1
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Chaiyachat P, Kaewseekhao B, Chaiprasert A, Kamolwat P, Nonghanphithak D, Phetcharaburanin J, Sirichoat A, Ong RTH, Faksri K. Metabolomic analysis of Mycobacterium tuberculosis reveals metabolic profiles for identification of drug-resistant tuberculosis. Sci Rep 2023; 13:8655. [PMID: 37244948 DOI: 10.1038/s41598-023-35882-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 05/25/2023] [Indexed: 05/29/2023] Open
Abstract
The detection of pre-extensively (pre-XDR) and extensively drug-resistant tuberculosis (XDR-TB) is challenging. Drug-susceptibility tests for some anti-TB drugs, especially ethambutol (ETH) and ethionamide (ETO), are problematic due to overlapping thresholds to differentiate between susceptible and resistant phenotypes. We aimed to identify possible metabolomic markers to detect Mycobacterium tuberculosis (Mtb) strains causing pre-XDR and XDR-TB. The metabolic patterns of ETH- and ETO-resistant Mtb isolates were also investigated. Metabolomics of 150 Mtb isolates (54 pre-XDR, 63 XDR-TB and 33 pan-susceptible; pan-S) were investigated. Metabolomics of ETH and ETO phenotypically resistant subgroups were analyzed using UHPLC-ESI-QTOF-MS/MS. Orthogonal partial least-squares discriminant analysis revealed distinct separation in all pairwise comparisons among groups. Two metabolites (meso-hydroxyheme and itaconic anhydride) were able to differentiate the pre-XDR and XDR-TB groups from the pan-S group with 100% sensitivity and 100% specificity. In comparisons of the ETH and ETO phenotypically resistant subsets, sets of increased (ETH = 15, ETO = 7) and decreased (ETH = 1, ETO = 6) metabolites specific for the resistance phenotype of each drug were found. We demonstrated the potential for metabolomics of Mtb to differentiate among types of DR-TB as well as between isolates that were phenotypically resistant to ETO and ETH. Thus, metabolomics might be further applied for DR-TB diagnosis and patient management.
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Affiliation(s)
- Pratchakan Chaiyachat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Benjawan Kaewseekhao
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Angkana Chaiprasert
- Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Phalin Kamolwat
- Bureau of Tuberculosis, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Ditthawat Nonghanphithak
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Jutarop Phetcharaburanin
- Department of Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Auttawit Sirichoat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand.
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2
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Wang Z, Song L, Liu X, Shen X, Li X. Bacterial second messenger c-di-GMP: Emerging functions in stress resistance. Microbiol Res 2023; 268:127302. [PMID: 36640720 DOI: 10.1016/j.micres.2023.127302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/07/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
In natural environments, bacteria constantly encounter various stressful conditions, including nutrient starvation, toxic chemicals, and oxidative stress. The ability to adapt to these adverse conditions is crucial for bacterial survival. Frequently, bacteria utilize nucleotide signaling molecules such as cyclic diguanylate (c-di-GMP) to regulate their behaviors when encounter stress conditions. c-di-GMP is a ubiquitous bacterial second messenger regulating the transition between the planktonic state and biofilm state. An essential feature of biofilms is the production of extracellular matrix that covers bacterial cells and offers a physical barrier protecting the cells from environmental assaults. Beyond that, accumulating evidences have demonstrated that changes in the environment, including stress stimuli, cause the alteration of intracellular levels of c-di-GMP in bacterial cells, which is immediately sensed by a variety of downstream effectors that induce an appropriate stress response. In this review, we summarize recent research on the role of c-di-GMP signaling in bacterial responses to diverse stress conditions.
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Affiliation(s)
- Zhuo Wang
- Yuncheng Key Laboratory of Halophiles Resources Utilization, College of Life Sciences, Yuncheng University, Yuncheng, Shanxi 044000, People's Republic of China
| | - Li Song
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Xiaozhen Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Xihui Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Xin Li
- Yuncheng Key Laboratory of Halophiles Resources Utilization, College of Life Sciences, Yuncheng University, Yuncheng, Shanxi 044000, People's Republic of China.
