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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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Bikmullin AG, Fatkhullin B, Stetsenko A, Gabdulkhakov A, Garaeva N, Nurullina L, Klochkova E, Golubev A, Khusainov I, Trachtmann N, Blokhin D, Guskov A, Validov S, Usachev K, Yusupov M. Yet Another Similarity between Mitochondrial and Bacterial Ribosomal Small Subunit Biogenesis Obtained by Structural Characterization of RbfA from S. aureus. Int J Mol Sci 2023; 24:ijms24032118. [PMID: 36768442 PMCID: PMC9917171 DOI: 10.3390/ijms24032118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
Ribosome biogenesis is a complex and highly accurate conservative process of ribosomal subunit maturation followed by association. Subunit maturation comprises sequential stages of ribosomal RNA and proteins' folding, modification and binding, with the involvement of numerous RNAses, helicases, GTPases, chaperones, RNA, protein-modifying enzymes, and assembly factors. One such assembly factor involved in bacterial 30S subunit maturation is ribosomal binding factor A (RbfA). In this study, we present the crystal (determined at 2.2 Å resolution) and NMR structures of RbfA as well as the 2.9 Å resolution cryo-EM reconstruction of the 30S-RbfA complex from Staphylococcus aureus (S. aureus). Additionally, we show that the manner of RbfA action on the small ribosomal subunit during its maturation is shared between bacteria and mitochondria. The obtained results clarify the function of RbfA in the 30S maturation process and its role in ribosome functioning in general. Furthermore, given that S. aureus is a serious human pathogen, this study provides an additional prospect to develop antimicrobials targeting bacterial pathogens.
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Affiliation(s)
- Aydar G. Bikmullin
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420021 Kazan, Russia
| | - Bulat Fatkhullin
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, 67400 Illkirch, France
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Artem Stetsenko
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9700 AB Groningen, The Netherlands
| | - Azat Gabdulkhakov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Natalia Garaeva
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420021 Kazan, Russia
| | - Liliia Nurullina
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, 67400 Illkirch, France
| | - Evelina Klochkova
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420021 Kazan, Russia
| | - Alexander Golubev
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420021 Kazan, Russia
| | | | - Natalie Trachtmann
- Institute of Microbiology, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Dmitriy Blokhin
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, 420008 Kazan, Russia
| | - Albert Guskov
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9700 AB Groningen, The Netherlands
| | - Shamil Validov
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420021 Kazan, Russia
- Federal Research Center “Kazan Scientific Center of Russian Academy of Sciences”, 420111 Kazan, Russia
| | - Konstantin Usachev
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420021 Kazan, Russia
- Federal Research Center “Kazan Scientific Center of Russian Academy of Sciences”, 420111 Kazan, Russia
| | - Marat Yusupov
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420021 Kazan, Russia
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, 67400 Illkirch, France
- Correspondence:
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3
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Identification and characterisation of sPEPs in Cryptococcus neoformans. Fungal Genet Biol 2022; 160:103688. [PMID: 35339703 DOI: 10.1016/j.fgb.2022.103688] [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: 01/04/2022] [Revised: 03/02/2022] [Accepted: 03/21/2022] [Indexed: 11/24/2022]
Abstract
Short open reading frame (sORF)-encoded peptides (sPEPs) have been found across a wide range of genomic locations in a variety of species. To date, their identification, validation, and characterisation in the human fungal pathogen Cryptococcus neoformans has been limited due to a lack of standardised protocols. We have developed an enrichment process that enables sPEP detection within a protein sample from this polysaccharide-encapsulated yeast, and implemented proteogenomics to provide insights into the validity of predicted and hypothetical sORFs annotated in the C. neoformans genome. Novel sORFs were discovered within the 5' and 3' UTRs of known transcripts as well as in "non-coding" RNAs. One novel candidate, dubbed NPB1, that resided in an RNA annotated as "non-coding", was chosen for characterisation. Through the creation of both specific point mutations and a full deletion allele, the function of the new sPEP, Npb1, was shown to resemble that of the bacterial trans-translation protein SmpB.
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4
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Switching at the ribosome: riboswitches need rProteins as modulators to regulate translation. Nat Commun 2021; 12:4723. [PMID: 34354064 PMCID: PMC8342710 DOI: 10.1038/s41467-021-25024-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/17/2021] [Indexed: 11/29/2022] Open
Abstract
Translational riboswitches are cis-acting RNA regulators that modulate the expression of genes during translation initiation. Their mechanism is considered as an RNA-only gene-regulatory system inducing a ligand-dependent shift of the population of functional ON- and OFF-states. The interaction of riboswitches with the translation machinery remained unexplored. For the adenine-sensing riboswitch from Vibrio vulnificus we show that ligand binding alone is not sufficient for switching to a translational ON-state but the interaction of the riboswitch with the 30S ribosome is indispensable. Only the synergy of binding of adenine and of 30S ribosome, in particular protein rS1, induces complete opening of the translation initiation region. Our investigation thus unravels the intricate dynamic network involving RNA regulator, ligand inducer and ribosome protein modulator during translation initiation. Translational regulation by riboswitches is an important mechanism for the modulation of gene expression in bacteria. Here the authors show that the ligand-induced allosteric switch in the adenine-sensing riboswitch from V. vulnificus is insufficient and leads only to a partial opening of the ribosome binding site and requires interaction with 30S-bound ribosomal protein S1, which acts as an RNA chaperone.
