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Lee OYC, Wu HHT, Besra GS. Professor David Minnikin Memorial Lecture: An era of the mycobacterial cell wall lipid biomarkers. Tuberculosis (Edinb) 2023; 143S:102415. [PMID: 38012929 DOI: 10.1016/j.tube.2023.102415] [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: 09/03/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 11/29/2023]
Abstract
This paper is dedicated to the memory of Professor David Ernest Minnikin (1939-2021). David was one of the key scientists who pioneered the field of Mycobacterium tuberculosis cell envelope research for over half a century. From the classification, identification, and extraction of the unusual lipids of the mycobacterial cell wall, to exploiting them as characteristic lipid biomarkers for sensitive detection, his ideas enlightened a whole world of possibilities within the tuberculosis (TB) field. In addition, his definition of the intricate models now forms a key milestone in our understanding of the M. tuberculosis cell envelope and has resolved many unanswered questions on the evolution of M. tuberculosis.
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Affiliation(s)
- Oona Y-C Lee
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, B15 2TT, United Kingdom; Coventry Road Medical Centre, Small Heath, Birmingham, B10 0UG, United Kingdom
| | - Houdini H T Wu
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, B15 2TT, United Kingdom; Coventry Road Medical Centre, Small Heath, Birmingham, B10 0UG, United Kingdom; UK Health Security Agency, Public Health Laboratory, Birmingham, B5 9SS, United Kingdom
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, B15 2TT, United Kingdom.
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2
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Wang K, Cui X, Ling X, Chen J, Zheng J, Xiang Y, Li W. D-Xylose Blocks the Broad Negative Regulation of XylR on Lipid Metabolism and Affects Multiple Physiological Characteristics in Mycobacteria. Int J Mol Sci 2023; 24:ijms24087086. [PMID: 37108247 PMCID: PMC10138657 DOI: 10.3390/ijms24087086] [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: 03/17/2023] [Revised: 04/01/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
D-xylose is the most abundant fermentable pentose, which usually represents an architectural component of the bacterial cell wall. However, its regulatory function and the involved signaling pathway in bacteria remain largely unclear. Here, we show that D-xylose can act as a signaling molecule to regulate the lipid metabolism and affect multiple physiological characteristics in mycobacteria. D-xylose directly interacts with XylR and inhibits its DNA-binding ability, thus blocking XylR-mediated repression. The xylose inhibitor, XylR, plays a global regulatory role and affects the expression of 166 mycobacterial genes that are involved in lipid synthesis and metabolism. Furthermore, we show that the xylose-dependent gene regulation of XylR affects the multiple physiological characteristics of Mycobacterium smegmatis, including bacterial size, colony phenotype, biofilm formation, cell aggregation, and antibiotic resistance. Finally, we found that XylR inhibited the survival of Mycobacterium bovis BCG in the host. Our findings provide novel insights into the molecular mechanism of lipid metabolism regulation and its correlation with bacterial physiological phenotypes.
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Affiliation(s)
- Kun Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Xujie Cui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Xiaocui Ling
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jiarui Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jiachen Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuling Xiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Weihui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
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3
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The search for organic compounds with TMAH thermochemolysis: From Earth analyses to space exploration experiments. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115896] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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4
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Arslan FN, Kolk A, Janssen H. Methods for one– and two–dimensional gas chromatography with flame ionization detection for identification of Mycobacterium tuberculosis in sputum. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1124:204-217. [DOI: 10.1016/j.jchromb.2019.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/03/2019] [Accepted: 06/06/2019] [Indexed: 11/24/2022]
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5
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Rana A, Thakur S, Kumar G, Akhter Y. Recent Trends in System-Scale Integrative Approaches for Discovering Protective Antigens Against Mycobacterial Pathogens. Front Genet 2018; 9:572. [PMID: 30538722 PMCID: PMC6277634 DOI: 10.3389/fgene.2018.00572] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/06/2018] [Indexed: 11/21/2022] Open
Abstract
Mycobacterial infections are one of the deadliest infectious diseases still posing a major health burden worldwide. The battle against these pathogens needs to focus on novel approaches and key interventions. In recent times, availability of genome scale data has revolutionized the fields of computational biology and immunoproteomics. Here, we summarize the cutting-edge ‘omics’ technologies and innovative system scale strategies exploited to mine the available data. These may be targeted using high-throughput technologies to expedite the identification of novel antigenic candidates for the rational next generation vaccines and serodiagnostic development against mycobacterial pathogens for which traditional methods have been failing.
