1
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Kim D, Crippen TL, Dhungel L, Delclos PJ, Tomberlin JK, Jordan HR. Behavioral interplay between mosquito and mycolactone produced by Mycobacterium ulcerans and bacterial gene expression induced by mosquito proximity. PLoS One 2023; 18:e0289768. [PMID: 37535670 PMCID: PMC10399876 DOI: 10.1371/journal.pone.0289768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/25/2023] [Indexed: 08/05/2023] Open
Abstract
Mycolactone is a cytotoxic lipid metabolite produced by Mycobacterium ulcerans, the environmental pathogen responsible for Buruli ulcer, a neglected tropical disease. Mycobacterium ulcerans is prevalent in West Africa, particularly found in lentic environments, where mosquitoes also occur. Researchers hypothesize mosquitoes could serve as a transmission mechanism resulting in infection by M. ulcerans when mosquitoes pierce skin contaminated with M. ulcerans. The interplay between the pathogen, mycolactone, and mosquito is only just beginning to be explored. A triple-choice assay was conducted to determine the host-seeking preference of Aedes aegypti between M. ulcerans wildtype (MU, mycolactone active) and mutant (MUlac-, mycolactone inactive). Both qualitative and quantitative differences in volatile organic compounds' (VOCs) profiles of MU and MUlac- were determined by GC-MS. Additionally, we evaluated the interplay between Ae. aegypti proximity and M. ulcerans mRNA expression. The results showed that mosquito attraction was significantly greater (126.0%) to an artificial host treated with MU than MUlac-. We found that MU and MUlac produced differential profiles of VOCs associated with a wide range of biological importance from quorum sensing (QS) to human odor components. RT-qPCR assays showed that mycolactone upregulation was 24-fold greater for MU exposed to Ae. aegypti in direct proximity. Transcriptome data indicated significant induction of ten chromosomal genes of MU involved in stress responses and membrane protein, compared to MUlac- when directly having access to or in near mosquito proximity. Our study provides evidence of possible interkingdom interactions between unicellular and multicellular species that MU present on human skin is capable of interreacting with unrelated species (i.e., mosquitoes), altering its gene expression when mosquitoes are in direct contact or proximity, potentially impacting the production of its VOCs, and consequently leading to the stronger attraction of mosquitoes toward human hosts. This study elucidates interkingdom interactions between viable M. ulcerans bacteria and Ae. aegypti mosquitoes, which rarely have been explored in the past. Our finding opens new doors for future research in terms of disease ecology, prevalence, and pathogen dispersal outside of the M. ulcerans system.
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Affiliation(s)
- Dongmin Kim
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
| | - Tawni L Crippen
- Southern Plains Agricultural Research Center, Agricultural Research Service, USDA, College Station, Texas, United States of America
| | - Laxmi Dhungel
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi, United States of America
| | - Pablo J Delclos
- Department of Natural Sciences, University of Houston-Downtown, Houston, Texas, United States of America
| | - Jeffery K Tomberlin
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
| | - Heather R Jordan
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi, United States of America
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2
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Alebouyeh S, Cárdenas-Pestana JA, Vazquez L, Prados-Rosales R, Del Portillo P, Sanz J, Menéndez MC, García MJ. Iron deprivation enhances transcriptional responses to in vitro growth arrest of Mycobacterium tuberculosis. Front Microbiol 2022; 13:956602. [PMID: 36267176 PMCID: PMC9577196 DOI: 10.3389/fmicb.2022.956602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/07/2022] [Indexed: 11/18/2022] Open
Abstract
The establishment of Mycobacterium tuberculosis (Mtb) long-term infection in vivo depends on several factors, one of which is the availability of key nutrients such as iron (Fe). The relation between Fe deprivation inside and outside the granuloma, and the capacity of Mtb to accumulate lipids and persist in the absence of growth is not well understood. In this context, current knowledge of how Mtb modifies its lipid composition in response to growth arrest, depending on iron availability, is scarce. To shed light on these matters, in this work we compare genome-wide transcriptomic and lipidomic profiles of Mtb at exponential and stationary growth phases using cultures with glycerol as a carbon source, in the presence or absence of iron. As a result, we found that transcriptomic responses to growth arrest, considered as the transition from exponential to stationary phase, are iron dependent for as many as 714 genes (iron-growth interaction contrast, FDR <0.05), and that, in a majority of these genes, iron deprivation enhances the magnitude of the transcriptional responses to growth arrest in either direction. On the one hand, genes whose upregulation upon growth arrest is enhanced by iron deprivation were enriched in functional terms related to homeostasis of ion metals, and responses to several stressful cues considered cardinal features of the intracellular environment. On the other hand, genes showing negative responses to growth arrest that are stronger in iron-poor medium were enriched in energy production processes (TCA cycle, NADH dehydrogenation and cellular respiration), and key controllers of ribosomal activity shut-down, such as the T/A system mazE6/F6. Despite of these findings, a main component of the cell envelope, lipid phthiocerol dimycocerosate (PDIM), was not detected in the stationary phase regardless of iron availability, suggesting that lipid changes during Mtb adaptation to non-dividing phenotypes appear to be iron-independent. Taken together, our results indicate that environmental iron levels act as a key modulator of the intensity of the transcriptional adaptations that take place in the bacterium upon its transition between dividing and dormant-like phenotypes in vitro.