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5
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Vallejos-Sánchez K, Lopez JM, Antiparra R, Toscano E, Saavedra H, Kirwan DE, Amzel LM, Gilman RH, Maruenda H, Sheen P, Zimic M. Mycobacterium tuberculosis ribosomal protein S1 (RpsA) and variants with truncated C-terminal end show absence of interaction with pyrazinoic acid. Sci Rep 2020; 10:8356. [PMID: 32433489 PMCID: PMC7239899 DOI: 10.1038/s41598-020-65173-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/29/2020] [Indexed: 01/31/2023] Open
Abstract
Pyrazinamide (PZA) is an antibiotic used in first- and second-line tuberculosis treatment regimens. Approximately 50% of multidrug-resistant tuberculosis and over 90% of extensively drug-resistant tuberculosis strains are also PZA resistant. Despite the key role played by PZA, its mechanisms of action are not yet fully understood. It has been postulated that pyrazinoic acid (POA), the hydrolyzed product of PZA, could inhibit trans-translation by binding to Ribosomal protein S1 (RpsA) and competing with tmRNA, the natural cofactor of RpsA. Subsequent data, however, indicate that these early findings resulted from experimental artifact. Hence, in this study we assess the capacity of POA to compete with tmRNA for RpsA. We evaluated RpsA wild type (WT), RpsA ∆A438, and RpsA ∆A438 variants with truncations towards the carboxy terminal end. Interactions were measured using Nuclear Magnetic Resonance spectroscopy (NMR), Isothermal Titration Calorimetry (ITC), Microscale Thermophoresis (MST), and Electrophoretic Mobility Shift Assay (EMSA). We found no measurable binding between POA and RpsA (WT or variants). This suggests that RpsA may not be involved in the mechanism of action of PZA in Mycobacterium tuberculosis, as previously thought. Interactions observed between tmRNA and RpsA WT, RpsA ∆A438, and each of the truncated variants of RpsA ∆A438, are reported.
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Affiliation(s)
- Katherine Vallejos-Sánchez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Juan M Lopez
- Pontificia Universidad Católica del Perú, Departamento de Ciencias, Sección Química, Centro de Espectroscopía de Resonancia Magnética Nuclear (CERMN), Lima, Perú
| | - Ricardo Antiparra
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Emily Toscano
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Harry Saavedra
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD., USA
| | - Daniela E Kirwan
- Infection and Immunity Research Institute, St George's, University of London, London, England
| | - L M Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD., USA
| | - R H Gilman
- International Health Department. Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Helena Maruenda
- Pontificia Universidad Católica del Perú, Departamento de Ciencias, Sección Química, Centro de Espectroscopía de Resonancia Magnética Nuclear (CERMN), Lima, Perú
| | - Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, Perú.
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6
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Lund PE, Chatterjee S, Daher M, Walter NG. Protein unties the pseudoknot: S1-mediated unfolding of RNA higher order structure. Nucleic Acids Res 2020; 48:2107-2125. [PMID: 31832686 PMCID: PMC7038950 DOI: 10.1093/nar/gkz1166] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/26/2019] [Accepted: 12/02/2019] [Indexed: 11/13/2022] Open
Abstract
Ribosomal protein S1 plays important roles in the translation initiation step of many Escherichia coli mRNAs, particularly those with weak Shine-Dalgarno sequences or structured 5′ UTRs, in addition to a variety of cellular processes beyond the ribosome. In all cases, the RNA-binding activity of S1 is a central feature of its function. While sequence determinants of S1 affinity and many elements of the interactions of S1 with simple secondary structures are known, mechanistic details of the protein's interactions with RNAs of more complex secondary and tertiary structure are less understood. Here, we investigate the interaction of S1 with the well-characterized H-type pseudoknot of a class-I translational preQ1 riboswitch as a highly structured RNA model whose conformation and structural dynamics can be tuned by the addition of ligands of varying binding affinity, particularly preQ1, guanine, and 2,6-diaminopurine. Combining biochemical and single molecule fluorescence approaches, we show that S1 preferentially interacts with the less folded form of the pseudoknot and promotes a dynamic, partially unfolded conformation. The ability of S1 to unfold the RNA is inversely correlated with the structural stability of the pseudoknot. These mechanistic insights delineate the scope and limitations of S1-chaperoned unfolding of structured RNAs.
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Affiliation(s)
- Paul E Lund
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Surajit Chatterjee
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - May Daher
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.,Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
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7
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Solution structure and backbone dynamics for S1 domain of ribosomal protein S1 from Mycobacterium tuberculosis. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:491-501. [PMID: 31165910 DOI: 10.1007/s00249-019-01372-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 04/01/2019] [Accepted: 05/17/2019] [Indexed: 12/17/2022]
Abstract
The pro-drug pyrazinamide is hydrolyzed to pyrazinoic acid (POA) in its use for the treatment of tuberculosis. As a molecule with bactericidal activity, POA binds to the C-terminal S1 domain of ribosomal protein S1 from Mycobacterium tuberculosis (MtRpsACTD_S1) to inhibit trans-translation. Trans-translation is a critical component of protein synthesis quality control, and is mediated by transfer-messenger RNA. Here, we have determined the solution structure of MtRpsACTD_S1(280-368), and analyzed its structural dynamics by NMR spectroscopy. The solution structure of MtRpsACTD_S1(280-368) mainly consists of five anti-parallel β strands, two α helices, and two 310 helices. Backbone dynamics reveals that the overall structure of MtRpsACTD_S1(280-368) is rigid, but segment L326-V333 undergoes large amplitude fluctuations on picosecond to nanosecond time scales. In addition, residues V321, H322, V331 and D335 with large Rex values exhibit significant chemical or conformational exchange on microsecond to millisecond time scale. Titration of the truncated MtRpsACTD_S1(280-368) with POA shows similar characteristics to titration of MtRpsACTD_S1(280-438) with POA. In addition, diverse length fragments of MtRpsACTD_S1 show various HN resonance signals, and we find that the interaction of MtRpsA(369-481) with MtRpsACTD_S1(280-368) [Kd = (4.25 ± 0.15) mM] is responsible for the structural difference between MtRpsACTD_S1(280-368) and MtRpsACTD_S1. This work may shed light on the underlying molecular mechanism of MtRpsACTD recognizing and binding POA or mRNA, as well as the detailed mechanism of interactions between MtRpsACTD_S1(280-368) and the additional C-terminal MtRpsA(369-481).
