory of Molecular Biology, Cambridge, U.K
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Affiliation(s)
- M Kozak
- Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260
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35
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Parsons GD, Donly BC, Mackie GA. Mutations in the leader sequence and initiation codon of the gene for ribosomal protein S20 (rpsT) affect both translational efficiency and autoregulation. J Bacteriol 1988; 170:2485-92. [PMID: 3286608 PMCID: PMC211160 DOI: 10.1128/jb.170.6.2485-2492.1988] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We have transferred the complete structural gene and part of the leader for ribosomal protein S20 of Escherichia coli to a controllable expression vector and have used oligonucleotide-directed mutagenesis to create mutations in the untranslated leader of the plasmid-borne gene. We have assayed for posttranscriptional regulation of the synthesis of S20 after inducing transcription of the mutant S20 mRNA from the expression vector. We found that two mutations lead to loss of feedback control of S20 synthesis: (i) a change of the initiation codon from UUG to AUG and (ii) a replacement of part of the S20 leader with a nonhomologous sequence including an AUG initiation codon. These mutations also lead to increases in both the intrinsic translational efficiency of the plasmid-encoded S20 mRNA in vitro and its half-life in vivo. A double mutation (GA to CT) at residues -3 and -4 relative to the initiation codon does not result in overproduction of S20. Rather, it reduces translational efficiency in vitro and mRNA stability in vivo. Our results demonstrate the fundamental importance of the UUG initiation codon in mediating autogenous repression of S20 synthesis.
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Affiliation(s)
- G D Parsons
- Department of Biochemistry, University of Western Ontario, London, Canada
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36
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Leibold EA, Munro HN. Cytoplasmic protein binds in vitro to a highly conserved sequence in the 5' untranslated region of ferritin heavy- and light-subunit mRNAs. Proc Natl Acad Sci U S A 1988; 85:2171-5. [PMID: 3127826 PMCID: PMC279951 DOI: 10.1073/pnas.85.7.2171] [Citation(s) in RCA: 525] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The mRNAs for the heavy and light subunits of the iron-storage protein ferritin occur in cells largely as inactive ribonucleoprotein particles, which are recruited for translation when iron enters the cell. Cytoplasmic extracts from rat tissues and hepatoma cells were shown by an electrophoretic separation procedure to form RNA-protein complexes involving a highly conserved sequence in the 5' untranslated region of both ferritin heavy- and light-subunit mRNAs. The pattern of complex formation was affected by pretreatment of rats or cells with iron. Crosslinking by UV irradiation showed that the complexes contained an 87-kDa protein interacting with the conserved sequence of the ferritin mRNA. We propose that intracellular iron levels regulate ferritin synthesis by causing changes in specific protein binding to the conserved sequence in the ferritin heavy- and light-subunit mRNAs.
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Affiliation(s)
- E A Leibold
- Department of Applied Biological Sciences, Massachusetts Institute of Technology, Cambridge 02139
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37
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Affiliation(s)
- W H Mager
- Biochemical Laboratorium, Vrije Universiteit, Amsterdam, The Netherlands
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38
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Kearney KR, Nomura M. Secondary structure of the autoregulatory mRNA binding site of ribosomal protein L1. MOLECULAR & GENERAL GENETICS : MGG 1987; 210:60-8. [PMID: 2448590 DOI: 10.1007/bf00337759] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The secondary structure of the autoregulatory mRNA binding site of Escherichia coli ribosomal protein L1 has been studied using enzymatic methods. The control region of the E. coli L11 operon was cloned into a vector under control of the Salmonella phage SP6 promoter, and RNA transcribed using SP6 RNA polymerase. The secondary structure of this RNA was probed using structure-specific nucleases, and by comparison of the data with computer predictions of RNA folding, secondary structural features were deduced. The proposed model is consistent with elements of some previously proposed models, but differs in other features. Finally, secondary structure information was obtained from two mutant mRNAs and the structural features correlated with observed phenotypes of the mutants.
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Affiliation(s)
- K R Kearney
- Institute for Enzyme Research, University of Wisconsin, Madison 53705
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Sor F, Nomura M. Cloning and DNA sequence determination of the L11 ribosomal protein operon of Serratia marcescens and Proteus vulgaris: translational feedback regulation of the Escherichia coli L11 operon by heterologous L1 proteins. MOLECULAR & GENERAL GENETICS : MGG 1987; 210:52-9. [PMID: 3323840 DOI: 10.1007/bf00337758] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In Escherichia coli the genes encoding ribosomal proteins L11 (rplK) and L1 (rplA) are contained in a single operon and their expression is translationally regulated by L1. We have cloned the homologous genes from two other enterobacteria, Serratia marcescens and Proteus vulgaris, and determined nucleotide sequences. The genes are organized in a similar way to that found in E. coli. Conservation of nucleotide and amino acid sequences relative to E. coli in the protein coding regions are 89.2% and 94.7% for S. marcescens, and 80.9% and 88.6% for P. vulgaris. Nucleotide sequences of L11 mRNA leader regions were strongly conserved for the primary as well as the secondary structures in the L1 target site. We have also constructed plasmids carrying E. coli L11 and either P. vulgaris or S. marcescens L1 genes fused to the lac promoter, with or without the E. coli leader containing the L1 target site. Induction of transcription of the operons possessing the E. coli mRNA leader did not lead to overproduction of L11, indicating translational regulation of the chimeric operon as well as the chromosomal operon by the plasmid encoded L1. Repression of the chromosomal L11 operon was directly demonstrated upon induction of the chimeric operons without the leader, which also lack the L11 initiation signal but have a mutation allowing L1 translation.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- F Sor
- Department of Biological Chemistry, California College of Medicine, University of California, Irvine 92717
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