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Affiliation(s)
- Aarti Rana
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Shweta Thakur
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Girish Kumar
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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Zhang J, Xu J, Lu H, Ding J, Yu D, Li P, Xiong J, Liu X, Chen H, Wei Y. Altered phosphatidylcholines expression in sputum for diagnosis of non-small cell lung cancer. Oncotarget 2018; 7:63158-63165. [PMID: 27542233 PMCID: PMC5325353 DOI: 10.18632/oncotarget.11283] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/19/2016] [Indexed: 11/25/2022] Open
Abstract
Non–small cell lung cancer (NSCLC) is a leading cause of cancer mortality worldwide, and early diagnosis needs to be improved. We examined whether neutral desorption extractive electrospray ionization mass spectrometry (ND-EESI-MS) could be used to detect sputum lipids expression changes to enable earlier diagnosis. Overall, 167 NSCLC patients and 140 controls were enrolled. The main peaks in the sputum of patients with NSCLC patients differed from controls (83.3% of total variability), and the signals were not associated with pathological type, TNM stage or smoking history. The relative abundance of peaks at m/z734, m/ z756, m/z772, m/z782, m/z798 and m/z803 reliably distinguished NSCLC sputum from control. Collision-induced dissociation confirmed that m/z734, m/z756, and m/z772 represented [DPPC + H]+, [DPPC + Na]+, and [DPPC + K]+, respectively, and m/z782, m/z798, and m/z803 represented sphingomyelin, phosphatidylglycerol, and phosphatidylglycerolphosphate, respectively. The relative abundance of DPPC was clearly lower in NSCLC sputum than in control, and the relative abundances of phosphatidylglycerol and phosphatidylglycerolphosphate were higher in NSCLC sputum than in control. The detection of changes in sputum lipids with ND-EESI-MS may be a noninvasive, radiation-free, relatively inexpensive, repeatable, and efficient method for diagnosis of NSCLC.
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Affiliation(s)
- Jianyong Zhang
- Department of Cardiothoracic Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, P. R. China
| | - Jianjun Xu
- Department of Cardiothoracic Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, P. R. China
| | - Haiyan Lu
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang, Jiangxi Province 330013, P. R. China
| | - Jianhua Ding
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang, Jiangxi Province 330013, P. R. China
| | - Dongliang Yu
- Department of Cardiothoracic Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, P. R. China
| | - Penghui Li
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang, Jiangxi Province 330013, P. R. China
| | - Jianwen Xiong
- Department of Cardiothoracic Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, P. R. China
| | - Xingxing Liu
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang, Jiangxi Province 330013, P. R. China
| | - Huanwen Chen
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang, Jiangxi Province 330013, P. R. China
| | - Yiping Wei
- Department of Cardiothoracic Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, P. R. China
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Zetola NM, Modongo C, Matsiri O, Tamuhla T, Mbongwe B, Matlhagela K, Sepako E, Catini A, Sirugo G, Martinelli E, Paolesse R, Di Natale C. Diagnosis of pulmonary tuberculosis and assessment of treatment response through analyses of volatile compound patterns in exhaled breath samples. J Infect 2016; 74:367-376. [PMID: 28017825 DOI: 10.1016/j.jinf.2016.12.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 12/12/2016] [Accepted: 12/18/2016] [Indexed: 12/11/2022]
Abstract
OBJECTIVES We determined the performance of a sensor array (an electronic nose) made of 8 metalloporphyrins coated quartz microbalances sensors for the diagnosis and prognosis of pulmonary tuberculosis (TB) using exhaled breath samples. METHODS TB cases and healthy controls were prospectively enrolled. Signals from volatile organic compounds (VOCs) in breath samples were measured at days 0, 2, 7, 14, and 30 of TB therapy and correlated with clinical and microbiological measurements. RESULTS Fifty one pulmonary TB cases and 20 healthy HIV-uninfected controls were enrolled in the study. 31 (61%) of the 51 pulmonary TB cases were coinfected with HIV. At day 0 (before TB treatment initiation) the sensitivity of our device was estimated at 94.1% (95% confidence interval [CI], 83.8-98.8%) and specificity was 90.0% (95% CI, 68.3-98.8%) for distinguishing TB cases from controls. Time-dependent changes in the breath signals were identified as time on TB treatment progressed. Time-dependent signal changes were more pronounced among HIV-uninfected patients. CONCLUSION The identification of VOCs' signals in breath samples using a sensor array achieved high sensitivity and specificity for the diagnosis of TB and allowed following signal changes during TB treatment.