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Tuyiringire N, Tusubira D, Munyampundu JP, Tolo CU, Muvunyi CM, Ogwang PE. Application of metabolomics to drug discovery and understanding the mechanisms of action of medicinal plants with anti-tuberculosis activity. Clin Transl Med 2018; 7:29. [PMID: 30270413 PMCID: PMC6165828 DOI: 10.1186/s40169-018-0208-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/29/2018] [Indexed: 11/10/2022] Open
Abstract
Human tuberculosis (TB) is amongst the oldest and deadliest human bacterial diseases that pose major health, social and economic burden at a global level. Current regimens for TB treatment are lengthy, expensive and ineffective to emerging drug resistant strains. Thus, there is an urgent need for identification and development of novel TB drugs and drug regimens with comprehensive and specific mechanisms of action. Many medicinal plants are traditionally used for TB treatment. While some of their phytochemical composition has been elucidated, their mechanisms of action are not well understood. Insufficient knowledge on Mycobacterium tuberculosis (M.tb) biology and the complex nature of its infection limit the effectiveness of current screening-based methods used for TB drug discovery. Nonetheless, application of metabolomics tools within the 'omics' approaches, could provide an alternative method of elucidating the mechanism of action of medicinal plants. Metabolomics aims at high throughput detection, quantification and identification of metabolites in biological samples. Changes in the concentration of specific metabolites in a biological sample indicate changes in the metabolic pathways. In this paper review and discuss novel methods that involve application of metabolomics to drug discovery and the understanding of mechanisms of action of medicinal plants with anti-TB activity. Current knowledge on TB infection, anti-TB drugs and mechanisms of action are also included. We further highlight metabolism of M. tuberculosis and the potential drug targets, as well as current approaches in the development of anti-TB drugs.
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Affiliation(s)
- Naasson Tuyiringire
- Pharm-BioTechnology and Traditional Medicine Centre (PHARMBIOTRAC), Mbarara University of Science & Technology, P.O. Box, 1410 Mbarara, Uganda
- College of Medicine and Health Sciences, University of Rwanda, University Avenue, P.O. Box 56, Butare, Rwanda
| | - Deusdedit Tusubira
- Pharm-BioTechnology and Traditional Medicine Centre (PHARMBIOTRAC), Mbarara University of Science & Technology, P.O. Box, 1410 Mbarara, Uganda
- Department of Biomedicine, University of Bergen, Jonas Lies Vei 91, 5020 Bergen, Norway
| | - Jean-Pierre Munyampundu
- School of Science, College of Science and Technology, University of Rwanda, Avenue de l’Armée, P.O. Box 3900, Kigali, Rwanda
| | - Casim Umba Tolo
- Pharm-BioTechnology and Traditional Medicine Centre (PHARMBIOTRAC), Mbarara University of Science & Technology, P.O. Box, 1410 Mbarara, Uganda
| | - Claude M. Muvunyi
- College of Medicine and Health Sciences, University of Rwanda, University Avenue, P.O. Box 56, Butare, Rwanda
| | - Patrick Engeu Ogwang
- Pharm-BioTechnology and Traditional Medicine Centre (PHARMBIOTRAC), Mbarara University of Science & Technology, P.O. Box, 1410 Mbarara, Uganda
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Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1. Nat Microbiol 2018; 3:1115-1121. [PMID: 30177741 DOI: 10.1038/s41564-018-0237-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/01/2018] [Indexed: 01/22/2023]
Abstract
To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles1. In γ-proteobacteria, such as Escherichia coli, 100S formation requires the ribosome modulation factor (RMF) and the hibernation promoting factor (HPF)2-4. Here we present single-particle cryo-electron microscopy structures of hibernating 70S and 100S particles isolated from stationary-phase E. coli cells at 3.0 Å and 7.9 Å resolution, respectively. The structures reveal the binding sites for HPF and RMF as well as the unexpected presence of deacylated E-site transfer RNA and ribosomal protein bS1. HPF interacts with the anticodon-stem-loop of the E-tRNA and occludes the binding site for the messenger RNA as well as A- and P-site tRNAs. RMF facilitates stabilization of a compact conformation of bS1, which together sequester the anti-Shine-Dalgarno sequence of the 16S ribosomal RNA (rRNA), thereby inhibiting translation initiation. At the dimerization interface, the C-terminus of uS2 probes the mRNA entrance channel of the symmetry-related particle, thus suggesting that dimerization inactivates ribosomes by blocking the binding of mRNA within the channel. The back-to-back E. coli 100S arrangement is distinct from 100S particles observed previously in Gram-positive bacteria5-8, and reveals a unique role for bS1 in translation regulation.
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An A/U-Rich Enhancer Region Is Required for High-Level Protein Secretion through the HlyA Type I Secretion System. Appl Environ Microbiol 2017; 84:AEM.01163-17. [PMID: 29030442 DOI: 10.1128/aem.01163-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 10/06/2017] [Indexed: 11/20/2022] Open
Abstract
Efficient protein secretion is often a valuable alternative to classic cellular expression to obtain homogenous protein samples. Early on, bacterial type I secretion systems (T1SS) were employed to allow heterologous secretion of fusion proteins. However, this approach was not fully exploited, as many proteins could not be secreted at all or only at low levels. Here, we present an engineered microbial secretion system which allows the effective production of proteins up to a molecular mass of 88 kDa. This system is based on the hemolysin A (HlyA) T1SS of the Gram-negative bacterium Escherichia coli, which exports polypeptides when fused to a hemolysin secretion signal. We identified an A/U-rich enhancer region upstream of hlyA required for effective expression and secretion of selected heterologous proteins irrespective of their prokaryotic, viral, or eukaryotic origin. We further demonstrate that the ribosomal protein S1 binds to the hlyA A/U-rich enhancer region and that this region is involved in the high yields of secretion of functional proteins, like maltose-binding protein or human interferon alpha-2.IMPORTANCE A 5' untranslated region of the mRNA of substrates of type I secretion systems (T1SS) drastically enhanced the secretion efficiency of the endogenously secreted protein. The identification of ribosomal protein S1 as the interaction partner of this 5' untranslated region provides a rationale for the enhancement. This strategy furthermore can be transferred to fusion proteins allowing a broader, and eventually a more general, application of this system for secreting heterologous fusion proteins.
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11
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Loveland AB, Korostelev AA. Structural dynamics of protein S1 on the 70S ribosome visualized by ensemble cryo-EM. Methods 2017; 137:55-66. [PMID: 29247757 DOI: 10.1016/j.ymeth.2017.12.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/06/2017] [Indexed: 10/18/2022] Open
Abstract
Bacterial ribosomal protein S1 is the largest and highly flexible protein of the 30S subunit, and one of a few core ribosomal proteins for which a complete structure is lacking. S1 is thought to participate in transcription and translation. Best understood is the role of S1 in facilitating translation of mRNAs with structured 5' UTRs. Here, we present cryo-EM analyses of the 70S ribosome that reveal multiple conformations of S1. Based on comparison of several 3D maximum likelihood classification approaches in Frealign, we propose a streamlined strategy for visualizing a highly dynamic component of a large macromolecular assembly that itself exhibits high compositional and conformational heterogeneity. The resulting maps show how S1 docks at the ribosomal protein S2 near the mRNA exit channel. The globular OB-fold domains sample a wide area around the mRNA exit channel and interact with mobile tails of proteins S6 and S18. S1 also interacts with the mRNA entrance channel, where an OB-fold domain can be localized near S3 and S5. Our analyses suggest that S1 cooperates with other ribosomal proteins to form a dynamic mesh near the mRNA exit and entrance channels to modulate the binding, folding and movement of mRNA.
