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Kumar GS, Dubey A, Panda SP, Alawi MM, Sindi AA, Azhar EI, Dwivedi VD, Agrawal S. Repurposing of antibacterial compounds for suppression of Mycobacterium tuberculosis dormancy reactivation by targeting resuscitation-promoting factors B. J Biomol Struct Dyn 2024; 42:6850-6862. [PMID: 37551014 DOI: 10.1080/07391102.2023.2245059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/08/2023] [Indexed: 08/09/2023]
Abstract
Tuberculosis infection has always been a global concern for public health, and the mortality rate has increased tremendously every year. The ability of the resuscitation Mycobacterium tuberculosis (Mtb) from the dormant state is one of the major reasons for the epidemic spread of tuberculosis infection, especially latent tuberculosis infection (LTBI). The element that encourages resuscitation, RpfB (resuscitation-promoting factors B), is mostly in charge of bringing Mtb out of slumber. This reason makes RpfB a promising target for developing tuberculosis drugs because of the effects of latent tuberculosis. Therefore, this work was executed using a computational three-level screening of the Selleckhem antibiotics database consisting of 462 antibiotics against the ligand binding region of the RpfB protein, followed by an estimation of binding free energy for ideal identification and confirmation of potential RpfB inhibitor. Subsequently, three antibiotic drug molecules, i.e., Amikacin hydrate (-66.87 kcal/mol), Isepamicin sulphate (-60.8 kcal/mol), and Bekanamycin (-46.89 kcal/mol), were selected on the basis of their binding free energy value for further computational studies in comparison to reference ligand, 4-benzoyl-2-nitrophenyl thiocyanate (NPT7). Based on the intermolecular interaction profiling, 200 ns molecular dynamic simulation (MD), post-simulation analysis and principal component analysis (PCA), the selected antibiotics showed substantial stability with the RpfB protein compared to the NPT7 inhibitor. Conclusively based on the computational results, the preferred drugs can be potent inhibitors of the RpfB protein, which can be further validated using in vivo research and in vitro enzyme inhibition to understand their therapeutic activity against tuberculosis infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Geethu S Kumar
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, India
| | - Amit Dubey
- Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida, India
| | - Siva Prasad Panda
- Institute of Pharmaceutical Research, GLA University, Mathura, India
| | - Maha M Alawi
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anees A Sindi
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Anesthesia and Critical Care, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Pulmonary and Critical Care Department, International Medical Center Hospital, Jeddah, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Sharad Agrawal
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, India
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2
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Jubilee R, Komala M, Patel S. Therapeutic Potential of Resveratrol and Lignans in the Management of Tuberculosis. Cell Biochem Biophys 2024:10.1007/s12013-024-01378-7. [PMID: 38914838 DOI: 10.1007/s12013-024-01378-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2024] [Indexed: 06/26/2024]
Abstract
This study aims to investigate the therapeutic potential of herbal remedies, specifically resveratrol and lignans, as alternative treatments for tuberculosis (TB), given the challenges posed by drug-resistant strains and adverse effects of conventional therapies. A comprehensive review of the literature was conducted to analyze the mechanisms of action, safety profiles, and efficacy of resveratrol and lignans in the context of TB management. This review focused on the bactericidal and bacteriostatic effects of these compounds, examining their interaction with Mycobacterium tuberculosis within macrophages. Resveratrol and lignans were found to exhibit significant antibacterial properties through mechanisms such as SIRT1 modulation, coenzyme A transferase inhibition, suppression of intracellular bacterial proliferation in macrophages, and induction of autophagy. These mechanisms contribute to their effectiveness in combating TB and highlight their potential as alternative therapeutic agents.
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Affiliation(s)
- R Jubilee
- Department of Pharmacology, Saveetha College of Pharmacy, Saveetha Institute of Medical and Technical Sciences, (Deemed to be University), Saveetha Nagar, Chennai, India
| | - M Komala
- Department of Pharmaceutical Pharmaceutics, School of Pharmaceutical Sciences, Vels Institute of Science, Technology and Advanced Studies (VISTAS), Pallavaram, Chennai, Tamil Nadu, India
| | - Saraswati Patel
- Department of Pharmacology, Saveetha College of Pharmacy, Saveetha Institute of Medical and Technical Sciences, (Deemed to be University), Saveetha Nagar, Chennai, India.
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3
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Garg R, Manhas I, Chaturvedi D. Unveiling the orchestration: mycobacterial small RNAs as key mediators in host-pathogen interactions. Front Microbiol 2024; 15:1399280. [PMID: 38903780 PMCID: PMC11188477 DOI: 10.3389/fmicb.2024.1399280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/21/2024] [Indexed: 06/22/2024] Open
Abstract
Small RNA (sRNA) molecules, a class of non-coding RNAs, have emerged as pivotal players in the regulation of gene expression and cellular processes. Mycobacterium tuberculosis and other pathogenic mycobacteria produce diverse small RNA species that modulate bacterial physiology and pathogenesis. Recent advances in RNA sequencing have enabled identification of novel small RNAs and characterization of their regulatory functions. This review discusses the multifaceted roles of bacterial small RNAs, covering their biogenesis, classification, and functional diversity. Small RNAs (sRNAs) play pivotal roles in orchestrating diverse cellular processes, ranging from gene silencing to epigenetic modifications, across a broad spectrum of organisms. While traditionally associated with eukaryotic systems, recent research has unveiled their presence and significance within bacterial domains as well. Unlike their eukaryotic counterparts, which primarily function within the context of RNA interference (RNAi) pathways, bacterial sRNAs predominantly act through base-pairing interactions with target mRNAs, leading to post-transcriptional regulation. This fundamental distinction underscores the necessity of elucidating the unique roles and regulatory mechanisms of bacterial sRNAs in bacterial adaptation and survival. By doing these myriad functions, they regulate bacterial growth, metabolism, virulence, and drug resistance. In Mycobacterium tuberculosis, apart from having various roles in the bacillus itself, small RNA molecules have emerged as key regulators of gene expression and mediators of host-pathogen interactions. Understanding sRNA regulatory networks in mycobacteria can drive our understanding of significant role they play in regulating virulence and adaptation to the host environment. Detailed functional characterization of Mtb sRNAs at the host-pathogen interface is required to fully elucidate the complex sRNA-mediated gene regulatory networks deployed by Mtb, to manipulate the host. A deeper understanding of this aspect could pave the development of novel diagnostic and therapeutic strategies for tuberculosis.
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Affiliation(s)
- Rajni Garg
- Department of Human Genetics and Molecular Medicine, Amity School of Health Sciences, Amity University, Mohali, Punjab, India
| | - Ishali Manhas
- Department of Biotechnology, Amity School of Biological Sciences, Amity University, Mohali, Punjab, India
| | - Diksha Chaturvedi
- Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela, Odisha, India
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4
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Krüger W. Diagnostic algorithm allows for a scientifically robust and reliable retrospective diagnosis using textual evidence from mid-19th century Basel, Switzerland. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2024; 44:105-111. [PMID: 38218023 DOI: 10.1016/j.ijpp.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 12/17/2023] [Accepted: 01/01/2024] [Indexed: 01/15/2024]
Abstract
OBJECTIVE Diagnosing disease from the past using historic textual sources can be controversial as to its accuracy. To overcome these objections, an empirical approach to the historical clinical data was developed. The approach follows a standardised, objective, and systematic evaluation, satisfying the requirements of the philosophy of science. MATERIAL Physician-managed medical records of mid-19th century patients reported to have suffered from tuberculosis. METHOD A diagnostic algorithm, quantifying clinical data into a scoring system, was developed based on criteria recorded in the medical sources. The findings were compared to the autopsy results using the Receiver Operating Characteristics method. RESULTS The generated scoring system correctly predicted the diagnosis of tuberculosis in 86% of patients in the study. 6% false negatives and 8% false positives were predicted. CONCLUSIONS It is possible to retrospectively diagnose in a reliable and scientifically robust manner under certain conditions. It is important to embed the clinical data into the historical context. A general rejection of retrospective diagnosis is unsubstantiated. Well-designed, disease-specific, and source adapted medical scoring systems are new approaches and overcome criticism raised against retrospective diagnosis. SIGNIFICANCE This new approach utilises diverse historic sources and potentially leads to reliable retrospective diagnosis of most common diseases of the past. LIMITATIONS Selection bias of the records allocated. Quality of the historic sources utilized. Restricted statistical assessment potential of historic sources. SUGGESTIONS FOR FURTHER RESEARCH Development of disease- and epoch-specific medical score systems.
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Affiliation(s)
- Wolfgang Krüger
- Biological Anthropology, Faculty of Medicine, University of Freiburg, Hebelstrasse 29, D-79104 Freiburg im Breisgau, Germany.
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5
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Ufimtseva EG, Eremeeva NI. Drug-Tolerant Mycobacterium tuberculosis Adopt Different Survival Strategies in Alveolar Macrophages of Patients with Pulmonary Tuberculosis. Int J Mol Sci 2023; 24:14942. [PMID: 37834390 PMCID: PMC10573496 DOI: 10.3390/ijms241914942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 08/31/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
The rapid spread of drug-resistant M. tuberculosis (Mtb) strains and the phenomenon of phenotypic tolerance to drugs present challenges toward achieving the goal of tuberculosis (TB) elimination worldwide. By using the ex vivo cultures of alveolar macrophages obtained from lung tissues of TB patients after intensive antimicrobial chemotherapy before surgery, different subpopulations of multidrug-tolerant Mtb with a spectrum of phenotypic and growth features were identified in the same TB lesions. Our results are indicative of not only passive mechanisms generating nonheritable resistance of Mtb to antibiotics, which are associated mainly with a lack of Mtb growth, but also some active mechanisms of Mtb persistence, such as cell wall and metabolic pathway remodeling. In one of the subpopulations, non-acid-fast Mtb have undergone significant reprogramming with the restoration of acid-fastness, lipoarabinomannan expression and replication in host cells of some patients after withdrawal of anti-TB drugs. Our data indicate the universal stress protein Rv2623 as a clinically relevant biomarker of Mtb that has lost acid-fastness in human lungs. The studies of Mtb survival, persistence, dormancy, and resumption and the identification of biomarkers characterizing these phenomena are very important concerning the development of vaccines and drug regimens with individualized management of patients for overcoming the resistance/tolerance crisis in anti-TB therapy.
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Affiliation(s)
- Elena G Ufimtseva
- Laboratory of Medical Biotechnology, Research Institute of Biochemistry, Federal Research Center of Fundamental and Translational Medicine, 2 Timakova Street, 630117 Novosibirsk, Russia
| | - Natalya I Eremeeva
- Institute of Disinfectology, F.F. Erisman Federal Scientific Center of Hygiene of the Federal Service on Surveillance for Consumer Rights Protection and Human Well-Being, 18a Nauchniy Proezd, 117246 Moscow, Russia
- Scientific Department, Ural Research Institute for Phthisiopulmonology, National Medical Research Center of Tuberculosis and Infectious Diseases of Ministry of Health of the Russian Federation, 50 XXII Partsyezda Street, 620039 Yekaterinburg, Russia
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6
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Wang Q, Li YL, Yin YL, Hu B, Yu CC, Wang ZD, Li YH, Xu CJ, Wang YB. Association of air pollutants and meteorological factors with tuberculosis: a national multicenter ecological study in China. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2023; 67:1629-1641. [PMID: 37535117 DOI: 10.1007/s00484-023-02524-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/17/2023] [Accepted: 07/14/2023] [Indexed: 08/04/2023]
Abstract
The impact of weather variability and air pollutants on tuberculosis (TB) has been a research hotspot. Previous studies have mostly been limited to a certain area or with a small sample size of cases, and multi-scale systematic studies are lacking. In this study, 14,816,329 TB cases were collected from 31 provinces in China between 2004 and 2018 to estimate the association between TB risk and meteorological factors and air pollutants using a two-stage time-series analysis. The impact and lagged time of meteorological factors and air pollutants on TB risk varied greatly in different provinces and regions. Overall cumulative exposure-response summary associations across 31 provinces suggested that high monthly mean relative humidity (RH) (66.8-82.4%, percentile56-100 (P56-100)), rainfall (316.5-331.1 mm, P96-100), PM2.5 exposure concentration (93.3-145.0 μg/m3, P58-100), and low monthly mean wind speed (1.6-2.1 m/s, P0-38) increased the risk of TB incidence, with a relative risk (RR) of 1.10 (95% CI: 1.04-1.16), 1.10 (95% CI: 1.03-1.16), 2.08 (95% CI: 1.18-3.65), and 2.06 (95% CI: 1.27-3.33), and attributable risk percent (AR%) of 9%, 9%, 52%, and 51%, respectively. Conversely, high monthly average wind speed (2.3-2.9 m/s, P54-100) and mean temperature (20.2-25.3 °C, P79-96), and low monthly average rainfall (2.4-25.2 mm, P0-7) and concentration of SO2 (8.1-21.2 μg/m3, P0-16) exposure decreased the risk of TB incidence, with an overall cumulative RR of 0.92 (95% CI: 0.87-0.98), 0.74 (95% CI: 0.59-0.94), 0.87 (95% CI: 0.79-0.95), and 0.72 (95% CI: 0.56-0.93), respectively. Our study provided insights into future planning of public health interventions for TB.
