1
|
Miller AH, Marks F, Chan L, Botella H, Schnappinger D, Ehrt S. Interruption of mycothiol synthesis and intracellular redox status impact iron-regulated reporter activation in Mycobacterium smegmatis. Microbiol Spectr 2024; 12:e0048724. [PMID: 38860795 PMCID: PMC11218476 DOI: 10.1128/spectrum.00487-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/04/2024] [Indexed: 06/12/2024] Open
Abstract
Iron scavenging is required for full virulence of mycobacterial pathogens. During infection, the host immune response restricts mycobacterial access to iron, which is essential for bacterial respiration and DNA synthesis. The Mycobacterium tuberculosis iron-dependent regulator (IdeR) responds to changes in iron accessibility by repressing iron-uptake genes when iron is available. In contrast, iron-uptake gene transcription is induced when iron is depleted. The ideR gene is essential in M. tuberculosis and is required for bacterial growth. To further study how iron regulates transcription, wee developed an iron responsive reporter system that relies on an IdeR-regulated promoter to drive Cre and loxP mediated recombination in Mycobacterium smegmatis. Recombination leads to the expression of an antibiotic resistance gene so that mutations that activate the IdeR-regulated promoter can be selected. A transposon library in the background of this reporter system was exposed to media containing iron and hemin, and this resulted in the selection of mutants in the antioxidant mycothiol synthesis pathway. We validated that inactivation of the mycothiol synthesis gene mshA results in increased recombination and increased IdeR-regulated promoter activity in the reporter system. Further, we show that vitamin C, which has been shown to oxidize iron through the Fenton reaction, can decrease promoter activity in the mshA mutant. We conclude that the intracellular redox state balanced by mycothiol can alter IdeR activity in the presence of iron.IMPORTANCEMycobacterium smegmatis is a tractable organism to study mycobacterial gene regulation. We used M. smegmatis to construct a novel recombination-based reporter system that allows for the selection of mutations that deregulate a promoter of interest. Transposon mutagenesis and insertion sequencing (TnSeq) in the recombination reporter strain identified genes that impact iron regulated promoter activity in mycobacteria. We found that the mycothiol synthesis gene mshA is required for IdeR mediated transcriptional regulation by maintaining intracellular redox balance. By affecting the oxidative state of the intracellular environment, mycothiol can modulate iron-dependent transcriptional activity. Taken more broadly, this novel reporter system can be used in combination with transposon mutagenesis to identify genes that are required by Mycobacterium tuberculosis to overcome temporary or local changes in iron availability during infection.
Collapse
Affiliation(s)
- Alexandra H Miller
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA
| | - Frances Marks
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
- Biochemistry and Structural Biology, Cell and Developmental Biology, and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA
| | - Luming Chan
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Helene Botella
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA
| |
Collapse
|
2
|
Santoshi M, Tare P, Nagaraja V. Nucleoid-associated proteins of mycobacteria come with a distinctive flavor. Mol Microbiol 2024. [PMID: 38922783 DOI: 10.1111/mmi.15287] [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: 02/16/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
In every bacterium, nucleoid-associated proteins (NAPs) play crucial roles in chromosome organization, replication, repair, gene expression, and other DNA transactions. Their central role in controlling the chromatin dynamics and transcription has been well-appreciated in several well-studied organisms. Here, we review the diversity, distribution, structure, and function of NAPs from the genus Mycobacterium. We highlight the progress made in our understanding of the effects of these proteins on various processes and in responding to environmental stimuli and stress of mycobacteria in their free-living as well as during distinctive intracellular lifestyles. We project them as potential drug targets and discuss future studies to bridge the information gap with NAPs from well-studied systems.
Collapse
Affiliation(s)
- Meghna Santoshi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Priyanka Tare
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| |
Collapse
|
3
|
Simwela NV, Johnston L, Pavinski Bitar P, Jaecklein E, Altier C, Sassetti CM, Russell DG. Genome-wide screen of Mycobacterium tuberculosis- infected macrophages identified the GID/CTLH complex as a determinant of intracellular bacterial growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592714. [PMID: 38766174 PMCID: PMC11100626 DOI: 10.1101/2024.05.06.592714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The eukaryotic GID/CTLH complex is a highly conserved E3 ubiquitin ligase involved in a broad range of biological processes. However, a role of this complex in host antimicrobial defenses has not been described. We exploited Mycobacterium tuberculosis ( Mtb ) induced cytotoxicity in macrophages in a FACS based CRISPR genetic screen to identify host determinants of intracellular Mtb growth restriction. Our screen identified 5 ( GID8 , YPEL5 , WDR26 , UBE2H , MAEA ) of the 10 predicted members of the GID/CTLH complex as determinants of intracellular growth of both Mtb and Salmonella serovar Typhimurium. We show that the antimicrobial properties of the GID/CTLH complex knockdown macrophages are mediated by enhanced GABAergic signaling, activated AMPK, increased autophagic flux and resistance to cell death. Meanwhile, Mtb isolated from GID/CTLH knockdown macrophages are nutritionally starved and oxidatively stressed. Our study identifies the GID/CTLH complex activity as broadly suppressive of host antimicrobial responses against intracellular bacterial infections. Graphical abstract
Collapse
|
4
|
Wang S, Fang R, Wang H, Li X, Xing J, Li Z, Song N. The role of transcriptional regulators in metal ion homeostasis of Mycobacterium tuberculosis. Front Cell Infect Microbiol 2024; 14:1360880. [PMID: 38529472 PMCID: PMC10961391 DOI: 10.3389/fcimb.2024.1360880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 02/27/2024] [Indexed: 03/27/2024] Open
Abstract
Metal ions are essential trace elements for all living organisms and play critical catalytic, structural, and allosteric roles in many enzymes and transcription factors. Mycobacterium tuberculosis (MTB), as an intracellular pathogen, is usually found in host macrophages, where the bacterium can survive and replicate. One of the reasons why Tuberculosis (TB) is so difficult to eradicate is the continuous adaptation of its pathogen. It is capable of adapting to a wide range of harsh environmental stresses, including metal ion toxicity in the host macrophages. Altering the concentration of metal ions is the common host strategy to limit MTB replication and persistence. This review mainly focuses on transcriptional regulatory proteins in MTB that are involved in the regulation of metal ions such as iron, copper and zinc. The aim is to offer novel insights and strategies for screening targets for TB treatment, as well as for the development and design of new therapeutic interventions.
Collapse
Affiliation(s)
- Shuxian Wang
- Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Ren Fang
- Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Hui Wang
- Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Xiaotian Li
- Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Jiayin Xing
- Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Zhaoli Li
- Drug Innovation Research Center, SAFE Pharmaceutical Technology Co. Ltd., Beijing, China
| | - Ningning Song
- Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| |
Collapse
|
5
|
Granados-Tristán AL, Hernández-Luna CE, González-Escalante LA, Camacho-Moll ME, Silva-Ramírez B, Bermúdez de León M, Peñuelas-Urquides K. ESX-3 secretion system in Mycobacterium: An overview. Biochimie 2024; 216:46-55. [PMID: 37879428 DOI: 10.1016/j.biochi.2023.10.013] [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: 04/17/2023] [Revised: 09/26/2023] [Accepted: 10/22/2023] [Indexed: 10/27/2023]
Abstract
Mycobacteria are microorganisms distributed in the environment worldwide, and some of them, such as Mycobacterium tuberculosis or M. leprae, are pathogenic. The hydrophobic mycobacterial cell envelope has low permeation and bacteria need to export products across their structure. Mycobacteria possess specialized protein secretion systems, such as the Early Secretory Antigenic Target 6 secretion (ESX) system. Five ESX loci have been described in M. tuberculosis, called ESX-1 to ESX-5. The ESX-3 secretion system has been associated with mycobacterial metabolism and growth. The locus of this system is highly conserved across mycobacterial species. Metallo-proteins regulate negative ESX-3 transcription in high conditions of iron and zinc. Moreover, this secretion system is part of an antioxidant regulatory pathway linked to Zinc. EccA3, EccB3, EccC3, EccD3, and EccE3 are components of the ESX-3 secretion machinery, whereas EsxG-EsxH, PE5-PPE4, and PE15-PPE20 are proteins secreted by this system. In addition, EspG3 and MycP3 are complementary proteins involved in transport and proteolysis respectively. This system is associated to mycobacterial virulence by releasing the bacteria from the phagosome and inhibiting endomembrane damage response. Furthermore, components of this system inhibit the host immune response by reducing the recognition of M. tuberculosis-infected cells. The components of the ESX-3 secretion system play a role in drug resistance and cell wall integrity. Moreover, the expression data of this system indicated that external and internal factors affect ESX-3 locus expression. This review provides an overview of new findings on the ESX-3 secretion system, its regulation, expression, and functions.
Collapse
Affiliation(s)
- Ana Laura Granados-Tristán
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico; Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, 66455, Nuevo León, Mexico.
| | - Carlos Eduardo Hernández-Luna
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, 66455, Nuevo León, Mexico.
| | - Laura Adiene González-Escalante
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - María Elena Camacho-Moll
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - Beatriz Silva-Ramírez
- Departamento de Inmunogenética, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - Mario Bermúdez de León
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - Katia Peñuelas-Urquides
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| |
Collapse
|
6
|
Keshavam CC, Naz S, Gupta A, Sanyal P, Kochar M, Gangwal A, Sangwan N, Kumar N, Tyagi E, Goel S, Singh NK, Sowpati DT, Khare G, Ganguli M, Raze D, Locht C, Basu-Modak S, Gupta M, Nandicoori VK, Singh Y. The heparin-binding hemagglutinin protein of Mycobacterium tuberculosis is a nucleoid-associated protein. J Biol Chem 2023; 299:105364. [PMID: 37865319 PMCID: PMC10665949 DOI: 10.1016/j.jbc.2023.105364] [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: 08/08/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023] Open
Abstract
Nucleoid-associated proteins (NAPs) regulate multiple cellular processes such as gene expression, virulence, and dormancy throughout bacterial species. NAPs help in the survival and adaptation of Mycobacterium tuberculosis (Mtb) within the host. Fourteen NAPs have been identified in Escherichia coli; however, only seven NAPs are documented in Mtb. Given its complex lifestyle, it is reasonable to assume that Mtb would encode for more NAPs. Using bioinformatics tools and biochemical experiments, we have identified the heparin-binding hemagglutinin (HbhA) protein of Mtb as a novel sequence-independent DNA-binding protein which has previously been characterized as an adhesion molecule required for extrapulmonary dissemination. Deleting the carboxy-terminal domain of HbhA resulted in a complete loss of its DNA-binding activity. Atomic force microscopy showed HbhA-mediated architectural modulations in the DNA, which may play a regulatory role in transcription and genome organization. Our results showed that HbhA colocalizes with the nucleoid region of Mtb. Transcriptomics analyses of a hbhA KO strain revealed that it regulates the expression of ∼36% of total and ∼29% of essential genes. Deletion of hbhA resulted in the upregulation of ∼73% of all differentially expressed genes, belonging to multiple pathways suggesting it to be a global repressor. The results show that HbhA is a nonessential NAP regulating gene expression globally and acting as a plausible transcriptional repressor.
Collapse
Affiliation(s)
| | - Saba Naz
- Department of Zoology, University of Delhi, Delhi, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Aanchal Gupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Priyadarshini Sanyal
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB) Campus, Hyderabad, India
| | - Manisha Kochar
- Department of Zoology, University of Delhi, Delhi, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | | | - Nitika Sangwan
- Department of Zoology, University of Delhi, Delhi, India
| | - Nishant Kumar
- Department of Zoology, University of Delhi, Delhi, India
| | - Ekta Tyagi
- Department of Zoology, University of Delhi, Delhi, India
| | - Simran Goel
- Department of Zoology, University of Delhi, Delhi, India
| | | | | | - Garima Khare
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Munia Ganguli
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Dominique Raze
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Centre for Infection and Immunity of Lille, Lille, France
| | - Camille Locht
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Centre for Infection and Immunity of Lille, Lille, France
| | | | - Meetu Gupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
| | - Vinay Kumar Nandicoori
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB) Campus, Hyderabad, India; National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India.