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3
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Zhang J, Hu L, Zhang H, He Z. Cyclic
di‐GMP
triggers the hypoxic adaptation of
Mycobacterium bovis
through a metabolic switching regulator
ArgR. Environ Microbiol 2022; 24:4382-4400. [DOI: 10.1111/1462-2920.15987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Jiaxun Zhang
- College of Life Science and Technology Huazhong Agricultural University Wuhan 430070 China
| | - Lihua Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresources, College of Life Science and Technology Guangxi University Nanning 530004 China
| | - Hua Zhang
- College of Life Science and Technology Huazhong Agricultural University Wuhan 430070 China
| | - Zheng‐Guo He
- 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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4
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Zhang J, Sun L, Zhang Q, Bartlam M. Crystal structure of oligoribonuclease from Vibrio cholerae O1 El Tor with bound peptide. Acta Crystallogr F Struct Biol Commun 2021; 77:437-443. [PMID: 34866598 PMCID: PMC8647215 DOI: 10.1107/s2053230x21011043] [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: 09/17/2021] [Accepted: 10/21/2021] [Indexed: 11/10/2022] Open
Abstract
Oligoribonuclease (Orn), a member of the DEDDh superfamily, can hydrolyse 2-5 nt nanoRNAs to mononucleotides. It is involved in maintaining the intracellular levels of RNA, c-di-GMP signalling and transcription initiation in many bacterial species. Here, the crystal structure of Orn from Vibrio cholerae O1 El Tor (VcOrn) is reported at a resolution of 1.7 Å. VcOrn, which consists of nine α-helices and six β-strands, crystallizes with a single monomer in the asymmetric unit but forms a homodimer via crystallographic twofold symmetry. Electron density is observed in the active pocket that corresponds to an intersubunit N-terminal expression tag with sequence GPLGSHHH. The positively charged N-terminal tag binds in the negatively charged nucleotide-binding pocket with a buried surface area of ∼500 Å2. The N-terminal tag interacts with VcOrn via π-π stacking with two conserved residues involved in nucleotide binding, as well as via salt bridges and hydrogen bonds. The structure reported here reveals that the active pocket can accommodate polypeptides in addition to nucleotides, thus providing an important starting point for investigation into substrate modification and inhibitor design targeting VcOrn.
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Affiliation(s)
- Jianyu Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin 300350, People’s Republic of China
| | - Liyuan Sun
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin 300350, People’s Republic of China
| | - Qionglin Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin 300350, People’s Republic of China
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin 300350, People’s Republic of China
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5
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Bonnet I, Enouf V, Morel F, Ok V, Jaffré J, Jarlier V, Aubry A, Robert J, Sougakoff W. A Comprehensive Evaluation of GeneLEAD VIII DNA Platform Combined to Deeplex Myc-TB ® Assay to Detect in 8 Days Drug Resistance to 13 Antituberculous Drugs and Transmission of Mycobacterium tuberculosis Complex Directly From Clinical Samples. Front Cell Infect Microbiol 2021; 11:707244. [PMID: 34778100 PMCID: PMC8586210 DOI: 10.3389/fcimb.2021.707244] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/04/2021] [Indexed: 11/21/2022] Open
Abstract