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Affiliation(s)
- Qian Wang
- School of Public Health, Xinxiang Medical University, Henan Province, Xinxiang, 453003, China
| | - Yan-Lin Li
- School of Public Health, Xinxiang Medical University, Henan Province, Xinxiang, 453003, China
| | - Ya-Ling Yin
- Sino-UK Joint Laboratory of Brain Function and Injury of Henan Province, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xinxiang Medical University, Henan Province, Xinxiang, 453003, China
| | - Bin Hu
- School of Public Health, Xinxiang Medical University, Henan Province, Xinxiang, 453003, China
| | - Chong-Chong Yu
- School of Public Health, Xinxiang Medical University, Henan Province, Xinxiang, 453003, China
| | - Zhen-de Wang
- School of Public Health, Weifang Medical University, Shandong Province, Weifang, 261053, China
- National Center for Tuberculosis Control and Prevention, China Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yu-Hong Li
- National Center for Tuberculosis Control and Prevention, China Center for Disease Control and Prevention, Beijing, 102206, China
| | - Chun-Jie Xu
- Institute of Medical Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical Sciences, Beijing, 100730, China.
| | - Yong-Bin Wang
- School of Public Health, Xinxiang Medical University, Henan Province, Xinxiang, 453003, China.
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7
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Pagani TD, Corrêa PR, Lima C, Gomes LHF, Schwarz MGA, Galvão TC, Degrave WM, Valadares NF, Mendonça-Lima L. Impact of Genomic Deletion RD16 on the Expression of the Mycobacterium bovis BCG Moreau VapBC47 Toxin-Antitoxin System. Curr Issues Mol Biol 2023; 45:6538-6549. [PMID: 37623231 PMCID: PMC10453824 DOI: 10.3390/cimb45080412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/23/2023] [Accepted: 05/27/2023] [Indexed: 08/26/2023] Open
Abstract
Mycobacterium bovis BCG is the only vaccine against tuberculosis. The variable forms of cultivation throughout the years, before seed-lots were developed, allowed in vitro evolution of the original strain, generating a family of vaccines with different phenotypic and genotypic characteristics. Molecular studies revealed regions of difference (RDs) in the genomes of the various BCG strains. This work aims to characterize the gene pair rv3407-rv3408 (vapB47-vapC47), coding for a toxin-antitoxin system of the VapBC family, and to evaluate possible transcriptional effects due to the adjacent BCG Moreau-specific genomic deletion RD16. We show that these genes are co-transcribed in BCG strains Moreau and Pasteur, and that the inactivation of an upstream transcriptional repressor (Rv3405c) due to RD16 has a polar effect, leading to increased vapBC47 expression. Furthermore, we detect VapB47 DNA binding in vitro, dependent on a 5' vapB47 sequence that contributes to a palindrome, spanning the promoter and coding region. Our data shed light on the regulation of VapBC systems and on the impact of the BCG Moreau RD16 deletion in the expression of adjacent genes, contributing to a better understanding of BCG Moreau physiology.
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Affiliation(s)
- Talita Duarte Pagani
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (T.D.P.); (P.R.C.); (C.L.); (L.H.F.G.); (M.G.A.S.); (W.M.D.)
| | - Paloma Rezende Corrêa
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (T.D.P.); (P.R.C.); (C.L.); (L.H.F.G.); (M.G.A.S.); (W.M.D.)
| | - Cristiane Lima
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (T.D.P.); (P.R.C.); (C.L.); (L.H.F.G.); (M.G.A.S.); (W.M.D.)
| | - Leonardo Henrique Ferreira Gomes
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (T.D.P.); (P.R.C.); (C.L.); (L.H.F.G.); (M.G.A.S.); (W.M.D.)
| | - Marcos Gustavo Araujo Schwarz
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (T.D.P.); (P.R.C.); (C.L.); (L.H.F.G.); (M.G.A.S.); (W.M.D.)
| | - Teca Calcagno Galvão
- Laboratório de Bacteriologia, Centro de Referência Prof. Hélio Fraga, Escola Nacional de Saúde Pública Sergio Arouca, Fiocruz, Rio de Janeiro 21041-210, RJ, Brazil;
| | - Wim Maurits Degrave
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (T.D.P.); (P.R.C.); (C.L.); (L.H.F.G.); (M.G.A.S.); (W.M.D.)
| | | | - Leila Mendonça-Lima
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (T.D.P.); (P.R.C.); (C.L.); (L.H.F.G.); (M.G.A.S.); (W.M.D.)
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8
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Sarkar S, Dyett B, Lakic B, Ball AS, Yeo LY, White JF, Soni S, Drummond CJ, Conn CE. Cubosome Lipid Nanocarriers As a Drug Delivery Vehicle for Intracellular Mycobacterium tuberculosis Infections. ACS APPLIED MATERIALS & INTERFACES 2023; 15:21819-21829. [PMID: 37018059 DOI: 10.1021/acsami.3c00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Mycobacterium tuberculosis (MTB) causes the infectious disease tuberculosis (TB), responsible for more deaths than any other single infectious disease in history. Intracellular MTB are slow growing and difficult to target with traditional antitubercular drugs, leading to the emergence of multidrug resistance in TB infection, which is a major global public health issue. Recent advances in innovative lipid nanotechnologies for drug delivery have demonstrated promising outcomes for chronic infectious diseases but have not yet been tested as potential delivery systems for intracellular infections such as TB. The current study evaluates the potential of monoolein (MO)-based cationic cubosomes for the encapsulation and delivery of the first line antitubercular drug rifampicin (RIF) against an MTB-H37Ra in vitro culture model. In particular, we show that the use of cationic cubosomes as delivery vehicles reduced the minimum inhibitory concentration (MIC) of RIF by 2-fold against actively replicating MTB-H37Ra (compared to that of the free drug) and also shortened the lifecycle duration of axenic MTB-H37Ra from 5 to 3 days. The cubosome-mediated delivery was also found to be effective against intracellular MTB-H37Ra within THP-1 human macrophages, with a 2.8 log reduction in viability of the bacilli after 6 days incubation at the MIC. The killing time was also reduced from 8 to 6 days without distressing the host macrophages. Mechanistic studies on the uptake of RIF-loaded cationic cubosomes using total internal reflection fluorescence microscopy (TIRFM) demonstrated the capacity of these lipid particles to effectively target intracellular bacteria. Overall, these results demonstrate that cationic cubosomes are a potent delivery system for the antitubercular drug RIF for therapeutic management of TB.
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Affiliation(s)
- Sampa Sarkar
- School of Science, STEM College, RMIT University, Melbourne, Victoria 3001, Australia
| | - Brendan Dyett
- School of Science, STEM College, RMIT University, Melbourne, Victoria 3001, Australia
| | - Biserka Lakic
- School of Science, STEM College, RMIT University, Melbourne, Victoria 3001, Australia
| | - Andrew S Ball
- School of Science, STEM College, RMIT University, Melbourne, Victoria 3001, Australia
| | - Leslie Y Yeo
- School of Engineering, STEM College, RMIT University, Melbourne, Victoria 3001, Australia
| | - Jacinta F White
- The Commonwealth Scientific and Industrial Research Organisation, Manufacturing, Clayton, Victoria 3169, Australia
| | - Sarvesh Soni
- School of Science, STEM College, RMIT University, Melbourne, Victoria 3001, Australia
| | - Calum J Drummond
- School of Science, STEM College, RMIT University, Melbourne, Victoria 3001, Australia
| | - Charlotte E Conn
- School of Science, STEM College, RMIT University, Melbourne, Victoria 3001, Australia
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9
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Rockstrom M, Lutz R, Dickeson K, O'Rorke EV, Narita M, Amram O, Chan ED. Fulminant pulmonary tuberculosis in a previously healthy young woman from the Marshall Islands: Potential risk factors. J Clin Tuberc Other Mycobact Dis 2023; 31:100351. [PMID: 36923241 PMCID: PMC10009541 DOI: 10.1016/j.jctube.2023.100351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
Abstract
A 19-year-old woman originally from the Republic of the Marshall Islands presented with diffuse pneumonia and acute hypoxemic respiratory failure. She dies one month into her hospitalization but the diagnosis of pulmonary tuberculosis (TB) was not made until one day before her demise. A contact investigation screened a total of 155 persons with 36 (23%) found to have latent TB infection and seven (4.5%) with active pulmonary TB. This unfortunate case provided the opportunity to analyze the epidemiology of TB in the state of Washington in the context of those who emigrated from the Marshall Islands. The development of fulminant pulmonary TB in this previously healthy young woman also provides a segue to discuss potential risk factors for TB in the index case that include: (i) foreign-born in a TB-endemic country; (ii) race and genetic factors; (iii) age; (iv) body habitus; (v) pregnancy; and (vi) use of glucocorticoids.
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Affiliation(s)
- Matthew Rockstrom
- University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Robert Lutz
- Washington State Department of Health, Tumwater, WA, United States
| | - Katie Dickeson
- Spokane Regional Health District, Spokane, WA, United States
| | - Erin V O'Rorke
- Elson S. Floyd College of Medicine, Spokane, WA, United States
| | - Masahiro Narita
- Public Health - Seattle & King County Public Health, and University of Washington, Seattle, WA, United States
| | - Ofer Amram
- Washington State University, Pullman, WA, United States
| | - Edward D Chan
- University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Academic Affairs, National Jewish Health, Denver, CO, United States.,Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, United States
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10
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Kia P, Ruman U, Pratiwi AR, Hussein MZ. Innovative Therapeutic Approaches Based on Nanotechnology for the Treatment and Management of Tuberculosis. Int J Nanomedicine 2023; 18:1159-1191. [PMID: 36919095 PMCID: PMC10008450 DOI: 10.2147/ijn.s364634] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 02/06/2023] [Indexed: 03/11/2023] Open
Abstract
Tuberculosis (TB), derived from bacterium named Mycobacterium tuberculosis, has become one of the worst infectious and contagious illnesses in the world after HIV/AIDS. Long-term therapy, a high pill burden, lack of compliance, and strict management regimens are disadvantages which resulted in the extensively drug-resistant (XDR) along with multidrug-resistant (MDR) in the treatment of TB. One of the main thrust areas for the current scenario is the development of innovative intervention tools for early diagnosis and therapeutics towards Mycobacterium tuberculosis (MTB). This review discusses various nanotherapeutic agents that have been developed for MTB diagnostics, anti-TB drugs and vaccine. Undoubtedly, the concept of employing nanoparticles (NPs) has strong potential in this therapy and offers impressive outcomes to conquer the disease. Nanocarriers with different types were designed for drug delivery applications via various administration methods. Controlling and maintaining the drug release might be an example of the benefits of utilizing a drug-loaded NP in TB therapy over conventional drug therapy. Furthermore, the drug-encapsulated NP is able to lessen dosage regimen and can resolve the problems of insufficient compliance. Over the past decade, NPs were developed in both diagnostic and therapeutic methods, while on the other hand, the therapeutic system has increased. These "theranostic" NPs were designed for nuclear imaging, optical imaging, ultrasound, imaging with magnetic resonance and the computed tomography, which includes both single-photon computed tomography and positron emission tomography. More specifically, the current manuscript focuses on the status of therapeutic and diagnostic approaches in the treatment of TB.