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, India; Delhi School of Public Health, Institution of Eminence, University of Delhi, Delhi, India.
| |
Collapse
|
7
|
Shaban AK, Gebretsadik G, Hakamata M, Takihara H, Inouchi E, Nishiyama A, Ozeki Y, Tateishi Y, Nishiuchi Y, Yamaguchi T, Ohara N, Okuda S, Matsumoto S. Mycobacterial DNA-binding protein 1 is critical for BCG survival in stressful environments and simultaneously regulates gene expression. Sci Rep 2023; 13:14157. [PMID: 37644087 PMCID: PMC10465568 DOI: 10.1038/s41598-023-40941-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/18/2023] [Indexed: 08/31/2023] Open
Abstract
Survival of the live attenuated Bacillus Calmette-Guérin (BCG) vaccine amidst harsh host environments is key for BCG effectiveness as it allows continuous immune response induction and protection against tuberculosis. Mycobacterial DNA binding protein 1 (MDP1), a nucleoid associated protein, is essential in BCG. However, there is limited knowledge on the extent of MDP1 gene regulation and how this influences BCG survival. Here, we demonstrate that MDP1 conditional knockdown (cKD) BCG grows slower than vector control in vitro, and dies faster upon exposure to antibiotics (bedaquiline) and oxidative stress (H2O2 and menadione). MDP1-cKD BCG also exhibited low infectivity and survival in THP-1 macrophages and mice indicating possible susceptibility to host mediated stress. Consequently, low in vivo survival resulted in reduced cytokine (IFN-gamma and TNF-alpha) production by splenocytes. Temporal transcriptome profiling showed more upregulated (81-240) than downregulated (5-175) genes in response to MDP1 suppression. Pathway analysis showed suppression of biosynthetic pathways that coincide with low in vitro growth. Notable was the deferential expression of genes involved in stress response (sigI), maintenance of DNA integrity (mutT1), REDOX balance (WhiB3), and host interactions (PE/PE_PGRS). Thus, this study shows MDP1's importance in BCG survival and highlights MDP1-dependent gene regulation suggesting its role in growth and stress adaptation.
Collapse
Affiliation(s)
- Amina K Shaban
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan.
| | - Gebremichal Gebretsadik
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan
- Department of Biology, Assosa University, Assosa, Ethiopia
| | - Mariko Hakamata
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan
- Department of Respiratory Medicine and Infectious Disease, School of Medicine, Niigata University, Niigata, Japan
| | - Hayato Takihara
- Bioinformatics Department, School of Medicine, Niigata University, Niigata, Japan
| | - Erina Inouchi
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan
| | - Akihito Nishiyama
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan
| | - Yuriko Ozeki
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan
| | - Yoshitaka Tateishi
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan
| | - Yukiko Nishiuchi
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan
- Toneyama Tuberculosis Research Institute, Osaka Metropolitan University, Osaka, Japan
- Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Hiroshima, Japan
| | - Takehiro Yamaguchi
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan
- Department of Pharmacology, Osaka Metropolitan University, Osaka, Japan
| | - Naoya Ohara
- Department of Oral Microbiology, Okayama University, Okayama, Japan
| | - Shujiro Okuda
- Bioinformatics Department, School of Medicine, Niigata University, Niigata, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan.
- Laboratory of Tuberculosis, Institute of Tropical Disease, Universitas Airlangga, Surabaya, East Java, Indonesia.
- Division of Research Aids, Hokkaido University Institute for Vaccine Research & Development, Sapporo, Japan.
| |
Collapse
|
8
|
Xu J, Li D, Shi J, Wang B, Ge F, Guo Z, Mu X, Nuermberger E, Lu Y. Bedquiline Resistance Mutations: Correlations with Drug Exposures and Impact on the Proteome in M. tuberculosis. Antimicrob Agents Chemother 2023; 67:e0153222. [PMID: 37255473 PMCID: PMC10353445 DOI: 10.1128/aac.01532-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 05/12/2023] [Indexed: 06/01/2023] Open
Abstract
Bedaquiline (BDQ) is an effective drug for the treatment of drug-resistant tuberculosis. Mutations in atpE, which encodes the target of BDQ, are associated with large increases in MICs. Mutations in Rv0678 that derepress the transcription of the MmpL5-MmpS5 efflux transporter are associated with smaller increases in MICs. However, Rv0678 mutations are the most common mutations that are associated with BDQ resistance in clinical isolates, and they also confer cross-resistance to clofazimine (CFZ). To investigate the mechanism of BDQ resistance and the correlation between Rv0678 mutations and target-based atpE mutations, M. tuberculosis strains were exposed to different concentrations of BDQ or CFZ to select Rv0678 mutations and atpE mutations. Gene overexpression strains were constructed to illustrate the roles of MmpL5 and MmpS5. A quantitative proteome analysis was performed to compare the BDQ-resistant mutants to the isogenic strain H37Rv. Here, we report that the Rv0678 mutations were more readily selected than were the atpE mutations at low concentrations of BDQ or CFZ. The atpE mutations were selected by high concentrations of BDQ exposure. The overexpression of both mmpL5 and mmpS5 reduced the susceptibility of Mycobacterium tuberculosis to BDQ and CFZ. Secreted immunogenic proteins and proteins involved in the biosynthesis and transport of phthiocerol dimycocerosates were associated with Rv0678 mutations conferring BDQ resistance in the proteome analysis. In conclusion, exposure to different bedaquiline concentrations resulted in the selection of different mutations. The coexpression of MmpL5 and MmpS5 contributed to drug resistance and upregulated pathogenic proteins in M. tuberculosis, suggesting MmpL5-MmpS5 as a new potential target for antituberculosis drug development. These results warrant further surveillance for the evolution of BDQ resistance during clinical usage.
Collapse
Affiliation(s)
- Jian Xu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, and Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Dongshuo Li
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, and Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Jinghua Shi
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, and Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Bin Wang
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, and Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Fei Ge
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, and Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Zhenyong Guo
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, and Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Xiaopan Mu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, and Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Eric Nuermberger
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Yu Lu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, and Beijing Chest Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
9
|
Chesnokov Y, Kamyshinsky R, Mozhaev A, Shtykova E, Vasiliev A, Orlov I, Dadinova L. Morphological Diversity of Dps Complex with Genomic DNA. Int J Mol Sci 2023; 24:ijms24108534. [PMID: 37239879 DOI: 10.3390/ijms24108534] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/26/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
In response to adverse environmental factors, Escherichia coli cells actively produce Dps proteins which form ordered complexes (biocrystals) with bacterial DNA to protect the genome. The effect of biocrystallization has been described extensively in the scientific literature; furthermore, to date, the structure of the Dps-DNA complex has been established in detail in vitro using plasmid DNA. In the present work, for the first time, Dps complexes with E. coli genomic DNA were studied in vitro using cryo-electron tomography. We demonstrate that genomic DNA forms one-dimensional crystals or filament-like assemblies which transform into weakly ordered complexes with triclinic unit cells, similar to what is observed for plasmid DNA. Changing such environmental factors as pH and KCl and MgCl2 concentrations leads to the formation of cylindrical structures.
Collapse
Affiliation(s)
- Yuri Chesnokov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia
- National Research Center "Kurchatov Institute", Akademika Kurchatova pl., 1, 123182 Moscow, Russia
| | - Roman Kamyshinsky
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia
- National Research Center "Kurchatov Institute", Akademika Kurchatova pl., 1, 123182 Moscow, Russia
| | - Andrey Mozhaev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Eleonora Shtykova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia
| | - Alexander Vasiliev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia
- National Research Center "Kurchatov Institute", Akademika Kurchatova pl., 1, 123182 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutsky per. 9, 141701 Dolgoprudny, Russia
| | - Ivan Orlov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia
| | - Liubov Dadinova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia
| |
Collapse
|
10
|
Pereira MMR, de Oliveira FM, da Costa AC, Junqueira-Kipnis AP, Kipnis A. Ferritin from Mycobacterium abscessus is involved in resistance to antibiotics and oxidative stress. Appl Microbiol Biotechnol 2023; 107:2577-2595. [PMID: 36862179 DOI: 10.1007/s00253-023-12420-8] [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: 11/02/2022] [Revised: 01/22/2023] [Accepted: 01/30/2023] [Indexed: 03/03/2023]
Abstract
Mycobacterium abscessus subsp. massiliense (Mycma) is a rapidly growing Mycobacterium belonging to the M. abscessus complex that is often associated with lung and soft tissue infection outbreaks. Mycma is resistant to many antimicrobials, including those used for treating tuberculosis. Therefore, Mycma infections are difficult to treat and may lead to high infectious complication rates. Iron is essential for bacterial growth and establishment of infection. During infection, the host reduces iron concentrations as a defense mechanism. To counteract the host-induced iron deficiency, Mycma produces siderophores to capture iron. Mycma has two ferritins (encoded by mycma_0076 and mycma_0077) modulated by different iron concentrations, which allow the survival of this pathogen during iron scarcity. In this study, we constructed knockout (Mycma 0076KO) and complemented (Mycma 0076KOc) gene strains for mycma_0076 to understand the function of 0076 ferritin. Deletion of mycma_0076 in Mycma led to the transition in colony morphology from smooth to rough, alteration of the glycopeptidolipids spectra, increased permeability of the envelope, reduction in biofilm formation, increased susceptibility to antimicrobials and hydrogen peroxide-induced oxidative stress, and decreased internalization by macrophages. This study shows that Mycma_0076 ferritin in Mycma is involved in resistance to oxidative stress and antimicrobials, and alteration of cell envelope architecture. KEY POINTS: • Deletion of the mycma_0076 gene altered colony morphology to rough; • Mycma 0076KO changed GPL profile; • Absence of Mycma_0076 ferritin results in increased susceptibility to antimicrobials and oxidative stress in Mycma. Legend: a In wild-type M. abscessus subsp. massiliense strain, iron is captured from the environment by carboxymycobactins and mycobactins (1). Iron-dependent regulator (IdeR) proteins bind to ferrous iron (Fe+2) in the bacterial cytoplasm leading to the activation of the IdeR-Fe+2 complex (2). The activated complex binds to the promoter regions of iron-dependent genes, called iron box, which in turn help in the recruitment of RNA polymerase to promote transcription of genes such as mycma_0076 and mycma_0077 ferritin genes (3). Mycma_0076 and Mycma_0077 ferritins bind to excess iron in the medium and promote Fe2+ oxidation into ferric iron (Fe3+) and store iron molecules to be released under iron scarcity conditions. (4) Genes related to biosynthesis and transport of glycopeptidolipids (GPL) are expressed normally and the cell envelope is composed of different GPL species (colored squares represented on the cell surface (GPLs). Consequently, WT Mycma present smooth colony phenotype (5). b In Mycma 0076KO strain, the lack of ferritin 0076 causes overexpression of mycma_0077 (6), but does not restore wild-type iron homeostasis and thus may result in free intracellular iron, even in the presence of miniferritins (MaDps). The excess iron potentiates oxidative stress (7) by generating hydroxyl radicals through Fenton Reaction. During this process, through an unknown mechanism, that could involve Lsr2 (8), the expression of GPL synthesis locus is regulated positively and/or negatively, resulting in alteration of GPL composition in the membrane (as represented by different colors of squares on the cell surface), resulting in a rough colony phenotype (9). The changes of GPL can increase cell wall permeability, contributing to antimicrobial susceptibility (10).
Collapse
Affiliation(s)
- Maria Micaella Rodrigues Pereira
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, GO, Brazil
- Tropical Medicine and Public Health Graduate Program at Federal, University of Goiás, Goiânia, GO, Brazil
| | - Fábio Muniz de Oliveira
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, GO, Brazil
- Tropical Medicine and Public Health Graduate Program at Federal, University of Goiás, Goiânia, GO, Brazil
- Indiana Center for Regenerative Medicine and Engineering, School of Medicine, Indiana University, Indianapolis, IN, USA
| | | | | | - André Kipnis
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, GO, Brazil.
| |
Collapse
|
11
|
Hadizadeh Tasbiti A, Badmasti F, Siadat SD, Fateh A, Yari F, GHzanfari Jajin M, Yari S. Recognition of specific immunogenic antigens with potential diagnostic value in multi-drug resistant Mycobacterium tuberculosis inducing humoral immunity in MDR-TB patients. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105328. [PMID: 35788051 DOI: 10.1016/j.meegid.2022.105328] [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: 07/05/2021] [Revised: 06/25/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Tuberculosis (TB) as a public health crisis is caused by the intracellular bacterium Mycobacterium tuberculosis. Detection of immunogenic proteins in TB is valuable for the development of diagnostic tests, vaccine formulations and monitoring treatment outcome. In this study, we differentiated the immune-reactivity of proteins in multidrug-resistant tuberculosis (MDRTB) and drug-susceptible strains using purified anti-MDRTB antibodies isolated from inpatients. Our data showed that the anti- MDRTB antibody was well able to detect the MDR strain in the patient's sputum. The immunogenic proteins of MDRTB were purified by affinity chromatography and subjected to matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. Analysis of the data revealed that seven MDRTB immunogenic proteins, including Rv2986c (HupB), Rv3699, Rv1133c (MetE), Rv0440 (GroEL), Rv3057c, Rv2558 and Rv2971 are involved in DNA stability, metabolism, cellular processes and some unknown functions. Similarities in the electrophoresis protein profiles were evident between the extracts of MDR and sensitive TB strains. However, the protein expression patterns of MDRTB isolates were distinguishable from that formed by susceptible TB strains.