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Affiliation(s)
- Sogol Alebouyeh
- Department of Preventive Medicine and Public Health and Microbiology, School of Medicine, Autonomous University of Madrid, Madrid, Spain
| | - Jorge A. Cárdenas-Pestana
- Department of Theoretical Physics, University of Zaragoza, Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
| | - Lucia Vazquez
- Department of Preventive Medicine and Public Health and Microbiology, School of Medicine, Autonomous University of Madrid, Madrid, Spain
| | - Rafael Prados-Rosales
- Department of Preventive Medicine and Public Health and Microbiology, School of Medicine, Autonomous University of Madrid, Madrid, Spain
| | | | - Joaquín Sanz
- Department of Theoretical Physics, University of Zaragoza, Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
- *Correspondence: Maria J. García,
| | - Maria Carmen Menéndez
- Department of Preventive Medicine and Public Health and Microbiology, School of Medicine, Autonomous University of Madrid, Madrid, Spain
- Maria Carmen Menéndez,
| | - Maria J. García
- Department of Preventive Medicine and Public Health and Microbiology, School of Medicine, Autonomous University of Madrid, Madrid, Spain
- Joaquín Sanz,
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3
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Campos-Silva R, D’Urso G, Delalande O, Giudice E, Macedo AJ, Gillet R. Trans-Translation Is an Appealing Target for the Development of New Antimicrobial Compounds. Microorganisms 2021; 10:3. [PMID: 35056452 PMCID: PMC8778911 DOI: 10.3390/microorganisms10010003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/09/2021] [Accepted: 12/16/2021] [Indexed: 01/06/2023] Open
Abstract
Because of the ever-increasing multidrug resistance in microorganisms, it is crucial that we find and develop new antibiotics, especially molecules with different targets and mechanisms of action than those of the antibiotics in use today. Translation is a fundamental process that uses a large portion of the cell's energy, and the ribosome is already the target of more than half of the antibiotics in clinical use. However, this process is highly regulated, and its quality control machinery is actively studied as a possible target for new inhibitors. In bacteria, ribosomal stalling is a frequent event that jeopardizes bacterial wellness, and the most severe form occurs when ribosomes stall at the 3'-end of mRNA molecules devoid of a stop codon. Trans-translation is the principal and most sophisticated quality control mechanism for solving this problem, which would otherwise result in inefficient or even toxic protein synthesis. It is based on the complex made by tmRNA and SmpB, and because trans-translation is absent in eukaryotes, but necessary for bacterial fitness or survival, it is an exciting and realistic target for new antibiotics. Here, we describe the current and future prospects for developing what we hope will be a novel generation of trans-translation inhibitors.
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Affiliation(s)
- Rodrigo Campos-Silva
- CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, University of Rennes, 35000 Rennes, France; (R.C.-S.); (G.D.); (O.D.); (E.G.)