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Affiliation(s)
- Pooneh Kia
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Umme Ruman
- Nanomaterials Synthesis and Characterization Laboratory (NSCL), Institute of Nanoscience and Nanotechnology (ION2), Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Ariyati Retno Pratiwi
- Department of Oral Biology, Faculty of Dentistry, Universitas Brawijaya, Malang, Indonesia
| | - Mohd Zobir Hussein
- Nanomaterials Synthesis and Characterization Laboratory (NSCL), Institute of Nanoscience and Nanotechnology (ION2), Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
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11
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Sonika S, Singh S, Mishra S, Verma S. Toxin-antitoxin systems in bacterial pathogenesis. Heliyon 2023; 9:e14220. [PMID: 37101643 PMCID: PMC10123168 DOI: 10.1016/j.heliyon.2023.e14220] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Toxin-Antitoxin (TA) systems are abundant in prokaryotes and play an important role in various biological processes such as plasmid maintenance, phage inhibition, stress response, biofilm formation, and dormant persister cell generation. TA loci are abundant in pathogenic intracellular micro-organisms and help in their adaptation to the harsh host environment such as nutrient deprivation, oxidation, immune response, and antimicrobials. Several studies have reported the involvement of TA loci in establishing successful infection, intracellular survival, better colonization, adaptation to host stresses, and chronic infection. Overall, the TA loci play a crucial role in bacterial virulence and pathogenesis. Nonetheless, there are some controversies about the role of TA system in stress response, biofilm and persister formation. In this review, we describe the role of the TA systems in bacterial virulence. We discuss the important features of each type of TA system and the recent discoveries identifying key contributions of TA loci in bacterial pathogenesis.
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Acetylation of Cyclic AMP Receptor Protein by Acetyl Phosphate Modulates Mycobacterial Virulence. Microbiol Spectr 2023; 11:e0400222. [PMID: 36700638 PMCID: PMC9927398 DOI: 10.1128/spectrum.04002-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The success of Mycobacterium tuberculosis (Mtb) as a pathogen is partly attributed to its ability to sense and respond to dynamic host microenvironments. The cyclic AMP (cAMP) receptor protein (CRP) is closely related to the pathogenicity of Mtb and plays an important role in this process. However, the molecular mechanisms guiding the autoregulation and downstream target genes of CRP while Mtb responds to its environment are not fully understood. Here, it is demonstrated that the acetylation of conserved lysine 193 (K193) within the C-terminal DNA-binding domain of CRP reduces its DNA-binding ability and inhibits transcriptional activity. The reversible acetylation status of CRP K193 was shown to significantly affect mycobacterial growth phenotype, alter the stress response, and regulate the expression of biologically relevant genes using a CRP K193 site-specific mutation. Notably, the acetylation level of K193 decreases under CRP-activating conditions, including the presence of cAMP, low pH, high temperature, and oxidative stress, suggesting that microenvironmental signals can directly regulate CRP K193 acetylation. Both cell- and murine-based infection assays confirmed that CRP K193 is critical to the regulation of Mtb virulence. Furthermore, the acetylation of CRP K193 was shown to be dependent on the intracellular metabolic intermediate acetyl phosphate (AcP), and deacetylation was mediated by NAD+-dependent deacetylases. These findings indicate that AcP-mediated acetylation of CRP K193 decreases CRP activity and negatively regulates the pathogenicity of Mtb. We believe that the underlying mechanisms of cross talk between transcription, posttranslational modifications, and metabolites are a common regulatory mechanism for pathogenic bacteria. IMPORTANCE Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, and the ability of Mtb to survive harsh host conditions has been the subject of intensive research. As a result, we explored the molecular mechanisms guiding downstream target genes of CRP when Mtb responds to its environment. Our study makes a contribution to the literature because we describe the role of acetylated K193 in regulating its binding affinity to target DNA and influencing the virulence of mycobacteria. We discovered that mycobacteria can regulate their pathogenicity through the reversible acetylation of CRP K193 and that this reversible acetylation is mediated by AcP and a NAD+-dependent deacetylase. The regulation of CRPMtb by posttranslational modifications, at the transcriptional level, and by metabolic intermediates contribute to a better understanding of its role in the survival and pathogenicity of mycobacteria.
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Chauhan NK, Anand A, Sharma A, Dhiman K, Gosain TP, Singh P, Singh P, Khan E, Chattopadhyay G, Kumar A, Sharma D, Ashish, Sharma TK, Singh R. Structural and Functional Characterization of Rv0792c from Mycobacterium tuberculosis: Identifying Small Molecule Inhibitor against HutC Protein. Microbiol Spectr 2023; 11:e0197322. [PMID: 36507689 PMCID: PMC9927256 DOI: 10.1128/spectrum.01973-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In order to adapt in host tissues, microbial pathogens regulate their gene expression through a variety of transcription factors. Here, we have functionally characterized Rv0792c, a HutC homolog from Mycobacterium tuberculosis. In comparison to the parental strain, a strain of M. tuberculosis with a Rv0792c mutant was compromised for survival upon exposure to oxidative stress and infection in guinea pigs. RNA sequencing analysis revealed that Rv0792c regulates the expression of genes involved in stress adaptation and virulence of M. tuberculosis. Solution small-angle X-ray scattering (SAXS) data-steered model building confirmed that the C-terminal region plays a pivotal role in dimer formation. Systematic evolution of ligands by exponential enrichment (SELEX) resulted in the identification of single-strand DNA (ssDNA) aptamers that can be used as a tool to identify small-molecule inhibitors targeting Rv0792c. Using SELEX and SAXS data-based modeling, we identified residues essential for Rv0792c's aptamer binding activity. In this study, we also identified I-OMe-Tyrphostin as an inhibitor of Rv0792c's aptamer and DNA binding activity. The identified small molecule reduced the growth of intracellular M. tuberculosis in macrophages. The present study thus provides a detailed shape-function characterization of a HutC family of transcription factor from M. tuberculosis. IMPORTANCE Prokaryotes encode a large number of GntR family transcription factors that are involved in various fundamental biological processes, including stress adaptation and pathogenesis. Here, we investigated the structural and functional role of Rv0792c, a HutC homolog from M. tuberculosis. We demonstrated that Rv0792c is essential for M. tuberculosis to adapt to oxidative stress and establish disease in guinea pigs. Using a systematic evolution of ligands by exponential enrichment (SELEX) approach, we identified ssDNA aptamers from a random ssDNA library that bound to Rv0792c protein. These aptamers were thoroughly characterized using biochemical and biophysical assays. Using SAXS, we determined the structural model of Rv0792c in both the presence and absence of the aptamers. Further, using a combination of SELEX and SAXS methodologies, we identified I-OMe-Tyrphostin as a potential inhibitor of Rv0792c. Here we provide a detailed functional characterization of a transcription factor belonging to the HutC family from M. tuberculosis.
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Affiliation(s)
- Neeraj Kumar Chauhan
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Anjali Anand
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Arun Sharma
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Kanika Dhiman
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Tannu Priya Gosain
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Prashant Singh
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Padam Singh
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Eshan Khan
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indoregrid.450280.b, Indore, India
| | | | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indoregrid.450280.b, Indore, India
| | - Deepak Sharma
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Ashish
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Tarun Kumar Sharma
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Ramandeep Singh
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
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Huang T, Wang L, Wang F, Shen X, Wang L. LC-MS/MS method assay for simultaneous determination of the pretomanid and pyrazinamide in rat plasma by LC-MS/MS: Assessment of pharmacokinetic drug-drug interaction study. ACTA CHROMATOGR 2022. [DOI: 10.1556/1326.2022.01087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
AbstractIn the present study, an LC-MS/MS method allowing to quantify pretomanid and pyrazinamide simultaneously in rat plasma was developed. Chromatographic separation was achieved on an Agilent Eclipse plus C18 column (100 mm × 2.1 mm, 3.5 μm; Agilent, USA) and maintained at 30 °C. Multiple reaction monitoring (MRM) using positive-ion ESI mode to monitor ion transitions of m/z 360.1 → m/z 175.1 for pretomanid, m/z 124.1 → m/z 81.0 for pyrazinamide, m/z 172.1 → m/z 128.1 for metronidazole (IS). The calibration curves showed good linear relationships over the concentration range of 50–7,500 ng mL−1 for pretomanid and 500–75,000 ng mL−1 for pyrazinamide. The precision and accuracy were below 15% and within ±15% of the nominal concentrations, respectively. The selectivity, recovery and matrix effect of this method were all within acceptable limits of bioanalytics. The method was applied to the analysis of plasma samples from pharmacokinetic studies in rats. The results show that the main pharmacokinetic parameters of pyrazinamide, namely, Tmax, t1/2, and AUC(0–t), decreased in the combined group than in the alone group.
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Affiliation(s)
- Tao Huang
- Medical School, Huanghe Science and Technology University, Zhengzhou, Henan Province 450063, PR China
| | - Li Wang
- Medical School, Huanghe Science and Technology University, Zhengzhou, Henan Province 450063, PR China
| | - Fang Wang
- School of Medicine, Shaanxi Energy Institute, Xianyang, Shaanxi Province 712000, PR China
| | - Xin Shen
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Libin Wang
- Medical School, Huanghe Science and Technology University, Zhengzhou, Henan Province 450063, PR China
- School of Medicine, Shaanxi Energy Institute, Xianyang, Shaanxi Province 712000, PR China
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Umar Ibrahim A, Al-Turjman F, Ozsoz M, Serte S. Computer aided detection of tuberculosis using two classifiers. BIOMED ENG-BIOMED TE 2022; 67:513-524. [PMID: 36165698 DOI: 10.1515/bmt-2021-0310] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 09/13/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Tuberculosis caused by Mycobacterium tuberculosis have been a major challenge for medical and healthcare sectors in many underdeveloped countries with limited diagnosis tools. Tuberculosis can be detected from microscopic slides and chest X-ray but as a result of the high cases of tuberculosis, this method can be tedious for both microbiologist and Radiologist and can lead to miss-diagnosis. The main objective of this study is to addressed these challenges by employing Computer Aided Detection (CAD) using Artificial Intelligence-driven models which learn features based on convolution and result in an output with high accuracy. METHOD In this paper, we described automated discrimination of X-ray and microscopic slide images of tuberculosis into positive and negative cases using pretrained AlexNet Models. The study employed Chest X-ray dataset made available on Kaggle repository and microscopic slide images from both Near East university hospital and Kaggle repository. RESULTS For classification of tuberculosis and healthy microscopic slide using AlexNet+Softmax, the model achieved accuracy of 98.14%. For classification of tuberculosis and healthy microscopic slide using AlexNet+SVM, the model achieved 98.73% accuracy. For classification of tuberculosis and healthy chest X-ray images using AlexNet+Softmax, the model achieved accuracy of 98.19%. For classification of tuberculosis and healthy chest X-ray images using AlexNet+SVM, the model achieved 98.38% accuracy. CONCLUSION The result obtained has shown to outperformed several studies in the current literature. Future studies will attempt to integrate Internet of Medical Things (IoMT) for the design of IoMT/AI-enabled platform for detection of Tuberculosis from both X-ray and Microscopic slide images.
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Affiliation(s)
| | - Fadi Al-Turjman
- Department of Artificial Intelligence, Research Center for AI and IoT, Near East University, Nicosia, Turkey
| | - Mehmet Ozsoz
- Department of Biomedical Engineering, Near East University, Nicosia, Turkey
| | - Sertan Serte
- Department of Electrical and Electronics Engineering, Near East University, Nicosia, Turkey
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Kuan MM. Applying SARIMA, ETS, and hybrid models for prediction of tuberculosis incidence rate in Taiwan. PeerJ 2022; 10:e13117. [PMID: 36164599 PMCID: PMC9508881 DOI: 10.7717/peerj.13117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/23/2022] [Indexed: 01/12/2023] Open
Abstract
Background Tuberculosis (TB) remained one of the world's most deadly chronic communicable diseases. Future TB incidence prediction is a benefit for intervention options and resource-allocation planning. We aimed to develop rapid univariate prediction models for epidemics forecasting employment. Methods The surveillance data regarding Taiwan monthly TB incidence rates which from January 2005 to June 2017 were utilized for simulation modelling and from July 2017 to December 2020 for model validation. The modeling approaches including the Seasonal Autoregressive Integrated Moving Average (SARIMA), the Exponential Smoothing (ETS), and SARIMA-ETS hybrid algorithms were constructed and compared. The modeling performance of in-sample simulating training sets and pseudo-out-of-sample validating sets were evaluated by metrics of the root mean square error (RMSE), mean absolute percentage error (MAPE), mean absolute error (MAE), and mean absolute scaled error (MASE). Results A total of 191,526 TB cases with a highest incidence rate in 2005 (72.5 per 100,000 person-year) and lowest in 2020 (33.2 per 100,000 person-year), from January-2005 to December-2020 showed a seasonality and steadily declining trend in Taiwan. The monthly incidence rates data were utilized to formulate these forecasting models. Through stepwise screening and assessing of the accuracy metrics, the optimized SARIMA(3,0,0)(2,1,0)12, ETS(A,A,A) and SARIMA-ETS-hybrid models were respectively selected as the candidate models. Regarding the outcome assessment of model performance, the SARIMA-ETS-hybrid model outperformed the ARIMA and ETS in the short term prediction with metrics of RMSE, MAE MAPE, and MASE of 0.084%, 0.067%, 0.646%, and 0.870%, during the pseudo-out-of-sample forecasting period. After projecting ahead to the long term forecasting TB incidence rates, ETS model showed the best performance resulting as a 41.69% (range: 22.1-56.38%) reduction of TB epidemics in 2025 and a 54.48% (range: 33.7-68.7%) reduction in 2030 compared with the 2015 levels. Conclusion This time series modeling might offer us a rapid surveillance tool for facilitating WHO's future TB elimination milestone. Our proposed SARIMA-ETS or ETS model outperformed the SARIMA in predicting less or 12-30 months ahead of epidemics, and all models showed better in short or medium-term forecasting than long-term forecasting.