Collapse
Affiliation(s)
- Alireza Hadizadeh Tasbiti
- Tuberculosis and Pulmonary Research Dept, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Farzad Badmasti
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran; Bacteriology Dept, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Tuberculosis and Pulmonary Research Dept, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Tuberculosis and Pulmonary Research Dept, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Yari
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion, Iran
| | | | - Shamsi Yari
- Tuberculosis and Pulmonary Research Dept, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
12
|
Singh N, Sharma N, Singh P, Pandey M, Ilyas M, Sisodiya L, Choudhury T, Gosain TP, Singh R, Atmakuri K. HupB, a nucleoid-associated protein, is critical for survival of Mycobacterium tuberculosis under host-mediated stresses and for enhanced tolerance to key first-line antibiotics. Front Microbiol 2022; 13:937970. [PMID: 36071978 PMCID: PMC9441915 DOI: 10.3389/fmicb.2022.937970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/12/2022] [Indexed: 11/30/2022] Open
Abstract
To survive and establish its niche, Mycobacterium tuberculosis (Mtb) engages in a steady battle against an array of host defenses and a barrage of antibiotics. Here, we demonstrate that Mtb employs HupB, a nucleoid-associated protein (NAP) as its key player to simultaneously battle and survive in these two stress-inducing fronts. Typically, NAPs are key to bacterial survival under a wide array of environmental or host-mediated stresses. Here, we report that for Mtb to survive under different macrophage-induced assaults including acidic pH, nutrient depletion, oxidative and nitrosative stresses, HupB presence is critical. As expected, the hupB knockout mutant is highly sensitive to these host-mediated stresses. Furthermore, Mtb aptly modulates HupB protein levels to overcome these stresses. We also report that HupB aids Mtb to gain tolerance to high levels of rifampicin (RIF) and isoniazid (INH) exposure. Loss of hupB makes Mtb highly susceptible to even short exposures to reduced amounts of RIF and INH. Overexpressing hupB in Mtb or complementing hupB in the hupB knockout mutant triggers enhanced survival of Mtb under these stresses. We also find that upon loss of hupB, Mtb significantly enhances the permeability of its cell wall by modulating the levels of several surface lipids including phthiocerol dimycocerosates (PDIMs), thus possibly influencing overall susceptibility to host-mediated stresses. Loss of hupB also downregulates efflux pump expression possibly influencing increased susceptibility to INH and RIF. Finally, we find that therapeutic targeting of HupB with SD1, a known small molecule inhibitor, significantly enhances Mtb susceptibility to INH and THP-1 macrophages and significantly reduces MIC to INH. Thus, our data strongly indicate that HupB is a highly promising therapeutic target especially for potential combinatorial shortened therapy with reduced INH and RIF doses.
Collapse
Affiliation(s)
- Niti Singh
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- Manipal University, Manipal, Karnataka, India
| | - Nishant Sharma
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Padam Singh
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Manitosh Pandey
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- Department of Life Sciences, ITM University, Gwalior, Madhya Pradesh, India
| | - Mohd Ilyas
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Lovely Sisodiya
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Tejaswini Choudhury
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Tannu Priya Gosain
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ramandeep Singh
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Krishnamohan Atmakuri
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- *Correspondence: Krishnamohan Atmakuri
| |
Collapse
|
13
|
Shyam M, Shilkar D, Rakshit G, Jayaprakash V. Approaches for Targeting the Mycobactin Biosynthesis Pathway for Novel Anti-tubercular Drug Discovery: Where We Stand. Expert Opin Drug Discov 2022; 17:699-715. [PMID: 35575503 DOI: 10.1080/17460441.2022.2077328] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Several decades of antitubercular drug discovery efforts have focused on novel antitubercular chemotherapies. However, recent efforts have greatly shifted towards countering extremely/multi/total drug-resistant species. Targeting the conditionally essential elements inside Mycobacterium is a relatively new approach against tuberculosis and has received lackluster attention. The siderophore, Mycobactin, is a conditionally essential molecule expressed by mycobacteria in iron-stress conditions. It helps capture the micronutrient iron, essential for the smooth functioning of cellular processes. AREAS COVERED The authors discuss opportunities to target the conditionally essential pathways to help develop newer drugs and prolong the shelf life of existing therapeutics, emphasizing the bottlenecks in fast-tracking antitubercular drug discovery. EXPERT OPINION While the lack of iron supply can cripple bacterial growth and multiplication, excess iron can cause oxidative overload. Constant up-regulation can strain the bacterial synthetic machinery, further slowing its growth. Mycobactin synthesis is tightly controlled by a genetically conserved mega enzyme family via up-regulation (HupB) or down-regulation (IdeR) based on iron availability in its microenvironment. Furthermore, the recycling of siderophores by the MmpL-MmpS4/5 orchestra provides endogenous drug targets to beat the bugs with iron-toxicity contrivance. These processes can be exploited as chinks in the armor of Mycobacterium and be used for new drug development.
Collapse
Affiliation(s)
- Mousumi Shyam
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Deepak Shilkar
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Gourav Rakshit
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Venkatesan Jayaprakash
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| |
Collapse
|
14
|
Rodriguez GM, Sharma N, Biswas A, Sharma N. The Iron Response of Mycobacterium tuberculosis and Its Implications for Tuberculosis Pathogenesis and Novel Therapeutics. Front Cell Infect Microbiol 2022; 12:876667. [PMID: 35646739 PMCID: PMC9132128 DOI: 10.3389/fcimb.2022.876667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/25/2022] [Indexed: 12/16/2022] Open
Abstract
Most pathogenic bacteria require iron for growth. However, this metal is not freely available in the mammalian host. Due to its poor solubility and propensity to catalyze the generation of reactive oxygen species, host iron is kept in solution bound to specialized iron binding proteins. Access to iron is an important factor in the outcome of bacterial infections; iron limitation frequently induces virulence and drives pathogenic interactions with host cells. Here, we review the response of Mycobacterium tuberculosis to changes in iron availability, the relevance of this response to TB pathogenesis, and its potential for the design of new therapeutic interventions.
Collapse
|
15
|
Choudhury M, Virivinti J, Kandi S, Sritharan V, Sritharan M. Th2 immune response by the iron-regulated protein HupB of Mycobacterium tuberculosis. Indian J Tuberc 2022; 69:90-99. [PMID: 35074158 DOI: 10.1016/j.ijtb.2021.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 04/06/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND HupB is an iron-regulated protein essential for the growth of Mycobacterium tuberculosis inside macrophages. To investigate if HupB induced a dominant Th2 type immune response, we studied the effect of rHupB on PBMCs from TB patients and by infecting mouse macrophages with wild type and hupB KO mutants. METHODS PBMCs from pulmonary TB (n = 60), extra pulmonary TB (n = 23) and healthy controls (n = 30) were stimulated with purified HupB and the cytokines secreted were assayed. The sera were screened for anti-HupB antibodies by ELISA. Mouse macrophages cell line (RAW 264.7) was infected with wild type, hupB KO and hupB-complemented strains of M. tuberculosis grown in high and low iron medium and the expression of cytokines was assayed by qRT-PCR. RESULTS Murine macrophages infected with the hupB KO strain produced low levels of the pro-inflammatory cytokines IFN-γ, TNF-α, IL-1, and IL-18 and high levels of IL-10. HupB induced IL-6 and IL-10 production in PBMCs of TB patients and down-regulated IFN-γ and TNF-α production. The influence of HupB was remarkable in the EPTB group. CONCLUSION HupB shifted the immune response to the Th2 type. Low IFN-γ and elevated IL-10 in EPTB patients is noteworthy.
Collapse
Affiliation(s)
- Mitali Choudhury
- Department of Animal Biology, University of Hyderabad, Hyderabad, 500046, India
| | - Jahnavi Virivinti
- Molecular Diagnostics and Biomarkers Lab, Global Hospitals, Hyderabad, 500004, India
| | - Subhakar Kandi
- Kamineni Academy of Medical Sciences and Research Centre, Hyderabad, 500038, India
| | | | - Manjula Sritharan
- Department of Animal Biology, University of Hyderabad, Hyderabad, 500046, India.
| |
Collapse
|
16
|
Baatjies L, Loxton AG, Williams MJ. Host and Bacterial Iron Homeostasis, an Underexplored Area in Tuberculosis Biomarker Research. Front Immunol 2021; 12:742059. [PMID: 34777355 PMCID: PMC8586213 DOI: 10.3389/fimmu.2021.742059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/14/2021] [Indexed: 01/10/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) "a human adapted pathogen" has found multiple ways to manipulate the host immune response during infection. The human immune response to Mtb infection is a highly complex cascade of reactions, with macrophages as preferred intracellular location. Interaction with the host through infection gives rise to expression of specific gene products for survival and multiplication within the host. The signals that the pathogens encounter during infection cause them to selectively express genes in response to signals. One strategy to identify Mtb antigens with diagnostic potential is to identify genes that are specifically induced during infection or in specific disease stages. The shortcomings of current immunodiagnostics include the failure to detect progression from latent infection to active tuberculosis disease, and the inability to monitor treatment efficacy. This highlights the need for new tuberculosis biomarkers. These biomarkers should be highly sensitive and specific diagnosing TB infection, specifically distinguishing between latent infection and active disease. The regulation of iron levels by the host plays a crucial role in the susceptibility and outcome of Mtb infection. Of interest are the siderophore biosynthetic genes, encoded by the mbt-1 and mbt-2 loci and the SUF (mobilization of sulphur) operon (sufR-sufB-sufD-sufC-csd-nifU-sufT), which encodes the primary iron-sulphur cluster biogenesis system. These genes are induced during iron limitation and intracellular growth of Mtb, pointing to their importance during infection.
Collapse
Affiliation(s)
- Lucinda Baatjies
- Department of Science and Innovation (DSI)-National Research Foundation (NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Andre G. Loxton
- Department of Science and Innovation (DSI)-National Research Foundation (NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Monique J. Williams
- Department of Science and Innovation (DSI)-National Research Foundation (NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| |
Collapse
|
17
|
Sarkar S, Dey U, Khohliwe TB, Yella VR, Kumar A. Analysis of nucleoid-associated protein-binding regions reveals DNA structural features influencing genome organization in Mycobacterium tuberculosis. FEBS Lett 2021; 595:2504-2521. [PMID: 34387867 DOI: 10.1002/1873-3468.14178] [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: 06/11/2021] [Revised: 08/01/2021] [Accepted: 08/11/2021] [Indexed: 11/10/2022]
Abstract
Nucleoid-associated proteins (NAPs) maintain bacterial nucleoid configuration through their architectural properties of DNA bending, wrapping, and bridging. However, the contribution of DNA structural alterations to DNA-NAP recognition at the genomic scale remains unresolved. Present work dissects the DNA sequence, shape and altered structural preferences at a genomic scale for six NAPs in Mycobacterium tuberculosis. Results suggest narrower minor groove width (MGW) and higher DNA rigidity are marked for the binding sites of EspR and Lsr2, while mIHF, MtHU and NapM have heterogeneous DNA structural predilections. In contrast, WhiB4-DNA-binding sites were characterized by wider MGW, highly deformable and less curved DNA. This work provides systematic insight into NAP-mediated genome organization as a function of DNA structural features.