The GeneLEAD VIII (Diagenode, Belgium) is a new, fully automated, sample-to-result precision instrument for the extraction of DNA and PCR detection of Mycobacterium tuberculosis complex (MTBC) directly from clinical samples. The Deeplex Myc-TB® assay (Genoscreen, France) is a diagnostic kit based on the deep sequencing of a 24-plexed amplicon mix allowing simultaneously the detection of resistance to 13 antituberculous (antiTB) drugs and the determination of spoligotype. We evaluated the performance of a strategy combining the both mentioned tools to detect directly from clinical samples, in 8 days, MTBC and its resistance to 13 antiTB drugs, and identify potential transmission of strains from patient-to-patient. Using this approach, we screened 112 clinical samples (65 smear-negative) and 94 MTBC cultured strains. The sensitivity and the specificity of the GeneLEAD/Deeplex Myc-TB approach for MTBC detection were 79.3% and 100%, respectively. One hundred forty successful Deeplex Myc-TB results were obtained for 46 clinical samples and 94 strains, a total of 85.4% of which had a Deeplex Myc-TB susceptibility and resistance prediction consistent with phenotypic drug susceptibility testing (DST). Importantly, the Deeplex Myc-TB assay was able to detect 100% of the multidrug-resistant (MDR) MTBC tested. The lowest concordance rates were for pyrazinamide, ethambutol, streptomycin, and ethionamide (84.5%, 81.5%, 73%, and 55%, respectively) for which the determination of susceptibility or resistance is generally difficult with current tools. One of the main difficulties of Deeplex Myc-TB is to interpret the non-synonymous uncharacterized variants that can represent up to 30% of the detected single nucleotide variants. We observed a good level of concordance between Deeplex Myc-TB-spoligotyping and MIRU-VNTR despite a lower discriminatory power for spoligotyping. The median time to obtain complete results from clinical samples was 8 days (IQR 7–13) provided a high-throughput NGS sequencing platform was available. Our results highlight that the GeneLEAD/Deeplex Myc-TB approach could be a breakthrough in rapid diagnosis of MDR TB in routine practice.
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Affiliation(s)
- Isabelle Bonnet
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Vincent Enouf
- Plateforme de Microbiologie Mutualisée (P2M), Pasteur International Bioresources network (PIBnet), Institut Pasteur, Paris, France
| | - Florence Morel
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Vichita Ok
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Jérémy Jaffré
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Vincent Jarlier
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France
| | - Alexandra Aubry
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Jérôme Robert
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Wladimir Sougakoff
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
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6
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Hariharan VN, Yadav R, Thakur C, Singh A, Gopinathan R, Singh DP, Sankhe G, Malhotra V, Chandra N, Bhatt A, Saini DK. Cyclic di-GMP sensing histidine kinase PdtaS controls mycobacterial adaptation to carbon sources. FASEB J 2021; 35:e21475. [PMID: 33772870 DOI: 10.1096/fj.202002537rr] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 11/11/2022]
Abstract
Cell signaling relies on second messengers to transduce signals from the sensory apparatus to downstream signaling pathway components. In bacteria, one of the most important and ubiquitous second messenger is the small molecule cyclic diguanosine monophosphate (c-di-GMP). While the biosynthesis, degradation, and regulatory pathways controlled by c-di-GMP are well characterized, the mechanisms through which c-di-GMP controls these processes are not entirely understood. Herein we present the report of a c-di-GMP sensing sensor histidine kinase PdtaS (Rv3220c), which binds to c-di-GMP at submicromolar concentrations, subsequently perturbing signaling of the PdtaS-PdtaR (Rv1626) two-component system. Aided by biochemical analysis, genetics, molecular docking, FRET microscopy, and structural modelling, we have characterized the binding of c-di-GMP in the GAF domain of PdtaS. We show that a pdtaS knockout in Mycobacterium smegmatis is severely compromised in growth on amino acid deficient media and exhibits global transcriptional dysregulation. The perturbation of the c-di-GMP-PdtaS-PdtaR axis results in a cascade of cellular changes recorded by a multiparametric systems' approach of transcriptomics, unbiased metabolomics, and lipid analyses.
