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Ranaei-Siadat E, Mérigoux C, Seijo B, Ponchon L, Saliou JM, Bernauer J, Sanglier-Cianférani S, Dardel F, Vachette P, Nonin-Lecomte S. In vivo tmRNA protection by SmpB and pre-ribosome binding conformation in solution. RNA (NEW YORK, N.Y.) 2014; 20:1607-20. [PMID: 25135523 PMCID: PMC4174442 DOI: 10.1261/rna.045674.114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/15/2014] [Indexed: 06/03/2023]
Abstract
TmRNA is an abundant RNA in bacteria with tRNA and mRNA features. It is specialized in trans-translation, a translation rescuing system. We demonstrate that its partner protein SmpB binds the tRNA-like region (TLD) in vivo and chaperones the fold of the TLD-H2 region. We use an original approach combining the observation of tmRNA degradation pathways in a heterologous system, the analysis of the tmRNA digests by MS and NMR, and co-overproduction assays of tmRNA and SmpB. We study the conformation in solution of tmRNA alone or in complex with one SmpB before ribosome binding using SAXS. Our data show that Mg(2+) drives compaction of the RNA structure and that, in the absence of Mg(2+), SmpB has a similar effect albeit to a lesser extent. Our results show that tmRNA is intrinsically structured in solution with identical topology to that observed on complexes on ribosomes which should facilitate its subsequent recruitment by the 70S ribosome, free or preloaded with one SmpB molecule.
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Affiliation(s)
- Ehsan Ranaei-Siadat
- CNRS-UMR 8015, Laboratoire de Cristallographie et RMN Biologiques, Faculté de Pharmacie, 75270 Paris Cedex 06, France Université Paris Descartes, LCRB, Faculté de Pharmacie, 75270 Paris Cedex 06, France
| | - Cécile Mérigoux
- Université Paris-Sud, IBBMC, UMR8619, 91405 Orsay, France CNRS, 91405 Orsay, France
| | - Bili Seijo
- CNRS-UMR 8015, Laboratoire de Cristallographie et RMN Biologiques, Faculté de Pharmacie, 75270 Paris Cedex 06, France Université Paris Descartes, LCRB, Faculté de Pharmacie, 75270 Paris Cedex 06, France
| | - Luc Ponchon
- CNRS-UMR 8015, Laboratoire de Cristallographie et RMN Biologiques, Faculté de Pharmacie, 75270 Paris Cedex 06, France Université Paris Descartes, LCRB, Faculté de Pharmacie, 75270 Paris Cedex 06, France
| | - Jean-Michel Saliou
- CNRS, IPHC-LSMBO, Université Louis Pasteur Bât, 67087 Strasbourg, France
| | - Julie Bernauer
- AMIB, INRIA Saclay-Île de France, 91120 Palaiseau, France LIX, CNRS UMR 7161, École Polytechnique, 91120 Palaiseau, France
| | | | - Fréderic Dardel
- CNRS-UMR 8015, Laboratoire de Cristallographie et RMN Biologiques, Faculté de Pharmacie, 75270 Paris Cedex 06, France Université Paris Descartes, LCRB, Faculté de Pharmacie, 75270 Paris Cedex 06, France
| | - Patrice Vachette
- Université Paris-Sud, IBBMC, UMR8619, 91405 Orsay, France CNRS, 91405 Orsay, France
| | - Sylvie Nonin-Lecomte
- CNRS-UMR 8015, Laboratoire de Cristallographie et RMN Biologiques, Faculté de Pharmacie, 75270 Paris Cedex 06, France Université Paris Descartes, LCRB, Faculté de Pharmacie, 75270 Paris Cedex 06, France
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Wower IK, Zwieb C, Wower J. Requirements for resuming translation in chimeric transfer-messenger RNAs of Escherichia coli and Mycobacterium tuberculosis. BMC Mol Biol 2014; 15:19. [PMID: 25220282 PMCID: PMC4236655 DOI: 10.1186/1471-2199-15-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 06/18/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trans-translation is catalyzed by ribonucleprotein complexes composed of SmpB protein and transfer-messenger RNA. They release stalled ribosomes from truncated mRNAs and tag defective proteins for proteolytic degradation. Comparative sequence analysis of bacterial tmRNAs provides considerable insights into their secondary structures in which a tRNA-like domain and an mRNA-like region are connected by a variable number of pseudoknots. Progress toward understanding the molecular mechanism of trans-translation is hampered by our limited knowledge about the structure of tmRNA:SmpB complexes. RESULTS Complexes consisting of M. tuberculosis tmRNA and E. coli SmpB tag truncated proteins poorly in E. coli. In contrast, the tagging activity of E. coli tmRNA is well supported by M. tuberculosis SmpB that is expressed in E. coli. To investigate this incompatibility, we constructed 12 chimeric tmRNA molecules composed of structural features derived from both E. coli and M. tuberculosis. Our studies demonstrate that replacing the hp5-pk2-pk3-pk4 segment of E. coli tmRNA with the equivalent segment of M. tuberculosis tmRNA has no significant effect on the tagging efficiency of chimeric tmRNAs in the presence of E. coli SmpB. Replacing either helices 2b-2d, the single-stranded part of the ORF, pk1, or residues 79-89 of E. coli tmRNA with the equivalent features of M. tuberculosis tmRNA yields chimeric tmRNAs that are tagged at 68 to 88 percent of what is observed with E. coli tmRNA. Exchanging segments composed of either pk1 and the single-stranded segment upstream of the ORF or helices 2b-2d and pk1 results in markedly impaired tagging activity. CONCLUSION Our observations demonstrate the existence of functionally important but as yet uncharacterized structural constraints in the segment of tmRNA that connects its TLD to the ORF used for resuming translation. As trans-translation is important for the survival of M. tuberculosis, our work provides a new target for pharmacological intervention against multidrug-resistant tuberculosis.
