1
|
Novel gene similar to nitrite reductase (NO forming) plays potentially important role in the latency of tuberculosis. Sci Rep 2021; 11:19813. [PMID: 34615967 PMCID: PMC8494734 DOI: 10.1038/s41598-021-99346-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 08/30/2021] [Indexed: 12/03/2022] Open
Abstract
The development of the latent phenotype of Mycobacterium tuberculosis (Mtb) in the human lungs is the major hurdle to eradicate Tuberculosis. We recently reported that exposure to nitrite (10 mM) for six days under in vitro aerobic conditions completely transforms the bacilli into a viable but non-cultivable phenotype. Herein, we show that nitrite (beyond 5 mM) treated Mtb produces nitric oxide (NO) within the cell in a dose-dependent manner. Our search for the conserved sequence of NO synthesizing enzyme in the bacterial system identified MRA2164 and MRA0854 genes, of which the former was found to be significantly up regulated after nitrite exposure. In addition, the purified recombinant MRA2164 protein shows significant nitrite dependent NO synthesizing activity. The knockdown of the MRA2164 gene at mRNA level expression resulted in a significantly reduced NO level compared to the wild type bacilli with a simultaneous return of its replicative capability. Therefore, this study first time reports that nitrite induces dormancy in Mtb cells through induced expression of the MRA2164 gene and productions of NO as a mechanism for maintaining non-replicative stage in Mtb. This observation could help to control the Tuberculosis disease, especially the latent phenotype of the bacilli.
Collapse
|
2
|
Using diphenyleneiodonium to induce a viable but non-culturable phenotype in Mycobacterium tuberculosis and its metabolomics analysis. PLoS One 2019; 14:e0220628. [PMID: 31369628 PMCID: PMC6675104 DOI: 10.1371/journal.pone.0220628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 07/19/2019] [Indexed: 11/19/2022] Open
Abstract
Depletion of oxygen levels is a well-accepted model for induction of non-replicating, persistent states in mycobacteria. Increasing the stress levels in mycobacterium bacilli facilitates their entry into a non-cultivable, dormant state. In this study, it was shown that diphenyleneiodonium, an inhibitor of NADH oxidase, induced a viable, but non-culturable state in mycobacteria, having similar features to dormant bacilli, like loss of acid-fastness, upregulation of stress-regulated genes and decreased superoxide levels as compared to actively growing bacilli. Comprehensive, untargeted metabolic profiling also confirmed a decrease in biogenesis of amino acids, NAD, unsaturated fatty acids and nucleotides. Additionally, an increase in the level of lactate, fumarate, succinate and pentose phosphate pathways along with increased mycothiol and sulfate metabolites, similar to dormant bacilli, was observed in the granuloma. These non-cultivable bacilli were resuscitated by supplementation of fetal bovine serum, regaining their culturability in liquid as well as on agar medium. This study focused on the effect of diphenyleneiodonium treatment in causing mycobacteria to rapidly transition from an active state into a viable, but non-cultivable state, and comparing their characteristics with dormant phenotypes.
Collapse
|
3
|
Gample SP, Agrawal S, Sarkar D. Evidence of nitrite acting as a stable and robust inducer of non-cultivability in Mycobacterium tuberculosis with physiological relevance. Sci Rep 2019; 9:9261. [PMID: 31239517 PMCID: PMC6593118 DOI: 10.1038/s41598-019-45652-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/30/2019] [Indexed: 11/21/2022] Open
Abstract
Tuberculosis (TB) is the ninth leading cause of death worldwide, ranking above human immunodeficiency virus. Latency is the major obstacle in the eradication of this disease. How the physiology of the pathogen changes in transition to the latent stage needs to be understood. The latent bacteria extracted from animal hosts exist in a nonculturable (NC) phase, whereas bacteria extracted from most in vitro models are culture-positive. In the present study, we observed that nitrite, up to a concentration of 5 mM, shows the growth of Mycobacterium tuberculosis (MTB) in liquid media, but this effect starts reversing at higher concentrations. At a concentration of 10 mM, nitrite induces rapid nonculturability of MTB at the aerobic stage. This noncultivable dormancy was confirmed by analyzing the characteristics of NC bacteria. Further differential gene expression analyses clearly supported the formation of a dormancy phenotype. This study will be helpful for the use of this bacillus as a dormancy model in future studies on TB latency.
Collapse
Affiliation(s)
- Suwarna P Gample
- CSIR-National Chemical Laboratory, Organic Chemistry Division, Pune, 411008, Maharashtra, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sonia Agrawal
- CSIR-National Chemical Laboratory, Organic Chemistry Division, Pune, 411008, Maharashtra, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Dhiman Sarkar
- CSIR-National Chemical Laboratory, Organic Chemistry Division, Pune, 411008, Maharashtra, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
4
|
Cai WM, Chionh YH, Hia F, Gu C, Kellner S, McBee ME, Ng CS, Pang YLJ, Prestwich EG, Lim KS, Babu IR, Begley TJ, Dedon PC. A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications. Methods Enzymol 2015; 560:29-71. [PMID: 26253965 DOI: 10.1016/bs.mie.2015.03.004] [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] [Indexed: 12/03/2022]
Abstract
Here we describe an analytical platform for systems-level quantitative analysis of modified ribonucleosides in any RNA species, with a focus on stress-induced reprogramming of tRNA as part of a system of translational control of cell stress response. This chapter emphasizes strategies and caveats for each of the seven steps of the platform workflow: (1) RNA isolation, (2) RNA purification, (3) RNA hydrolysis to individual ribonucleosides, (4) chromatographic resolution of ribonucleosides, (5) identification of the full set of modified ribonucleosides, (6) mass spectrometric quantification of ribonucleosides, (6) interrogation of ribonucleoside datasets, and (7) mapping the location of stress-sensitive modifications in individual tRNA molecules. We have focused on the critical determinants of analytical sensitivity, specificity, precision, and accuracy in an effort to ensure the most biologically meaningful data on mechanisms of translational control of cell stress response. The methods described here should find wide use in virtually any analysis involving RNA modifications.