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Affiliation(s)
- Vignesh Narayan Hariharan
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Rahul Yadav
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Albel Singh
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Renu Gopinathan
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Devendra Pratap Singh
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Gaurav Sankhe
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Vandana Malhotra
- Department of Biochemistry, Sri Venkateswara College, Delhi University, Delhi, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Deepak Kumar Saini
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
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7
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Xiao Y, Nie L, Chen H, He M, Liang Q, Nie H, Chen W, Huang Q. The two-component system TarR-TarS is regulated by c-di-GMP/FleQ and FliA and modulates antibiotic susceptibility in Pseudomonas putida. Environ Microbiol 2021; 23:5239-5257. [PMID: 33938113 DOI: 10.1111/1462-2920.15555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/19/2021] [Accepted: 04/30/2021] [Indexed: 11/29/2022]
Abstract
Two-component systems (TCSs) are predominant means by which bacteria sense and respond to environment signals. Genome of Pseudomonas putida contains dozens of putative TCS-encoding genes, but phenotypical-genotypical correlation and transcriptional regulation of these genes are largely unknown. Herein, we characterized function and transcriptional regulation of a conserved P. putida TCS, named TarR-TarS. TarS (PP_0769) encodes a potential histidine kinase, and tarR (PP_0768) encodes a potential response regulator. Protein-protein interaction assay and phosphorylation assay confirmed that TarR-TarS was a functional TCS. Growth assay under antibiotics revealed that TarR-TarS positively regulated bacterial resistance to multiple antibiotics. Pull-down assay revealed that TarR directly interacted with PP_0800 (a hypothetical protein) and GroEL (the chaperonin). GroEL played a positive role in antibiotic resistance, while PP_0800 seemed to have no effect on antibiotic resistance. The regulator FleQ indirectly activated tarR-tarS transcription. However, the second messenger c-di-GMP antagonized FleQ activation to inhibit tarR-tarS transcription. The sigma factor FliA directly activated tarR-tarS transcription via a consensus motif. These findings reveal function and transcriptional regulation of TarR-TarS, and enrich knowledge regarding the relationship between c-di-GMP and antibiotic susceptibility in P. putida.
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Affiliation(s)
- Yujie Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liang Nie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haozhe Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meina He
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingyuan Liang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hailing Nie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.,Hubei Key Laboratory of Soil Environment and Pollution Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
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8
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Transcriptional portrait of M. bovis BCG during biofilm production shows genes differentially expressed during intercellular aggregation and substrate attachment. Sci Rep 2020; 10:12578. [PMID: 32724037 PMCID: PMC7387457 DOI: 10.1038/s41598-020-69152-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis and M. smegmatis form drug-tolerant biofilms through dedicated genetic programs. In support of a stepwise process regulating biofilm production in mycobacteria, it was shown elsewhere that lsr2 participates in intercellular aggregation, while groEL1 was required for biofilm maturation in M. smegmatis. Here, by means of RNA-Seq, we monitored the early steps of biofilm production in M. bovis BCG, to distinguish intercellular aggregation from attachment to a surface. Genes encoding for the transcriptional regulators dosR and BCG0114 (Rv0081) were significantly regulated and responded differently to intercellular aggregation and surface attachment. Moreover, a M. tuberculosis H37Rv deletion mutant in the Rv3134c-dosS-dosR regulon, formed less biofilm than wild type M. tuberculosis, a phenotype reverted upon reintroduction of this operon into the mutant. Combining RT-qPCR with microbiological assays (colony and surface pellicle morphologies, biofilm quantification, Ziehl–Neelsen staining, growth curve and replication of planktonic cells), we found that BCG0642c affected biofilm production and replication of planktonic BCG, whereas ethR affected only phenotypes linked to planktonic cells despite its downregulation at the intercellular aggregation step. Our results provide evidence for a stage-dependent expression of genes that contribute to biofilm production in slow-growing mycobacteria.