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Affiliation(s)
- Nicola M Zetola
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, USA; School of Medicine, University of Botswana, Gaborone, Botswana; Botswana-UPenn Partnership, University of Pennsylvania, Gaborone, Botswana.
| | - Chawangwa Modongo
- Botswana-UPenn Partnership, University of Pennsylvania, Gaborone, Botswana.
| | - Ogopotse Matsiri
- Botswana-UPenn Partnership, University of Pennsylvania, Gaborone, Botswana.
| | - Tsaone Tamuhla
- Botswana-UPenn Partnership, University of Pennsylvania, Gaborone, Botswana.
| | - Bontle Mbongwe
- Department of Environmental Sciences, University of Botswana, Gaborone, Botswana.
| | | | - Enoch Sepako
- School of Medicine, University of Botswana, Gaborone, Botswana.
| | - Alexandro Catini
- Department of Electronic Engineering, University of Rome Tor Vergata, Rome, Italy.
| | - Giorgio Sirugo
- Centro di Ricerca, Ospedale San Pietro Fatebenefratelli, Rome, Italy.
| | - Eugenio Martinelli
- Department of Electronic Engineering, University of Rome Tor Vergata, Rome, Italy.
| | - Roberto Paolesse
- Department of Chemical Science and Technology, University of Rome Tor Vergata, Rome, Italy.
| | - Corrado Di Natale
- Department of Electronic Engineering, University of Rome Tor Vergata, Rome, Italy.
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8
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Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria. Clin Microbiol Rev 2016; 29:239-90. [PMID: 26912567 DOI: 10.1128/cmr.00055-15] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.
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Abstract
Until recently, the study of mycobacterial diseases was trapped in culture-based technology that is more than a century old. The use of nucleic acid amplification is changing this, and powerful new technologies are on the horizon. Metabolomics, which is the study of sets of metabolites of both the bacteria and host, is being used to clarify mechanisms of disease, and can identify changes leading to better diagnosis, treatment, and prognostication of mycobacterial diseases. Metabolomic profiles are arrays of biochemical products of genes in their environment. These complex patterns are biomarkers that can allow a more complete understanding of cell function, dysfunction, and perturbation than genomics or proteomics. Metabolomics could herald sweeping advances in personalized medicine and clinical trial design, but the challenges in metabolomics are also great. Measured metabolite concentrations vary with the timing within a condition, the intrinsic biology, the instruments, and the sample preparation. Metabolism profoundly changes with age, sex, variations in gut microbial flora, and lifestyle. Validation of biomarkers is complicated by measurement accuracy, selectivity, linearity, reproducibility, robustness, and limits of detection. The statistical challenges include analysis, interpretation, and description of the vast amount of data generated. Despite these drawbacks, metabolomics provides great opportunity and the potential to understand and manage mycobacterial diseases.