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia and Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 90610-000, Brazil;
| | - Gaetano D’Urso
- CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, University of Rennes, 35000 Rennes, France; (R.C.-S.); (G.D.); (O.D.); (E.G.)
| | - Olivier Delalande
- CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, University of Rennes, 35000 Rennes, France; (R.C.-S.); (G.D.); (O.D.); (E.G.)
| | - Emmanuel Giudice
- CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, University of Rennes, 35000 Rennes, France; (R.C.-S.); (G.D.); (O.D.); (E.G.)
| | - Alexandre José Macedo
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia and Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 90610-000, Brazil;
| | - Reynald Gillet
- CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, University of Rennes, 35000 Rennes, France; (R.C.-S.); (G.D.); (O.D.); (E.G.)
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4
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Burgos R, Weber M, Gallo C, Lluch-Senar M, Serrano L. Widespread ribosome stalling in a genome-reduced bacterium and the need for translational quality control. iScience 2021; 24:102985. [PMID: 34485867 PMCID: PMC8403727 DOI: 10.1016/j.isci.2021.102985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/22/2021] [Accepted: 08/11/2021] [Indexed: 11/21/2022] Open
Abstract
Trans-translation is a ubiquitous bacterial mechanism of ribosome rescue mediated by a transfer-messenger RNA (tmRNA) that adds a degradation tag to the truncated nascent polypeptide. Here, we characterize this quality control system in a genome-reduced bacterium, Mycoplasma pneumoniae (MPN), and perform a comparative analysis of protein quality control components in slow and fast-growing prokaryotes. We show in vivo that in MPN the sole quality control cytoplasmic protease (Lon) degrades efficiently tmRNA-tagged proteins. Analysis of tmRNA-mutants encoding a tag resistant to proteolysis reveals extensive tagging activity under normal growth. Unlike knockout strains, these mutants are viable demonstrating the requirement of tmRNA-mediated ribosome recycling. Chaperone and Lon steady-state levels maintain proteostasis in these mutants suggesting a model in which co-evolution of Lon and their substrates offer simple mechanisms of regulation without specialized degradation machineries. Finally, comparative analysis shows relative increase in Lon/Chaperone levels in slow-growing bacteria suggesting physiological adaptation to growth demand. Lon degrades efficiently tmRNA-tagged proteins in a genome-reduced bacterium tmRNA-tag mutants are viable and reveal extensive tagging activity in M. pneumoniae Co-evolution of Lon and their substrates offer simple mechanisms of regulation Chaperone and Lon relative levels correlate with bacterial growth rates
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Affiliation(s)
- Raul Burgos
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Corresponding author
| | - Marc Weber
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Carolina Gallo
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
- Corresponding author
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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: 10] [Impact Index Per Article: 2.5] [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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Behra PRK, Pettersson BMF, Das S, Dasgupta S, Kirsebom LA. Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA. BMC Evol Biol 2019; 19:124. [PMID: 31215393 PMCID: PMC6582537 DOI: 10.1186/s12862-019-1447-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 05/27/2019] [Indexed: 02/07/2023] Open
Abstract
Background Mycobacteria occupy various ecological niches and can be isolated from soil, tap water and ground water. Several cause diseases in humans and animals. To get deeper insight into our understanding of mycobacterial evolution focusing on tRNA and non-coding (nc)RNA, we conducted a comparative genome analysis of Mycobacterium mucogenicum (Mmuc) and Mycobacterium neoaurum (Mneo) clade members. Results Genome sizes for Mmuc- and Mneo-clade members vary between 5.4 and 6.5 Mbps with the complete MmucT (type strain) genome encompassing 6.1 Mbp. The number of tRNA genes range between 46 and 79 (including one pseudo tRNA gene) with 39 tRNA genes common among the members of these clades, while additional tRNA genes were probably acquired through horizontal gene transfer. Selected tRNAs and ncRNAs (RNase P RNA, tmRNA, 4.5S RNA, Ms1 RNA and 6C RNA) are expressed, and the levels for several of these are higher in stationary phase compared to exponentially growing cells. The rare tRNAIleTAT isoacceptor and two for mycobacteria novel ncRNAs: the Lactobacillales-derived GOLLD RNA and a homolog to the antisense Salmonella typhimurium phage Sar RNA, were shown to be present and expressed in certain Mmuc-clade members. Conclusions Phages, IS elements, horizontally transferred tRNA gene clusters, and phage-derived ncRNAs appears to have influenced the evolution of the Mmuc- and Mneo-clades. While the number of predicted coding sequences correlates with genome size, the number of tRNA coding genes does not. The majority of the tRNA genes in mycobacteria are transcribed mainly from single genes and the levels of certain ncRNAs, including RNase P RNA (essential for the processing of tRNAs), are higher at stationary phase compared to exponentially growing cells. We provide supporting evidence that Ms1 RNA represents a mycobacterial 6S RNA variant. The evolutionary routes for the ncRNAs RNase P RNA, tmRNA and Ms1 RNA are different from that of the core genes. Electronic supplementary material The online version of this article (10.1186/s12862-019-1447-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Phani Rama Krishna Behra
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden
| | - B M Fredrik Pettersson
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden
| | - Sarbashis Das
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden
| | - Santanu Dasgupta
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden
| | - Leif A Kirsebom
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden.