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9
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la Cruz MAD, Ares MA, Rodríguez-Valverde D, Vallejo-Cardona AA, Flores-Valdez MA, Núñez IDC, Aceves-Sánchez MDJ, Lira-Chávez J, Rodríguez-Campos J, Bravo-Madrigal J. Transcriptional and Mycolic Acid Profiling in Mycobacterium bovis BCG In Vitro Show an Effect for c-di-GMP and Overlap between Dormancy and Biofilms. J Microbiol Biotechnol 2020; 30:811-821. [PMID: 32238759 PMCID: PMC9728378 DOI: 10.4014/jmb.1911.11043] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/12/2020] [Indexed: 12/15/2022]
Abstract
Mycobacterium tuberculosis produces mycolic acids which are relevant for persistence, recalcitrance to antibiotics and defiance to host immunity. c-di-GMP is a second messenger involved in transition from planktonic cells to biofilms, whose levels are controlled by diguanylate cyclases (DGC) and phosphodiesterases (PDE). The transcriptional regulator dosR, is involved in response to low oxygen, a condition likely happening to a subset of cells within biofilms. Here, we found that in M. bovis BCG, expression of both BCG1416c and BCG1419c genes, which code for a DGC and a PDE, respectively, decreased in both stationary phase and during biofilm production. The kasA, kasB, and fas genes, which are involved in mycolic acid biosynthesis, were induced in biofilm cultures, as was dosR, therefore suggesting an inverse correlation in their expression compared with that of genes involved in c-di-GMP metabolism. The relative abundance within trehalose dimycolate (TDM) of α-mycolates decreased during biofilm maturation, with methoxy mycolates increasing over time, and keto species remaining practically stable. Moreover, addition of synthetic c-di-GMP to mid-log phase BCG cultures reduced methoxy mycolates, increased keto species and practically did not affect α-mycolates, showing a differential effect of c-di-GMP on keto- and methoxy-mycolic acid metabolism.
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Affiliation(s)
- Miguel A. De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Centro Médico Nacional (CMN) Siglo XXI, Instituto Mexicano de Seguro Social (IMSS), Ciudad de México, México
| | - Miguel A. Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Centro Médico Nacional (CMN) Siglo XXI, Instituto Mexicano de Seguro Social (IMSS), Ciudad de México, México
| | - Diana Rodríguez-Valverde
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Centro Médico Nacional (CMN) Siglo XXI, Instituto Mexicano de Seguro Social (IMSS), Ciudad de México, México
| | - Alba Adriana Vallejo-Cardona
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco (CIATEJ) A.C., Biotecnología Médica y Farmacéutica, Av. Normalistas No. 800. Colinas de la Normal, C.P. 4470 Guadalajara, Jalisco, México,Alba Adriana Vallejo-Cardona Phone: +52-33-33-45-52-00 E-mail:
| | - Mario Alberto Flores-Valdez
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco (CIATEJ) A.C., Biotecnología Médica y Farmacéutica, Av. Normalistas No. 800. Colinas de la Normal, C.P. 4470 Guadalajara, Jalisco, México,Corresponding authors Mario Alberto Flores-Valdez Phone: +52-33-33-45-52-00 E-mail:
| | - Iris Denisse Cota Núñez
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco (CIATEJ) A.C., Biotecnología Médica y Farmacéutica, Av. Normalistas No. 800. Colinas de la Normal, C.P. 4470 Guadalajara, Jalisco, México
| | - Michel de Jesús Aceves-Sánchez
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco (CIATEJ) A.C., Biotecnología Médica y Farmacéutica, Av. Normalistas No. 800. Colinas de la Normal, C.P. 4470 Guadalajara, Jalisco, México
| | - Jonahtan Lira-Chávez
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco (CIATEJ) A.C., Biotecnología Médica y Farmacéutica, Av. Normalistas No. 800. Colinas de la Normal, C.P. 4470 Guadalajara, Jalisco, México
| | - Jacobo Rodríguez-Campos
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco (CIATEJ) A.C, Unidad de Servicios Analíticos y Metrológicos, Av. Normalistas No. 800. Colinas de la Normal, C.P. 44270 Guadalajara, Jalisco, México
| | - Jorge Bravo-Madrigal
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco (CIATEJ) A.C., Biotecnología Médica y Farmacéutica, Av. Normalistas No. 800. Colinas de la Normal, C.P. 4470 Guadalajara, Jalisco, México
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10