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Affiliation(s)
- Anna B Loveland
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation St., Worcester, MA 01605, USA
| | - Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation St., Worcester, MA 01605, USA.
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12
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Sheen P, Requena D, Gushiken E, Gilman RH, Antiparra R, Lucero B, Lizárraga P, Cieza B, Roncal E, Grandjean L, Pain A, McNerney R, Clark TG, Moore D, Zimic M. A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance. BMC Genomics 2017; 18:769. [PMID: 29020922 PMCID: PMC5637355 DOI: 10.1186/s12864-017-4146-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 10/02/2017] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) is a major global health problem and drug resistance compromises the efforts to control this disease. Pyrazinamide (PZA) is an important drug used in both first and second line treatment regimes. However, its complete mechanism of action and resistance remains unclear. RESULTS We genotyped and sequenced the complete genomes of 68 M. tuberculosis strains isolated from unrelated TB patients in Peru. No clustering pattern of the strains was verified based on spoligotyping. We analyzed the association between PZA resistance with non-synonymous mutations and specific genes. We found mutations in pncA and novel genes significantly associated with PZA resistance in strains without pncA mutations. These included genes related to transportation of metal ions, pH regulation and immune system evasion. CONCLUSIONS These results suggest potential alternate mechanisms of PZA resistance that have not been found in other populations, supporting that the antibacterial activity of PZA may hit multiple targets.
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Affiliation(s)
- Patricia Sheen
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - David Requena
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Eduardo Gushiken
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Robert H. Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe St., Room 5515, Baltimore, MD 21205 USA
| | - Ricardo Antiparra
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Bryan Lucero
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Pilar Lizárraga
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Basilio Cieza
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Elisa Roncal
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Louis Grandjean
- Department of Infection, Immunology and Rheumatology, Institute of Child Health, University College London, 30 Guilford St, London, WC1N 1EH UK
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science & Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
| | - David Moore
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
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Fan Y, Dai Y, Hou M, Wang H, Yao H, Guo C, Lin D, Liao X. Structural basis for ribosome protein S1 interaction with RNA in trans-translation of Mycobacterium tuberculosis. Biochem Biophys Res Commun 2017; 487:268-273. [PMID: 28412369 DOI: 10.1016/j.bbrc.2017.04.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 04/11/2017] [Indexed: 11/24/2022]
Abstract
Ribosomal protein S1 (RpsA), the largest 30S protein in ribosome, plays a significant role in translation and trans-translation. In Mycobacterium tuberculosis, the C-terminus of RpsA is known as tuberculosis drug target of pyrazinoic acid, which inhibits the interaction between MtRpsA and tmRNA in trans-translation. However, the molecular mechanism underlying the interaction of MtRpsA with tmRNA remains unknown. We herein analyzed the interaction of the C-terminal domain of MtRpsA with three RNA fragments poly(A), sMLD and pre-sMLD. NMR titration analysis revealed that the RNA binding sites on MtRpsACTD are mainly located in the β2, β3 and β5 strands and the adjacent L3 loop of the S1 domain. Fluorescence experiments determined the MtRpsACTD binding to RNAs are in the micromolar affinity range. Sequence analysis also revealed conserved residues in the mapped RNA binding region. Residues L304, V305, G308, F310, H322, I323, R357 and I358 were verified to be the key residues influencing the interaction between MtRpsACTD and pre-sMLD. Molecular docking further confirmed that the poly(A)-like sequence and sMLD of tmRNA are all involved in the protein-RNA interaction, through charged interaction and hydrogen bonds. The results will be beneficial for designing new anti-tuberculosis drugs.
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Affiliation(s)
- Yi Fan
- Key Laboratory of Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yazhuang Dai
- School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Meijing Hou
- Key Laboratory of Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Huilin Wang
- Key Laboratory of Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Hongwei Yao
- Key Laboratory of Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chenyun Guo
- Key Laboratory of Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Donghai Lin
- Key Laboratory of Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Xinli Liao
- Key Laboratory of Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
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14
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Huang B, Fu J, Guo C, Wu X, Lin D, Liao X. (1)H, (15)N, (13)C resonance assignments for pyrazinoic acid binding domain of ribosomal protein S1 from Mycobacterium tuberculosis. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:321-324. [PMID: 27412769 DOI: 10.1007/s12104-016-9692-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
Ribosomal protein S1 of Mycobacterium tuberculosis (MtRpsA) binds to ribosome and mRNA, and plays significant role in the regulation of translation initiation, conventional protein synthesis and transfer-messenger RNA (tmRNA) mediated trans-translation. It has been identified as the target of pyrazinoic acid (POA), a bactericidal moiety from hydrolysis of pyrazinamide, which is a mainstay of combination therapy for tuberculosis. POA prevented the interactions between the C-terminal S1 domain of MtRpsA (residues 280-368, MtRpsA(CTD)_S1) and tmRNA; so that POA can inhibit the trans-translation, which is a key component of multiple quality control pathways in bacteria. However, the details of molecular mechanism and dynamic characteristics for MtRpsA(CTD)_S1 interactions with POA, tmRNA or mRNA are still unclear. Here we present the (1)H, (15)N, (13)C resonance assignments of MtRpsA(CTD)_S1 as well as the secondary structure information based on backbone chemical shifts, which lay foundation for further solution structure determination, dynamic properties characterization and interactions investigation between MtRpsA(CTD)_S1 and tmRNA, RNA or POA.
