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Gap-Gaupool B, Glenn SM, Milburn E, Turapov O, Crosatti M, Hincks J, Stewart B, Bacon J, Kendall SL, Voskuil MI, Riabova O, Monakhova N, Green J, Waddell SJ, Makarov VA, Mukamolova GV. Nitric oxide induces the distinct invisibility phenotype of Mycobacterium tuberculosis. Commun Biol 2024; 7:1206. [PMID: 39342050 PMCID: PMC11439070 DOI: 10.1038/s42003-024-06912-0] [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: 11/30/2023] [Accepted: 09/17/2024] [Indexed: 10/01/2024] Open
Abstract
During infection Mycobacterium tuberculosis (Mtb) forms physiologically distinct subpopulations that are recalcitrant to treatment and undetectable using standard diagnostics. These difficult to culture or differentially culturable (DC) Mtb are revealed in liquid media, their revival is often stimulated by resuscitation-promoting factors (Rpf) and prevented by Rpf inhibitors. Here, we investigated the role of nitric oxide (NO) in promoting the DC phenotype. Rpf-dependent DC Mtb were detected following infection of interferon-γ-induced macrophages capable of producing NO, but not when inducible NO synthase was inactivated. After exposure of Mtb to a new donor for sustained NO release (named NOD), the majority of viable cells were Rpf-dependent and undetectable on solid media. Gene expression analyses revealed a broad transcriptional response to NOD, including down-regulation of all five rpf genes. The DC phenotype was partially reverted by over-expression of Rpfs which promoted peptidoglycan remodelling. Thus, NO plays a central role in the generation of Rpf-dependent Mtb, with implications for improving tuberculosis diagnostics and treatments.
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Affiliation(s)
- Brindha Gap-Gaupool
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE1 9HN, UK
| | - Sarah M Glenn
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE1 9HN, UK
| | - Emily Milburn
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE1 9HN, UK
| | - Obolbek Turapov
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE1 9HN, UK
| | - Marialuisa Crosatti
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE1 9HN, UK
| | - Jennifer Hincks
- FACS Facility Core Biotechnology Services, University of Leicester, Leicester, LE1 9HN, UK
| | - Bradley Stewart
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE1 9HN, UK
| | - Joanna Bacon
- Discovery Group, Vaccine Development and Evaluation Centre, UK Health Security Agency, Porton Down, SP4 0JG, UK
| | - Sharon L Kendall
- Centre for Endemic, Emerging and Exotic Disease, the Royal Veterinary College, Hatfield, Hertfordshire, AL9 7TA, UK
| | - Martin I Voskuil
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Olga Riabova
- Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Natalia Monakhova
- Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Jeffrey Green
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Simon J Waddell
- Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK.
| | - Vadim A Makarov
- Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia.
| | - Galina V Mukamolova
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE1 9HN, UK.
- The National Institute for Health and Care Research Leicester Biomedical Research Centre, University of Leicester, Leicester, LE1 9HN, UK.
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2
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Alqaseer K, Turapov O, Barthe P, Jagatia H, De Visch A, Roumestand C, Wegrzyn M, Bartek IL, Voskuil MI, O'Hare HM, Ajuh P, Bottrill AR, Witney AA, Cohen-Gonsaud M, Waddell SJ, Mukamolova GV. Protein kinase B controls Mycobacterium tuberculosis growth via phosphorylation of the transcriptional regulator Lsr2 at threonine 112. Mol Microbiol 2019; 112:1847-1862. [PMID: 31562654 PMCID: PMC6906086 DOI: 10.1111/mmi.14398] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2019] [Indexed: 01/23/2023]
Abstract
Mycobacterium tuberculosis (Mtb) is able to persist in the body through months of multi‐drug therapy. Mycobacteria possess a wide range of regulatory proteins, including the protein kinase B (PknB) which controls peptidoglycan biosynthesis during growth. Here, we observed that depletion of PknB resulted in specific transcriptional changes that are likely caused by reduced phosphorylation of the H‐NS‐like regulator Lsr2 at threonine 112. The activity of PknB towards this phosphosite was confirmed with purified proteins, and this site was required for adaptation of Mtb to hypoxic conditions, and growth on solid media. Like H‐NS, Lsr2 binds DNA in sequence‐dependent and non‐specific modes. PknB phosphorylation of Lsr2 reduced DNA binding, measured by fluorescence anisotropy and electrophoretic mobility shift assays, and our NMR structure of phosphomimetic T112D Lsr2 suggests that this may be due to increased dynamics of the DNA‐binding domain. Conversely, the phosphoablative T112A Lsr2 had increased binding to certain DNA sites in ChIP‐sequencing, and Mtb containing this variant showed transcriptional changes that correspond with the change in DNA binding. In summary, PknB controls Mtb growth and adaptations to the changing host environment by phosphorylating the global transcriptional regulator Lsr2.