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7
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Mishra S, Ahmed T, Tyagi A, Shi J, Bhushan S. Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA. Sci Rep 2018; 8:13587. [PMID: 30206241 PMCID: PMC6133939 DOI: 10.1038/s41598-018-31850-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/23/2018] [Indexed: 11/09/2022] Open
Abstract
Ribosomes are the dynamic protein synthesis machineries of the cell. They may exist in different functional states in the cell. Therefore, it is essential to have structural information on these different functional states of ribosomes to understand their mechanism of action. Here, we present single particle cryo-EM reconstructions of the Mycobacterium smegmatis 70S ribosomes in the hibernating state (with HPF), trans-translating state (with tmRNA), and the P/P state (with P-tRNA) resolved to 4.1, 12.5, and 3.4 Å, respectively. A comparison of the P/P state with the hibernating state provides possible functional insights about the Mycobacteria-specific helix H54a rRNA segment. Interestingly, densities for all the four OB domains of bS1 protein is visible in the hibernating 70S ribosome displaying the molecular details of bS1-70S interactions. Our structural data shows a Mycobacteria-specific H54a-bS1 interaction which seems to prevent subunit dissociation and degradation during hibernation without the formation of 100S dimer. This indicates a new role of bS1 protein in 70S protection during hibernation in Mycobacteria in addition to its conserved function during translation initiation.
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MESH Headings
- Binding Sites
- Cryoelectron Microscopy
- Models, Molecular
- Mycobacterium smegmatis/genetics
- Mycobacterium smegmatis/metabolism
- Mycobacterium smegmatis/ultrastructure
- Nucleic Acid Conformation
- Protein Binding
- Protein Biosynthesis
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
- Ribosomes/ultrastructure
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Affiliation(s)
- Satabdi Mishra
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Tofayel Ahmed
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Anu Tyagi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jian Shi
- Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Shashi Bhushan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.
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8
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Alumasa JN, Manzanillo PS, Peterson ND, Lundrigan T, Baughn AD, Cox JS, Keiler KC. Ribosome Rescue Inhibitors Kill Actively Growing and Nonreplicating Persister Mycobacterium tuberculosis Cells. ACS Infect Dis 2017; 3:634-644. [PMID: 28762275 PMCID: PMC5594445 DOI: 10.1021/acsinfecdis.7b00028] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
The
emergence of Mycobacterium tuberculosis (MTB) strains
that are resistant to most or all available antibiotics has created
a severe problem for treating tuberculosis and has spurred a quest
for new antibiotic targets. Here, we demonstrate that trans-translation is essential for growth of MTB and is a viable target
for development of antituberculosis drugs. We also show that an inhibitor
of trans-translation, KKL-35, is bactericidal against
MTB under both aerobic and anoxic conditions. Biochemical experiments
show that this compound targets helix 89 of the 23S rRNA. In silico molecular docking predicts a binding pocket for
KKL-35 adjacent to the peptidyl-transfer center in a region not targeted
by conventional antibiotics. Computational solvent mapping suggests
that this pocket is a druggable hot spot for small molecule binding.
Collectively, our findings reveal a new target for antituberculosis
drug development and provide critical insight on the mechanism of
antibacterial action for KKL-35 and related 1,3,4-oxadiazole benzamides.