Collapse
Affiliation(s)
- Weiling Maggie Cai
- Department of Microbiology, National University of Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore
| | - Yok Hian Chionh
- Department of Microbiology, National University of Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore
| | - Fabian Hia
- Singapore-MIT Alliance for Research and Technology, Singapore
| | - Chen Gu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Stefanie Kellner
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Megan E McBee
- Singapore-MIT Alliance for Research and Technology, Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Chee Sheng Ng
- Singapore-MIT Alliance for Research and Technology, Singapore; School of Biological Sciences, Nanyang Technological Institute, Singapore
| | - Yan Ling Joy Pang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Erin G Prestwich
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kok Seong Lim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - I Ramesh Babu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Thomas J Begley
- College of Nanoscale Engineering and Science, State University of New York, Albany, New York, USA
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
| |
Collapse
|
5
|
Hia F, Chionh YH, Pang YLJ, DeMott MS, McBee ME, Dedon PC. Mycobacterial RNA isolation optimized for non-coding RNA: high fidelity isolation of 5S rRNA from Mycobacterium bovis BCG reveals novel post-transcriptional processing and a complete spectrum of modified ribonucleosides. Nucleic Acids Res 2014; 43:e32. [PMID: 25539917 PMCID: PMC4357692 DOI: 10.1093/nar/gku1317] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
A major challenge in the study of mycobacterial RNA biology is the lack of a comprehensive RNA isolation method that overcomes the unusual cell wall to faithfully yield the full spectrum of non-coding RNA (ncRNA) species. Here, we describe a simple and robust procedure optimized for the isolation of total ncRNA, including 5S, 16S and 23S ribosomal RNA (rRNA) and tRNA, from mycobacteria, using Mycobacterium bovis BCG to illustrate the method. Based on a combination of mechanical disruption and liquid and solid-phase technologies, the method produces all major species of ncRNA in high yield and with high integrity, enabling direct chemical and sequence analysis of the ncRNA species. The reproducibility of the method with BCG was evident in bioanalyzer electrophoretic analysis of isolated RNA, which revealed quantitatively significant differences in the ncRNA profiles of exponentially growing and non-replicating hypoxic bacilli. The method also overcame an historical inconsistency in 5S rRNA isolation, with direct sequencing revealing a novel post-transcriptional processing of 5S rRNA to its functional form and with chemical analysis revealing seven post-transcriptional ribonucleoside modifications in the 5S rRNA. This optimized RNA isolation procedure thus provides a means to more rigorously explore the biology of ncRNA species in mycobacteria.
Collapse
Affiliation(s)
- Fabian Hia
- Singapore MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore
| | - Yok Hian Chionh
- Singapore MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore Department of Microbiology and Immunology Programme, National University of Singapore, 117456, Singapore
| | - Yan Ling Joy Pang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Megan E McBee
- Singapore MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore
| | - Peter C Dedon
- Singapore MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
6
|
Nitrite reductase NirBD is induced and plays an important role during in vitro dormancy of Mycobacterium tuberculosis. J Bacteriol 2013; 195:4592-9. [PMID: 23935045 DOI: 10.1128/jb.00698-13] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Mycobacterium tuberculosis is one of the strongest reducers of nitrate among all mycobacteria. Reduction of nitrate to nitrite, mediated by nitrate reductase (NarGHJI) of M. tuberculosis, is induced during the dormant stage, and the enzyme has a respiratory function in the absence of oxygen. Nitrite reductase (NirBD) is also functional during aerobic growth when nitrite is the sole nitrogen source. However, the role of NirBD-mediated nitrite reduction during the dormancy is not yet characterized. Here, we analyzed nitrite reduction during aerobic growth as well as in a hypoxic dormancy model of M. tuberculosis in vitro. When nitrite was used as the sole nitrogen source in the medium, the organism grew and the reduction of nitrite was evident in both hypoxic and aerobic cultures of M. tuberculosis. Remarkably, the hypoxic culture of M. tuberculosis, compared to the aerobic culture, showed 32- and 4-fold-increased expression of nitrite reductase (NirBD) at the transcription and protein levels, respectively. More importantly, a nirBD mutant of M. tuberculosis was unable to reduce nitrite and compared to the wild-type (WT) strain had a >2-log reduction in viability after 240 h in the Wayne model of hypoxic dormancy. Dependence of M. tuberculosis on nitrite reductase (NirBD) was also seen in a human macrophage-based dormancy model where the nirBD mutant was impaired for survival compared to the WT strain. Overall, the increased expression and essentiality of nitrite reductase in the in vitro dormancy models suggested that NirBD-mediated nitrite reduction could be critical during the persistent stage of M. tuberculosis.
Collapse
|