Collapse
Affiliation(s)
- Sharmilee Sarkar
- Department of Molecular Biology and Biotechnology, Tezpur University, India
| | - Upalabdha Dey
- Department of Molecular Biology and Biotechnology, Tezpur University, India
| | | | - Venkata Rajesh Yella
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, India
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, India
| |
Collapse
|
18
|
Lewin A, Kamal E, Semmler T, Winter K, Kaiser S, Schäfer H, Mao L, Eschenhagen P, Grehn C, Bender J, Schwarz C. Genetic diversification of persistent Mycobacterium abscessus within cystic fibrosis patients. Virulence 2021; 12:2415-2429. [PMID: 34546836 PMCID: PMC8526041 DOI: 10.1080/21505594.2021.1959808] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mycobacterium (M.) abscessus infections in Cystic Fibrosis (CF) patients cause a deterioration of lung function. Treatment of these multidrug-resistant pathogens is associated with severe side-effects, while frequently unsuccessful. Insight on M. abscessus genomic evolvement during chronic lung infection would be beneficial for improving treatment strategies. A longitudinal study enrolling 42 CF patients was performed at a CF center in Berlin, Germany, to elaborate phylogeny and genomic diversification of in-patient M. abscessus. Eleven of the 42 CF patients were infected with M. abscessus. Five of these 11 patients were infected with global human-transmissible M. abscessus cluster strains. Phylogenetic analysis of 88 genomes from isolates of the 11 patients excluded occurrence of M. abscessus transmission among members of the study group. Genome sequencing and variant analysis of 30 isolates from 11 serial respiratory samples collected over 4.5 years from a chronically infected patient demonstrated accumulation of gene mutations. In total, 53 genes exhibiting non-synonymous variations were identified. Enrichment analysis emphasized genes involved in synthesis of glycopeptidolipids, genes from the embABC (arabinosyltransferase) operon, betA (glucose-methanol-choline oxidoreductase) and choD (cholesterol oxidase). Genetic diversity evolved in a variety of virulence- and resistance-associated genes. The strategy of M. abscessus populations in chronic lung infection is not clonal expansion of dominant variants, but to sustain simultaneously a wide range of genetic variants facilitating adaptation of the population to changing living conditions in the lung. Genomic diversification during chronic infection requires increased attention when new control strategies against M. abscessus infections are explored.
Collapse
Affiliation(s)
- Astrid Lewin
- Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Elisabeth Kamal
- Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- Unit NG 1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Katja Winter
- Unit MF1 Bioinformatics, Robert Koch Institute, Berlin, Germany
| | - Sandra Kaiser
- Unit MF1 Bioinformatics, Robert Koch Institute, Berlin, Germany
| | - Hubert Schäfer
- Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Lei Mao
- Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany.,Unit 31 Infectious Disease Data Science Unit, Robert Koch Institute, Berlin, Germany
| | - Patience Eschenhagen
- Klinikum Westbrandenburg, Campus Potsdam, Cystic Fibrosis Section, Potsdam, Germany.,Pediatric Respiratory Medicine, Immunology and Intensive Care Medicine, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Claudia Grehn
- Department of Pediatrics, Division of Pulmonology, Immunology and Intensive Care Medicine, Division of Cystic Fibrosis, Charité - Universitätsmedizin, Berlin, Germany
| | - Jennifer Bender
- Unit 13 Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany.,ECDC Fellowship Programme, Public Health Microbiology Path (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Carsten Schwarz
- Klinikum Westbrandenburg, Campus Potsdam, Cystic Fibrosis Section, Potsdam, Germany.,Pediatric Respiratory Medicine, Immunology and Intensive Care Medicine, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| |
Collapse
|
19
|
Vatlin AA, Shitikov EA, Shahbaaz M, Bespiatykh DA, Klimina KM, Christoffels A, Danilenko VN, Maslov DA. Transcriptomic Profile of Mycobacterium smegmatis in Response to an Imidazo[1,2- b][1,2,4,5]tetrazine Reveals Its Possible Impact on Iron Metabolism. Front Microbiol 2021; 12:724042. [PMID: 34421882 PMCID: PMC8371482 DOI: 10.3389/fmicb.2021.724042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/14/2021] [Indexed: 12/03/2022] Open
Abstract
Tuberculosis (TB), caused by the Mycobacterium tuberculosis complex bacteria, is one of the most pressing health problems. The development of new drugs and new therapeutic regimens effective against the pathogen is one of the greatest challenges in the way of tuberculosis control. Imidazo[1,2-b][1,2,4,5]tetrazines have shown promising activity against M. tuberculosis and M. smegmatis strains. Mutations in MSMEG_1380 lead to mmpS5–mmpL5 operon overexpression, which provides M. smegmatis with efflux-mediated resistance to imidazo[1,2-b][1,2,4,5]tetrazines, but the exact mechanism of action of these compounds remains unknown. To assess the mode of action of imidazo[1,2-b][1,2,4,5]tetrazines, we analyzed the transcriptomic response of M. smegmatis to three different concentrations of 3a compound: 1/8×, 1/4×, and 1/2× MIC. Six groups of genes responsible for siderophore synthesis and transport were upregulated in a dose-dependent manner, while virtual docking revealed proteins involved in siderophore synthesis as possible targets for 3a. Thus, we suggest that imidazo[1,2-b][1,2,4,5]tetrazines may affect mycobacterial iron metabolism.
Collapse
Affiliation(s)
- Aleksey A Vatlin
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia.,Peoples' Friendship University of Russia (RUDN University), Moscow, Russia
| | - Egor A Shitikov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Mohd Shahbaaz
- South Africa Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Dmitry A Bespiatykh
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Ksenia M Klimina
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia.,Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Alan Christoffels
- South Africa Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Valery N Danilenko
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A Maslov
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
20
|
Srivastava S, Abraham PR, Mukhopadhyay S. Aptamers: An Emerging Tool for Diagnosis and Therapeutics in Tuberculosis. Front Cell Infect Microbiol 2021; 11:656421. [PMID: 34277465 PMCID: PMC8280756 DOI: 10.3389/fcimb.2021.656421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/09/2021] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) has been plaguing human civilization for centuries, and currently around one-third of the global population is affected with TB. Development of novel intervention tools for early diagnosis and therapeutics against Mycobacterium tuberculosis (M.tb) is the main thrust area in today's scenario. In this direction global efforts were made to use aptamers, the chemical antibodies as tool for TB diagnostics and therapeutics. This review describes the various aptamers introduced for targeting M.tb and highlights the need for development of novel aptamers to selectively target virulent proteins of M.tb for vaccine and anti-TB drugs. The objective of this review is to highlight the diagnostic and therapeutic application of aptamers used for tuberculosis. The discovery of aptamers, SELEX technology, different types of SELEX development processes, DNA and RNA aptamers reported for diseases and pathogenic agents as well have also been described in detail. But the emphasis of this review is on the development of aptamers which can block the function of virulent mycobacterial components for developing newer TB vaccine candidates and/or drug targets. Aptamers designed to target M.tb cell wall proteins, virulent factors, secretory proteins, or combination could orchestrate advanced diagnosis and therapeutic measures for tuberculosis.
Collapse
Affiliation(s)
- Shruti Srivastava
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Philip Raj Abraham
- Unit of OMICS, ICMR-Vector Control Research Centre (VCRC), Puducherry, India
| | - Sangita Mukhopadhyay
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| |
Collapse
|
21
|
Klebba PE, Newton SMC, Six DA, Kumar A, Yang T, Nairn BL, Munger C, Chakravorty S. Iron Acquisition Systems of Gram-negative Bacterial Pathogens Define TonB-Dependent Pathways to Novel Antibiotics. Chem Rev 2021; 121:5193-5239. [PMID: 33724814 PMCID: PMC8687107 DOI: 10.1021/acs.chemrev.0c01005] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Iron is an indispensable metabolic cofactor in both pro- and eukaryotes, which engenders a natural competition for the metal between bacterial pathogens and their human or animal hosts. Bacteria secrete siderophores that extract Fe3+ from tissues, fluids, cells, and proteins; the ligand gated porins of the Gram-negative bacterial outer membrane actively acquire the resulting ferric siderophores, as well as other iron-containing molecules like heme. Conversely, eukaryotic hosts combat bacterial iron scavenging by sequestering Fe3+ in binding proteins and ferritin. The variety of iron uptake systems in Gram-negative bacterial pathogens illustrates a range of chemical and biochemical mechanisms that facilitate microbial pathogenesis. This document attempts to summarize and understand these processes, to guide discovery of immunological or chemical interventions that may thwart infectious disease.
Collapse
Affiliation(s)
- Phillip E Klebba
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Salete M C Newton
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - David A Six
- Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States
| | - Ashish Kumar
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Taihao Yang
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Brittany L Nairn
- Department of Biological Sciences, Bethel University, 3900 Bethel Drive, St. Paul, Minnesota 55112, United States
| | - Colton Munger
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Somnath Chakravorty
- Jacobs School of Medicine and Biomedical Sciences, SUNY Buffalo, Buffalo, New York 14203, United States
| |
Collapse
|
22
|
Iron uptake and transport by the carboxymycobactin-mycobactin siderophore machinery of Mycobacterium tuberculosis is dependent on the iron-regulated protein HupB. Biometals 2021; 34:511-528. [PMID: 33609202 DOI: 10.1007/s10534-021-00292-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 02/07/2021] [Indexed: 12/27/2022]
Abstract
Iron-starved Mycobacterium tuberculosis utilises the carboxymycobactin-mycobactin siderophore machinery to acquire iron. These two siderophores have high affinity for ferric iron and can withdraw the metal ion from insoluble iron hydroxides and iron-binding proteins. We first reported HupB, a multi-functional mycobacterial protein to be associated with iron acquisition in M. tuberculosis. This 28 kDa cell wall protein, up regulated upon iron limitation functions as a transcriptional activator of mycobactin biosynthesis and is essential for the pathogen to survive inside macrophages. The focus of this study is to understand the role of HupB in iron uptake and transport by the carboxmycobactin-mycobactin siderophore machinery in M. tuberculosis. Experimental approaches included radiolabelled iron uptake studies by viable organisms and protein-ligand binding studies using the purified HupB and the two siderophores. Uptake of 55Fe-carboxymycobactin by wild type M. tuberculosis (WT M.tb.H37Rv) and not by the hupB KO mutant (M.tb.ΔhupB) showed that HupB is necessary for the uptake of ferri-carboxymycobactin. Additionally, the radiolabel recovery was high in HupB-incorporated liposomes upon addition of the labelled siderophore. Bioinformatic and experimental studies using spectrofluorimetry, CD analysis and surface plasmon resonance not only confirmed the binding of HupB with ferri-carboxymycobactin and ferri-mycobactin but also with free iron. In conclusion, HupB is established as a ferri- carboxymycobactin receptor and by virtue of its property to bind ferric iron, functions as a transporter of the ferric iron from the extracellular siderophore to mycobactin within the cell envelope.
Collapse
|
23
|
Kumar N, Sritharan M. Role of a 21-kDa iron-regulated protein IrpA in the uptake of ferri-exochelin by Mycobacterium smegmatis. J Appl Microbiol 2020; 129:1733-1743. [PMID: 32472729 DOI: 10.1111/jam.14728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/17/2020] [Accepted: 05/25/2020] [Indexed: 11/30/2022]
Abstract
AIMS To characterize the 21-kDa iron-regulated cell wall protein in Mycobacterium smegmatis co-expressed with the siderophores mycobactin, exochelin and carboxymycobactin upon iron limitation. METHODS AND RESULTS Mycobacterium smegmatis, grown in the presence of 0·02 μg Fe ml-1 (low iron) produced high levels of all the three siderophores, which were repressed in bacteria supplemented with 8 μg Fe ml-1 (high iron). Exochelin, the major extracellular siderophore was the first to rise and was expressed at high levels during log phase of growth. Carboxymycobactin, a minor component in log phase iron-starved M. smegmatis continued to rise when cultured for longer periods, reaching levels greater than exochelin. Iron-starved bacteria expressed a 21-kDa iron-regulated protein (IrpA) that was identified as Clp protease subunit (MSMEG_3671) and characterized as a receptor for ferri-exochelin. CONCLUSIONS Ferri-exochelin is the preferred siderophore in M. smegmatis and this ferri-exochelin: IrpA machinery is absent in Mycobacterium tuberculosis. SIGNIFICANCE AND IMPACT OF THE STUDY Exochelin machinery is functional in M. smegmatis and the carboxymycobactin-mycobactin machinery is the sole iron uptake system in M. tuberculosis. The absence of the ferri-exochelin: IrpA system in the pathogen signifies the importance of the carboxymycobactin-mycobactin system machinery in M. tuberculosis.
Collapse
Affiliation(s)
- N Kumar
- Department of Animal Biology, University of Hyderabad, Hyderabad, Telangana, India
| | - M Sritharan
- Department of Animal Biology, University of Hyderabad, Hyderabad, Telangana, India
| |
Collapse
|
24
|
Hołówka J, Zakrzewska-Czerwińska J. Nucleoid Associated Proteins: The Small Organizers That Help to Cope With Stress. Front Microbiol 2020; 11:590. [PMID: 32373086 PMCID: PMC7177045 DOI: 10.3389/fmicb.2020.00590] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 03/18/2020] [Indexed: 12/11/2022] Open
Abstract
The bacterial chromosome must be efficiently compacted to fit inside the small and crowded cell while remaining accessible for the protein complexes involved in replication, transcription, and DNA repair. The dynamic organization of the nucleoid is a consequence of both intracellular factors (i.e., simultaneously occurring cell processes) and extracellular factors (e.g., environmental conditions, stress agents). Recent studies have revealed that the bacterial chromosome undergoes profound topological changes under stress. Among the many DNA-binding proteins that shape the bacterial chromosome structure in response to various signals, NAPs (nucleoid associated proteins) are the most abundant. These small, basic proteins bind DNA with low specificity and can influence chromosome organization under changing environmental conditions (i.e., by coating the chromosome in response to stress) or regulate the transcription of specific genes (e.g., those involved in virulence).