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Affiliation(s)
- Kawther Alqaseer
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE2 9HN, UK.,Department of Basic Science, Faculty of Nursing, University of Kufa, Najaf Governorate, P.O. Box 21, Kufa, Najaf, Iraq
| | - Obolbek Turapov
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE2 9HN, UK
| | - Philippe Barthe
- Centre de Biochimie Structurale, CNRS, INSERM, University of Montpellier, 34090, Montpellier, France
| | - Heena Jagatia
- Wellcome Trust Brighton and Sussex Centre for Global Health Research, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK
| | - Angélique De Visch
- Centre de Biochimie Structurale, CNRS, INSERM, University of Montpellier, 34090, Montpellier, France
| | - Christian Roumestand
- Centre de Biochimie Structurale, CNRS, INSERM, University of Montpellier, 34090, Montpellier, France
| | - Malgorzata Wegrzyn
- Core Biotechnology Services, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Iona L Bartek
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Martin I Voskuil
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Helen M O'Hare
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE2 9HN, UK.,LISCB, Department of Molecular and Cell Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Paul Ajuh
- Gemini Biosciences Ltd, Liverpool Science Park, Liverpool, L7 8TX, UK
| | - Andrew R Bottrill
- Protein Nucleic Acid Laboratory, University of Leicester, Leicester, LE1 7RH, UK
| | - Adam A Witney
- Institute for Infection and Immunity, St George's University of London, London, SW17 0RE, UK
| | - Martin Cohen-Gonsaud
- Centre de Biochimie Structurale, CNRS, INSERM, University of Montpellier, 34090, Montpellier, France
| | - Simon J Waddell
- Wellcome Trust Brighton and Sussex Centre for Global Health Research, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK
| | - Galina V Mukamolova
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE2 9HN, UK
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3
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Choi HH, Kwon KW, Han SJ, Kang SM, Choi E, Kim A, Cho SN, Shin SJ. PPE39 of the Mycobacterium tuberculosis strain Beijing/K induces Th1-cell polarization through dendritic cell maturation. J Cell Sci 2019; 132:jcs.228700. [PMID: 31371491 DOI: 10.1242/jcs.228700] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 07/17/2019] [Indexed: 12/22/2022] Open
Abstract
In a previous study, we have identified MTBK_24820, the complete protein form of PPE39 in the hypervirulent Mycobacterium tuberculosis (Mtb) strain Beijing/K by using comparative genomic analysis. PPE39 exhibited vaccine potential against Mtb challenge in a murine model. Thus, in this present study, we characterize PPE39-induced immunological features by investigating the interaction of PPE39 with dendritic cells (DCs). PPE39-treated DCs display reduced dextran uptake and enhanced MHC-I, MHC-II, CD80 and CD86 expression, indicating that this PPE protein induces phenotypic DC maturation. In addition, PPE39-treated DCs produce TNF-α, IL-6 and IL-12p70 to a similar and/or greater extent than lipopolysaccharide-treated DCs in a dose-dependent manner. The activating effect of PPE39 on DCs was mediated by TLR4 through downstream MAPK and NF-κB signaling pathways. Moreover, PPE39-treated DCs promoted naïve CD4+ T-cell proliferation accompanied by remarkable increases of IFN-γ and IL-2 secretion levels, and an increase in the Th1-related transcription factor T-bet but not in Th2-associated expression of GATA-3, suggesting that PPE39 induces Th1-type T-cell responses through DC activation. Collectively, the results indicate that the complete form of PPE39 is a so-far-unknown TLR4 agonist that induces Th1-cell biased immune responses by interacting with DCs.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Hong-Hee Choi
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Kee Woong Kwon
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, South Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Seung Jung Han
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Soon Myung Kang
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, South Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Eunsol Choi
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, South Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Ahreum Kim
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Sang-Nae Cho
- Institute for Immunology and Immunological Disease, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, South Korea .,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea.,Institute for Immunology and Immunological Disease, Yonsei University College of Medicine, Seoul 03722, South Korea