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Affiliation(s)
- Biling Huang
- Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Jinglin Fu
- Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Chenyun Guo
- Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Xueji Wu
- Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Donghai Lin
- Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Xinli Liao
- Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
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15
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Nguyen L. Antibiotic resistance mechanisms in M. tuberculosis: an update. Arch Toxicol 2016; 90:1585-604. [PMID: 27161440 DOI: 10.1007/s00204-016-1727-6] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 04/27/2016] [Indexed: 12/16/2022]
Abstract
Treatment of tuberculosis (TB) has been a therapeutic challenge because of not only the naturally high resistance level of Mycobacterium tuberculosis to antibiotics but also the newly acquired mutations that confer further resistance. Currently standardized regimens require patients to daily ingest up to four drugs under direct observation of a healthcare worker for a period of 6-9 months. Although they are quite effective in treating drug susceptible TB, these lengthy treatments often lead to patient non-adherence, which catalyzes for the emergence of M. tuberculosis strains that are increasingly resistant to the few available anti-TB drugs. The rapid evolution of M. tuberculosis, from mono-drug-resistant to multiple drug-resistant, extensively drug-resistant and most recently totally drug-resistant strains, is threatening to make TB once again an untreatable disease if new therapeutic options do not soon become available. Here, I discuss the molecular mechanisms by which M. tuberculosis confers its profound resistance to antibiotics. This knowledge may help in developing novel strategies for weakening drug resistance, thus enhancing the potency of available antibiotics against both drug susceptible and resistant M. tuberculosis strains.
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Affiliation(s)
- Liem Nguyen
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
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16
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17
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Nguta JM, Appiah-Opong R, Nyarko AK, Yeboah-Manu D, Addo PGA. Current perspectives in drug discovery against tuberculosis from natural products. Int J Mycobacteriol 2015; 4:165-83. [PMID: 27649863 DOI: 10.1016/j.ijmyco.2015.05.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/03/2015] [Accepted: 05/06/2015] [Indexed: 10/23/2022] Open
Abstract
Currently, one third of the world's population is latently infected with Mycobacterium tuberculosis (MTB), while 8.9-9.9 million new and relapse cases of tuberculosis (TB) are reported yearly. The renewed research interests in natural products in the hope of discovering new and novel antitubercular leads have been driven partly by the increased incidence of multidrug-resistant strains of MTB and the adverse effects associated with the first- and second-line antitubercular drugs. Natural products have been, and will continue to be a rich source of new drugs against many diseases. The depth and breadth of therapeutic agents that have their origins in the secondary metabolites produced by living organisms cannot be compared with any other source of therapeutic agents. Discovery of new chemical molecules against active and latent TB from natural products requires an interdisciplinary approach, which is a major challenge facing scientists in this field. In order to overcome this challenge, cutting edge techniques in mycobacteriology and innovative natural product chemistry tools need to be developed and used in tandem. The present review provides a cross-linkage to the most recent literature in both fields and their potential to impact the early phase of drug discovery against TB if seamlessly combined.
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Affiliation(s)
- Joseph Mwanzia Nguta
- Department of Clinical Pathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Ghana; Department of Public Health, Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Nairobi, Kenya
| | - Regina Appiah-Opong
- Department of Clinical Pathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Ghana
| | - Alexander K Nyarko
- Department of Clinical Pathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Ghana
| | - Dorothy Yeboah-Manu
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Ghana
| | - Phyllis G A Addo
- Department of Animal Experimentation, Noguchi Memorial Institute for Medical Research, University of Ghana, Ghana
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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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19
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Trends in discovery of new drugs for tuberculosis therapy. J Antibiot (Tokyo) 2014; 67:655-9. [PMID: 25095807 DOI: 10.1038/ja.2014.109] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 07/18/2014] [Accepted: 07/18/2014] [Indexed: 11/09/2022]
Abstract
After the introduction of isoniazid and rifampicin, the second one discovered in the Lepetit Research Laboratories (Milan, Italy), under the supervision of Professor Piero Sensi, tuberculosis (TB) was considered an illness of the past. Unfortunately, this infectious disease is still a global health fear, due to the multidrug-resistant Mycobacterium tuberculosis and extensively circulating drug-resistant strains, as well as the unrecognized TB transmission, especially in regions with high HIV incidence. In the last few years, new antitubercular molecules appeared on the horizon both in preclinical and clinical stage of evaluation. In this review, we focus on a few of them and on their mechanism of action. Two new promising drug targets, DprE1 and MmpL3, are also discussed.
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20
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Himeno H, Kurita D, Muto A. Mechanism of trans-translation revealed by in vitro studies. Front Microbiol 2014; 5:65. [PMID: 24600445 PMCID: PMC3929946 DOI: 10.3389/fmicb.2014.00065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 02/04/2014] [Indexed: 11/28/2022] Open
Abstract
tmRNA is a bacterial small RNA having a structure resembling the upper half of tRNA and its 3′ end accepts alanine followed by binding to EF-Tu like tRNA. Instead of lacking a lower half of the cloverleaf structure including the anticodon, tmRNA has a short coding sequence for tag-peptide that serves as a target of cellular proteases. An elaborate coordination of two functions as tRNA and mRNA facilitates an irregular translation termed trans-translation: a single polypeptide is synthesized from two mRNA molecules. It allows resumption of translation stalled on a truncated mRNA, producing a chimeric polypeptide comprising the C-terminally truncated polypeptide derived from truncated mRNA and the C-terminal tag-peptide encoded by tmRNA. Trans-translation promotes recycling of the stalled ribosomes in the cell, and the resulting C-terminally tagged polypeptide is preferentially degraded by cellular proteases. Biochemical studies using in vitro trans-translation systems together with structural studies have unveiled the molecular mechanism of trans-translation, during which the upper and lower halves of tRNA are mimicked by the tRNA-like structure of tmRNA and a tmRNA-specific binding protein called SmpB, respectively. They mimic not only the tRNA structure but also its behavior perhaps at every step of the trans-translation process in the ribosome. Furthermore, the C-terminal tail of SmpB, which is unstructured in solution, occupies the mRNA path in the ribosome to play a crucial role in trans-translation, addressing how tmRNA·SmpB recognizes the ribosome stalled on a truncated mRNA.