Collapse
Affiliation(s)
- Joanna Hołówka
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | | |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
Ferguson L, Wells G, Bhakta S, Johnson J, Guzman J, Parish T, Prentice RA, Brucoli F. Integrated Target-Based and Phenotypic Screening Approaches for the Identification of Anti-Tubercular Agents That Bind to the Mycobacterial Adenylating Enzyme MbtA. ChemMedChem 2019; 14:1735-1741. [PMID: 31454170 PMCID: PMC6800809 DOI: 10.1002/cmdc.201900217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 08/20/2019] [Indexed: 12/27/2022]
Abstract
Iron is essential for the pathogenicity and virulence of Mycobacterium tuberculosis, which synthesises salicyl-capped siderophores (mycobactins) to acquire this element from the host. MbtA is the adenylating enzyme that catalyses the initial reaction of mycobactin biosynthesis and is solely expressed by mycobacteria. A 3200-member library comprised of lead-like, structurally diverse compounds was screened against M. tuberculosis for whole-cell inhibitory activity. A set of 846 compounds that inhibited the tubercle bacilli growth were then tested for their ability to bind to MbtA using a fluorescence-based thermal shift assay and NMR-based Water-LOGSY and saturation transfer difference (STD) experiments. We identified an attractive hit molecule, 5-hydroxyindol-3-ethylamino-(2-nitro-4-trifluoromethyl)benzene (5), that bound with high affinity to MbtA and produced a MIC90 value of 13 μm. The ligand was docked into the MbtA crystal structure and displayed an excellent fit within the MbtA active pocket, adopting a binding mode different from that of the established MbtA inhibitor Sal-AMS.
Collapse
Affiliation(s)
- Lindsay Ferguson
- School of Science, University of the West of Scotland, Paisley, PA1 2BE, Scotland, UK
| | - Geoff Wells
- UCL School of Pharmacy, University College London, 29/39 Brunswick Square, London, WC1N 1AX, UK
| | - Sanjib Bhakta
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, WC1E 7HX, UK
| | - James Johnson
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, WA 98102, USA
| | - Junitta Guzman
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, WA 98102, USA
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, WA 98102, USA
| | - Robin A. Prentice
- Seattle Structural Genomics Center for Infectious Disease, Seattle WA, USA
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA
| | - Federico Brucoli
- Leicester School of Pharmacy, De Montfort University, Leicester, LE1 9BH, UK
| |
Collapse
|
27
|
Dragset MS, Ioerger TR, Zhang YJ, Mærk M, Ginbot Z, Sacchettini JC, Flo TH, Rubin EJ, Steigedal M. Genome-wide Phenotypic Profiling Identifies and Categorizes Genes Required for Mycobacterial Low Iron Fitness. Sci Rep 2019; 9:11394. [PMID: 31388080 PMCID: PMC6684656 DOI: 10.1038/s41598-019-47905-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/18/2019] [Indexed: 11/26/2022] Open
Abstract
Iron is vital for nearly all living organisms, but during infection, not readily available to pathogens. Infectious bacteria therefore depend on specialized mechanisms to survive when iron is limited. These mechanisms make attractive targets for new drugs. Here, by genome-wide phenotypic profiling, we identify and categorize mycobacterial genes required for low iron fitness. Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), can scavenge host-sequestered iron by high-affinity iron chelators called siderophores. We take advantage of siderophore redundancy within the non-pathogenic mycobacterial model organism M. smegmatis (Msmeg), to identify genes required for siderophore dependent and independent fitness when iron is low. In addition to genes with a potential function in recognition, transport or utilization of mycobacterial siderophores, we identify novel putative low iron survival strategies that are separate from siderophore systems. We also identify the Msmeg in vitro essential gene set, and find that 96% of all growth-required Msmeg genes have a mutual ortholog in Mtb. Of these again, nearly 90% are defined as required for growth in Mtb as well. Finally, we show that a novel, putative ferric iron ABC transporter contributes to low iron fitness in Msmeg, in a siderophore independent manner.
Collapse
Affiliation(s)
- Marte S Dragset
- NTNU Norwegian University of Science and Technology, Centre of Molecular Inflammation Research and Department of Clinical and Molecular Medicine, Trondheim, 7491, Norway. .,Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA, 02115, USA. .,Germans Trias i Pujol Research Institute, Tuberculosis Research Unit, Badalona, 80916, Spain.
| | - Thomas R Ioerger
- Texas A&M University, Department of Computer Science, College Station, TX, 77843, USA
| | - Yanjia J Zhang
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA, 02115, USA
| | - Mali Mærk
- NTNU Norwegian University of Science and Technology, Centre of Molecular Inflammation Research and Department of Clinical and Molecular Medicine, Trondheim, 7491, Norway
| | - Zekarias Ginbot
- NTNU Norwegian University of Science and Technology, Centre of Molecular Inflammation Research and Department of Clinical and Molecular Medicine, Trondheim, 7491, Norway
| | - James C Sacchettini
- Texas A&M University, Department of Biochemistry and Biophysics, College Station, TX, 77843, USA
| | - Trude H Flo
- NTNU Norwegian University of Science and Technology, Centre of Molecular Inflammation Research and Department of Clinical and Molecular Medicine, Trondheim, 7491, Norway
| | - Eric J Rubin
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA, 02115, USA
| | - Magnus Steigedal
- NTNU Norwegian University of Science and Technology, Centre of Molecular Inflammation Research and Department of Clinical and Molecular Medicine, Trondheim, 7491, Norway.,Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA, 02115, USA.,St. Olavs University Hospital, Department of Medical Microbiology, Trondheim, 7030, Norway
| |
Collapse
|
28
|
Iron Supplementation Therapy, A Friend and Foe of Mycobacterial Infections? Pharmaceuticals (Basel) 2019; 12:ph12020075. [PMID: 31108902 PMCID: PMC6630247 DOI: 10.3390/ph12020075] [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] [Received: 04/28/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 12/21/2022] Open
Abstract
Iron is an essential element that is required for oxygen transfer, redox, and metabolic activities in mammals and bacteria. Mycobacteria, some of the most prevalent infectious agents in the world, require iron as growth factor. Mycobacterial-infected hosts set up a series of defense mechanisms, including systemic iron restriction and cellular iron distribution, whereas mycobacteria have developed sophisticated strategies to acquire iron from their hosts and to protect themselves from iron’s harmful effects. Therefore, it is assumed that host iron and iron-binding proteins, and natural or synthetic chelators would be keys targets to inhibit mycobacterial proliferation and may have a therapeutic potential. Beyond this hypothesis, recent evidence indicates a host protective effect of iron against mycobacterial infections likely through promoting remodeled immune response. In this review, we discuss experimental procedures and clinical observations that highlight the role of the immune response against mycobacteria under various iron availability conditions. In addition, we discuss the clinical relevance of our knowledge regarding host susceptibility to mycobacteria in the context of iron availability and suggest future directions for research on the relationship between host iron and the immune response and the use of iron as a therapeutic agent.
Collapse
|
29
|
de Oliveira FM, Corrêa VLR, Corrêa AF, da Costa AC, Procopio VO, Junqueira-Kipnis AP, Kipnis A. The mycma_1113 Gene from Mycobacterium abscessus subsp. massiliense is Related to Siderophore Synthesis. Indian J Microbiol 2019; 59:180-187. [PMID: 31031432 DOI: 10.1007/s12088-019-00788-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/22/2019] [Indexed: 12/13/2022] Open
Abstract
Iron (Fe) homeostasis control is important for both pathogen and the host. During infection, the host reduces the access of microorganisms to iron, however, studies have shown that virulent pathogens are capable to sequester Fe from host proteins, and establish the infection. M. abscessus subsp. massiliense (Mycma), that is resistant to most drugs used against tuberculosis, was responsible for outbreaks around the world showing increased virulence when compared to other rapidly growing mycobacteria. The goal of this study was to determine whether Mycma produce siderophores and if the mycma_1113 gene expression, a putative homolog of M. tuberculosis mbtB gene located in the mbt gene cluster, is related to the synthesis of these molecules. For that, the effect of different iron concentrations on the growth of Mycma, the expression of mycma_1113 gene, and the production of siderophores was evaluated in vitro and in vivo. It is shown that Mycma produce siderophores under iron deprivation conditions and mycma_1113 gene expression was influenced by iron availability. The mycma_1113 gene expression was also increased after macrophage or in vivo infection indicating that mycobactin synthesis by Mycma could participate in the Fe sequestration from the host during infection. In conclusion, we show that Mycma produces siderophores under iron deprivation conditions and that the mycma_1113 gene is involved in this process, furthermore, this gene expression is induced during infection.
Collapse
Affiliation(s)
- Fábio Muniz de Oliveira
- Tropical Institute of Pathology and Public Health, Federal University of Goiás, Rua 235 esquina com 1a avenida S/N, Setor Universitário, Goiânia, Goiás CEP 7405-050 Brazil
| | - Viviane Lopes Rocha Corrêa
- Tropical Institute of Pathology and Public Health, Federal University of Goiás, Rua 235 esquina com 1a avenida S/N, Setor Universitário, Goiânia, Goiás CEP 7405-050 Brazil
| | - André França Corrêa
- Tropical Institute of Pathology and Public Health, Federal University of Goiás, Rua 235 esquina com 1a avenida S/N, Setor Universitário, Goiânia, Goiás CEP 7405-050 Brazil
| | - Adeliane Castro da Costa
- Tropical Institute of Pathology and Public Health, Federal University of Goiás, Rua 235 esquina com 1a avenida S/N, Setor Universitário, Goiânia, Goiás CEP 7405-050 Brazil
| | - Victor Oliveira Procopio
- Tropical Institute of Pathology and Public Health, Federal University of Goiás, Rua 235 esquina com 1a avenida S/N, Setor Universitário, Goiânia, Goiás CEP 7405-050 Brazil
| | - Ana Paula Junqueira-Kipnis
- Tropical Institute of Pathology and Public Health, Federal University of Goiás, Rua 235 esquina com 1a avenida S/N, Setor Universitário, Goiânia, Goiás CEP 7405-050 Brazil
| | - André Kipnis
- Tropical Institute of Pathology and Public Health, Federal University of Goiás, Rua 235 esquina com 1a avenida S/N, Setor Universitário, Goiânia, Goiás CEP 7405-050 Brazil
| |
Collapse
|
30
|
Datta C, Jha RK, Ahmed W, Ganguly S, Ghosh S, Nagaraja V. Physical and functional interaction between nucleoid-associated proteins HU and Lsr2 of Mycobacterium tuberculosis: altered DNA binding and gene regulation. Mol Microbiol 2019; 111:981-994. [PMID: 30633392 DOI: 10.1111/mmi.14202] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2019] [Indexed: 12/15/2022]
Abstract
Nucleoid-associated proteins (NAPs) in bacteria contribute to key activities such as DNA compaction, chromosome organization and regulation of gene expression. HU and Lsr2 are two principal NAPs in Mycobacterium tuberculosis (Mtb). HU is essential for Mtb survival and is one of the most abundant NAPs. It differs from other eubacterial HU proteins in having a long, flexible lysine- and arginine-rich carboxy-terminal domain. Lsr2 of Mtb is the functional analogue of the bacterial NAP commonly called H-NS. Lsr2 binds to and regulates expression of A/T-rich portions of the otherwise G/C-rich mycobacterial chromosome. Here, we demonstrate that HU and Lsr2 interact to form a complex. The interaction occurs primarily through the flexible carboxy-terminal domain of HU and the acidic amino-terminal domain of Lsr2. The resulting complex, upon binding to DNA, forms thick nucleoprotein rods, in contrast to the DNA bridging seen with Lsr2 and the DNA compaction seen with HU. Furthermore, transcription assays indicate that the HU-Lsr2 complex is a regulator of gene expression. This physical and functional interaction between two NAPs, which has not been reported previously, is likely to be important for DNA organization and gene expression in Mtb and perhaps other bacterial species.