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Ncube P, Bagheri B, Goosen WJ, Miller MA, Sampson SL. Evidence, Challenges, and Knowledge Gaps Regarding Latent Tuberculosis in Animals. Microorganisms 2022; 10:microorganisms10091845. [PMID: 36144447 PMCID: PMC9503773 DOI: 10.3390/microorganisms10091845] [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: 08/12/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 01/30/2023] Open
Abstract
Mycobacterium bovis and other Mycobacterium tuberculosis complex (MTBC) pathogens that cause domestic animal and wildlife tuberculosis have received considerably less attention than M. tuberculosis, the primary cause of human tuberculosis (TB). Human TB studies have shown that different stages of infection can exist, driven by host–pathogen interactions. This results in the emergence of heterogeneous subpopulations of mycobacteria in different phenotypic states, which range from actively replicating (AR) cells to viable but slowly or non-replicating (VBNR), viable but non-culturable (VBNC), and dormant mycobacteria. The VBNR, VBNC, and dormant subpopulations are believed to underlie latent tuberculosis (LTB) in humans; however, it is unclear if a similar phenomenon could be happening in animals. This review discusses the evidence, challenges, and knowledge gaps regarding LTB in animals, and possible host–pathogen differences in the MTBC strains M. tuberculosis and M. bovis during infection. We further consider models that might be adapted from human TB research to investigate how the different phenotypic states of bacteria could influence TB stages in animals. In addition, we explore potential host biomarkers and mycobacterial changes in the DosR regulon, transcriptional sigma factors, and resuscitation-promoting factors that may influence the development of LTB.
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18
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Weng Y, Shepherd D, Liu Y, Krishnan N, Robertson BD, Platt N, Larrouy-Maumus G, Platt FM. Inhibition of the Niemann-Pick C1 protein is a conserved feature of multiple strains of pathogenic mycobacteria. Nat Commun 2022; 13:5320. [PMID: 36085278 PMCID: PMC9463166 DOI: 10.1038/s41467-022-32553-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 08/04/2022] [Indexed: 11/12/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) survives and replicates within host macrophages (MΦ) and subverts multiple antimicrobial defense mechanisms. Previously, we reported that lipids shed by pathogenic mycobacteria inhibit NPC1, the lysosomal membrane protein deficient in the lysosomal storage disorder Niemann-Pick disease type C (NPC). Inhibition of NPC1 leads to a drop in lysosomal calcium levels, blocking phagosome-lysosome fusion leading to mycobacterial survival. We speculated that the production of specific cell wall lipid(s) that inhibit NPC1 could have been a critical step in the evolution of pathogenicity. We therefore investigated whether lipid extracts from clinical Mtb strains from multiple Mtb lineages, Mtb complex (MTBC) members and non-tubercular mycobacteria (NTM) inhibit the NPC pathway. We report that inhibition of the NPC pathway was present in all clinical isolates from Mtb lineages 1, 2, 3 and 4, Mycobacterium bovis and the NTM, Mycobacterium abscessus and Mycobacterium avium. However, lipid extract from Mycobacterium canettii, which is considered to resemble the common ancestor of the MTBC did not inhibit the NPC1 pathway. We conclude that the evolution of NPC1 inhibitory mycobacterial cell wall lipids evolved early and post divergence from Mycobacterium canettii-related mycobacteria and that this activity contributes significantly to the promotion of disease.
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Affiliation(s)
- Yuzhe Weng
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Dawn Shepherd
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Yi Liu
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Nitya Krishnan
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Imperial College London, Flowers Building, London, SW7 2AZ, UK
| | - Brian D Robertson
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Imperial College London, Flowers Building, London, SW7 2AZ, UK
| | - Nick Platt
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Frances M Platt
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.
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Liu Y, Lu Y, Xu Z, Ma X, Chen X, Liu W. Repurposing of the gold drug auranofin and a review of its derivatives as antibacterial therapeutics. Drug Discov Today 2022; 27:1961-1973. [DOI: 10.1016/j.drudis.2022.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/22/2022] [Accepted: 02/16/2022] [Indexed: 12/18/2022]
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20
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Zorzan I, Del Favero S, Giaretta A, Manganelli R, Di Camillo B, Schenato L. Mathematical modelling of SigE regulatory network reveals new insights into bistability of mycobacterial stress response. BMC Bioinformatics 2021; 22:558. [PMID: 34798803 PMCID: PMC8605609 DOI: 10.1186/s12859-021-04372-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 09/11/2021] [Indexed: 12/19/2022] Open
Abstract
Background The ability to rapidly adapt to adverse environmental conditions represents the key of success of many pathogens and, in particular, of Mycobacterium tuberculosis. Upon exposition to heat shock, antibiotics or other sources of stress, appropriate responses in terms of genes transcription and proteins activity are activated leading part of a genetically identical bacterial population to express a different phenotype, namely to develop persistence. When the stress response network is mathematically described by an ordinary differential equations model, development of persistence in the bacterial population is associated with bistability of the model, since different emerging phenotypes are represented by different stable steady states. Results In this work, we develop a mathematical model of SigE stress response network that incorporates interactions not considered in mathematical models currently available in the literature. We provide, through involved analytical computations, accurate approximations of the system’s nullclines, and exploit the obtained expressions to determine, in a reliable though computationally efficient way, the number of equilibrium points of the system. Conclusions Theoretical analysis and perturbation experiments point out the crucial role played by the degradation pathway involving RseA, the anti-sigma factor of SigE, for coexistence of two stable equilibria and the emergence of bistability. Our results also indicate that a fine control on RseA concentration is a necessary requirement in order for the system to exhibit bistability. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04372-5.
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Affiliation(s)
- Irene Zorzan
- Department of Information Engineering, University of Padova, 35131, Padova, Italy.
| | - Simone Del Favero
- Department of Information Engineering, University of Padova, 35131, Padova, Italy
| | - Alberto Giaretta
- Department of Information Engineering, University of Padova, 35131, Padova, Italy
| | - Riccardo Manganelli
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, 35131, Padova, Italy.,Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro (Padova), Italy
| | - Luca Schenato
- Department of Information Engineering, University of Padova, 35131, Padova, Italy
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21
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Patra P, Klumpp S. Role of bacterial persistence in spatial population expansion. Phys Rev E 2021; 104:034401. [PMID: 34654134 DOI: 10.1103/physreve.104.034401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/19/2021] [Indexed: 11/07/2022]
Abstract
Bacterial persistence, tolerance to antibiotics via stochastic phenotype switching, provides a survival strategy and a fitness advantage in temporally fluctuating environments. Here we study its possible benefit in spatially varying environments using a Fisher wave approach. We study the spatial expansion of a population with stochastic switching between two phenotypes in spatially homogeneous conditions and in the presence of an antibiotic barrier. Our analytical results show that the expansion speed in growth-supporting conditions depends on the fraction of persister cells at the leading edge of the population wave. The leading edge contains a small fraction of persister cells, keeping the effect on the expansion speed minimal. The fraction of persisters increases gradually in the interior of the wave. This persister pool benefits the population when it is stalled by an antibiotic environment. In that case, the presence of persister enables the population to spread deeper into the antibiotic region and to cross an antibiotic region more rapidly. Further we observe that optimal switching rates maximize the expansion speed of the population in spatially varying environments with alternating regions of growth permitting conditions and antibiotics. Overall, our results show that stochastic switching can promote population expansion in the presence of antibiotic barriers or other stressful environments.
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Affiliation(s)
- Pintu Patra
- Institute for Theoretical Physics, Heidelberg University, Heidelberg 69120, Germany
| | - Stefan Klumpp
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen 37077, Germany
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Interception of host fatty acid metabolism by mycobacteria under hypoxia to suppress anti-TB immunity. Cell Discov 2021; 7:90. [PMID: 34608123 PMCID: PMC8490369 DOI: 10.1038/s41421-021-00301-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/01/2021] [Indexed: 02/08/2023] Open
Abstract
Pathogenic mycobacteria induce the formation of hypoxic granulomas during latent tuberculosis (TB) infection, in which the immune system contains, but fails to eliminate the mycobacteria. Fatty acid metabolism-related genes are relatively overrepresented in the mycobacterial genome and mycobacteria favor host-derived fatty acids as nutrient sources. However, whether and how mycobacteria modulate host fatty acid metabolism to drive granuloma progression remains unknown. Here, we report that mycobacteria under hypoxia markedly secrete the protein Rv0859/MMAR_4677 (Fatty-acid degradation A, FadA), which is also enriched in tuberculous granulomas. FadA acts as an acetyltransferase that converts host acetyl-CoA to acetoacetyl-CoA. The reduced acetyl-CoA level suppresses H3K9Ac-mediated expression of the host proinflammatory cytokine Il6, thus promoting granuloma progression. Moreover, supplementation of acetate increases the level of acetyl-CoA and inhibits the formation of granulomas. Our findings suggest an unexpected mechanism of a hypoxia-induced mycobacterial protein suppressing host immunity via modulation of host fatty acid metabolism and raise the possibility of a novel therapeutic strategy for TB infection.
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Wang X, Bittner T, Milanov M, Kaul L, Mundinger S, Koch HG, Jessen-Trefzer C, Jessen HJ. Pyridinium Modified Anthracenes and Their Endoperoxides Provide a Tunable Scaffold with Activity against Gram-Positive and Gram-Negative Bacteria. ACS Infect Dis 2021; 7:2073-2080. [PMID: 34291902 DOI: 10.1021/acsinfecdis.1c00263] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Due to the emergence of multidrug resistant bacteria, the development of new antibiotics is required. We introduce here asymmetrically modified positively charged bis(methylpyridinium) anthracenes as a novel tunable scaffold, in which the two positive charges can be placed at a defined distance and angle. Our structure-activity relationship reveals that coupling the methylpyridiniums with alkynyl linkers to the central anthracene unit yields antibacterial compounds against a wide range of bacteria, including Escherichia coli, Staphylococcus aureus, and Staphylococcus epidermidis. Also, different mycobacteria, such as Mycobacterium smegmatis and Mycobacterium tuberculosis, are efficiently targeted by these compounds. The antibacterial activity depends on the number of alkynyl linkers and consequently also on the distance of the positive charges in the rigid anthracene scaffold. Additionally, the formation of an anthracene endoperoxide further increases the antibacterial activity, likely due to the release of toxic singlet oxygen that converts the endoperoxide back to the antibacterial anthracene scaffold with half-lives of several hours.
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Affiliation(s)
- Xuan Wang
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Tamara Bittner
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Martin Milanov
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
| | - Laurine Kaul
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Technology and Biopharmacy, University of Freiburg, 79104 Freiburg, Germany
- Richter Lab, Department of Surgery, Basil Hetzel Institute for Translational Health Research, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5000, Australia
| | - Stephan Mundinger
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Claudia Jessen-Trefzer
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Henning J. Jessen
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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Wang H, Conover GM, Han SI, Sacchettini JC, Han A. Development of single-cell-level microfluidic technology for long-term growth visualization of living cultures of Mycobacterium smegmatis. MICROSYSTEMS & NANOENGINEERING 2021; 7:37. [PMID: 34567751 PMCID: PMC8433163 DOI: 10.1038/s41378-021-00262-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 01/15/2021] [Accepted: 02/01/2021] [Indexed: 06/13/2023]
Abstract
Analysis of growth and death kinetics at single-cell resolution is a key step in understanding the complexity of the nonreplicating growth phenotype of the bacterial pathogen Mycobacterium tuberculosis. Here, we developed a single-cell-resolution microfluidic mycobacterial culture device that allows time-lapse microscopy-based long-term phenotypic visualization of the live replication dynamics of mycobacteria. This technology was successfully applied to monitor the real-time growth dynamics of the fast-growing model strain Mycobacterium smegmatis (M. smegmatis) while subjected to drug treatment regimens during continuous culture for 48 h inside the microfluidic device. A clear morphological change leading to significant swelling at the poles of the bacterial membrane was observed during drug treatment. In addition, a small subpopulation of cells surviving treatment by frontline antibiotics was observed to recover and achieve robust replicative growth once regular culture media was provided, suggesting the possibility of identifying and isolating nonreplicative mycobacteria. This device is a simple, easy-to-use, and low-cost solution for studying the single-cell phenotype and growth dynamics of mycobacteria, especially during drug treatment.