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Affiliation(s)
- John N. Alumasa
- Department of Biochemistry
and Molecular Biology, The Pennsylvania State University, 401 Althouse Laboratory, University Park, Pennsylvania 16802, United States
| | - Paolo S. Manzanillo
- Department
of Molecular and Cell Biology, University of California, Berkeley, #3370, 375E Li Ka Shing Center, Berkeley, California 94720, United States
| | - Nicholas D. Peterson
- Department of Microbiology and Immunology,
Microbiology Research Facility, University of Minnesota, Rm4-115, 689 23rd Ave. SE, Minneapolis, Minnesota 55455, United States
| | - Tricia Lundrigan
- Department
of Molecular and Cell Biology, University of California, Berkeley, #3370, 375E Li Ka Shing Center, Berkeley, California 94720, United States
| | - Anthony D. Baughn
- Department of Microbiology and Immunology,
Microbiology Research Facility, University of Minnesota, Rm4-115, 689 23rd Ave. SE, Minneapolis, Minnesota 55455, United States
| | - Jeffery S. Cox
- Department
of Molecular and Cell Biology, University of California, Berkeley, #3370, 375E Li Ka Shing Center, Berkeley, California 94720, United States
| | - Kenneth C. Keiler
- Department of Biochemistry
and Molecular Biology, The Pennsylvania State University, 401 Althouse Laboratory, University Park, Pennsylvania 16802, United States
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Abstract
La synthèse des protéines, également appelée traduction, est assurée dans chaque cellule par des machines moléculaires très sophistiquées : les ribosomes. Compte tenu de l’immense quantité de données biologiques à traiter, il arrive régulièrement que ces machines se bloquent et mettent en péril la survie de la cellule. Chez les bactéries, le principal processus de sauvetage des ribosomes bloqués est la trans-traduction. Il est assuré par un acide ribonucléique (ARN) hybride, l’ARN transfert-messager (ARNtm), associé à une petite protéine basique, SmpB (small protein B). Plusieurs autres systèmes de contrôle qualité ont récemment été mis en évidence, révélant un réseau de maintien de la survie cellulaire très sophistiqué. Cette machinerie du contrôle qualité de la synthèse protéique est une cible très prometteuse pour le développement de futurs antibiotiques.
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10
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Irla M, Neshat A, Brautaset T, Rückert C, Kalinowski J, Wendisch VF. Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape. BMC Genomics 2015; 16:73. [PMID: 25758049 PMCID: PMC4342826 DOI: 10.1186/s12864-015-1239-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/12/2015] [Indexed: 01/27/2023] Open
Abstract
Background Bacillus methanolicus MGA3 is a thermophilic, facultative ribulose monophosphate (RuMP) cycle methylotroph. Together with its ability to produce high yields of amino acids, the relevance of this microorganism as a promising candidate for biotechnological applications is evident. The B. methanolicus MGA3 genome consists of a 3,337,035 nucleotides (nt) circular chromosome, the 19,174 nt plasmid pBM19 and the 68,999 nt plasmid pBM69. 3,218 protein-coding regions were annotated on the chromosome, 22 on pBM19 and 82 on pBM69. In the present study, the RNA-seq approach was used to comprehensively investigate the transcriptome of B. methanolicus MGA3 in order to improve the genome annotation, identify novel transcripts, analyze conserved sequence motifs involved in gene expression and reveal operon structures. For this aim, two different cDNA library preparation methods were applied: one which allows characterization of the whole transcriptome and another which includes enrichment of primary transcript 5′-ends. Results Analysis of the primary transcriptome data enabled the detection of 2,167 putative transcription start sites (TSSs) which were categorized into 1,642 TSSs located in the upstream region (5′-UTR) of known protein-coding genes and 525 TSSs of novel antisense, intragenic, or intergenic transcripts. Firstly, 14 wrongly annotated translation start sites (TLSs) were corrected based on primary transcriptome data. Further investigation of the identified 5′-UTRs resulted in the detailed characterization of their length distribution and the detection of 75 hitherto unknown cis-regulatory RNA elements. Moreover, the exact TSSs positions were utilized to define conserved sequence motifs for translation start sites, ribosome binding sites and promoters in B. methanolicus MGA3. Based on the whole transcriptome data set, novel transcripts, operon structures and mRNA abundances were determined. The analysis of the operon structures revealed that almost half of the genes are transcribed monocistronically (940), whereas 1,164 genes are organized in 381 operons. Several of the genes related to methylotrophy had highly abundant transcripts. Conclusion The extensive insights into the transcriptional landscape of B. methanolicus MGA3, gained in this study, represent a valuable foundation for further comparative quantitative transcriptome analyses and possibly also for the development of molecular biology tools which at present are very limited for this organism. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1239-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marta Irla
- Genetics of Prokaryotes, Faculty of Biology & Center for Biotechnology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany.