Collapse
Affiliation(s)
- Chandreyee Datta
- Department of Microbiology and Cell Biology, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India
| | - Rajiv Kumar Jha
- Department of Microbiology and Cell Biology, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India
| | - Wareed Ahmed
- Department of Microbiology and Cell Biology, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India
| | - Sohini Ganguly
- Department of Microbiology and Cell Biology, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India
| | - Soumitra Ghosh
- Department of Microbiology and Cell Biology, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India
| |
Collapse
|
31
|
Essential Nucleoid Associated Protein mIHF (Rv1388) Controls Virulence and Housekeeping Genes in Mycobacterium tuberculosis. Sci Rep 2018; 8:14214. [PMID: 30242166 PMCID: PMC6155035 DOI: 10.1038/s41598-018-32340-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/20/2018] [Indexed: 12/14/2022] Open
Abstract
Tight control of gene expression is crucial for Mycobacterium tuberculosis to adapt to the changing environments encountered when infecting or exiting human cells. While three nucleoid associated proteins (NAPs) EspR, HupB and Lsr2 have been investigated, the role of a fourth, the mycobacterial integration host factor (mIHF), remains elusive. Here, we report a multidisciplinary functional analysis that exploits a conditional mIHF mutant. Gene silencing was bactericidal and resulted in elongated cells devoid of septa, with only one nucleoid. ChIP-sequencing identified 153 broad peaks distributed around the chromosome, which were often situated upstream of transcriptional start sites where EspR also bound. RNA-sequencing showed expression of 209 genes to be heavily affected upon mIHF depletion, including those for many tRNAs, DNA synthesis and virulence pathways. Consistent with NAP function, mIHF acts as a global regulator by directly and indirectly controlling genes required for pathogenesis and for housekeeping functions.
Collapse
|
32
|
Kalra P, Mishra SK, Kaur S, Kumar A, Prasad HK, Sharma TK, Tyagi JS. G-Quadruplex-Forming DNA Aptamers Inhibit the DNA-Binding Function of HupB and Mycobacterium tuberculosis Entry into Host Cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 13:99-109. [PMID: 30245472 PMCID: PMC6148841 DOI: 10.1016/j.omtn.2018.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 08/16/2018] [Accepted: 08/16/2018] [Indexed: 01/26/2023]
Abstract
The entry and survival of Mycobacterium tuberculosis (Mtb) within host cells is orchestrated partly by an essential histone-like protein HupB (Rv2986c). Despite being an essential drug target, the lack of structural information has impeded the development of inhibitors targeting the indispensable and multifunctional C-terminal domain (CTD) of HupB. To bypass the requirement for structural information in the classical drug discovery route, we generated a panel of DNA aptamers against HupB protein through systemic evolution of ligands by exponential (SELEX) enrichment. Two G-quadruplex-forming high-affinity aptamers (HupB-4T and HupB-13T) were identified, each of which bound two distinct sites on full-length HupB, with an estimated KD of ∼1.72 μM and ∼0.17 μM, respectively, for the high-affinity sites. While HupB-4T robustly inhibited DNA-binding activity of HupB in vitro, both the aptamers recognized surface-located HupB and significantly blocked Mtb entry into THP-1 monocytic cells (p < 0.0001). In summary, DNA aptamers generated in this study block DNA-binding activity of HupB, inhibit virulent Mtb infection in host cells, and demonstrate aptamers to be inhibitors of HupB functions. This study also illustrates the utility of SELEX in developing inhibitors against essential targets for whom structural information is not available.
Collapse
Affiliation(s)
- Priya Kalra
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, Delhi 110029, India
| | - Subodh Kumar Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Madhya Pradesh 453552, India
| | - Surinder Kaur
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, Delhi 110029, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Madhya Pradesh 453552, India
| | | | - Tarun Kumar Sharma
- Centre for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India.
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, Delhi 110029, India; Centre for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India.
| |
Collapse
|
33
|
Two dd-Carboxypeptidases from Mycobacterium smegmatis Affect Cell Surface Properties through Regulation of Peptidoglycan Cross-Linking and Glycopeptidolipids. J Bacteriol 2018; 200:JB.00760-17. [PMID: 29735762 DOI: 10.1128/jb.00760-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 04/25/2018] [Indexed: 11/20/2022] Open
Abstract
During the peptidoglycan (PG) maturation of mycobacteria, the glycan strands are interlinked by both 3-3 (between two meso-diaminopimelic acids [meso-DAPs]) and 4-3 cross-links (between d-Ala and meso-DAP), though there is a predominance (60 to 80%) of 3-3 cross-links. The dd-carboxypeptidases (dd-CPases) act on pentapeptides to generate tetrapeptides that are used by ld-transpeptidases as substrates to form 3-3 cross-links. Therefore, dd-CPases play a crucial role in mycobacterial PG cross-link formation. However, the physiology of dd-CPases in mycobacteria is relatively unexplored. In this study, we deleted two dd-CPase genes, msmeg_2433 and msmeg_2432, both individually and in combination, from Mycobacterium smegmatis mc2155. Though the single dd-CPase gene deletions had no significant impact on the mycobacterial physiology, many interesting functional alterations were observed in the double-deletion mutant, viz, a predominance in PG cross-link formation was shifted from 3-3 cross-links to 4-3, cell surface glycopeptidolipid (GPL) expression was reduced, and susceptibility to β-lactams and antitubercular agents was enhanced. Moreover, the survival rate of the double mutant within murine macrophages was higher than that of the parent. Interestingly, the complementation with any one of the dd-CPase genes could restore the wild-type phenotype. In a nutshell, we infer that the altered ratio of 4-3 to 3-3 PG cross-links might have influenced the expression of surface GPLs, colony morphology, biofilm formation, drug susceptibility, and subsistence of the cells within macrophages.IMPORTANCE The glycan strands in mycobacterial peptidoglycan (PG) are interlinked by both 3-3 and 4-3 cross-links. The dd-CPases generate tetrapeptides by acting on the pentapeptides, and ld-transpeptidases use tetrapeptides as substrates to form 3-3 cross-links. In this study, we showed that simultaneous deletions of two dd-CPases alter the nature of PG cross-linking from 3-3 cross-links to 4-3 cross-links. The deletions subsequently decrease the expression of glycopeptidolipids (significant surface lipid present in many nontuberculous mycobacteria, including Mycobacterium smegmatis) and affect other physiological parameters, like cell morphology, growth rate, biofilm formation, antibiotic susceptibility, and survival within murine macrophages. Thus, unraveling the physiology of dd-CPases might help us design antimycobacterial therapeutics in the future.
Collapse
|
34
|
Oliveira FM, Da Costa AC, Procopio VO, Garcia W, Araújo JN, Da Silva RA, Junqueira-Kipnis AP, Kipnis A. Mycobacterium abscessus subsp. massiliense mycma_0076 and mycma_0077 Genes Code for Ferritins That Are Modulated by Iron Concentration. Front Microbiol 2018; 9:1072. [PMID: 29910777 PMCID: PMC5992710 DOI: 10.3389/fmicb.2018.01072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/04/2018] [Indexed: 12/19/2022] Open
Abstract
Mycobacterium abscessus complex has been characterized in the last decade as part of a cluster of mycobacteria that evolved from an opportunistic to true human pathogen; however, the factors responsible for pathogenicity are still undefined. It appears that the success of mycobacterial infection is intrinsically related with the capacity of the bacteria to regulate intracellular iron levels, mostly using iron storage proteins. This study evaluated two potential M. abscessus subsp. massiliense genes involved in iron storage. Unlike other opportunist or pathogenic mycobacteria studied, M. abscessus complex has two genes similar to ferritins from M. tuberculosis (Rv3841), and in M. abscessus subsp. massiliense, those genes are annotated as mycma_0076 and mycma_0077. Molecular dynamic analysis of the predicted expressed proteins showed that they have a ferroxidase center. The expressions of mycma_0076 and mycma_0077 genes were modulated by the iron levels in both in vitro cultures as well as infected macrophages. Structural studies using size-exclusion chromatography, circular dichroism spectroscopy and dynamic light scattering showed that r0076 protein has a structure similar to those observed in the ferritin family. The r0076 forms oligomers in solution most likely composed of 24 subunits. Functional studies with recombinant proteins, obtained from heterologous expression of mycma_0076 and mycma_0077 genes in Escherichia coli, showed that both proteins were capable of oxidizing Fe2+ into Fe3+, demonstrating that these proteins have a functional ferroxidase center. In conclusion, two ferritins proteins were shown, for the first time, to be involved in iron storage in M. abscessus subsp. massiliense and their expressions were modulated by the iron levels.
Collapse
Affiliation(s)
- Fábio M. Oliveira
- Tropical Institute of Pathology and Public Health, Department of Microbiology, Immunology, Parasitology and Pathology, Federal University of Goiás, Goiânia, Brazil
| | - Adeliane C. Da Costa
- Tropical Institute of Pathology and Public Health, Department of Microbiology, Immunology, Parasitology and Pathology, Federal University of Goiás, Goiânia, Brazil
| | - Victor O. Procopio
- Tropical Institute of Pathology and Public Health, Department of Microbiology, Immunology, Parasitology and Pathology, Federal University of Goiás, Goiânia, Brazil
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Federal University of ABC (UFABC), Santo André, Brazil
| | - Juscemácia N. Araújo
- Centro de Ciências Naturais e Humanas, Federal University of ABC (UFABC), Santo André, Brazil
| | - Roosevelt A. Da Silva
- Collaborative Center of Biosystems, Regional Jataí, Federal University of Goiás, Goiânia, Brazil
| | - Ana Paula Junqueira-Kipnis
- Tropical Institute of Pathology and Public Health, Department of Microbiology, Immunology, Parasitology and Pathology, Federal University of Goiás, Goiânia, Brazil
| | - André Kipnis
- Tropical Institute of Pathology and Public Health, Department of Microbiology, Immunology, Parasitology and Pathology, Federal University of Goiás, Goiânia, Brazil
| |
Collapse
|
35
|
The Origin of Chromosomal Replication Is Asymmetrically Positioned on the Mycobacterial Nucleoid, and the Timing of Its Firing Depends on HupB. J Bacteriol 2018. [PMID: 29531181 DOI: 10.1128/jb.00044-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The bacterial chromosome undergoes dynamic changes in response to ongoing cellular processes and adaptation to environmental conditions. Among the many proteins involved in maintaining this dynamism, the most abundant is the nucleoid-associated protein (NAP) HU. In mycobacteria, the HU homolog, HupB, possesses an additional C-terminal domain that resembles that of eukaryotic histones H1/H5. Recently, we demonstrated that the highly abundant HupB protein occupies the entirety of the Mycobacterium smegmatis chromosome and that the HupB-binding sites exhibit a bias from the origin (oriC) to the terminus (ter). In this study, we used HupB fused with enhanced green fluorescent protein (EGFP) to perform the first analysis of chromosome dynamics and to track the oriC and replication machinery directly on the chromosome during the mycobacterial cell cycle. We show that the chromosome is located in an off-center position that reflects the unequal division and growth of mycobacterial cells. Moreover, unlike the situation in E. coli, the sister oriC regions of M. smegmatis move asymmetrically along the mycobacterial nucleoid. Interestingly, in this slow-growing organism, the initiation of the next round of replication precedes the physical separation of sister chromosomes. Finally, we show that HupB is involved in the precise timing of replication initiation.IMPORTANCE Although our view of mycobacterial nucleoid organization has evolved considerably over time, we still know little about the dynamics of the mycobacterial nucleoid during the cell cycle. HupB is a highly abundant mycobacterial nucleoid-associated protein (NAP) with an indispensable histone-like tail. It was previously suggested as a potential target for antibiotic therapy against tuberculosis. Here, we fused HupB with enhanced green fluorescent protein (EGFP) to study the dynamics of the mycobacterial chromosome in real time and to monitor the replication process directly on the chromosome. Our results reveal that, unlike the situation in Escherichia coli, the nucleoid of an apically growing mycobacterium is positioned asymmetrically within the cell throughout the cell cycle. We show that HupB is involved in controlling the timing of replication initiation. Since tuberculosis remains a serious health problem, studies concerning mycobacterial cell biology are of great importance.
Collapse
|
36
|
Zondervan NA, van Dam JCJ, Schaap PJ, Martins Dos Santos VAP, Suarez-Diez M. Regulation of Three Virulence Strategies of Mycobacterium tuberculosis: A Success Story. Int J Mol Sci 2018; 19:E347. [PMID: 29364195 PMCID: PMC5855569 DOI: 10.3390/ijms19020347] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/19/2018] [Accepted: 01/21/2018] [Indexed: 12/28/2022] Open
Abstract
Tuberculosis remains one of the deadliest diseases. Emergence of drug-resistant and multidrug-resistant M. tuberculosis strains makes treating tuberculosis increasingly challenging. In order to develop novel intervention strategies, detailed understanding of the molecular mechanisms behind the success of this pathogen is required. Here, we review recent literature to provide a systems level overview of the molecular and cellular components involved in divalent metal homeostasis and their role in regulating the three main virulence strategies of M. tuberculosis: immune modulation, dormancy and phagosomal rupture. We provide a visual and modular overview of these components and their regulation. Our analysis identified a single regulatory cascade for these three virulence strategies that respond to limited availability of divalent metals in the phagosome.