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Affiliation(s)
- Han Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, 100084 Beijing, China
| | - Gloria M. Conover
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843 USA
- Present Address: Department of Medical Education, Health Sciences Center, Texas A&M University, Bryan, TX 77807 USA
| | - Song-I Han
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843 USA
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843 USA
| | - Arum Han
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843 USA
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843 USA
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Rohman A, Dijkstra BW. Application of microbial 3-ketosteroid Δ 1-dehydrogenases in biotechnology. Biotechnol Adv 2021; 49:107751. [PMID: 33823268 DOI: 10.1016/j.biotechadv.2021.107751] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/27/2021] [Accepted: 04/02/2021] [Indexed: 11/19/2022]
Abstract
3-Ketosteroid Δ1-dehydrogenase catalyzes the 1(2)-dehydrogenation of 3-ketosteroid substrates using flavin adenine dinucleotide as a cofactor. The enzyme plays a crucial role in microbial steroid degradation, both under aerobic and anaerobic conditions, by initiating the opening of the steroid nucleus. Indeed, many microorganisms are known to possess one or more 3-ketosteroid Δ1-dehydrogenases. In the pharmaceutical industry, 3-ketosteroid Δ1-dehydrogenase activity is exploited to produce Δ1-3-ketosteroids, a class of steroids that display various biological activities. Many of them are used as active pharmaceutical ingredients in drug products, or as key precursors to produce pharmaceutically important steroids. Since 3-ketosteroid Δ1-dehydrogenase activity requires electron acceptors, among other considerations, Δ1-3-ketosteroid production has been industrially implemented using whole-cell fermentation with growing or metabolically active resting cells, in which the electron acceptors are available, rather than using the isolated enzyme. In this review we discuss biotechnological applications of microbial 3-ketosteroid Δ1-dehydrogenases, covering commonly used steroid-1(2)-dehydrogenating microorganisms, the bioprocess for preparing Δ1-3-ketosteroids, genetic engineering of 3-ketosteroid Δ1-dehydrogenases and related genes for constructing new, productive industrial strains, and microbial fermentation strategies for enhancing the product yield. Furthermore, we also highlight the recent development in the use of isolated 3-ketosteroid Δ1-dehydrogenases combined with a FAD cofactor regeneration system. Finally, in a somewhat different context, we summarize the role of 3-ketosteroid Δ1-dehydrogenase in cholesterol degradation by Mycobacterium tuberculosis and other mycobacteria. Because the enzyme is essential for the pathogenicity of these organisms, it may be a potential target for drug development to combat mycobacterial infections.
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Affiliation(s)
- Ali Rohman
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia; Laboratory of Proteomics, Research Center for Bio-Molecule Engineering (BIOME), Universitas Airlangga, Surabaya 60115, Indonesia; Laboratory of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, the Netherlands.
| | - Bauke W Dijkstra
- Laboratory of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, the Netherlands.
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Chaperone-Mediated Stress Sensing in Mycobacterium tuberculosis Enables Fast Activation and Sustained Response. mSystems 2021; 6:6/1/e00979-20. [PMID: 33594002 PMCID: PMC8561658 DOI: 10.1128/msystems.00979-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dynamical properties of gene regulatory networks are tuned to ensure bacterial survival. In mycobacteria, the MprAB-σE network responds to the presence of stressors, such as surfactants that cause surface stress. Positive feedback loops in this network were previously predicted to cause hysteresis, i.e., different responses to identical stressor levels for prestressed and unstressed cells. Here, we show that hysteresis does not occur in nonpathogenic Mycobacterium smegmatis but does occur in Mycobacterium tuberculosis However, the observed rapid temporal response in M. tuberculosis is inconsistent with the model predictions. To reconcile these observations, we implement a recently proposed mechanism for stress sensing, namely, the release of MprB from the inhibitory complex with the chaperone DnaK upon the stress exposure. Using modeling and parameter fitting, we demonstrate that this mechanism can accurately describe the experimental observations. Furthermore, we predict perturbations in DnaK expression that can strongly affect dynamical properties. Experiments with these perturbations agree with model predictions, confirming the role of DnaK in fast and sustained response.IMPORTANCE Gene regulatory networks controlling stress response in mycobacterial species have been linked to persistence switches that enable bacterial dormancy within a host. However, the mechanistic basis of switching and stress sensing is not fully understood. In this paper, combining quantitative experiments and mathematical modeling, we uncover how interactions between two master regulators of stress response-the MprAB two-component system (TCS) and the alternative sigma factor σE-shape the dynamical properties of the surface stress network. The result show hysteresis (history dependence) in the response of the pathogenic bacterium M. tuberculosis to surface stress and lack of hysteresis in nonpathogenic M. smegmatis Furthermore, to resolve the apparent contradiction between the existence of hysteresis and fast activation of the response, we utilize a recently proposed role of chaperone DnaK in stress sensing. These result leads to a novel system-level understanding of bacterial stress response dynamics.
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Sawyer EB, Phelan JE, Clark TG, Cortes T. A snapshot of translation in Mycobacterium tuberculosis during exponential growth and nutrient starvation revealed by ribosome profiling. Cell Rep 2021; 34:108695. [PMID: 33535039 PMCID: PMC7856553 DOI: 10.1016/j.celrep.2021.108695] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/20/2020] [Accepted: 01/05/2021] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis, which causes tuberculosis, can undergo prolonged periods of non-replicating persistence in the host. The mechanisms underlying this are not fully understood, but translational regulation is thought to play a role. A large proportion of mRNA transcripts expressed in M. tuberculosis lack canonical bacterial translation initiation signals, but little is known about the implications of this for fine-tuning of translation. Here, we perform ribosome profiling to characterize the translational landscape of M. tuberculosis under conditions of exponential growth and nutrient starvation. Our data reveal robust, widespread translation of non-canonical transcripts and point toward different translation initiation mechanisms compared to canonical Shine-Dalgarno transcripts. During nutrient starvation, patterns of ribosome recruitment vary, suggesting that regulation of translation in this pathogen is more complex than originally thought. Our data represent a rich resource for others seeking to understand translational regulation in bacterial pathogens.
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Affiliation(s)
- Elizabeth B Sawyer
- TB Centre and Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Jody E Phelan
- TB Centre and Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Taane G Clark
- TB Centre and Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK; Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Teresa Cortes
- TB Centre and Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
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Pathak L, Das B. Initiation of Post-Primary Tuberculosis of the Lungs: Exploring the Secret Role of Bone Marrow Derived Stem Cells. Front Immunol 2021; 11:594572. [PMID: 33584661 PMCID: PMC7873989 DOI: 10.3389/fimmu.2020.594572] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/03/2020] [Indexed: 01/01/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative organism of pulmonary tuberculosis (PTB) now infects more than half of the world population. The efficient transmission strategy of the pathogen includes first remaining dormant inside the infected host, next undergoing reactivation to cause post-primary tuberculosis of the lungs (PPTBL) and then transmit via aerosol to the community. In this review, we are exploring recent findings on the role of bone marrow (BM) stem cell niche in Mtb dormancy and reactivation that may underlie the mechanisms of PPTBL development. We suggest that pathogen's interaction with the stem cell niche may be relevant in potential inflammation induced PPTBL reactivation, which need significant research attention for the future development of novel preventive and therapeutic strategies for PPTBL, especially in a post COVID-19 pandemic world. Finally, we put forward potential animal models to study the stem cell basis of Mtb dormancy and reactivation.
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Affiliation(s)
- Lekhika Pathak
- Department of Stem Cell and Infectious Diseases, KaviKrishna Laboratory, Guwahati Biotech Park, Indian Institute of Technology, Guwahati, India
- KaviKrishna Telemedicine Care, Sualkuchi, India
| | - Bikul Das
- Department of Stem Cell and Infectious Diseases, KaviKrishna Laboratory, Guwahati Biotech Park, Indian Institute of Technology, Guwahati, India
- KaviKrishna Telemedicine Care, Sualkuchi, India
- Department of Stem Cell and Infection, Thoreau Laboratory for Global Health, M2D2, University of Massachusetts, Lowell, MA, United States
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Danelishvili L, Armstrong E, Miyasako E, Jeffrey B, Bermudez LE. Exposure of Mycobacterium avium subsp. homonissuis to Metal Concentrations of the Phagosome Environment Enhances the Selection of Persistent Subpopulation to Antibiotic Treatment. Antibiotics (Basel) 2020; 9:antibiotics9120927. [PMID: 33352715 PMCID: PMC7767021 DOI: 10.3390/antibiotics9120927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/15/2020] [Accepted: 12/18/2020] [Indexed: 01/20/2023] Open
Abstract
Mycobacterium avium subspecies hominissuis (MAH) is an opportunistic intracellular pathogen causing infections in individuals with chronic lung conditions and patients with immune-deficient disorders. The treatment of MAH infections is prolonged and outcomes many times are suboptimal. The reason for the extended treatment is complex and reflects the inability of current antimicrobials to clear diverse phenotypes of MAH quickly, particularly, the subpopulation of susceptible but drug-tolerant bacilli where the persistent fitness to anti-MAH drugs is stimulated and enhanced by the host environmental stresses. In order to enhance the pathogen killing, we need to understand the fundamentals of persistence mechanism and conditions that can initiate the drug-tolerance phenotype in mycobacteria. MAH can influence the intracellular environment through manipulation of the metal concentrations in the phagosome of infected macrophages. While metals play important role and are crucial for many cellular functions, little is known how vacuole elements influence persistence state of MAH during intracellular growth. In this study, we utilized the in vitro model mimicking the metal concentrations and pH of MAH phagosome at 1 h and 24 h post-infection to distinguish if metals encountered in phagosome could act as a trigger factor for persistence phenotype. Antibiotic treatment of metal mix exposed MAH demonstrates that metals of the phagosome environment can enhance the persistence state, and greater number of tolerant bacteria is recovered from the 24 h metal mix when compared to the viable pathogen number in the 1 h metal mix and 7H9 growth control. In addition, bacterial phenotype induced by the 24 h metal mix increases MAH tolerance to macrophage killing in TNF-α and IFN-γ activated cells, confirming presence of persistent MAH in the 24 h metal mix condition. This work shows that the phagosome environment can promote persistence population in MAH, and that the population differs dependent on a concentration of metals.
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Affiliation(s)
- Lia Danelishvili
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA; (E.A.); (E.M.)
- Correspondence: (L.D.); (L.E.B.); Tel.: +1-(541)-737-6544 (L.D.); +1-(541)-737-6532 (L.E.B.); Fax: +1-(541)-737-2730 (L.D.); +1-(541)-737-2730 (L.E.B.)
| | - Elyssa Armstrong
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA; (E.A.); (E.M.)
| | - Emily Miyasako
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA; (E.A.); (E.M.)
| | - Brendan Jeffrey
- Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA;
| | - Luiz E. Bermudez
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA; (E.A.); (E.M.)
- Department of Microbiology, College of Sciences, Oregon State University, Corvallis, OR 97331, USA
- Correspondence: (L.D.); (L.E.B.); Tel.: +1-(541)-737-6544 (L.D.); +1-(541)-737-6532 (L.E.B.); Fax: +1-(541)-737-2730 (L.D.); +1-(541)-737-2730 (L.E.B.)
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Kostyuk AI, Panova AS, Kokova AD, Kotova DA, Maltsev DI, Podgorny OV, Belousov VV, Bilan DS. In Vivo Imaging with Genetically Encoded Redox Biosensors. Int J Mol Sci 2020; 21:E8164. [PMID: 33142884 PMCID: PMC7662651 DOI: 10.3390/ijms21218164] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
Redox reactions are of high fundamental and practical interest since they are involved in both normal physiology and the pathogenesis of various diseases. However, this area of research has always been a relatively problematic field in the context of analytical approaches, mostly because of the unstable nature of the compounds that are measured. Genetically encoded sensors allow for the registration of highly reactive molecules in real-time mode and, therefore, they began a new era in redox biology. Their strongest points manifest most brightly in in vivo experiments and pave the way for the non-invasive investigation of biochemical pathways that proceed in organisms from different systematic groups. In the first part of the review, we briefly describe the redox sensors that were used in vivo as well as summarize the model systems to which they were applied. Next, we thoroughly discuss the biological results obtained in these studies in regard to animals, plants, as well as unicellular eukaryotes and prokaryotes. We hope that this work reflects the amazing power of this technology and can serve as a useful guide for biologists and chemists who work in the field of redox processes.