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10
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Mourão MP, Denekamp I, Kuijper S, Kolk AH, Janssen HG. Hyphenated and comprehensive liquid chromatography ÿ gas chromatographymass spectrometry for the identification of Mycobacterium tuberculosis. J Chromatogr A 2016; 1439:152-160. [DOI: 10.1016/j.chroma.2015.10.054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 09/24/2015] [Accepted: 10/19/2015] [Indexed: 12/14/2022]
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11
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Mourão MPB, Kuijper S, Dang NA, Walters E, Janssen HG, Kolk AHJ. Direct detection of Mycobacterium tuberculosis in sputum: A validation study using solid phase extraction-gas chromatography-mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1012-1013:50-4. [PMID: 26807702 DOI: 10.1016/j.jchromb.2015.12.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 12/11/2015] [Accepted: 12/13/2015] [Indexed: 10/22/2022]
Abstract
Tuberculosis (TB) remains a worldwide health problem, especially in developing countries. Correct identification of Mycobacterium tuberculosis (MTB) infection is extremely important for providing appropriate treatment and care to patients. Here we describe a solid phase extraction-gas chromatography-mass spectrometry method (SPE-THM-GC-MS) for the detection of five biomarkers for M. tuberculosis. The method for classification is developed and validated through the analysis of 112 sputum samples from patients suspected of having TB. Twenty of twenty-five MTB culture-positive sputum samples were correctly classified as positive by our improved SPE-THM-GC-MS method. Eighty-five of eighty-seven MTB culture-negative samples were also negative by SPE-THM-GC-MS. The overall sensitivity of the new SPE-THM-GC-MS method is 80% (20/25) and the specificity is 98% (85/87) compared with culture. The method proved to be reliable and, although complex in principle, easy to operate due to the high degree of automation.
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Affiliation(s)
- Marta P B Mourão
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences, Analytical Chemistry Group, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands.
| | - Sjoukje Kuijper
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences, Analytical Chemistry Group, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Ngoc A Dang
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences, Analytical Chemistry Group, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Elisabetta Walters
- Desmond Tutu TB Centre, Stellenbosch University, P.O. Box 19063, Tygerberg 7505, South Africa
| | - Hans-Gerd Janssen
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences, Analytical Chemistry Group, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands; Unilever Research and Development, P.O. Box 114, 3130 AC Vlaardingen, The Netherlands
| | - Arend H J Kolk
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences, Analytical Chemistry Group, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
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Pan SJ, Tapley A, Adamson J, Little T, Urbanowski M, Cohen K, Pym A, Almeida D, Dorasamy A, Layre E, Young DC, Singh R, Patel VB, Wallengren K, Ndung'u T, Wilson D, Moody DB, Bishai W. Biomarkers for Tuberculosis Based on Secreted, Species-Specific, Bacterial Small Molecules. J Infect Dis 2015; 212:1827-34. [PMID: 26014799 PMCID: PMC4633767 DOI: 10.1093/infdis/jiv312] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/09/2015] [Indexed: 01/06/2023] Open
Abstract
Improved biomarkers are needed for tuberculosis. To develop tests based on products secreted by tubercle bacilli that are strictly associated with viability, we evaluated 3 bacterial-derived, species-specific, small molecules as biomarkers: 2 mycobactin siderophores and tuberculosinyladenosine. Using liquid chromatography-tandem mass spectrometry, we demonstrated the presence of 1 or both mycobactins and/or tuberculosinyladenosine in serum and whole lung tissues from infected mice and sputum, cerebrospinal fluid (CSF), or lymph nodes from infected patients but not uninfected controls. Detection of the target molecules distinguished host infection status in 100% of mice with both serum and lung as the target sample. In human subjects, we evaluated detection of the bacterial small molecules (BSMs) in multiple body compartments in 3 patient cohorts corresponding to different forms of tuberculosis. We detected at least 1 of the 3 molecules in 90%, 71%, and 40% of tuberculosis patients' sputum, CSF, and lymph node samples, respectively. In paucibacillary forms of human tuberculosis, which are difficult to diagnose even with culture, detection of 1 or more BSM was rapid and compared favorably to polymerase chain reaction-based detection. Secreted BSMs, detectable in serum, warrant further investigation as a means for diagnosis and therapeutic monitoring in patients with tuberculosis.