Collapse
Affiliation(s)
- Niels A Zondervan
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Jesse C J van Dam
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
- LifeGlimmer GmbH, Markelstrasse 38, 12163 Berlin, Germany.
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| |
Collapse
|
37
|
Green KD, Biswas T, Pang AH, Willby MJ, Reed MS, Stuchlik O, Pohl J, Posey JE, Tsodikov OV, Garneau-Tsodikova S. Acetylation by Eis and Deacetylation by Rv1151c of Mycobacterium tuberculosis HupB: Biochemical and Structural Insight. Biochemistry 2018; 57:781-790. [PMID: 29345920 DOI: 10.1021/acs.biochem.7b01089] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial nucleoid-associated proteins (NAPs) are critical to genome integrity and chromosome maintenance. Post-translational modifications of bacterial NAPs appear to function similarly to their better studied mammalian counterparts. The histone-like NAP HupB from Mycobacterium tuberculosis (Mtb) was previously observed to be acetylated by the acetyltransferase Eis, leading to genome reorganization. We report biochemical and structural aspects of acetylation of HupB by Eis. We also found that the SirT-family NAD+-dependent deacetylase Rv1151c from Mtb deacetylated HupB in vitro and characterized the deacetylation kinetics. We propose that activities of Eis and Rv1151c could regulate the acetylation status of HupB to remodel the mycobacterial chromosome in response to environmental changes.
Collapse
Affiliation(s)
- Keith D Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | - Tapan Biswas
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Allan H Pang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | | | | | | | | | | | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| |
Collapse
|
38
|
Kriel NL, Gallant J, van Wyk N, van Helden P, Sampson SL, Warren RM, Williams MJ. Mycobacterial nucleoid associated proteins: An added dimension in gene regulation. Tuberculosis (Edinb) 2018. [DOI: 10.1016/j.tube.2017.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
39
|
Yaseen I, Choudhury M, Sritharan M, Khosla S. Histone methyltransferase SUV39H1 participates in host defense by methylating mycobacterial histone-like protein HupB. EMBO J 2017; 37:183-200. [PMID: 29170282 DOI: 10.15252/embj.201796918] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 09/25/2017] [Accepted: 10/18/2017] [Indexed: 12/22/2022] Open
Abstract
Host cell defense against an invading pathogen depends upon various multifactorial mechanisms, several of which remain undiscovered. Here, we report a novel defense mechanism against mycobacterial infection that utilizes the histone methyltransferase, SUV39H1. Normally, a part of the host chromatin, SUV39H1, was also found to be associated with the mycobacterial bacilli during infection. Its binding to bacilli was accompanied by trimethylation of the mycobacterial histone-like protein, HupB, which in turn reduced the cell adhesion capability of the bacilli. Importantly, SUV39H1-mediated methylation of HupB reduced the mycobacterial survival inside the host cell. This was also true in mice infection experiments. In addition, the ability of mycobacteria to form biofilms, a survival strategy of the bacteria dependent upon cell-cell adhesion, was dramatically reduced in the presence of SUV39H1. Thus, this novel defense mechanism against mycobacteria represents a surrogate function of the epigenetic modulator, SUV39H1, and operates by interfering with their cell-cell adhesion ability.
Collapse
Affiliation(s)
- Imtiyaz Yaseen
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India.,Graduate Studies, Manipal University, Manipal, India
| | - Mitali Choudhury
- Department of Animal Biology, University of Hyderabad, Hyderabad, India
| | - Manjula Sritharan
- Department of Animal Biology, University of Hyderabad, Hyderabad, India
| | - Sanjeev Khosla
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| |
Collapse
|
40
|
Abstract
In bacteria, chromosomal DNA must be efficiently compacted to fit inside the small cell compartment while remaining available for the proteins involved in replication, segregation, and transcription. Among the nucleoid-associated proteins (NAPs) responsible for maintaining this highly organized and yet dynamic chromosome structure, the HU protein is one of the most conserved and highly abundant. HupB, a homologue of HU, was recently identified in mycobacteria. This intriguing mycobacterial NAP is composed of two domains: an N-terminal domain that resembles bacterial HU, and a long and distinctive C-terminal domain that contains several PAKK/KAAK motifs, which are characteristic of the H1/H5 family of eukaryotic histones. In this study, we analyzed the in vivo binding of HupB on the chromosome scale. By using PALM (photoactivated localization microscopy) and ChIP-Seq (chromatin immunoprecipitation followed by deep sequencing), we observed that the C-terminal domain is indispensable for the association of HupB with the nucleoid. Strikingly, the in vivo binding of HupB displayed a bias from the origin (oriC) to the terminus (ter) of the mycobacterial chromosome (numbers of binding sites decreased toward ter). We hypothesized that this binding mode reflects a role for HupB in organizing newly replicated oriC regions. Thus, HupB may be involved in coordinating replication with chromosome segregation.IMPORTANCE We currently know little about the organization of the mycobacterial chromosome and its dynamics during the cell cycle. Among the mycobacterial nucleoid-associated proteins (NAPs) responsible for chromosome organization and dynamics, HupB is one of the most intriguing. It contains a long and distinctive C-terminal domain that harbors several PAKK/KAAK motifs, which are characteristic of the eukaryotic histone H1/H5 proteins. The HupB protein is also known to be crucial for the survival of tubercle bacilli during infection. Here, we provide in vivo experimental evidence showing that the C-terminal domain of HupB is crucial for its DNA binding. Our results suggest that HupB may be involved in organizing newly replicated regions and could help coordinate chromosome replication with segregation. Given that tuberculosis (TB) remains a serious worldwide health problem (10.4 million new TB cases were diagnosed in 2015, according to WHO) and new multidrug-resistant Mycobacterium tuberculosis strains are continually emerging, further studies of the biological function of HupB are needed to determine if this protein could be a prospect for novel antimicrobial drug development.
Collapse
|
41
|
Enany S, Yoshida Y, Tateishi Y, Ozeki Y, Nishiyama A, Savitskaya A, Yamaguchi T, Ohara Y, Yamamoto T, Ato M, Matsumoto S. Mycobacterial DNA-binding protein 1 is critical for long term survival of Mycobacterium smegmatis and simultaneously coordinates cellular functions. Sci Rep 2017; 7:6810. [PMID: 28754952 PMCID: PMC5533761 DOI: 10.1038/s41598-017-06480-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 06/13/2017] [Indexed: 11/09/2022] Open
Abstract
Bacteria can proliferate perpetually without ageing, but they also face conditions where they must persist. Mycobacteria can survive for a long period. This state appears during mycobacterial diseases such as tuberculosis and leprosy, which are chronic and develop after long-term persistent infections. However, the fundamental mechanisms of the long-term living of mycobacteria are unknown. Every Mycobacterium species expresses Mycobacterial DNA-binding protein 1 (MDP1), a histone-like nucleoid associated protein. Mycobacterium smegmatis is a saprophytic fast grower and used as a model of mycobacterial persistence, since it shares the characteristics of the long-term survival observed in pathogenic mycobacteria. Here we show that MDP1-deficient M. smegmatis dies more rapidly than the parental strain after entering stationary phase. Proteomic analyses revealed 21 upregulated proteins with more than 3-fold in MDP1-deficient strain, including DnaA, a replication initiator, NDH, a NADH dehydrogenase that catalyzes downhill electron transfer, Fas1, a critical fatty acid synthase, and antioxidants such as AhpC and KatG. Biochemical analyses showed elevated levels of DNA and ATP syntheses, a decreased NADH/NAD+ ratio, and a loss of resistance to oxidative stress in the MDP1-knockout strain. This study suggests the importance of MDP1-dependent simultaneous control of the cellular functions in the long-term survival of mycobacteria.
Collapse
Affiliation(s)
- Shymaa Enany
- Department of Bacteriology, Niigata University School of Medicine, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, Niigata, 951-9510, Japan.,Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, 41522, Ismailia, Egypt
| | - Yutaka Yoshida
- Department of Structural Pathology, Kidney Research Center, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, Niigata, 951-9510, Japan
| | - Yoshitaka Tateishi
- Department of Bacteriology, Niigata University School of Medicine, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, Niigata, 951-9510, Japan
| | - Yuriko Ozeki
- Department of Bacteriology, Niigata University School of Medicine, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, Niigata, 951-9510, Japan
| | - Akihito Nishiyama
- Department of Bacteriology, Niigata University School of Medicine, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, Niigata, 951-9510, Japan.
| | - Anna Savitskaya
- Department of Bacteriology, Niigata University School of Medicine, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, Niigata, 951-9510, Japan
| | - Takehiro Yamaguchi
- Department of Bacteriology, Niigata University School of Medicine, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, Niigata, 951-9510, Japan
| | - Yukiko Ohara
- Department of Bacteriology, Niigata University School of Medicine, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, Niigata, 951-9510, Japan
| | - Tadashi Yamamoto
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata, Niigata, 950-2181, Japan
| | - Manabu Ato
- Department of Immunology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, Niigata University School of Medicine, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, Niigata, 951-9510, Japan.
| |
Collapse
|
42
|
Yan S, Xu M, Wang R, Li Q, Yu Z, Xie J. Overexpression of Rv2788 increases mycobacterium stresses survival. Microbiol Res 2016; 195:51-59. [PMID: 28024526 DOI: 10.1016/j.micres.2016.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/11/2016] [Accepted: 11/14/2016] [Indexed: 11/18/2022]
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis-one of the most devastating infectious diseases, is a successful intracellular pathogen capable of surviving diverse stresses. Unveiling the molecular mechanisms governing this superior adaptation will inspire better control measures against tuberculosis. To define the role of Rv2788, a manganese-dependent transcriptional repressor, M.smegmatis was used as the host strain for heterologous expression Rv2788. Rv2788 can significantly change the colony morphology and fatty acids and permeability of cell wall, enhance the growth of the recombinants and resistance to diverse stresses, such as hydrogen peroxide (H₂O₂), diamide exposure, surface stress, acidic condition, multiple antibiotics treatment including chloramphenicol, vancomycin and amikacin. The dysregulation of the target genes of Rv2788, such as whiB1 and lexA, might underpin such phenotypes. The results implicate important roles of Rv2788 in the survival of Mycobacterium under stresses, and might represent ideal novel antibiotics target candidate.
Collapse
Affiliation(s)
- Shuangquan Yan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Mengmeng Xu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Rui Wang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Qiming Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Zhaoxiao Yu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China.
| |
Collapse
|
43
|
Vergnolle O, Xu H, Tufariello JM, Favrot L, Malek AA, Jacobs WR, Blanchard JS. Post-translational Acetylation of MbtA Modulates Mycobacterial Siderophore Biosynthesis. J Biol Chem 2016; 291:22315-22326. [PMID: 27566542 PMCID: PMC5064009 DOI: 10.1074/jbc.m116.744532] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/17/2016] [Indexed: 11/06/2022] Open
Abstract
Iron is an essential element for life, but its soluble form is scarce in the environment and is rarer in the human body. Mtb (Mycobacterium tuberculosis) produces two aryl-capped siderophores, mycobactin (MBT) and carboxymycobactin (cMBT), to chelate intracellular iron. The adenylating enzyme MbtA catalyzes the first step of mycobactin biosynthesis in two half-reactions: activation of the salicylic acid as an acyl-adenylate and ligation onto the acyl carrier protein (ACP) domain of MbtB to form covalently salicylated MbtB-ACP. We report the first apo-MbtA structure from Mycobacterium smegmatis at 2.3 Å. We demonstrate here that MbtA activity can be reversibly, post-translationally regulated by acetylation. Indeed the mycobacterial Pat (protein lysine acetyltransferase), Rv0998, specifically acetylates MbtA on lysine 546, in a cAMP-dependent manner, leading to enzyme inhibition. MbtA acetylation can be reversed by the NAD+-dependent DAc (deacetyltransferase), Rv1151c. Deletion of Pat and DAc genes in Mtb revealed distinct phenotypes for strains lacking one or the other gene at low pH and limiting iron conditions. This study establishes a direct connection between the reversible acetylation system Pat/DAc and the ability of Mtb to adapt in limited iron conditions, which is critical for mycobacterial infection.