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Affiliation(s)
- Hyouta Himeno
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University Hirosaki, Japan ; RNA Research Center, Hirosaki University Hirosaki, Japan
| | - Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University Hirosaki, Japan ; RNA Research Center, Hirosaki University Hirosaki, Japan
| | - Akira Muto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University Hirosaki, Japan
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21
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Ribosomal protein S1 unwinds double-stranded RNA in multiple steps. Proc Natl Acad Sci U S A 2012; 109:14458-63. [PMID: 22908248 DOI: 10.1073/pnas.1208950109] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The sequence and secondary structure of the 5'-end of mRNAs regulate translation by controlling ribosome initiation on the mRNA. Ribosomal protein S1 is crucial for ribosome initiation on many natural mRNAs, particularly for those with structured 5'-ends, or with no or weak Shine-Dalgarno sequences. Besides a critical role in translation, S1 has been implicated in several other cellular processes, such as transcription recycling, and the rescuing of stalled ribosomes by tmRNA. The mechanisms of S1 functions are still elusive but have been widely considered to be linked to the affinity of S1 for single-stranded RNA and its corresponding destabilization of mRNA secondary structures. Here, using optical tweezers techniques, we demonstrate that S1 promotes RNA unwinding by binding to the single-stranded RNA formed transiently during the thermal breathing of the RNA base pairs and that S1 dissociation results in RNA rezipping. We measured the dependence of the RNA unwinding and rezipping rates on S1 concentration, and the force applied to the ends of the RNA. We found that each S1 binds 10 nucleotides of RNA in a multistep fashion implying that S1 can facilitate ribosome initiation on structured mRNA by first binding to the single strand next to an RNA duplex structure ("stand-by site") before subsequent binding leads to RNA unwinding. Unwinding by multiple small substeps is much less rate limited by thermal breathing than unwinding in a single step. Thus, a multistep scheme greatly expedites S1 unwinding of an RNA structure compared to a single-step mode.
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22
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Multiple activities of RNA-binding proteins S1 and Hfq. Biochimie 2012; 94:1544-53. [DOI: 10.1016/j.biochi.2012.02.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 02/10/2012] [Indexed: 01/16/2023]
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Byrgazov K, Manoharadas S, Kaberdina AC, Vesper O, Moll I. Direct interaction of the N-terminal domain of ribosomal protein S1 with protein S2 in Escherichia coli. PLoS One 2012; 7:e32702. [PMID: 22412910 PMCID: PMC3296737 DOI: 10.1371/journal.pone.0032702] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 01/30/2012] [Indexed: 11/19/2022] Open
Abstract
Despite of the high resolution structure available for the E. coli ribosome, hitherto the structure and localization of the essential ribosomal protein S1 on the 30 S subunit still remains to be elucidated. It was previously reported that protein S1 binds to the ribosome via protein-protein interaction at the two N-terminal domains. Moreover, protein S2 was shown to be required for binding of protein S1 to the ribosome. Here, we present evidence that the N-terminal domain of S1 (amino acids 1-106; S1(106)) is necessary and sufficient for the interaction with protein S2 as well as for ribosome binding. We show that over production of protein S1(106) affects E. coli growth by displacing native protein S1 from its binding pocket on the ribosome. In addition, our data reveal that the coiled-coil domain of protein S2 (S2α(2)) is sufficient to allow protein S1 to bind to the ribosome. Taken together, these data uncover the crucial elements required for the S1/S2 interaction, which is pivotal for translation initiation on canonical mRNAs in gram-negative bacteria. The results are discussed in terms of a model wherein the S1/S2 interaction surface could represent a possible target to modulate the selectivity of the translational machinery and thereby alter the translational program under distinct conditions.
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Affiliation(s)
- Konstantin Byrgazov
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Center for Molecular Biology, University of Vienna, Vienna, Austria
| | - Salim Manoharadas
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Center for Molecular Biology, University of Vienna, Vienna, Austria
| | - Anna C. Kaberdina
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Center for Molecular Biology, University of Vienna, Vienna, Austria
| | - Oliver Vesper
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Center for Molecular Biology, University of Vienna, Vienna, Austria
| | - Isabella Moll
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Center for Molecular Biology, University of Vienna, Vienna, Austria
- * E-mail:
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Kalinda AS, Aldrich CC. Pyrazinamide: A Frontline Drug Used for Tuberculosis. Molecular Mechanism of Action Resolved after 50 Years? ChemMedChem 2012; 7:558-60. [DOI: 10.1002/cmdc.201100587] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Indexed: 11/10/2022]
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25
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Smith T, Wolff KA, Nguyen L. Molecular biology of drug resistance in Mycobacterium tuberculosis. Curr Top Microbiol Immunol 2012. [PMID: 23179675 DOI: 10.1007/82_2012_279] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Tuberculosis (TB) has become a curable disease, thanks to the discovery of antibiotics. However, it has remained one of the most difficult infections to treat. Most current TB regimens consist of 6-9 months of daily doses of four drugs that are highly toxic to patients. The purpose of these lengthy treatments is to completely eradicate Mycobacterium tuberculosis, notorious for its ability to resist most antibacterial agents, thereby preventing the formation of drug resistant mutants. On the contrary, the prolonged therapies have led to poor patient adherence. This, together with a severe limit of drug choices, has resulted in the emergence of strains that are increasingly resistant to the few available antibiotics. Here, we review our current understanding of molecular mechanisms underlying the profound drug resistance of M. tuberculosis. This knowledge is essential for the development of more effective antibiotics, which are not only potent against drug resistant M. tuberculosis strains but also help shorten the current treatment courses required for drug susceptible TB.
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Affiliation(s)
- Tasha Smith
- Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
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26
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Abstract
Trans-translation is a bacterial quality control system in protein synthesis facilitated by transfer-messenger RNA (tmRNA). Here, we describe the in vitro system using purified factors to evaluate the two steps of trans-translation: peptidyl-transfer from peptidyl-tRNA to alanyl-tmRNA and decoding of the resume codon on tmRNA.
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Affiliation(s)
- Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Hirosaki University, Hirosaki, Japan
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27
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Shi W, Zhang X, Jiang X, Ruan H, Barry CE, Wang H, Zhang W, Zhang Y. Pyrazinamide inhibits trans-translation in Mycobacterium tuberculosis. Science 2011; 333:1630-2. [PMID: 21835980 PMCID: PMC3502614 DOI: 10.1126/science.1208813] [Citation(s) in RCA: 371] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Pyrazinamide (PZA) is a first-line tuberculosis drug that plays a unique role in shortening the duration of tuberculosis chemotherapy. PZA is hydrolyzed intracellularly to pyrazinoic acid (POA) by pyrazinamidase (PZase, encoded by pncA), an enzyme frequently lost in PZA-resistant strains, but the target of POA in Mycobacterium tuberculosis has remained elusive. Here, we identify a previously unknown target of POA as the ribosomal protein S1 (RpsA), a vital protein involved in protein translation and the ribosome-sparing process of trans-translation. Three PZA-resistant clinical isolates without pncA mutation harbored RpsA mutations. RpsA overexpression conferred increased PZA resistance, and we confirmed that POA bound to RpsA (but not a clinically identified ΔAla mutant) and subsequently inhibited trans-translation rather than canonical translation. Trans-translation is essential for freeing scarce ribosomes in nonreplicating organisms, and its inhibition may explain the ability of PZA to eradicate persisting organisms.