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Affiliation(s)
- Shih-Jung Pan
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Asa Tapley
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- San Francisco School of Medicine, University of California, Oakland
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - John Adamson
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tessa Little
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Michael Urbanowski
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Keira Cohen
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Alexander Pym
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Deepak Almeida
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Afton Dorasamy
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Emilie Layre
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - David C. Young
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ravesh Singh
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine
| | | | - Kristina Wallengren
- Tuberculosis & HIV Investigative Network in KwaZulu-Natal (THINK), Durban, South Africa
| | - Thumbi Ndung'u
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine
- Max Planck Institute for Infection Biology, Berlin, Germany
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge
| | - Douglas Wilson
- Department of Medicine, Edendale Hospital, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - D. Branch Moody
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - William Bishai
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Howard Hughes Medical Institute, Chevy Chase, Maryland
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13
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Crick PJ, Guan XL. Lipid metabolism in mycobacteria--Insights using mass spectrometry-based lipidomics. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1861:60-67. [PMID: 26515252 DOI: 10.1016/j.bbalip.2015.10.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 10/14/2015] [Accepted: 10/23/2015] [Indexed: 11/18/2022]
Abstract
Diseases including tuberculosis and leprosy are caused by species of the Mycobacterium genus and are a huge burden on global health, aggravated by the emergence of drug resistant strains. Mycobacteria have a high lipid content and complex lipid profile including several unique classes of lipid. Recent years have seen a growth in research focused on lipid structures, metabolism and biological functions driven by advances in mass spectrometry techniques and instrumentation, particularly the use of electrospray ionization. Here we review the contributions of lipidomics towards the advancement of our knowledge of lipid metabolism in mycobacterial species.
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Affiliation(s)
- Peter J Crick
- Swiss Tropical and Public Health Institute, CH-4051 Basel, Switzerland; University of Basel, CH-4000 Basel, Switzerland
| | - Xue Li Guan
- Swiss Tropical and Public Health Institute, CH-4051 Basel, Switzerland; University of Basel, CH-4000 Basel, Switzerland; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.
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14
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Nicoara SC, Turner NW, Minnikin DE, Lee OYC, O'Sullivan DM, McNerney R, Mutetwa R, Corbett LE, Morgan GH. Development of sample clean up methods for the analysis of Mycobacterium tuberculosis methyl mycocerosate biomarkers in sputum extracts by gas chromatography-mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 986-987:135-42. [PMID: 25728371 PMCID: PMC4381843 DOI: 10.1016/j.jchromb.2015.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 02/05/2015] [Accepted: 02/08/2015] [Indexed: 11/23/2022]
Abstract
We developed a sample clean-up method to detect tuberculosis from sputum by GC–MS. Biomarkers recovered: 64–70% (standards solution), and 36–68% (sputum extracts). Cholesterol removed: 93–98% (standards solution) and 62–92% (sputum extracts). Less cholesterol in the filtered extracts avoids overloading of the analytical system. Analyzing large sample batches will need fewer interruptions for system cleaning.
A proof of principle gas chromatography–mass spectrometry method is presented, in combination with clean up assays, aiming to improve the analysis of methyl mycocerosate tuberculosis biomarkers from sputum. Methyl mycocerosates are generated from the transesterification of phthiocerol dimycocerosates (PDIMs), extracted in petroleum ether from sputum of tuberculosis suspect patients. When a high matrix background is present in the sputum extracts, the identification of the chromatographic peaks corresponding to the methyl derivatives of PDIMs analytes may be hindered by the closely eluting methyl ether of cholesterol, usually an abundant matrix constituent frequently present in sputum samples. The purification procedures involving solid phase extraction (SPE) based methods with both commercial Isolute-Florisil cartridges, and purpose designed molecularly imprinted polymeric materials (MIPs), resulted in cleaner chromatograms, while the mycocerosates are still present. The clean-up performed on solutions of PDIMs and cholesterol standards in petroleum ether show that, depending on the solvent mix and on the type of SPE used, the recovery of PDIMs is between 64 and 70%, whilst most of the cholesterol is removed from the system. When applied to petroleum ether extracts from representative sputum samples, the clean-up procedures resulted in recoveries of 36–68% for PDIMs, allowing some superior detection of the target analytes.