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Affiliation(s)
- Alexander I. Kostyuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Anastasiya S. Panova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Aleksandra D. Kokova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Daria A. Kotova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Dmitry I. Maltsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Federal Center for Cerebrovascular Pathology and Stroke, 117997 Moscow, Russia
| | - Oleg V. Podgorny
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Vsevolod V. Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Federal Center for Cerebrovascular Pathology and Stroke, 117997 Moscow, Russia
- Institute for Cardiovascular Physiology, Georg August University Göttingen, D-37073 Göttingen, Germany
| | - Dmitry S. Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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Tao Y, Yun J, Wang J, Xu P, Li C, Liu H, Lan Y, Pan J, Du W. High-performance detection of Mycobacterium bovis in milk using digital LAMP. Food Chem 2020; 327:126945. [DOI: 10.1016/j.foodchem.2020.126945] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/21/2020] [Accepted: 04/28/2020] [Indexed: 11/24/2022]
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Suárez I, Fünger SM, Kröger S, Rademacher J, Fätkenheuer G, Rybniker J. The Diagnosis and Treatment of Tuberculosis. DEUTSCHES ARZTEBLATT INTERNATIONAL 2020; 116:729-735. [PMID: 31755407 DOI: 10.3238/arztebl.2019.0729] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 04/21/2019] [Accepted: 08/01/2019] [Indexed: 11/27/2022]
Abstract
BACKGROUND Around 10 million people worldwide contract tuberculosis every year. According to the World Health Organization (WHO), approximately one-quarter of the world's population is latently infected with Mycobacterium tuberculosis. In Ger- many, the incidence of tuberculosis was in decline over several decades but rose in 2015 to 7.3 new cases per 100 000 persons. In 2018, a total of 5429 new cases were documented, corresponding to 6.5 new cases per 100 000 persons. METHODS This article is based on literature retrieved by a selective search in PubMed and on the authors' clinical experience. RESULTS Tuberculosis involves the lungs in almost 75% of patients but can generally involve any organ. In Germany, the majority of patients come from high-incidence countries. If a patient's differential diagnosis includes tuberculosis, the main tests for the detection of the pathogen in sputum and tissue samples are culture (the gold standard), microscopy, and nucleic acid amplification tests. Imaging studies are also used for diagnosis and follow-up. The standard treatment consists of a combination of isoniazid, rifampicin, ethambutol, and pyrazinamide, followed by a combination of isoniazid and rifampicin only. Liver damage is one of the more common adverse effects of this treatment, arising in 2.4% of patients. Multidrug-resistant tuberculosis, which is rare in Germany (around 100 cases per year), should be treated in special- ized centers. CONCLUSION Rapid diagnosis and targeted treatment are essential to prevent an unfavorable course of the disease as well as its transmission to other individuals. In patients presenting with unclear symptoms, tuberculosis should always be considered as a differential diagnosis. The diagnosis of latent tuberculosis and decision-making regarding its treatment are difficult because of the lack of specific biomarkers and of relevant data from clinical trials.
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Affiliation(s)
- Isabelle Suárez
- Division of Infectious Diseases, Department of Internal Medicine I, University Hospital Cologne; German Center for Infection Research, Cologne-Bonn, Partner Site Cologne; Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin; Department of Pneumonology, Hanover Medical School
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Casanova JL, Abel L. The human genetic determinism of life-threatening infectious diseases: genetic heterogeneity and physiological homogeneity? Hum Genet 2020; 139:681-694. [PMID: 32462426 PMCID: PMC7251220 DOI: 10.1007/s00439-020-02184-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Multicellular eukaryotes emerged late in evolution from an ocean of viruses, bacteria, archaea, and unicellular eukaryotes. These macroorganisms are exposed to and infected by a tremendous diversity of microorganisms. Those that are large enough can even be infected by multicellular fungi and parasites. Each interaction is unique, if only because it operates between two unique living organisms, in an infinite diversity of circumstances. This is neatly illustrated by the extraordinarily high level of interindividual clinical variability in human infections, even for a given pathogen, ranging from a total absence of clinical manifestations to death. We discuss here the idea that the determinism of human life-threatening infectious diseases can be governed by single-gene inborn errors of immunity, which are rarely Mendelian and frequently display incomplete penetrance. We briefly review the evidence in support of this notion obtained over the last two decades, referring to a number of focused and thorough reviews published by eminent colleagues in this issue of Human Genetics. It seems that almost any life-threatening infectious disease can be driven by at least one, and, perhaps, a great many diverse monogenic inborn errors, which may nonetheless be immunologically related. While the proportions of monogenic cases remain unknown, a picture in which genetic heterogeneity is combined with physiological homogeneity is emerging from these studies. A preliminary sketch of the human genetic architecture of severe infectious diseases is perhaps in sight.
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Affiliation(s)
- Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France.
- Paris University, Imagine Institute, Paris, France.
- Pediatric Hematology and Immunology Unit, Necker Hospital for Sick Children, Paris, France.
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France
- Paris University, Imagine Institute, Paris, France
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Shukla R, Shukla H, Tripathi T. Structure-based discovery of phenyl-diketo acids derivatives as Mycobacterium tuberculosis malate synthase inhibitors. J Biomol Struct Dyn 2020; 39:2945-2958. [PMID: 32306850 DOI: 10.1080/07391102.2020.1758787] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Mycobacterium tuberculosis remains one of the most successful bacterial pathogens worldwide. The development of drug-resistant strains and the ability of the bacteria to persist in a latent form in the host are major problems for tuberculosis (TB) control. Glyoxylate shunt is a metabolic bypass of the Krebs cycle and is the key for M. tuberculosis to survive under latent conditions. Malate synthase (MtbMS) catalyzes the second step of the glyoxylate cycle and converts glyoxylate into malate. Phenyl-diketo acid (PDKA) is a potent inhibitor of MtbMS, and its efficacy is validated in a mouse model of TB. To identify novel PDKA analogs as anti-TB compounds, PDKA analogs that obeyed the Lipinski rules (n = 5473) were analyzed and docked with MtbMS structure in three sequential modes. These compounds were then assessed for ADMET parameters. Of the compounds examined, 19 were found to fit well for redocking studies. After optimization, four prospective inhibitors were identified, that along with the reference compound PDKA were subjected to 50 ns molecular dynamics simulation and binding-free energy analyses to evaluate the complex dynamics after ligand binding, the stability of the bound complexes, and the intermolecular interactions between the complexes. The MtbMS-PDKA complex showed the binding free energy of -57.16 kJ·mol-1. After a thorough analysis, our results suggested that three compounds which had binding-free energy of -127.96, -97.60, and -83.98 kJ·mol-1, with PubChem IDs 91937661, 14016246, and 126487337, respectively, have the potential to inhibit MtbMS and can be taken as lead compounds for drug discovery against TB.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rohit Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
| | - Harish Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
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Microparticles in the pathogenesis of TB: Novel perspectives for diagnostic and therapy management of Mycobacterium tuberculosis infection. Microb Pathog 2020; 144:104176. [PMID: 32244042 DOI: 10.1016/j.micpath.2020.104176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 03/23/2020] [Accepted: 03/27/2020] [Indexed: 01/05/2023]
Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis, usually chronic and has a progressive clinical course. Despite the availability of effective chemotherapy, TB is a leading killer of young adults worldwide and the global multi-drug resistant TB is reaching epidemic proportions. Interrupt transmission through early detection and treatment of the patients is a main element of the drug-resistant TB control strategy. However, many drugable targets in pathogens are already inhibited by current antibiotics and there is not a biomarker that indicate normal or pathogenic biological processes, or pharmacological responses to therapeutic intervention. Studies directed at evaluate key elements of host response to infection may identify biomarkers with measurable characteristics that indicate pathogenic biological processes. Cell-derived microparticles (MPs) are membrane-coated vesicles that represent subcellular elements and have been identified increasingly in a broad range of diseases and emerging as potential novel biomarker to pathological processes. In addition, MPs carry contents from their cells of origin as bioactive molecules as cytokines, enzymes, surface receptors, antigens and genetic information and may provide a means of communication between cells. Molecules-loaded MPs may interplay with the immune system and therefore can acts on inflammation, cell activation and migration. Therefore, MPs may be an important factor to immune process during Mtb infection, especially in pulmonary granulomas and influence the outcome of infection. Their characterization may facilitate an appropriate diagnosis, optimize pharmacological strategies and might be further explored as potential targets for future clinical interventions.
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Morales-Espinosa R, Delgado G, Serrano LR, Castillo E, Santiago CA, Hernández-Castro R, Gonzalez-Pedraza A, Mendez JL, Mundo-Gallardo LF, Manzo-Merino J, Ayala S, Cravioto A. High expression of Helicobacter pylori VapD in both the intracellular environment and biopsies from gastric patients with severity. PLoS One 2020; 15:e0230220. [PMID: 32163505 PMCID: PMC7067408 DOI: 10.1371/journal.pone.0230220] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/24/2020] [Indexed: 12/15/2022] Open
Abstract
Helicobacter pylori is a Gram-negative bacterium that causes chronic atrophic gastritis and peptic ulcers and it has been associated with the development of gastric adenocarcinoma and mucosa-associated lymphoid tissue (MALT). One of the more remarkable characteristics of H. pylori is its ability to survive in the hostile environment of the stomach. H. pylori regulates the expression of specific sets of genes allowing it to survive high acidity levels and nutrient scarcity. In the present study, we determined the expression of virulence associated protein D (VapD) of H. pylori inside adenocarcinoma gastric (AGS) cells and in gastric biopsies. Using qRT-PCR, VapD expression was quantified in intracellular H. pylori-AGS cell cultures at different time points and in gastric mucosa biopsies from patients suffering from chronic atrophic gastritis, follicular gastritis, peptic ulcers, gastritis precancerous intestinal metaplasia and adenocarcinoma. Our results show that vapD of H. pylori presented high transcription levels inside AGS cells, which increased up to two-fold above basal values across all assays over time. Inside AGS cells, H. pylori acquired a coccoid form that is metabolically active in expressing VapD as a protection mechanism, thereby maintaining its permanence in a viable non-cultivable state. VapD of H. pylori was expressed in all gastric biopsies, however, higher expression levels (p = 0.029) were observed in gastric antrum biopsies from patients with follicular gastritis. The highest VapD expression levels were found in both antrum and corpus gastric biopsies from older patients (>57 years old). We observed that VapD in H. pylori is a protein that is only produced in response to interactions with eukaryotic cells. Our results suggest that VapD contributes to the persistence of H. pylori inside the gastric epithelial cells, protecting the microorganism from the intracellular environment, reducing its growth rate, enabling long-term infection and treatment resistance.
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Affiliation(s)
- Rosario Morales-Espinosa
- Facultad de Medicina, Departamento de Microbiología y Parasitología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Gabriela Delgado
- Facultad de Medicina, Departamento de Microbiología y Parasitología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis-Roberto Serrano
- Facultad de Medicina, Departamento de Microbiología y Parasitología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Elizabeth Castillo
- Facultad de Medicina, Departamento de Microbiología y Parasitología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Carlos A. Santiago
- Facultad de Medicina, Departamento de Microbiología y Parasitología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Alberto Gonzalez-Pedraza
- Facultad de Medicina, Departamento de Microbiología y Parasitología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jose L. Mendez
- Facultad de Medicina, Departamento de Microbiología y Parasitología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | | | - Sergio Ayala
- Cátedras CONACyT-Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Alejandro Cravioto
- Facultad de Medicina, Departamento de Microbiología y Parasitología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Geier B, Sogin EM, Michellod D, Janda M, Kompauer M, Spengler B, Dubilier N, Liebeke M. Spatial metabolomics of in situ host-microbe interactions at the micrometre scale. Nat Microbiol 2020; 5:498-510. [PMID: 32015496 DOI: 10.1038/s41564-019-0664-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 12/16/2019] [Indexed: 11/09/2022]
Abstract
Spatial metabolomics describes the location and chemistry of small molecules involved in metabolic phenotypes, defence molecules and chemical interactions in natural communities. Most current techniques are unable to spatially link the genotype and metabolic phenotype of microorganisms in situ at a scale relevant to microbial interactions. Here, we present a spatial metabolomics pipeline (metaFISH) that combines fluorescence in situ hybridization (FISH) microscopy and high-resolution atmospheric-pressure matrix-assisted laser desorption/ionization mass spectrometry to image host-microbe symbioses and their metabolic interactions. The metaFISH pipeline aligns and integrates metabolite and fluorescent images at the micrometre scale to provide a spatial assignment of host and symbiont metabolites on the same tissue section. To illustrate the advantages of metaFISH, we mapped the spatial metabolome of a deep-sea mussel and its intracellular symbiotic bacteria at the scale of individual epithelial host cells. Our analytical pipeline revealed metabolic adaptations of the epithelial cells to the intracellular symbionts and variation in metabolic phenotypes within a single symbiont 16S rRNA phylotype, and enabled the discovery of specialized metabolites from the host-microbe interface. metaFISH provides a culture-independent approach to link metabolic phenotypes to community members in situ and is a powerful tool for microbiologists across fields.