Collapse
Affiliation(s)
| | - Hua Xu
- From the Department of Biochemistry and
| | - JoAnn M Tufariello
- the Department of Microbiology and Immunology, Howard Hughes Medical Institute, Albert Einstein College of Medicine, Bronx, New York 10461
| | | | - Adel A Malek
- the Department of Microbiology and Immunology, Howard Hughes Medical Institute, Albert Einstein College of Medicine, Bronx, New York 10461
| | - William R Jacobs
- the Department of Microbiology and Immunology, Howard Hughes Medical Institute, Albert Einstein College of Medicine, Bronx, New York 10461
| | | |
Collapse
|
44
|
Iron Homeostasis in Mycobacterium tuberculosis: Mechanistic Insights into Siderophore-Mediated Iron Uptake. J Bacteriol 2016; 198:2399-409. [PMID: 27402628 DOI: 10.1128/jb.00359-16] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mycobacterium tuberculosis requires iron for normal growth but faces a limitation of the metal ion due to its low solubility at biological pH and the withholding of iron by the mammalian host. The pathogen expresses the Fe(3+)-specific siderophores mycobactin and carboxymycobactin to chelate the metal ion from insoluble iron and the host proteins transferrin, lactoferrin, and ferritin. Siderophore-mediated iron uptake is essential for the survival of M. tuberculosis, as knockout mutants, which were defective in siderophore synthesis or uptake, failed to survive in low-iron medium and inside macrophages. But as excess iron is toxic due to its catalytic role in the generation of free radicals, regulation of iron uptake is necessary to maintain optimal levels of intracellular iron. The focus of this review is to present a comprehensive overview of iron homeostasis in M. tuberculosis that is discussed in the context of mycobactin biosynthesis, transport of iron across the mycobacterial cell envelope, and storage of excess iron. The clinical significance of the serum iron status and the expression of the iron-regulated protein HupB in tuberculosis (TB) patients is presented here, highlighting the potential of HupB as a marker, notably in extrapulmonary TB cases.
Collapse
|
45
|
Liu Y, Wang H, Cui T, Zhou X, Jia Y, Zhang H, He ZG. NapM, a new nucleoid-associated protein, broadly regulates gene expression and affects mycobacterial resistance to anti-tuberculosis drugs. Mol Microbiol 2016; 101:167-81. [DOI: 10.1111/mmi.13383] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Yu Liu
- National Key Laboratory of Agricultural Microbiology, Department of Biological Science, College of Life Science and Technology, Huazhong Agricultural University; Wuhan 430070 China
| | - Hongyang Wang
- National Key Laboratory of Agricultural Microbiology, Department of Biological Science, College of Life Science and Technology, Huazhong Agricultural University; Wuhan 430070 China
| | - Tao Cui
- National Key Laboratory of Agricultural Microbiology, Department of Biological Science, College of Life Science and Technology, Huazhong Agricultural University; Wuhan 430070 China
| | - Xiling Zhou
- National Key Laboratory of Agricultural Microbiology, Department of Biological Science, College of Life Science and Technology, Huazhong Agricultural University; Wuhan 430070 China
| | - Yanxia Jia
- Division of Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences; Beijing 100101 China
| | - Hua Zhang
- National Key Laboratory of Agricultural Microbiology, Department of Biological Science, College of Life Science and Technology, Huazhong Agricultural University; Wuhan 430070 China
| | - Zheng-Guo He
- National Key Laboratory of Agricultural Microbiology, Department of Biological Science, College of Life Science and Technology, Huazhong Agricultural University; Wuhan 430070 China
| |
Collapse
|
46
|
de Keijzer J, Mulder A, de Beer J, de Ru AH, van Veelen PA, van Soolingen D. Mechanisms of Phenotypic Rifampicin Tolerance in Mycobacterium tuberculosis Beijing Genotype Strain B0/W148 Revealed by Proteomics. J Proteome Res 2016; 15:1194-204. [PMID: 26930559 DOI: 10.1021/acs.jproteome.5b01073] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The "successful" Russian clone B0/W148 of Mycobacterium tuberculosis Beijing is well-known for its capacity to develop antibiotic resistance. During treatment, resistant mutants can occur that have inheritable resistance to specific antibiotics. Next to mutations, M. tuberculosis has several mechanisms that increase their tolerance to a variety of antibiotics. Insights in the phenotypic mechanisms that contribute to drug tolerance will increase our understanding of how antibiotic resistance develops in M. tuberculosis. In this study, we examined the (phospho)proteome dynamics in M. tuberculosis Beijing strain B0/W148 when exposed to a high dose of rifampicin; one of the most potent first-line antibiotics. A total of 2,534 proteins and 191 phosphorylation sites were identified, and revealed the differential regulation of DosR regulon proteins, which are necessary for the development of a dormant phenotype that is less susceptible to antibiotics. By examining independent phenotypic markers of dormancy, we show that persisters of in vitro rifampicin exposure entered a metabolically hypoactive state, which yields rifampicin and other antibiotics largely ineffective. These new insights in the role of protein regulation and post-translational modifications during the initial phase of rifampicin treatment reveal a shortcoming in the antituberculosis regimen that is administered to 8-9 million individuals annually.
Collapse
Affiliation(s)
- Jeroen de Keijzer
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC) , Leiden 2300 RC, The Netherlands
| | - Arnout Mulder
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM) , Bilthoven 3720 BA, The Netherlands
| | - Jessica de Beer
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM) , Bilthoven 3720 BA, The Netherlands
| | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC) , Leiden 2300 RC, The Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC) , Leiden 2300 RC, The Netherlands
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM) , Bilthoven 3720 BA, The Netherlands.,Departments of Pulmonary Diseases and Medical Microbiology, Radboud University Medical Center , Nijmegen 6500 HB, The Netherlands
| |
Collapse
|
47
|
Syal K, Chakraborty S, Bhattacharyya R, Banerjee D. Combined inhalation and oral supplementation of Vitamin A and Vitamin D: A possible prevention and therapy for tuberculosis. Med Hypotheses 2015; 84:199-203. [DOI: 10.1016/j.mehy.2014.12.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/26/2014] [Indexed: 11/25/2022]
|
48
|
Minchella PA, Donkor S, McDermid JM, Sutherland JS. Iron homeostasis and progression to pulmonary tuberculosis disease among household contacts. Tuberculosis (Edinb) 2015; 95:288-93. [PMID: 25764944 DOI: 10.1016/j.tube.2015.02.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/16/2015] [Indexed: 12/26/2022]
Abstract
Early identification of individuals at risk for progressing to active tuberculosis (TB) disease may limit new transmission and improve clinical outcomes. Evidence indicates altered iron homeostasis may identify those at greater risk of disease progression in HIV co-infection. We aimed to investigate iron homeostasis biomarkers as risk factors for progression to TB. Archived plasma samples were analyzed from household contacts of pulmonary TB index cases in The Gambia. Contacts were classified as asymptomatic non-progressors (n = 17) or TB-progressors (n = 10), which included two HIV-infected participants. Iron homeostasis (hemoglobin, ferritin, hepcidin, soluble transferrin receptor, transferrin) was assessed in all contacts at study recruitment. Plasma was collected a median of 910 days prior to TB diagnosis. Low transferrin around the time of known exposure to infectious TB was a disease progression risk factor among all TB-progressors (Poisson incidence rate ratio: 0.55; 95% CI: 0.35-0.89). Iron homeostasis also differed between early and delayed TB-progressors, with higher ferritin and hepcidin concentrations observed among early TB-progressors (mean ferritin 50.2 vs. 26.2 ng/ml; P = 0.027; mean hepcidin 37.7 vs. 5.6 ng/ml; P = 0.036). Iron homeostasis is associated with progression to TB among household contacts. Further studies are needed to elucidate mechanisms and determine the clinical utility of monitoring iron homeostasis biomarkers.
Collapse
Affiliation(s)
| | - Simon Donkor
- Vaccinology Theme, Medical Research Council Unit, Fajara, Gambia
| | - Joann M McDermid
- Division of Nutritional Sciences, Cornell University, Ithaca, USA.
| | | |
Collapse
|
49
|
Sritharan N, Choudhury M, Sivakolundu S, Chaurasia R, Chouhan N, Rao PP, Sritharan M. Highly immunoreactive antibodies against the rHup-F2 fragment (aa 63-161) of the iron-regulated HupB protein of Mycobacterium tuberculosis and its potential for the serodiagnosis of extrapulmonary and recurrent tuberculosis. Eur J Clin Microbiol Infect Dis 2014; 34:33-40. [PMID: 25037869 DOI: 10.1007/s10096-014-2203-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 06/30/2014] [Indexed: 11/30/2022]
Abstract
HupB is an iron-regulated protein in Mycobacterium tuberculosis that functions as a positive regulator of mycobactin biosynthesis. It is essential for the growth and survival of the pathogen inside macrophages. Previously, using the full-length rHupB of M. tuberculosis, we demonstrated high levels of anti-HupB antibodies in the serum of pulmonary tuberculosis (TB) and, interestingly, extrapulmonary TB patients with negligible levels in household contacts and healthy controls. Here, we used three antigenic fragments of HupB, namely the recombinant HupB-F1 (aa 1-71), HupB-F2 (aa 63-161) and HupB-F3 (aa 164-214), as antigens in enzyme-linked immunosorbent assay (ELISA) to screen serum from TB patients. HupB-F2 showed enhanced immunoreactivity with serum from patients with pulmonary TB (three groups consisting of new cases, defaulters and recurrent cases) and extrapulmonary TB, with negligible levels in normal healthy controls. The negative correlation of the anti-(HupB-F2) antibodies with serum iron was maximal, with a Pearson's correlation coefficient value of -0.415. The study, in addition to strengthening the diagnostic potential of HupB, reflected the superior performance of HupB-F2 as an antigen in screening pulmonary and extrapulmonary TB.
Collapse
Affiliation(s)
- N Sritharan
- NRI Academy of Sciences, Guntur, Andhra Pradesh, India
| | - M Choudhury
- Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Prof. CR Rao Road, Gachibowli, Hyderabad, 500 046, India
| | - S Sivakolundu
- Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Prof. CR Rao Road, Gachibowli, Hyderabad, 500 046, India
| | - R Chaurasia
- Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Prof. CR Rao Road, Gachibowli, Hyderabad, 500 046, India
| | - N Chouhan
- Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Prof. CR Rao Road, Gachibowli, Hyderabad, 500 046, India
| | - P P Rao
- NRI Academy of Sciences, Guntur, Andhra Pradesh, India
| | - M Sritharan
- Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Prof. CR Rao Road, Gachibowli, Hyderabad, 500 046, India.
| |
Collapse
|
50
|
Pandey SD, Choudhury M, Sritharan M. Transcriptional regulation of Mycobacterium tuberculosis hupB gene expression. MICROBIOLOGY-SGM 2014; 160:1637-1647. [PMID: 24858079 DOI: 10.1099/mic.0.079640-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The influence of iron levels on the transcription of the hupB gene in Mycobacterium tuberculosis is the focus of this study. Studies in our laboratory showed HupB to be co-expressed with the two siderophores in low-iron organisms. Mycobactin biosynthesis is repressed by the IdeR-Fe(2+) complex that binds the IdeR box in the mbtB promoter. Recently, we demonstrated the positive regulatory effect of HupB on mycobactin biosynthesis by demonstrating its binding to a 10 bp HupB box in the mbtB promoter. Earlier, we observed that HupB, expressed maximally in low-iron media (0.02 µg Fe ml(-1); 0.36 µM Fe) was still detectable at 8 µg Fe ml(-1) (144 µM Fe) when the siderophores were absent and complete repression was seen only at 12 µg Fe ml(-1) (216 µM Fe). In this study, we observed elevated levels of hupB transcripts in iron-limited organisms. IdeR, and not FurA, functioned as the iron regulator, by binding to two IdeR boxes in the hupB promoter. Interestingly, the 10 bp HupB box, first reported in the mbtB promoter, was identified in the hupB promoter. Using DNA footprinting and electrophoretic mobility shift assays, we demonstrated the functionality of the HupB box and the two IdeR boxes. The high hupB transcript levels expressed by the organism and the in vitro protein-DNA interaction studies led us to hypothesize the sequence of events occurring in response to changes in the intracellular iron concentration, emphasizing the roles played by IdeR and HupB in iron homeostasis.
Collapse
Affiliation(s)
- Satya Deo Pandey
- Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad 500046, India
| | - Mitali Choudhury
- Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad 500046, India
| | - Manjula Sritharan
- Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad 500046, India
| |
Collapse
|