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Kwon KW, Choi HH, Han SJ, Kim JS, Kim WS, Kim H, Kim LH, Kang SM, Park J, Shin SJ. Vaccine efficacy of a Mycobacterium tuberculosis Beijing-specific proline-glutamic acid (PE) antigen against highly virulent outbreak isolates. FASEB J 2019; 33:6483-6496. [PMID: 30753099 DOI: 10.1096/fj.201802604r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacillus Calmette-Guerin vaccine confers insufficient pulmonary protection against tuberculosis (TB), particularly the Mycobacterium tuberculosis (Mtb) Beijing strain infection. Identification of vaccine antigens (Ags) by considering Mtb genetic diversity is crucial for the development of improved TB vaccine. MTBK_20640, a new Beijing genotype-specific proline-glutamic acid-family Ag, was identified by comparative genomic analysis. Its immunologic features were characterized by evaluating interactions with dendritic cells (DCs), and immunogenicity and vaccine efficacy were determined against highly virulent Mtb Beijing outbreak Korean Beijing (K) strain and HN878 strain in murine infection model. MTBK_20640 induced DCs via TLR2 and downstream MAPK and NF-κB signaling pathways, effectively promoting naive CD4-positive (CD4+) T-cell proliferation and IFN-γ production. Different IFN-γ response was observed in mice infected with Mtb K or reference H37Rv strain. Significant induction of T helper type 1 cell-polarized Ag-specific multifunctional CD4+ T cells and a marked Ag-specific IgG2c response were observed in mice immunized with MTBK_20640/glucopyranosyl lipid adjuvant-stable emulsion. The immunization conferred long-term protection against 2 Mtb Beijing outbreak strains, as evidenced by a significant reduction in colony-forming units in the lung and spleen and reduced lung inflammation. MTBK_20640 vaccination conferred long-term protection against highly virulent Mtb Beijing strains. MTBK_20640 may be developed into a novel Ag component in multisubunit TB vaccines in the future.-Kwon, K. W., Choi, H.-H., Han, S. J., Kim, J.-S., Kim, W. S., Kim, H., Kim, L.-H., Kang, S. M., Park, J., Shin, S. J. Vaccine efficacy of a Mycobacterium tuberculosis Beijing-specific proline-glutamic acid (PE) antigen against highly virulent outbreak isolates.
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Affiliation(s)
- Kee Woong Kwon
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Hong-Hee Choi
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Seung Jung Han
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Jong-Seok Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.,Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon, South Korea
| | - Woo Sik Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.,Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Hongmin Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Lee-Han Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Soon Myung Kang
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Jaehun Park
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
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5
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Kim WS, Kim JS, Kim HM, Kwon KW, Eum SY, Shin SJ. Comparison of immunogenicity and vaccine efficacy between heat-shock proteins, HSP70 and GrpE, in the DnaK operon of Mycobacterium tuberculosis. Sci Rep 2018; 8:14411. [PMID: 30258084 PMCID: PMC6158166 DOI: 10.1038/s41598-018-32799-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/13/2018] [Indexed: 12/17/2022] Open
Abstract
Antigens (Ags) in Mycobacterium tuberculosis (Mtb) that are constitutively expressed, overexpressed during growth, essential for survival, and highly conserved may be good vaccine targets if they induce the appropriate anti-Mtb Th1 immune response. In this context, stress response-related antigens of Mtb might serve as attractive targets for vaccine development as they are rapidly expressed and are up-regulated during Mtb infection in vivo. Our group recently demonstrated that GrpE, encoded by rv0351 as a cofactor of heat-shock protein 70 (HSP70) in the DnaK operon, is a novel immune activator that interacts with DCs to generate Th1-biased memory T cells in an antigen-specific manner. In this study, GrpE was evaluated as a subunit vaccine in comparison with the well-known HSP70 against the hyper-virulent Mtb Beijing K-strain. Both HSP70- and GrpE-specific effector/memory T cells expanded to a similar extent as those stimulated with ESAT-6 in the lung and spleen of Mtb-infected mice, but GrpE only produced a similar level of IFN-γ to that produced by ESAT-6 stimulation during the late phase and the early phase of Mtb K infection, indicating that GrpE is highly-well recognised by the host immune system as a T cell antigen. Mice immunised with the GrpE subunit vaccine displayed enhanced antigen-specific IFN-γ and serum IgG2c responses along with antigen-specific effector/memory T cell expansion in the lungs. In addition, GrpE-immunisation markedly induced multifunctional Th1-type CD4+ T cells co-expressing IFN-γ, TNF-α, and IL-2 in the lungs of Mtb K-infected mice, whereas HSP70-immunisation induced mixed Th1/Th2 immune responses. GrpE-immunisation conferred a more significant protective effect than that of HSP70-immunisation in terms of bacterial reduction and improved inflammation, accompanied by the remarkable persistence of GrpE-specific multifunctional CD4+ T cells. These results suggest that GrpE is an excellent vaccine antigen component for the development of a multi-antigenic Mtb subunit vaccine by generating Th1-biased memory T cells with multifunctional capacity, and confers durable protection against the highly virulent Mtb K.