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Affiliation(s)
- Wanliang Shi
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Xuelian Zhang
- Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Xin Jiang
- Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Haiming Ruan
- Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Clifton E. Barry
- Tuberculosis Research Section, NIAID, NIH, Bethesda, MD 20892, USA
| | - Honghai Wang
- Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Ying Zhang
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
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29
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Kurita D, Muto A, Himeno H. tRNA/mRNA Mimicry by tmRNA and SmpB in Trans-Translation. J Nucleic Acids 2011; 2011:130581. [PMID: 21253384 PMCID: PMC3022190 DOI: 10.4061/2011/130581] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 12/15/2010] [Indexed: 11/20/2022] Open
Abstract
Since accurate translation from mRNA to protein is critical to survival, cells have developed translational quality control systems. Bacterial ribosomes stalled on truncated mRNA are rescued by a system involving tmRNA and SmpB referred to as trans-translation. Here, we review current understanding of the mechanism of trans-translation. Based on results obtained by using directed hydroxyl radical probing, we propose a new type of molecular mimicry during trans-translation. Besides such chemical approaches, biochemical and cryo-EM studies have revealed the structural and functional aspects of multiple stages of trans-translation. These intensive works provide a basis for studying the dynamics of tmRNA/SmpB in the ribosome.
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Affiliation(s)
- Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
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Kurita D, Muto A, Himeno H. Role of the C-terminal tail of SmpB in the early stage of trans-translation. RNA (NEW YORK, N.Y.) 2010; 16:980-990. [PMID: 20348441 PMCID: PMC2856891 DOI: 10.1261/rna.1916610] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2009] [Accepted: 02/11/2010] [Indexed: 05/29/2023]
Abstract
Trans-translation relieves a stalled translation on the bacterial ribosome by transfer-messenger RNA (tmRNA) with the help of SmpB, an essential cofactor of tmRNA. Here, we examined the role of the unstructured C-terminal tail of SmpB using an in vitro trans-translation system. It was found that truncation of the C-terminal tail or substitution of tryptophan residue at 147 in the middle of the C-terminal tail affected the activity in the early stage of trans-translation. Our investigations also revealed that the C-terminal tail is not required for the events until GTP is hydrolyzed by EF-Tu in complex with tmRNA-SmpB. A synthetic peptide corresponding to the C-terminal tail of SmpB inhibited peptidyl-transfer of alanyl-tmRNA and A-site binding of SmpB, but not GTP hydrolysis. These results suggest that the C-terminal tail has a role in the step of accommodation of alanyl-tmRNA-SmpB into the A-site. Directed hydroxyl radical probing indicated that tryptophan residue at 147 is located just downstream of the decoding center in the mRNA path when SmpB is in the A-site.
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MESH Headings
- Amino Acid Substitution
- Base Sequence
- Binding Sites/genetics
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Guanosine Triphosphate/metabolism
- Kinetics
- Models, Biological
- Models, Molecular
- Mutagenesis, Site-Directed
- Peptide Elongation Factor Tu/metabolism
- Peptide Fragments/chemistry
- Peptide Fragments/genetics
- Peptide Fragments/metabolism
- Protein Biosynthesis
- Protein Structure, Tertiary
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Ribosomes/metabolism
- Sequence Deletion
- Tryptophan/chemistry
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Affiliation(s)
- Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
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Watts T, Cazier D, Healey D, Buskirk A. SmpB contributes to reading frame selection in the translation of transfer-messenger RNA. J Mol Biol 2009; 391:275-81. [PMID: 19540849 DOI: 10.1016/j.jmb.2009.06.037] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Revised: 06/09/2009] [Accepted: 06/16/2009] [Indexed: 11/26/2022]
Abstract
Transfer-messenger RNA (tmRNA) acts first as a tRNA and then as an mRNA template to rescue stalled ribosomes in eubacteria. Together with its protein partner, SmpB (small protein B), tmRNA enters stalled ribosomes and transfers an Ala residue to the growing polypeptide chain. A remarkable step then occurs: the ribosome leaves the stalled mRNA and resumes translation using tmRNA as a template, adding a short peptide tag that destines the aborted protein for destruction. Exactly how the ribosome switches templates, resuming translation on tmRNA in the proper reading frame, remains unknown. Within the tmRNA sequence itself, five nucleotides (U85AGUC) immediately upstream of the first codon appear to direct frame selection. In particular, mutation of the conserved A86 results in severe loss of function both in vitro and in vivo. The A86C mutation causes translation to resume exclusively in the +1 frame. Several candidate binding partners for this upstream sequence have been identified in vitro. Using a genetic selection for tmRNA activity in Escherichia coli, we identified mutations in the SmpB protein that restore the function of A86C tmRNA in vivo. The SmpB mutants increase tagging in the normal reading frame and reduce tagging in the +1 frame. These results demonstrate that SmpB is functionally linked with the sequence upstream of the tmRNA template; both contribute to reading frame selection on tmRNA.