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McClain MS, Duncan SS, Gaddy JA, Cover TL. Control of gene expression in Helicobacter pylori using the Tet repressor. J Microbiol Methods 2013; 95:336-41. [PMID: 24113399 PMCID: PMC3856897 DOI: 10.1016/j.mimet.2013.09.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 09/25/2013] [Accepted: 09/30/2013] [Indexed: 01/15/2023]
Abstract
The lack of a versatile system to control gene expression in Helicobacter pylori has hampered efforts to study H. pylori physiology and pathogenesis. To overcome these limitations, we evaluated the utility of an inducible system based on the well-characterized Tet repressor (TetR) and Tet operator (tetO). As validation of this system, we introduced three copies of tetO into the promoter region upstream of the cagUT operon (encoding two virulence factors required for function of the H. pylori Cag type IV secretion system) and expressed tetR by introducing a codon-optimized gene into the chromosomal ureA locus. Introduction of the tetO copies upstream of cagUT did not disrupt promoter activity, as determined by immunoblotting for CagT. The subsequent introduction of tetR, however, did repress CagT synthesis. Production of CagT was restored when strains were cultured in the presence of the inducer, anhydrotetracycline. To demonstrate one potential application of this new tool, we analyzed the function of the Cag type IV secretion system. When the modified H. pylori strains were co-cultured with AGS cells, activity of the Cag type IV secretion system was dependent on the presence of anhydrotetracycline as evidenced by inducer-dependent induction of IL-8 secretion, CagA translocation, and appearance of type IV secretion system pili at the bacteria-host interface. These studies demonstrate the effectiveness of the tetR-tetO system to control gene expression in H. pylori and provide an improved system for studying H. pylori physiology and pathogenesis.
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Affiliation(s)
- Mark S. McClain
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Stacy S. Duncan
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Jennifer A. Gaddy
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, United States of America
| | - Timothy L. Cover
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, United States of America
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Development of a tetracycline-inducible gene expression system for the study of Helicobacter pylori pathogenesis. Appl Environ Microbiol 2013; 79:7351-9. [PMID: 24056453 DOI: 10.1128/aem.02701-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Deletion mutants and animal models have been instrumental in the study of Helicobacter pylori pathogenesis. Conditional mutants, however, would enable the study of the temporal gene requirement during H. pylori colonization and chronic infection. To achieve this goal, we adapted the Escherichia coli Tn10-derived tetracycline-inducible expression system for use in H. pylori. The ureA promoter was modified by inserting one or two tet operators to generate tetracycline-responsive promoters, named uPtetO, and these promoters were then fused to the reporter gfpmut2 and inserted into different loci. The expression of the tetracycline repressor (tetR) was placed under the control of one of three promoters and inserted into the chromosome. Conditional expression of green fluorescent protein (GFP) in strains harboring tetR and uPtetO-GFP was characterized by measuring GFP activity and by immunoblotting. The two tet-responsive uPtetO promoters differ in strength, and induction of these promoters was inducer concentration and time dependent, with maximum expression achieved after induction for 8 to 16 h. Furthermore, the chromosomal location of the uPtetO-GFP construct and the nature of the promoter driving expression of tetR influenced the strength of the uPtetO promoters upon induction. Integration of uPtetO-GFP and tetR constructs at different genomic loci was stable in vivo and did not affect colonization. Finally, we demonstrate tetracycline-dependent induction of GFP expression in vivo during chronic infection. These results open new experimental avenues for dissecting H. pylori pathogenesis using animal models and for testing the roles of specific genes in colonization of, adaptation to, and persistence in the host.
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Redko Y, Aubert S, Stachowicz A, Lenormand P, Namane A, Darfeuille F, Thibonnier M, De Reuse H. A minimal bacterial RNase J-based degradosome is associated with translating ribosomes. Nucleic Acids Res 2012; 41:288-301. [PMID: 23093592 PMCID: PMC3592473 DOI: 10.1093/nar/gks945] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Protein complexes directing messenger RNA (mRNA) degradation are present in all kingdoms of life. In Escherichia coli, mRNA degradation is performed by an RNA degradosome organized by the major ribonuclease RNase E. In bacteria lacking RNase E, the existence of a functional RNA degradosome is still an open question. Here, we report that in the bacterial pathogen Helicobacter pylori, RNA degradation is directed by a minimal RNA degradosome consisting of Hp-RNase J and the only DExD-box RNA helicase of H. pylori, RhpA. We show that the protein complex promotes faster degradation of double-stranded RNA in vitro in comparison with Hp-RNase J alone. The ATPase activity of RhpA is stimulated in the presence of Hp-RNase J, demonstrating that the catalytic capacity of both partners is enhanced upon interaction. Remarkably, both proteins are associated with translating ribosomes and not with individual 30S and 50S subunits. Moreover, Hp-RNase J is not recruited to ribosomes to perform rRNA maturation. Together, our findings imply that in H. pylori, the mRNA-degrading machinery is associated with the translation apparatus, a situation till now thought to be restricted to eukaryotes and archaea.
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Affiliation(s)
- Yulia Redko
- Département de Microbiologie, Unité Pathogenèse de Helicobacter, Institut Pasteur, 75724 Paris Cedex 15, France
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