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Affiliation(s)
- Woo Sik Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.,Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Jong-Seok Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.,Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon, South Korea
| | - Hong Min Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Kee Woong Kwon
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Seok-Yong Eum
- Division of Immunopathology and Cellular Immunology, International Tuberculosis Research Center, Changwon, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.
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Novel vaccine potential of Rv3131, a DosR regulon-encoded putative nitroreductase, against hyper-virulent Mycobacterium tuberculosis strain K. Sci Rep 2017; 7:44151. [PMID: 28272457 PMCID: PMC5341159 DOI: 10.1038/srep44151] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/03/2017] [Indexed: 12/12/2022] Open
Abstract
Accumulating evidence indicates that latency-associated Mycobacterium tuberculosis (Mtb)-specific antigens from the dormancy survival regulator regulon (DosR) may be promising novel vaccine target antigens for the development of an improved tuberculosis vaccine. After transcriptional profiling of DosR-related genes in the hyper-virulent Beijing Mtb strain K and the reference Mtb strain H37Rv, we selected Rv3131, a hypothetical nitroreductase, as a vaccine antigen and evaluated its vaccine efficacy against Mtb K. Mtb K exhibited stable and constitutive up-regulation of rv3131 relative to Mtb H37Rv under three different growth conditions (at least 2-fold induction) including exponential growth in normal culture conditions, hypoxia, and inside macrophages. Mice immunised with Rv3131 formulated in GLA-SE, a well-defined TLR4 adjuvant, displayed enhanced Rv3131-specific IFN-γ and serum IgG2c responses along with effector/memory T cell expansion and remarkable generation of Rv3131-specific multifunctional CD4+ T cells co-producing TNF-α, IFN-γ and IL-2 in both spleen and lung. Following challenge with Mtb K, the Rv3131/GLA-SE-immunised group exhibited a significant reduction in bacterial number and less extensive lung inflammation accompanied by the obvious persistence of Rv3131-specific multifunctional CD4+ T cells. These results suggest that Rv3131 could be an excellent candidate for potential use in a multi-antigenic Mtb subunit vaccine, especially against Mtb Beijing strains.
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7
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Wang Y, Hayatsu M, Fujii T. Extraction of bacterial RNA from soil: challenges and solutions. Microbes Environ 2012; 27:111-21. [PMID: 22791042 PMCID: PMC4036013 DOI: 10.1264/jsme2.me11304] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Detection of bacterial gene expression in soil emerged in the early 1990s and provided information on bacterial responses in their original soil environments. As a key procedure in the detection, extraction of bacterial RNA from soil has attracted much interest, and many methods of soil RNA extraction have been reported in the past 20 years. In addition to various RT-PCR-based technologies, new technologies for gene expression analysis, such as microarrays and high-throughput sequencing technologies, have recently been applied to examine bacterial gene expression in soil. These technologies are driving improvements in RNA extraction protocols. In this mini-review, progress in the extraction of bacterial RNA from soil is summarized with emphasis on the major difficulties in the development of methodologies and corresponding strategies to overcome them.
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Affiliation(s)
- Yong Wang
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan.
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8
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Alternative DNA amplification methods to PCR and their application in GMO detection: a review. Eur Food Res Technol 2008. [DOI: 10.1007/s00217-008-0850-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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9
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Abstract
Metagenomics is expanding our knowledge of the gene content, functional significance, and genetic variability in natural microbial communities. Still, there exists limited information concerning the regulation and dynamics of genes in the environment. We report here global analysis of expressed genes in a naturally occurring microbial community. We first adapted RNA amplification technologies to produce large amounts of cDNA from small quantities of total microbial community RNA. The fidelity of the RNA amplification procedure was validated with Prochlorococcus cultures and then applied to a microbial assemblage collected in the oligotrophic Pacific Ocean. Microbial community cDNAs were analyzed by pyrosequencing and compared with microbial community genomic DNA sequences determined from the same sample. Pyrosequencing-based estimates of microbial community gene expression compared favorably to independent assessments of individual gene expression using quantitative PCR. Genes associated with key metabolic pathways in open ocean microbial species-including genes involved in photosynthesis, carbon fixation, and nitrogen acquisition-and a number of genes encoding hypothetical proteins were highly represented in the cDNA pool. Genes present in the variable regions of Prochlorococcus genomes were among the most highly expressed, suggesting these encode proteins central to cellular processes in specific genotypes. Although many transcripts detected were highly similar to genes previously detected in ocean metagenomic surveys, a significant fraction ( approximately 50%) were unique. Thus, microbial community transcriptomic analyses revealed not only indigenous gene- and taxon-specific expression patterns but also gene categories undetected in previous DNA-based metagenomic surveys.