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Affiliation(s)
- Benedikt Geier
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Emilia M Sogin
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Dolma Michellod
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Moritz Janda
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Mario Kompauer
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, University of Bremen, Bremen, Germany
| | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
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Jiang J, Lin C, Zhang J, Wang Y, Shen L, Yang K, Xiao W, Li Y, Zhang L, Liu J. Transcriptome Changes of Mycobacterium marinum in the Process of Resuscitation From Hypoxia-Induced Dormancy. Front Genet 2020; 10:1359. [PMID: 32117415 PMCID: PMC7025489 DOI: 10.3389/fgene.2019.01359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/11/2019] [Indexed: 12/22/2022] Open
Abstract
Nearly one-third of the world's population is latently infected with Mycobacterium tuberculosis (M. tb), which represents a huge disease reservoir for reactivation and a major obstacle for effective control of tuberculosis. During latent infection, M. tb is thought to enter nonreplicative dormant states by virtue of its response to hypoxia and nutrient-deprived conditions. Knowledge of the genetic programs used to facilitate entry into and exit from the nonreplicative dormant states remains incomplete. In this study, we examined the transcriptional changes of Mycobacterium marinum (M. marinum), a pathogenic mycobacterial species closely related to M. tb, at different stages of resuscitation from hypoxia-induced dormancy. RNA-seq analyses were performed on M. marinum cultures recovered at multiple time points after resuscitation. Differentially expressed genes (DEGs) at each time period were identified and analyzed. Co-expression networks of transcription factors and DEGs in each period were constructed. In addition, we performed a weighted gene co-expression network analysis (WGCNA) on all genes and obtained 12 distinct gene modules. Collectively, these data provided valuable insight into the transcriptome changes of M. marinum upon resuscitation as well as gene module function of the bacteria during active metabolism and growth.
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Affiliation(s)
- Jun Jiang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Chen Lin
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Junli Zhang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Yuchen Wang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Lifang Shen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Kunpeng Yang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Wenxuan Xiao
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Yao Li
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Lu Zhang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Science, Fudan University, Shanghai, China
| | - Jun Liu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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Hegde SR. Computational Identification of the Proteins Associated With Quorum Sensing and Biofilm Formation in Mycobacterium tuberculosis. Front Microbiol 2020; 10:3011. [PMID: 32038515 PMCID: PMC6988586 DOI: 10.3389/fmicb.2019.03011] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 12/16/2019] [Indexed: 12/23/2022] Open
Abstract
With prolonged therapy and increased instances of drug resistance, tuberculosis is viewed as a serious infectious disease causing high mortality. Emerging concepts in Mycobacterium tuberculosis pathogenicity include biofilm formation, which endows bacterial survival in the host for a long time. To tackle chronic tuberculosis infection, a detailed understanding of the bacterial survival mechanisms is crucial. Using comparative genomics and literature mining, 115 M. tuberculosis proteins were shortlisted for their likely association with biofilm formation or quorum sensing. These include essential genes such as secA2, lpqY-sugABC, Rv1176c, and Rv0195, many of which are also known virulence factors. Furthermore, the functional relationship among these proteins was established by considering known protein-protein interactions, regulatory interactions, and gene expression correlation data/information. Graph centrality and motif analyses predicted the importance of proteins, such as Rv0081, DevR, RegX3, Rv0097, and Rv1996 in M. tuberculosis biofilm formation. Analysis of conservation across other biofilm-forming bacteria suggests that most of these genes are conserved in mycobacteria. As the processes, such as quorum sensing, leading to biofilm formation involve diverse pathways and interactions between proteins, these system-wide studies provide a novel perspective toward understanding mycobacterial persistence.
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Affiliation(s)
- Shubhada R Hegde
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
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40
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Enniatin A1, A Natural Compound with Bactericidal Activity against Mycobacterium tuberculosis In Vitro. Molecules 2019; 25:molecules25010038. [PMID: 31861925 PMCID: PMC6982829 DOI: 10.3390/molecules25010038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 12/12/2022] Open
Abstract
Background: Tuberculosis remains a global disease that poses a serious threat to human health, but there is lack of new and available anti-tuberculosis agents to prevent the emergence of drug-resistant strains. To address this problem natural products are still potential sources for the development of novel drugs. Methods: A whole-cell screening approach was utilized to obtain a natural compound enniatin A1 from a natural products library. The target compound’s antibacterial activity against Mycobacterium tuberculosis (M. tuberculosis) was evaluated by using the resazurin reduction micro-plate assay (REMA) method. The cytotoxicity of the compound against Vero cells was measured to calculate the selectivity index. The intracellular inhibition activity of enniatin A1 was determined. We performed its time-kill kinetic assay against M. tuberculosis. We first tested its synergistic effect in combination with the first and second-line anti-tuberculosis drugs. Finally, we measured the membrane potential and intracellular ATP levels of M. tuberculosis after exposure to enniatin A1. Results: We identified enniatinA1 as a potential antibacterial agent against M. tuberculosis, against which it showed strong selectivity. Enniatin A1 exhibited a time-concentration-dependent bactericidal effect against M. tuberculosis, and it displayed synergy with rifamycin, amikacin, and ethambutol. After exposure to enniatinA1, the membrane potential and intracellular ATP levels of M. tuberculosis was significantly decreased. Conclusions: Enniatin A1 exhibits the positive potential anti-tuberculosis agent characteristics.
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Salina EG, Grigorov A, Skvortsova Y, Majorov K, Bychenko O, Ostrik A, Logunova N, Ignatov D, Kaprelyants A, Apt A, Azhikina T. MTS1338, A Small Mycobacterium tuberculosis RNA, Regulates Transcriptional Shifts Consistent With Bacterial Adaptation for Entering Into Dormancy and Survival Within Host Macrophages. Front Cell Infect Microbiol 2019; 9:405. [PMID: 31850238 PMCID: PMC6901956 DOI: 10.3389/fcimb.2019.00405] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 11/12/2019] [Indexed: 11/13/2022] Open
Abstract
Small non-coding RNAs play a significant role in bacterial adaptation to changing environmental conditions. We investigated the dynamics of expression of MTS1338, a small non-coding RNA of Mycobacterium tuberculosis, in the mouse model in vivo, regulation of its expression in the infected macrophages, and the consequences of its overexpression in bacterial cultures. Here we demonstrate that MTS1338 significantly contributes to host-pathogen interactions. Activation of the host immune system triggered NO-inducible up-regulation of MTS1338 in macrophage-engulfed mycobacteria. Constitutive overexpression of MTS1338 in cultured mycobacteria improved their survival in vitro under low pH conditions. MTS1338 up-regulation launched a spectrum of shifts in the transcriptome profile similar to those reported for M. tuberculosis adaptation to hostile intra-macrophage environment. Using the RNA-seq approach, we demonstrate that gene expression changes accompanying MTS1338 overexpression indicate reduction in translational activity and bacterial growth. These changes indicate mycobacteria entering the dormant state. Taken together, our results suggest a direct involvement of this sRNA in the interplay between mycobacteria and the host immune system during infectious process.
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Affiliation(s)
- Elena G. Salina
- Laboratory of Biochemistry of Stresses in Microorganisms, Bach Institute of Biochemistry, Research Center of Biotechnology, Moscow, Russia
| | - Artem Grigorov
- Laboratory of Regulatory Transcriptomics, Department of Genomics and Postgenomic Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Yulia Skvortsova
- Laboratory of Regulatory Transcriptomics, Department of Genomics and Postgenomic Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Konstantin Majorov
- Laboratory for Immunogenetics, Department of Immunology, Central Institute for Tuberculosis, Moscow, Russia
| | - Oksana Bychenko
- Laboratory of Regulatory Transcriptomics, Department of Genomics and Postgenomic Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Albina Ostrik
- Laboratory of Biochemistry of Stresses in Microorganisms, Bach Institute of Biochemistry, Research Center of Biotechnology, Moscow, Russia
| | - Nadezhda Logunova
- Laboratory for Immunogenetics, Department of Immunology, Central Institute for Tuberculosis, Moscow, Russia
| | - Dmitriy Ignatov
- Laboratory of Regulatory Transcriptomics, Department of Genomics and Postgenomic Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Arseny Kaprelyants
- Laboratory of Biochemistry of Stresses in Microorganisms, Bach Institute of Biochemistry, Research Center of Biotechnology, Moscow, Russia
| | - Alexander Apt
- Laboratory for Immunogenetics, Department of Immunology, Central Institute for Tuberculosis, Moscow, Russia
| | - Tatyana Azhikina
- Laboratory of Regulatory Transcriptomics, Department of Genomics and Postgenomic Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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Kushwaha GS, Oyeyemi BF, Bhavesh NS. Stringent response protein as a potential target to intervene persistent bacterial infection. Biochimie 2019; 165:67-75. [PMID: 31302165 DOI: 10.1016/j.biochi.2019.07.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/07/2019] [Indexed: 01/25/2023]
Abstract
More than half of the world's population is infected with persistent bacterial infections, consequently, persisters are gradually becoming a major public health concern. During the persistent phase, bacterial pathogens deploy many regulatory strategies to compensate unfavorable host environmental conditions. The stringent response is one of such gene regulatory mechanisms which is stimulated by nutrient starvation. It is regulated by the synthesis of highly phosphorylated signaling nucleotides, (p)ppGpp or alarmone. (p)ppGpp is synthesized by ppGpp synthetases, and these proteins are classified as RelA/SpoT homolog (RSH) proteins. Subsequently, (p)ppGpp modulate several molecular and biochemical processes ranging from transcription to metabolism. Imperativeness of (p)ppGpp synthetases has been investigated by numerous approaches including microbiology and animal studies, thereby establishing that Rel enzyme deleted strains of pathogenic bacteria were unable to transform in persister form. In this review, we summarize recent findings to corroborate the rationality to consider (p)ppGpp synthetase as a potential target in discovering a novel class of antimicrobial agents to combat persistent infections. Moreover, inhibition studies on Mycobacterium tuberculosis (p)ppGpp synthetase shows that these inhibitors prevent dormant state transition and biofilm formation. Also, we have highlighted the structural biology of (p)ppGpp synthetases, which may provide significant information that could be used in structure-based inhibitor design.
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Affiliation(s)
- Gajraj Singh Kushwaha
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Bolaji Fatai Oyeyemi
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Neel Sarovar Bhavesh
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Batyrshina YR, Schwartz YS. Modeling of Mycobacterium tuberculosis dormancy in bacterial cultures. Tuberculosis (Edinb) 2019; 117:7-17. [DOI: 10.1016/j.tube.2019.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/18/2019] [Accepted: 05/22/2019] [Indexed: 10/26/2022]
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Vandevenne M, Delmarcelle M, Galleni M. RNA Regulatory Networks as a Control of Stochasticity in Biological Systems. Front Genet 2019; 10:403. [PMID: 31134128 PMCID: PMC6514243 DOI: 10.3389/fgene.2019.00403] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/12/2019] [Indexed: 01/24/2023] Open
Abstract
The discovery that the non-protein coding part of human genome, dismissed as "junk DNA," is actively transcripted and carries out crucial functions is probably one of the most important discoveries of the past decades. These transcripts are becoming the rising stars of modern biology. In this review, we have casted a new light on RNAs. We have placed these molecules in the context of life origins, evolution with a big emphasize on the "RNA networks" concept. We discuss how this view can help us to understand the global role of RNA networks in modern cells, and can change our perception of the cell biology and therapy. Finally, although high-throughput methods as well as traditional case-to-case studies have laid the groundwork for our current knowledge of transcriptomes, we would like to discuss new strategies that are better suited to uncover and tackle these integrated and complex RNA networks.