| | - Armin Neshat
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätstr. 27, 33615, Bielefeld, Germany.
| | - Trygve Brautaset
- Department of Molecular Biology, SINTEF Materials and Chemistry, Sem Selands vei 2, 7465, Trondheim, Norway. .,Department of Biotechnology, Norwegian University of Science and Technology, Sem Sælands vei 6/8, 7491, Trondheim, Norway.
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätstr. 27, 33615, Bielefeld, Germany. .,Technology Platform Genomics, Center for Biotechnology, Bielefeld University, Universitätsstr. 27, 33615, Bielefeld, Germany.
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätstr. 27, 33615, Bielefeld, Germany. .,Technology Platform Genomics, Center for Biotechnology, Bielefeld University, Universitätsstr. 27, 33615, Bielefeld, Germany.
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology & Center for Biotechnology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany.
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Schwientek P, Neshat A, Kalinowski J, Klein A, Rückert C, Schneiker-Bekel S, Wendler S, Stoye J, Pühler A. Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts. J Biotechnol 2014; 190:85-95. [PMID: 24642337 DOI: 10.1016/j.jbiotec.2014.03.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/25/2014] [Accepted: 03/01/2014] [Indexed: 11/16/2022]
Abstract
Actinoplanes sp. SE50/110 is the producer of the alpha-glucosidase inhibitor acarbose, which is an economically relevant and potent drug in the treatment of type-2 diabetes mellitus. In this study, we present the detection of transcription start sites on this genome by sequencing enriched 5'-ends of primary transcripts. Altogether, 1427 putative transcription start sites were initially identified. With help of the annotated genome sequence, 661 transcription start sites were found to belong to the leader region of protein-coding genes with the surprising result that roughly 20% of these genes rank among the class of leaderless transcripts. Next, conserved promoter motifs were identified for protein-coding genes with and without leader sequences. The mapped transcription start sites were finally used to improve the annotation of the Actinoplanes sp. SE50/110 genome sequence. Concerning protein-coding genes, 41 translation start sites were corrected and 9 novel protein-coding genes could be identified. In addition to this, 122 previously undetermined non-coding RNA (ncRNA) genes of Actinoplanes sp. SE50/110 were defined. Focusing on antisense transcription start sites located within coding genes or their leader sequences, it was discovered that 96 of those ncRNA genes belong to the class of antisense RNA (asRNA) genes. The remaining 26 ncRNA genes were found outside of known protein-coding genes. Four chosen examples of prominent ncRNA genes, namely the transfer messenger RNA gene ssrA, the ribonuclease P class A RNA gene rnpB, the cobalamin riboswitch RNA gene cobRS, and the selenocysteine-specific tRNA gene selC, are presented in more detail. This study demonstrates that sequencing of enriched 5'-ends of primary transcripts and the identification of transcription start sites are valuable tools for advanced genome annotation of Actinoplanes sp. SE50/110 and most probably also for other bacteria.