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Affiliation(s)
- Talina Watts
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
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Chapter 1 A Phylogenetic View of Bacterial Ribonucleases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 85:1-41. [DOI: 10.1016/s0079-6603(08)00801-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Briani F, Curti S, Rossi F, Carzaniga T, Mauri P, Dehò G. Polynucleotide phosphorylase hinders mRNA degradation upon ribosomal protein S1 overexpression in Escherichia coli. RNA (NEW YORK, N.Y.) 2008; 14:2417-29. [PMID: 18824515 PMCID: PMC2578868 DOI: 10.1261/rna.1123908] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The exoribonuclease polynucleotide phosphorylase (PNPase, encoded by pnp) is a major player in bacterial RNA decay. In Escherichia coli, PNPase expression is post-transcriptionally regulated at the level of mRNA stability. The primary transcript is very efficiently processed by the endonuclease RNase III at a specific site and the processed pnp mRNA is rapidly degraded in a PNPase-dependent manner. While investigating the PNPase autoregulation mechanism we found, by UV-cross-linking experiments, that the ribosomal protein S1 in crude extracts binds to the pnp-mRNA leader region. We assayed the potential role of S1 protein in pnp gene regulation by modulating S1 expression from depletion to overexpression. We found that S1 depletion led to a sharp decrease of the amount of pnp and other tested mRNAs, as detected by Northern blotting, whereas S1 overexpression caused a strong stabilization of pnp and the other transcripts. Surprisingly, mRNA stabilization depended on PNPase, as it was not observed in a pnp deletion strain. PNPase-dependent stabilization, however, was not detected by chemical decay assay of bulk mRNA. Overall, our data suggest that PNPase exonucleolytic activity may be modulated by the translation potential of the target mRNAs and that, upon ribosomal protein S1 overexpression, PNPase protects from degradation a set of full-length mRNAs. It thus appears that a single mRNA species may be differentially targeted to either decay or PNPase-dependent stabilization, thus preventing its depletion in conditions of fast turnover.
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Affiliation(s)
- Federica Briani
- Dipartimento di Scienze biomolecolari e Biotecnologie, Università degli Studi di Milano, 20133 Milano, Italy.
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Miller MR, Healey DW, Robison SG, Dewey JD, Buskirk AR. The role of upstream sequences in selecting the reading frame on tmRNA. BMC Biol 2008; 6:29. [PMID: 18590561 PMCID: PMC2481249 DOI: 10.1186/1741-7007-6-29] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Accepted: 06/30/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND tmRNA acts first as a tRNA and then as an mRNA to rescue stalled ribosomes in eubacteria. Two unanswered questions about tmRNA function remain: how does tmRNA, lacking an anticodon, bypass the decoding machinery and enter the ribosome? Secondly, how does the ribosome choose the proper codon to resume translation on tmRNA? According to the -1 triplet hypothesis, the answer to both questions lies in the unique properties of the three nucleotides upstream of the first tmRNA codon. These nucleotides assume an A-form conformation that mimics the codon-anticodon interaction, leading to recognition by the decoding center and choice of the reading frame. The -1 triplet hypothesis is important because it is the most credible model in which direct binding and recognition by the ribosome sets the reading frame on tmRNA. RESULTS Conformational analysis predicts that 18 triplets cannot form the correct structure to function as the -1 triplet of tmRNA. We tested the tmRNA activity of all possible -1 triplet mutants using a genetic assay in Escherichia coli. While many mutants displayed reduced activity, our findings do not match the predictions of this model. Additional mutagenesis identified sequences further upstream that are required for tmRNA function. An immunoblot assay for translation of the tmRNA tag revealed that certain mutations in U85, A86, and the -1 triplet sequence result in improper selection of the first codon and translation in the wrong frame (-1 or +1) in vivo. CONCLUSION Our findings disprove the -1 triplet hypothesis. The -1 triplet is not required for accommodation of tmRNA into the ribosome, although it plays a minor role in frame selection. Our results strongly disfavor direct ribosomal recognition of the upstream sequence, instead supporting a model in which the binding of a separate ligand to A86 is primarily responsible for frame selection.
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Affiliation(s)
- Mickey R Miller
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA.
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Mikulík K, Palečková P, Felsberg J, Bobek J, Zídková J, Halada P. SsrA
genes of streptomycetes and association of proteins to the tmRNA during development and cellular differentiation. Proteomics 2008; 8:1429-41. [DOI: 10.1002/pmic.200700560] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Abstract
Small regulatory RNAs have been identified in a wide range of organisms, where they modify mRNA stability, translation or protein function. Small RNA regulators (sRNAs) either pair with mRNA targets or modify protein activities. Here we discuss current knowledge of the various proteins that interact with RNA regulators and review the physiologic implications of sRNA-protein complexes in DNA, RNA and protein metabolism, as well as in RNA and protein quality control in prokaryotes. Proteins that interact with the sRNAs can possess catalytic activity, induce conformational changes of the sRNA, or be sequestered by the sRNA to prevent the action of the protein.
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Affiliation(s)
- Christophe Pichon
- INSERM U835, Upres JE2311, Biochimie Pharmaceutique, Université de Rennes 1, Rennes, France
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Skorski P, Proux F, Cheraiti C, Dreyfus M, Hermann-Le Denmat S. The deleterious effect of an insertion sequence removing the last twenty percent of the essential Escherichia coli rpsA gene is due to mRNA destabilization, not protein truncation. J Bacteriol 2007; 189:6205-12. [PMID: 17616604 PMCID: PMC1951931 DOI: 10.1128/jb.00445-07] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ribosomal protein S1, the product of the essential rpsA gene, consists of six imperfect repeats of the same motif. Besides playing a critical role in translation initiation on most mRNAs, S1 also specifically autoregulates the translation of its own messenger. ssyF29 is a viable rpsA allele that carries an IS10R insertion within the coding sequence, resulting in a protein lacking the last motif (S1DeltaC). The growth of ssyF29 cells is slower than that of wild-type cells. Moreover, translation of a reporter rpsA-lacZ fusion is specifically stimulated, suggesting that the last motif is necessary for autoregulation. However, in ssyF29 cells the rpsA mRNA is also strongly destabilized; this destabilization, by causing S1DeltaC shortage, might also explain the observed slow-growth and autoregulation defect. To fix this ambiguity, we have introduced an early stop codon in the rpsA chromosomal gene, resulting in the synthesis of the S1DeltaC protein without an IS10R insertion (rpsADeltaC allele). rpsADeltaC cells grow much faster than their ssyF29 counterparts; moreover, in these cells S1 autoregulation and mRNA stability are normal. In vitro, the S1DeltaC protein binds mRNAs (including its own) almost as avidly as wild-type S1. These results demonstrate that the last S1 motif is dispensable for translation and autoregulation: the defects seen with ssyF29 cells reflect an IS10R-mediated destabilization of the rpsA mRNA, probably due to facilitated exonucleolytic degradation.
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Affiliation(s)
- Patricia Skorski
- Ecole Normale Supérieure, Laboratoire de Génétique Moléculaire-CNRS UMR8541, Paris, France
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