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Affiliation(s)
- Simona C Nicoara
- Centre for Earth, Planetary, Space and Astronomical Research CEPSAR, The Open University, Milton Keynes, UK.
| | - Nicholas W Turner
- Life, Health and Chemical Sciences, The Open University, Milton Keynes, UK
| | - David E Minnikin
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, UK
| | - Oona Y-C Lee
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, UK
| | | | - Ruth McNerney
- London School of Hygiene & Tropical Medicine, London, UK
| | - Reggie Mutetwa
- Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Liz E Corbett
- Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Geraint H Morgan
- Centre for Earth, Planetary, Space and Astronomical Research CEPSAR, The Open University, Milton Keynes, UK
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15
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Dang NA, Mourão M, Kuijper S, Walters E, Janssen HG, Kolk AHJ. Direct detection of Mycobacterium tuberculosis in sputum using combined solid phase extraction-gas chromatography-mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 986-987:115-22. [PMID: 25728368 DOI: 10.1016/j.jchromb.2015.01.045] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 01/28/2015] [Accepted: 01/30/2015] [Indexed: 10/24/2022]
Abstract
Recently, thermally-assisted hydrolysis and methylation followed by gas chromatography-mass spectrometry (THM-GC-MS) in combination with chemometrics has been used to develop a 20-compound model for fast differentiation of Mycobacterium tuberculosis (MTB) from Non-tuberculous mycobacteria (NTM) in bacterial cultures. This model provided better than 95% accuracy. In our current work a hexane/methanol/water extraction followed by a solid phase extraction (SPE) clean-up procedure was developed for use before THM-GC-MS, to make the test suitable for the identification of mycobacteria in sputum. The 20 biomarker model had to be adapted since many compounds were also found in the sputum of non-tuberculosis patients. An algorithm was established based on tuberculostearic acid, hexacosanoic acid and mycoserosates. The detection limit of the method was approximately 1×10(4) bacteria/mL sputum. Sputum specimens from 32 patients from South Africa who were suspected of having tuberculosis were blindly tested using the new method. Eight of the nine culture-positive sputum specimens were detected by the new SPE-THM-GC-MS method, resulting in a sensitivity of 89%. The specimen that was missed by the new method was also microscopy negative. The specificity of the test was 100%; all 23 microscopy- and culture-negative specimens were correctly identified as negative by SPE-THM-GC-MS.
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Affiliation(s)
- Ngoc A Dang
- Analytical Chemistry & Forensic Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Marta Mourão
- Analytical Chemistry & Forensic Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Sjoukje Kuijper
- Analytical Chemistry & Forensic Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Elisabetta Walters
- Desmond Tutu TB Centre, Stellenbosch University, P.O. Box 19063, Tygerberg 7505, South Africa
| | - Hans-Gerd Janssen
- Analytical Chemistry & Forensic Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; Unilever Research and Development, P.O. Box 114, 3130 AC Vlaardingen, The Netherlands
| | - Arend H J Kolk
- Analytical Chemistry & Forensic Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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16
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Fleurbaaij F, van Leeuwen HC, Klychnikov OI, Kuijper EJ, Hensbergen PJ. Mass Spectrometry in Clinical Microbiology and Infectious Diseases. Chromatographia 2015. [DOI: 10.1007/s10337-014-2839-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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17
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Abstract
The search continues for a rapid diagnostic test for TB that has high sensitivity and specificity and is useable in sophisticated environments and in deprived regions with poor infrastructure. We discuss here the modern bioanalytical techniques that can be used to discover biomarkers of infection with Mycobacterium tuberculosis, focusing on techniques using GC. We will also discuss the use of GC-MS to identify volatile organic compounds in the headspace of bacterial culture or in samples of breath, serum or urine. Biomarkers discovered in the 'clean' environment of culture may differ from those in patients. A number of biomarkers have been found in patients, with little consistency in the various studies to date. Reproducibility is difficult; the impressive results found initially with a few patients are rarely repeatable when a larger sample series is tested. Mycobacterial lipids offer promise for distinguishing M. tuberculosis from nontuberculous mycobacteria directly in sputum.