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Mycobacterial Cell Wall: A Source of Successful Targets for Old and New Drugs. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10072278] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Eighty years after the introduction of the first antituberculosis (TB) drug, the treatment of drug-susceptible TB remains very cumbersome, requiring the use of four drugs (isoniazid, rifampicin, ethambutol and pyrazinamide) for two months followed by four months on isoniazid and rifampicin. Two of the drugs used in this “short”-course, six-month chemotherapy, isoniazid and ethambutol, target the mycobacterial cell wall. Disruption of the cell wall structure can enhance the entry of other TB drugs, resulting in a more potent chemotherapy. More importantly, inhibition of cell wall components can lead to mycobacterial cell death. The complexity of the mycobacterial cell wall offers numerous opportunities to develop drugs to eradicate Mycobacterium tuberculosis, the causative agent of TB. In the past 20 years, researchers from industrial and academic laboratories have tested new molecules to find the best candidates that will change the face of TB treatment: drugs that will shorten TB treatment and be efficacious against active and latent, as well as drug-resistant TB. Two of these new TB drugs block components of the mycobacterial cell wall and have reached phase 3 clinical trial. This article reviews TB drugs targeting the mycobacterial cell wall in use clinically and those in clinical development.
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11
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Qi H, Wang F, Tao SC. Proteome microarray technology and application: higher, wider, and deeper. Expert Rev Proteomics 2019; 16:815-827. [PMID: 31469014 DOI: 10.1080/14789450.2019.1662303] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Introduction: Protein microarray is a powerful tool for both biological study and clinical research. The most useful features of protein microarrays are their miniaturized size (low reagent and sample consumption), high sensitivity and their capability for parallel/high-throughput analysis. The major focus of this review is functional proteome microarray. Areas covered: For proteome microarray, this review will discuss some recently constructed proteome microarrays and new concepts that have been used for constructing proteome microarrays and data interpretation in past few years, such as PAGES, M-NAPPA strategy, VirD technology, and the first protein microarray database. this review will summarize recent proteomic scale applications and address the limitations and future directions of proteome microarray technology. Expert opinion: Proteome microarray is a powerful tool for basic biological and clinical research. It is expected to see improvements in the currently used proteome microarrays and the construction of more proteome microarrays for other species by using traditional strategies or novel concepts. It is anticipated that the maximum number of features on a single microarray and the number of possible applications will be increased, and the information that can be obtained from proteome microarray experiments will more in-depth in the future.
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Affiliation(s)
- Huan Qi
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University , Shanghai , China
| | - Fei Wang
- School of Pharmacy, Shanghai Jiao Tong University , Shanghai , China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University , Shanghai , China
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12
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Wei S, Wang D, Li H, Bi L, Deng J, Zhu G, Zhang J, Li C, Li M, Fang Y, Zhang G, Chen J, Tao S, Zhang XE. Fatty acylCoA synthetase FadD13 regulates proinflammatory cytokine secretion dependent on the NF-κB signalling pathway by binding to eEF1A1. Cell Microbiol 2019; 21:e13090. [PMID: 31364251 PMCID: PMC6899955 DOI: 10.1111/cmi.13090] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/26/2019] [Accepted: 07/28/2019] [Indexed: 12/17/2022]
Abstract
Mycobacterium tuberculosis (Mtb) manipulates multiple host defence pathways to survive and persist in host cells. Understanding Mtb–host cell interaction is crucial to develop an efficient means to control the disease. Here, we applied the Mtb proteome chip, through separately interacting with H37Ra and H37Rv stimulated macrophage lysates, screened 283 Mtb differential proteins. Through primary screening, we focused on fatty acylCoA synthetase FadD13. Mtb FadD13 is a potential drug target, but its role in infection remains unclear. Deletion of FadD13 in Mtb reduced the production of proinflammatory cytokines IL‐1β, IL‐18, and IL‐6. Bimolecular fluorescence complementation and colocalization showed that the binding partner of FadD13 in macrophage was eEF1A1 (a translation elongation factor). Knockdown eEF1A1 expression in macrophage abrogated the promotion of proinflammatory cytokines induced by FadD13. In addition, ΔfadD13 mutant decreased the expression of the NF‐κB signalling pathway related proteins p50 and p65, so did the eEF1A1 knockdown macrophage infected with H37Rv. Meanwhile, we found that deletion of FadD13 reduced Mtb survival in macrophages during Mtb infection, and purified FadD13 proteins induced broken of macrophage membrane. Taken together, FadD13 is crucial for Mtb proliferation in macrophages, and it plays a key role in the production of proinflammatory cytokines during Mtb infection.