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Affiliation(s)
- Marylène Vandevenne
- InBioS - Center for Protein Engineering, University of Liège, Liège, Belgium
| | - Michael Delmarcelle
- InBioS - Center for Protein Engineering, University of Liège, Liège, Belgium
| | - Moreno Galleni
- InBioS - Center for Protein Engineering, University of Liège, Liège, Belgium
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Rossi I, Buttini F, Sonvico F, Affaticati F, Martinelli F, Annunziato G, Machado D, Viveiros M, Pieroni M, Bettini R. Sodium Hyaluronate Nanocomposite Respirable Microparticles to Tackle Antibiotic Resistance with Potential Application in Treatment of Mycobacterial Pulmonary Infections. Pharmaceutics 2019; 11:pharmaceutics11050203. [PMID: 31052403 PMCID: PMC6571635 DOI: 10.3390/pharmaceutics11050203] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/19/2019] [Accepted: 04/21/2019] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis resistant cases have been estimated to grow every year. Besides Mycobacterium tuberculosis, other mycobacterial species are responsible for an increasing number of difficult-to-treat infections. To increase efficacy of pulmonary treatment of mycobacterial infections an inhalable antibiotic powder targeting infected alveolar macrophages (AMs) and including an efflux pump inhibitor was developed. Low molecular weight sodium hyaluronate sub-micron particles were efficiently loaded with rifampicin, isoniazid and verapamil, and transformed in highly respirable microparticles (mean volume diameter: 1 μm) by spray drying. These particles were able to regenerate their original size upon contact with aqueous environment with mechanical stirring or sonication. The in vitro drugs release profile from the powder was characterized by a slow release rate, favorable to maintain a high drug level inside AMs. In vitro antimicrobial activity and ex vivo macrophage infection assays employing susceptible and drug resistant strains were carried out. No significant differences were observed when the powder, which did not compromise the AMs viability after a five-day exposure, was compared to the same formulation without verapamil. However, both preparations achieved more than 80% reduction in bacterial viability irrespective of the drug resistance profile. This approach can be considered appropriate to treat mycobacterial respiratory infections, regardless the level of drug resistance.
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Affiliation(s)
- Irene Rossi
- Food and Drug Department, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy.
- Interdipartmental Center for Innovation in Health Products, BIOPHARMANET TEC, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy.
| | - Francesca Buttini
- Food and Drug Department, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy.
- Interdipartmental Center for Innovation in Health Products, BIOPHARMANET TEC, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy.
| | - Fabio Sonvico
- Food and Drug Department, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy.
- Interdipartmental Center for Innovation in Health Products, BIOPHARMANET TEC, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy.
| | - Filippo Affaticati
- Food and Drug Department, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy.
| | - Francesco Martinelli
- Food and Drug Department, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy.
| | - Giannamaria Annunziato
- Food and Drug Department, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy.
| | - Diana Machado
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, 1349-008 Lisbon, Portugal.
| | - Miguel Viveiros
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, 1349-008 Lisbon, Portugal.
| | - Marco Pieroni
- Food and Drug Department, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy.
| | - Ruggero Bettini
- Food and Drug Department, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy.
- Interdipartmental Center for Innovation in Health Products, BIOPHARMANET TEC, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy.
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Sun X, Zhang L, Jiang J, Ng M, Cui Z, Mai J, Ahn SK, Liu J, Zhang J, Liu J, Li Y. Transcription factors Rv0081 and Rv3334 connect the early and the enduring hypoxic response of Mycobacterium tuberculosis. Virulence 2019; 9:1468-1482. [PMID: 30165798 PMCID: PMC6177252 DOI: 10.1080/21505594.2018.1514237] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The ability of Mycobacterium tuberculosis (M. tb) to survive and persist in the host for decades in an asymptomatic state is an important aspect of tuberculosis pathogenesis. Although adaptation to hypoxia is thought to play a prominent role underlying M. tb persistence, how the bacteria achieve this goal is largely unknown. Rv0081, a member of the DosR regulon, is induced at the early stage of hypoxia while Rv3334 is one of the enduring hypoxic response genes. In this study, we uncovered genetic interactions between these two transcription factors. RNA-seq analysis of ΔRv0081 and ΔRv3334 revealed that the gene expression profiles of these two mutants were highly similar. We also found that under hypoxia, Rv0081 positively regulated the expression of Rv3334 while Rv3334 repressed transcription of Rv0081. In addition, we demonstrated that Rv0081 formed dimer and bound to the promoter region of Rv3334. Taken together, these data suggest that Rv0081 and Rv3334 work in the same regulatory pathway and that Rv3334 functions immediately downstream of Rv0081. We also found that Rv3334 is a bona fide regulator of the enduring hypoxic response genes. Our study has uncovered a regulatory pathway that connects the early and the enduring hypoxic response, revealing a transcriptional cascade that coordinates the temporal response of M. tb to hypoxia.
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Affiliation(s)
- Xian Sun
- a State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science , Fudan University , Shanghai , China
| | - Lu Zhang
- a State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science , Fudan University , Shanghai , China
| | - Jun Jiang
- a State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science , Fudan University , Shanghai , China
| | - Mark Ng
- b Department of Molecular Genetics , University of Toronto , Toronto , Canada
| | - Zhenling Cui
- c Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Medical School , Tongji University , Shanghai , China
| | - Juntao Mai
- b Department of Molecular Genetics , University of Toronto , Toronto , Canada
| | - Sang Kyun Ahn
- b Department of Molecular Genetics , University of Toronto , Toronto , Canada
| | - Jingqian Liu
- b Department of Molecular Genetics , University of Toronto , Toronto , Canada
| | - Jinyu Zhang
- a State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science , Fudan University , Shanghai , China
| | - Jun Liu
- a State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science , Fudan University , Shanghai , China.,b Department of Molecular Genetics , University of Toronto , Toronto , Canada
| | - Yao Li
- a State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science , Fudan University , Shanghai , China
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47
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Development of a Synthetic 3-ketosteroid Δ 1-dehydrogenase for the Generation of a Novel Catabolic Pathway Enabling Cholesterol Degradation in Human Cells. Sci Rep 2019; 9:5969. [PMID: 30979909 PMCID: PMC6461610 DOI: 10.1038/s41598-019-42046-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 03/22/2019] [Indexed: 01/05/2023] Open
Abstract
Cholesterol is an essential component of membranes, which is acquired by cells via receptor-mediated endocytosis of lipoproteins or via de novo synthesis. In specialized cells, anabolic enzymes metabolize cholesterol, generating steroid hormones or bile acids. However, surplus cholesterol cannot be catabolized due to the lack of enzymes capable of degrading the cholestane ring. The inability to degrade cholesterol becomes evident in the development and progression of cardiovascular disease, where the accumulation of cholesterol/cholesteryl-esters in macrophages can elicit a maladaptive immune response leading to the development and progression of atherosclerosis. The discovery of cholesterol catabolic pathways in Actinomycetes led us to the hypothesis that if enzymes enabling cholesterol catabolism could be genetically engineered and introduced into human cells, the atherosclerotic process may be prevented or reversed. Comparison of bacterial enzymes that degrade cholesterol to obtain carbon and generate energy with the action of human enzymes revealed that humans lack a 3-ketosteroid Δ1-dehydrogenase (Δ1-KstD), which catalyzes the C-1 and C-2 desaturation of ring A. Here we describe the construction, heterologous expression, and actions of a synthetic humanized Δ1-KstD expressed in Hep3B and U-937 cells, providing proof that one of three key enzymes required for cholesterol ring opening can be functionally expressed in human cells.
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48
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Choudhary E, Sharma R, Kumar Y, Agarwal N. Conditional Silencing by CRISPRi Reveals the Role of DNA Gyrase in Formation of Drug-Tolerant Persister Population in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2019; 9:70. [PMID: 30972304 PMCID: PMC6443821 DOI: 10.3389/fcimb.2019.00070] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 03/04/2019] [Indexed: 12/21/2022] Open
Abstract
Drug tolerance in mycobacterial pathogens is a global concern. Fluoroquinolone (FQ) treatment is widely used for induction of persisters in bacteria. Although FQs that target DNA gyrase are currently used as second-line anti-tuberculosis (TB) drugs, little is known about their impact on Mycobacterium tuberculosis (Mtb) persister formation. Here we explored the CRISPRi-based genetic repression for better understanding the effect of DNA gyrase depletion on Mtb physiology and response to anti-TB drugs. We find that suppression of DNA gyrase drastically affects intra- and extracellular growth of Mtb. Interestingly, gyrase depletion in Mtb leads to activation of RecA/LexA-mediated SOS response and drug tolerance via induction of persister subpopulation. Chemical inhibition of RecA in gyrase-depleted bacteria results in reversion of persister phenotype and better killing by antibiotics. This study provides evidence that inhibition of SOS response can be advantageous in improving the efficacy of anti-TB drugs and shortening the duration of current TB treatment.
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Affiliation(s)
- Eira Choudhary
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India.,Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Rishabh Sharma
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Yashwant Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
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49
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Liu Y, Xie Z, Zhou X, Li W, Zhang H, He ZG. NapM enhances the survival of Mycobacterium tuberculosis under stress and in macrophages. Commun Biol 2019; 2:65. [PMID: 30793043 PMCID: PMC6377630 DOI: 10.1038/s42003-019-0314-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/18/2019] [Indexed: 11/09/2022] Open
Abstract
Hostile environmental cues cause Mycobacterium tuberculosis to enter a state of slow growth for survival. However, the underlying regulatory mechanism remains unclear. DnaA is essential for DNA replication initiation and represents an efficient target for growth regulation in bacteria. Here, we show that the nucleoid-associated protein NapM is a DnaA antagonist, protecting M. tuberculosis from stress-mediated killing. NapM can be induced by diverse stressful signals. It binds to DnaA to inhibit both its DNA replication origin-binding and ATP hydrolysis activity. As a DnaA antagonist, NapM inhibits the mycobacterial DNA synthesis in vitro and in vivo in M. tuberculosis. Furthermore, we show that NapM contributes to the survival of M. tuberculosis under stress and within macrophages during infection. Our findings provide a previously unidentified mechanism of mycobacterial survival under stress and also suggest NapM as a potential drug target for tuberculosis control.
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Affiliation(s)
- Yu Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhiwei Xie
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiling Zhou
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weihui Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hua Zhang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Zheng-Guo He
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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50
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Jeon AB, Ackart DF, Li W, Jackson M, Melander RJ, Melander C, Abramovitch RB, Chicco AJ, Basaraba RJ, Obregón-Henao A. 2-aminoimidazoles collapse mycobacterial proton motive force and block the electron transport chain. Sci Rep 2019; 9:1513. [PMID: 30728417 PMCID: PMC6365497 DOI: 10.1038/s41598-018-38064-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/18/2018] [Indexed: 12/22/2022] Open
Abstract
There is an urgent need to develop new drugs against tuberculosis. In particular, it is critical to target drug tolerant Mycobacterium tuberculosis (M. tuberculosis), responsible, in part, for the lengthy antibiotic regimen required for treatment. We previously postulated that the presence of in vivo biofilm-like communities of M. tuberculosis could contribute to this drug tolerance. Consistent with this hypothesis, certain 2-aminoimidazole (2-AIs) molecules with anti-biofilm activity were shown to revert mycobacterial drug tolerance in an in vitro M. tuberculosis biofilm model. While exploring their mechanism of action, it was serendipitously observed that these 2-AI molecules also potentiated β-lactam antibiotics by affecting mycobacterial protein secretion and lipid export. As these two bacterial processes are energy-dependent, herein it was evaluated if 2-AI compounds affect mycobacterial bioenergetics. At low concentrations, 2B8, the lead 2-AI compound, collapsed both components of the proton motive force, similar to other cationic amphiphiles. Interestingly, however, the minimum inhibitory concentration of 2B8 against M. tuberculosis correlated with a higher drug concentration determined to interfere with the mycobacterial electron transport chain. Collectively, this study elucidates the mechanism of action of 2-AIs against M. tuberculosis, providing a tool to better understand mycobacterial bioenergetics and develop compounds with improved anti-mycobacterial activity.
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Affiliation(s)
- Albert Byungyun Jeon
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, 80523, USA
- College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave, Gainesville, Florida, 32608, USA
| | - David F Ackart
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Wei Li
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Roberta J Melander
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695, USA
- Department of Chemistry & Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana, 46556, USA
| | - Christian Melander
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695, USA
- Department of Chemistry & Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana, 46556, USA
| | - Robert B Abramovitch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Adam J Chicco
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Randall J Basaraba
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, 80523, USA.
| | - Andrés Obregón-Henao
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, 80523, USA.
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