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18
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Abstract
ABSTRACT
Lipidomics is a distinct subspecialty of metabolomics concerned with hydrophobic molecules that organize into membranes. Most of the lipid classes present in
Mycobacterium tuberculosis
are found only in
Actinobacteria
and show extreme structural diversity. This article highlights the conceptual basis and the practical challenges associated with the mass spectrometry–based lipidomic study of
M. tuberculosis
to solve basic questions about the virulence of this lipid-laden organism.
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19
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Nicoara SC, Minnikin DE, Lee OCY, O'Sullivan DM, McNerney R, Pillinger CT, Wright IP, Morgan GH. Development and optimization of a gas chromatography/mass spectrometry method for the analysis of thermochemolytic degradation products of phthiocerol dimycocerosate waxes found in Mycobacterium tuberculosis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:2374-2382. [PMID: 24097393 PMCID: PMC3824232 DOI: 10.1002/rcm.6694] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 07/18/2013] [Accepted: 07/20/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE The phthiocerol dimycocerosates (PDIMs) are certain stable and hydrophobic waxes found in the cell membrane of Mycobacterium tuberculosis, bacteria that cause an infectious disease of growing concern worldwide. Previous studies report the analysis of derivatives of the hydrolysed PDIMs from biological samples, following complex extraction and offline derivatization of PDIMs biomarkers, prior to their analysis by gas chromatography/mass spectrometry (GC/MS). METHODS We developed and optimized a GC/MS method based on selected ion monitoring (SIM) to detect the derivatives produced via the thermally assisted hydrolysis and methylation (THM) of the PDIMs from the cell membrane of M. tuberculosis. The extraction of PDIMs from culture is simple, and their thermochemolysis is carried out automatically online, thus avoiding the time-consuming derivatization steps of hydrolysis and esterification, usually performed offline. RESULTS For standard PDIMs in petroleum ether, our optimized method gave an excellent linearity (R(2) = 0.99) at concentrations between 0.172 and 27.5 ng/mL, a good precision (RSD = 11.42%), and a limit of detection (LOD) of 100 pg/mL. For the PDIMs extracted from dilutions of M. tuberculosis culture, the method gave good linearity (R(2) = 0.9685) and an estimated LOD of 400 CFU/mL (CFU = colony forming units) in sterile distilled water. CONCLUSIONS A GC/MS(SIM) method is presented for the rapid and quantitative detection of M. tuberculosis, based on the online thermochemolysis of lipidic biomarkers extracted from the bacterial culture. The method has the potential to be applied in human and veterinary clinical laboratories for the rapid diagnosis of tuberculosis in infected biological samples.
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Affiliation(s)
- Simona C Nicoara
- Department of Physical Sciences, Faculty of Science, The Open UniversityWalton Hall, Milton Keynes, MK7 6AA, UK
- Technical University38 Memorandumului Bld., 400114, Cluj-Napoca, Romania
| | - David E Minnikin
- School of Biosciences, University of BirminghamEdgbaston, Birmingham, B15 2TT, UK
| | - Oona C Y Lee
- School of Biosciences, University of BirminghamEdgbaston, Birmingham, B15 2TT, UK
| | - Denise M O'Sullivan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineKeppel Street, London, WC1E 7HT, UK
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineKeppel Street, London, WC1E 7HT, UK
- LGCQueens Road, Teddington, London, TW11 0LY, UK
| | - Collin T Pillinger
- Department of Physical Sciences, Faculty of Science, The Open UniversityWalton Hall, Milton Keynes, MK7 6AA, UK
| | - Ian P Wright
- Department of Physical Sciences, Faculty of Science, The Open UniversityWalton Hall, Milton Keynes, MK7 6AA, UK
| | - Geraint H Morgan
- Department of Physical Sciences, Faculty of Science, The Open UniversityWalton Hall, Milton Keynes, MK7 6AA, UK
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20