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Affiliation(s)
- Sha Wei
- State Key Laboratory of Agromicrobiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Dianbing Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hua Li
- State Key Laboratory of Agromicrobiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lijun Bi
- Key Laboratory of Non-Coding RNA and State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jiaoyu Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Guofeng Zhu
- Key Laboratory of Non-Coding RNA and State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jibin Zhang
- State Key Laboratory of Agromicrobiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chuanyou Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Min Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yuan Fang
- College of Life Science, Hubei University, Wuhan, China
| | - Guimin Zhang
- College of Life Science, Hubei University, Wuhan, China
| | - Jian Chen
- College of Life Science, Hubei University, Wuhan, China
| | - Shengce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Xian-En Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Science, Beijing, China
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13
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A DNA-Binding Protein Tunes Septum Placement during Bacillus subtilis Sporulation. J Bacteriol 2019; 201:JB.00287-19. [PMID: 31160399 PMCID: PMC6657595 DOI: 10.1128/jb.00287-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/15/2019] [Indexed: 01/07/2023] Open
Abstract
Bacillus subtilis is a bacterium capable of differentiating into a spore form more resistant to environmental stress. Early in sporulation, each cell possesses two copies of a circular chromosome. A polar FtsZ ring (Z ring) directs septation over one of the chromosomes, generating two cell compartments. The smaller "forespore" compartment initially contains only 25 to 30% of one chromosome, and this transient genetic asymmetry is required for differentiation. Timely assembly of polar Z rings and precise capture of the chromosome in the forespore both require the DNA-binding protein RefZ. To mediate its role in chromosome capture, RefZ must bind to specific DNA motifs (RBMs) that localize near the poles at the time of septation. Cells artificially induced to express RefZ during vegetative growth cannot assemble Z rings, an effect that also requires DNA binding. We hypothesized that RefZ-RBM complexes mediate precise chromosome capture by modulating FtsZ function. To investigate, we isolated 10 RefZ loss-of-function (rLOF) variants unable to inhibit cell division yet still capable of binding RBMs. Sporulating cells expressing the rLOF variants in place of wild-type RefZ phenocopied a ΔrefZ mutant, suggesting that RefZ acts through an FtsZ-dependent mechanism. The crystal structure of RefZ was solved, and wild-type RefZ and the rLOF variants were further characterized. Our data suggest that RefZ's oligomerization state and specificity for the RBMs are critical determinants influencing RefZ's ability to affect FtsZ dynamics. We propose that RBM-bound RefZ complexes function as a developmentally regulated nucleoid occlusion system for fine-tuning the position of the septum relative to the chromosome during sporulation.IMPORTANCE The bacterial nucleoid forms a large, highly organized structure. Thus, in addition to storing the genetic code, the nucleoid harbors positional information that can be leveraged by DNA-binding proteins to spatially constrain cellular activities. During B. subtilis sporulation, the nucleoid undergoes reorganization, and the cell division protein FtsZ assembles polarly to direct septation over one chromosome. The TetR family protein RefZ binds DNA motifs (RBMs) localized near the poles at the time of division and is required for both timely FtsZ assembly and precise capture of DNA in the future spore compartment. Our data suggest that RefZ exploits nucleoid organization by associating with polarly localized RBMs to modulate the positioning of FtsZ relative to the chromosome during sporulation.