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Affiliation(s)
- Patrick Schwientek
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; Genome Informatics Research Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Armin Neshat
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Andreas Klein
- Bayer HealthCare AG, Friedrich-Ebert-Str. 475, 42117 Wuppertal, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Susanne Schneiker-Bekel
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Sergej Wendler
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jens Stoye
- Genome Informatics Research Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany; Institute for Bioinformatics, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Alfred Pühler
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
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Personne Y, Parish T. Mycobacterium tuberculosis possesses an unusual tmRNA rescue system. Tuberculosis (Edinb) 2013; 94:34-42. [PMID: 24145139 DOI: 10.1016/j.tube.2013.09.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 09/23/2013] [Accepted: 09/28/2013] [Indexed: 12/31/2022]
Abstract
Trans-translation is a key process in bacteria which recycles stalled ribosomes and tags incomplete nascent proteins for degradation. This ensures the availability of ribosomes for protein synthesis and prevents the accumulation of dysfunctional proteins. The tmRNA, ssrA, is responsible for both recovering stalled ribosomes and encodes the degradation tag; ssrA associates and functions with accessory proteins such as SmpB. Although ssrA and smpB are ubiquitous in bacteria, they are not essential for the viability of many species. The Mycobacterium tuberculosis genome has homologues of both ssrA and smpB. We demonstrated that ssrA is essential in M. tuberculosis, since the chromosomal copy of the gene could only be deleted in the presence of a functional copy integrated elsewhere. However, we were able to delete the proteolytic tagging function by constructing strains carrying a mutant allele (ssrADD). This demonstrates that ribosome rescue by ssrA is the essential function in M. tuberculosis, SmpB was not required for aerobic growth, since we were able to construct a deletion strain. However, the smpBΔ strain was more sensitive to antibiotics targeting the ribosome. Strains with deletion of smpB or mutations in ssrA did not show increased sensitivity (or resistance) to pyrazinamide suggesting that this antibiotic does not directly target these components of the tmRNA tagging system.
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Affiliation(s)
- Yoann Personne
- Queen Mary University of London, Barts & The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Tanya Parish
- Queen Mary University of London, Barts & The London School of Medicine and Dentistry, London E1 2AT, UK.
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Schuessler DL, Cortes T, Fivian-Hughes AS, Lougheed KEA, Harvey E, Buxton RS, Davis EO, Young DB. Induced ectopic expression of HigB toxin in Mycobacterium tuberculosis results in growth inhibition, reduced abundance of a subset of mRNAs and cleavage of tmRNA. Mol Microbiol 2013; 90:195-207. [PMID: 23927792 PMCID: PMC3912914 DOI: 10.1111/mmi.12358] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2013] [Indexed: 01/20/2023]
Abstract
In Mycobacterium tuberculosis, the genes Rv1954A-Rv1957 form an operon that includes Rv1955 and Rv1956 which encode the HigB toxin and the HigA antitoxin respectively. We are interested in the role and regulation of this operon, since toxin-antitoxin systems have been suggested to play a part in the formation of persister cells in mycobacteria. To investigate the function of the higBA locus, effects of toxin expression on mycobacterial growth and transcript levels were assessed in M. tuberculosis H37Rv wild type and in an operon deletion background. We show that expression of HigB toxin in the absence of HigA antitoxin arrests growth and causes cell death in M. tuberculosis. We demonstrate HigB expression to reduce the abundance of IdeR and Zur regulated mRNAs and to cleave tmRNA in M. tuberculosis, Escherichia coli and Mycobacterium smegmatis. This study provides the first identification of possible target transcripts of HigB in M. tuberculosis.
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Affiliation(s)
- Dorothée L Schuessler
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
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Mishra S, Anand D, Vijayarangan N, Ajitkumar P. An accurate method for the qualitative detection and quantification of mycobacterial promoter activity. Open Microbiol J 2013; 7:1-5. [PMID: 23359792 PMCID: PMC3553492 DOI: 10.2174/1874285801307010001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 11/07/2012] [Accepted: 11/20/2012] [Indexed: 11/22/2022] Open
Abstract
The present study was designed to determine the half-life of gfpm2+ mRNA, which encodes mycobacterial co-don-optimised highly fluorescent GFPm2+ protein, and to find out whether mycobacterial promoter activity can be quanti-tated more accurately using the mRNA levels of the reporter gene, gfpm2+, than the fluorescence intensity of the GFPm2+ protein. Quantitative PCR of gfpm2+ mRNA in the pulse-chased samples of the rifampicin-treated Mycobacterium smegmatis/gfpm2+ transformant showed the half-life of gfpm2+ mRNA to be 4.081 min. The levels of the gfpm2+ mRNA and the fluorescence intensity of the GFPm2+ protein, which were expressed by the promoters of Mycobacterium tuberculosis cell division gene, ftsZ (MtftsZ), were determined using quantitative PCR and fluorescence spectrophotometry, respectively. The data revealed that quantification of mycobacterial promoter activity by determining the gfpm2+ mRNA levels is more accurate and statistically significant than the measurement of GFPm2+ fluorescence intensity, especially for weak promoters.
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Affiliation(s)
- Saurabh Mishra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore - 560012, Karnataka, India
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