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Dang NA, Kuijper S, Walters E, Claassens M, van Soolingen D, Vivo-Truyols G, Janssen HG, Kolk AHJ. Validation of biomarkers for distinguishing Mycobacterium tuberculosis from non-tuberculous mycobacteria using gas chromatography-mass spectrometry and chemometrics. PLoS One 2013; 8:e76263. [PMID: 24146846 PMCID: PMC3798606 DOI: 10.1371/journal.pone.0076263] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 08/22/2013] [Indexed: 02/07/2023] Open
Abstract
Tuberculosis (TB) remains a major international health problem. Rapid differentiation of Mycobacterium tuberculosis complex (MTB) from non-tuberculous mycobacteria (NTM) is critical for decisions regarding patient management and choice of therapeutic regimen. Recently we developed a 20-compound model to distinguish between MTB and NTM. It is based on thermally assisted hydrolysis and methylation gas chromatography-mass spectrometry and partial least square discriminant analysis. Here we report the validation of this model with two independent sample sets, one consisting of 39 MTB and 17 NTM isolates from the Netherlands, the other comprising 103 isolates (91 MTB and 12 NTM) from Stellenbosch, Cape Town, South Africa. All the MTB strains in the 56 Dutch samples were correctly identified and the model had a sensitivity of 100% and a specificity of 94%. For the South African samples the model had a sensitivity of 88% and specificity of 100%. Based on our model, we have developed a new decision-tree that allows the differentiation of MTB from NTM with 100% accuracy. Encouraged by these findings we will proceed with the development of a simple, rapid, affordable, high-throughput test to identify MTB directly in sputum.
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Affiliation(s)
- Ngoc A. Dang
- Analytical Chemistry and Forensic Science, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
| | - Sjoukje Kuijper
- Analytical Chemistry and Forensic Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Elisabetta Walters
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Tygerberg, South Africa
| | - Mareli Claassens
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Tygerberg, South Africa
| | - Dick van Soolingen
- National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Department of Clinical Microbiology and Department of Pulmonary Diseases, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Gabriel Vivo-Truyols
- Analytical Chemistry and Forensic Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Hans-Gerd Janssen
- Analytical Chemistry and Forensic Science, University of Amsterdam, Amsterdam, The Netherlands
- Unilever Research and Development, Vlaardingen, The Netherlands
| | - Arend H. J. Kolk
- Analytical Chemistry and Forensic Science, University of Amsterdam, Amsterdam, The Netherlands
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21
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Zhang L, Li W, He ZG. DarR, a TetR-like transcriptional factor, is a cyclic di-AMP-responsive repressor in Mycobacterium smegmatis. J Biol Chem 2012; 288:3085-96. [PMID: 23250743 DOI: 10.1074/jbc.m112.428110] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cyclic dinucleotides, including cyclic di-AMP (c-di-AMP), are known to be ubiquitous second messengers involved in bacterial signal transduction. However, no transcriptional regulator has been characterized as a c-di-AMP receptor/effector to date. In the present study, using a c-di-AMP/transcription factor binding screen, we identified Ms5346, a TetR family regulator in Mycobacterium smegmatis, as a c-di-AMP receptor in bacteria. Ms5346 could specifically bind c-di-AMP with K(d) of 2.3 ± 0.5 μM. Using EMSA and DNase I footprinting assays, c-di-AMP was found to stimulate the DNA binding activity of Ms5346 and to enhance its ability to protect its target DNA sequence. A conserved 14-bp palindromic motif was identified as the DNA-binding site for Ms5346. Further, Ms5346 was found to negatively regulate expression of three target genes including Ms5347 (encoding a major facilitator family transporter), Ms5348 (encoding a medium chain fatty acyl-CoA ligase), and Ms5696 (encoding a cold shock protein, CspA). Ms5346 is the first cyclic di-AMP receptor regulator to be identified in bacteria, and we have designated it as DarR. Our findings enhance our understanding of the function and regulatory mechanism of the second messenger c-di-AMP in bacteria.
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Affiliation(s)
- Lei Zhang
- National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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