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10
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Waddell SJ, Laing K, Senner C, Butcher PD. Microarray analysis of defined Mycobacterium tuberculosis populations using RNA amplification strategies. BMC Genomics 2008; 9:94. [PMID: 18298834 PMCID: PMC2276497 DOI: 10.1186/1471-2164-9-94] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Accepted: 02/25/2008] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The amplification of bacterial RNA is required if complex host-pathogen interactions are to be studied where the recovery of bacterial RNA is limited. Here, using a whole genome Mycobacterium tuberculosis microarray to measure cross-genome representation of amplified mRNA populations, we have investigated two approaches to RNA amplification using different priming strategies. The first using oligo-dT primers after polyadenylation of the bacterial RNA, the second using a set of mycobacterial amplification-directed primers both linked to T7 polymerase in vitro run off transcription. RESULTS The reproducibility, sensitivity, and the representational bias introduced by these amplification systems were examined by contrasting expression profiles of the amplified products from inputs of 500, 50 and 5 ng total M. tuberculosis RNA with unamplified RNA from the same source. In addition, as a direct measure of the effectiveness of bacterial amplification for identifying biologically relevant changes in gene expression, a model M. tuberculosis system of microaerophilic growth and non-replicating persistence was used to assess the capability of amplified RNA microarray comparisons. Mycobacterial RNA was reproducibly amplified using both methods from as little as 5 ng total RNA (~equivalent to 2 x 105 bacilli). Differential gene expression patterns observed with unamplified RNA in the switch from aerobic to microaerophilic growth were also reflected in the amplified expression profiles using both methods. CONCLUSION Here we describe two reproducible methods of bacterial RNA amplification that will allow previously intractable host-pathogen interactions during bacterial infection to be explored at the whole genome level by RNA profiling.
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Affiliation(s)
- Simon J Waddell
- Medical Microbiology, Centre for Infection, Division of Cellular & Molecular Medicine, St, George's University of London, Cranmer Terrace, Tooting, London, UK.
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11
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Lee JS, Krause R, Schreiber J, Mollenkopf HJ, Kowall J, Stein R, Jeon BY, Kwak JY, Song MK, Patron JP, Jorg S, Roh K, Cho SN, Kaufmann SH. Mutation in the Transcriptional Regulator PhoP Contributes to Avirulence of Mycobacterium tuberculosis H37Ra Strain. Cell Host Microbe 2008; 3:97-103. [DOI: 10.1016/j.chom.2008.01.002] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Revised: 09/26/2007] [Accepted: 01/03/2008] [Indexed: 12/11/2022]
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12
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Rachman H, Kaufmann SHE. Exploring functional genomics for the development of novel intervention strategies against tuberculosis. Int J Med Microbiol 2007; 297:559-67. [PMID: 17467338 DOI: 10.1016/j.ijmm.2007.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Revised: 02/28/2007] [Accepted: 03/01/2007] [Indexed: 11/28/2022] Open
Abstract
Tuberculosis (TB) remains a serious threat to humankind, and humans have encountered the causative agent of TB, Mycobacterium tuberculosis (MTB), for more than 10,000 years. Despite rapid advances in technology, efforts to besiege this robust pathogen seem to fail. The availability of genome sequences of several MTB complex strains open a new era of MTB research, the functional genomics, which will provide guidelines for novel control measures. In recent years, a series of methods have been developed to explore the mechanisms employed by MTB to persist and cause disease in the host. DNA array technology enables us to perform comparative genomics of different MTB strains and to examine the gene expression profiles of MTB growing under diverse living conditions. The generated transcriptome data can be exploited for design of new drugs, especially against multidrug-resistant (MDR) strains, development of more efficient vaccines, and identification of biomarkers for better diagnosis.
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Affiliation(s)
- Helmy Rachman
- Department of Immunology, Max Planck Institute for Infection Biology, Schumannstr. 21/22, D-10117 Berlin, Germany
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