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14
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Johnson RM, McDonough KA. Cyclic nucleotide signaling in Mycobacterium tuberculosis: an expanding repertoire. Pathog Dis 2019; 76:4995197. [PMID: 29905867 DOI: 10.1093/femspd/fty048] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/08/2018] [Indexed: 12/25/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) is one of the most successful microbial pathogens, and currently infects over a quarter of the world's population. Mtb's success depends on the ability of the bacterium to sense and respond to dynamic and hostile environments within the host, including the ability to regulate bacterial metabolism and interactions with the host immune system. One of the ways Mtb senses and responds to conditions it faces during infection is through the concerted action of multiple cyclic nucleotide signaling pathways. This review will describe how Mtb uses cyclic AMP, cyclic di-AMP and cyclic di-GMP to regulate important physiological processes, and how these signaling pathways can be exploited for the development of novel thereapeutics and vaccines.
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Affiliation(s)
- Richard M Johnson
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201-2002, USA
| | - Kathleen A McDonough
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201-2002, USA.,Wadsworth Center, New York State Department of Health, Albany, NY 12201-2002, USA
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15
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Integrated analysis of ethionamide resistance loci in Mycobacterium tuberculosis clinical isolates. Tuberculosis (Edinb) 2018; 113:163-174. [DOI: 10.1016/j.tube.2018.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/15/2018] [Accepted: 08/22/2018] [Indexed: 01/31/2023]
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16
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Discovery of Two Native Baeyer-Villiger Monooxygenases for Asymmetric Synthesis of Bulky Chiral Sulfoxides. Appl Environ Microbiol 2018; 84:AEM.00638-18. [PMID: 29752270 DOI: 10.1128/aem.00638-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/07/2018] [Indexed: 01/25/2023] Open
Abstract
Two Baeyer-Villiger monooxygenases (BVMOs), designated BoBVMO and AmBVMO, were discovered from Bradyrhizobium oligotrophicum and Aeromicrobium marinum, respectively. Both monooxygenases displayed novel features for catalyzing the asymmetric sulfoxidation of bulky and pharmaceutically relevant thioethers. Evolutionary relationship and sequence analysis revealed that the two BVMOs belong to the family of typical type I BVMOs and the subtype ethionamide monooxygenase. Both BVMOs are active toward medium- and long-chain aliphatic ketones as well as various thioether substrates but are ineffective toward cyclohexanone, aromatic ketones, and other typical BVMO substrates. BoBVMO and AmBVMO showed the highest activities (0.117 and 0.025 U/mg protein, respectively) toward thioanisole among the tested substrates. Furthermore, these BVMOs exhibited distinct activity and excellent stereoselectivity toward bulky and prochiral prazole thioethers, which is a unique feature of this family of BVMOs. No native enzyme has been reported for the asymmetric sulfoxidation of bulky prazole thioethers into chiral sulfoxides. The identification of BoBVMO and AmBVMO provides an important scaffold for discovering enzymes capable of asymmetrically oxidizing bulky thioether substrates by genome mining.IMPORTANCE Baeyer-Villiger monooxygenases (BVMOs) are valuable enzyme catalysts that are an alternative to the chemical Baeyer-Villiger oxidation reaction. Although BVMOs display broad substrate ranges, no native enzymes were reported to have activity toward the asymmetric oxidation of bulky prazole-like thioether substrates. Herein, we report the discovery of two type I BVMOs from Bradyrhizobium oligotrophicum (BoBVMO) and Aeromicrobium marinum (AmBVMO) which are able to catalyze the asymmetric sulfoxidation of bulky prazole thioethers (proton pump inhibitors [PPIs], a group of drugs whose main action is a pronounced and long-lasting reduction of gastric acid production). Efficient catalysis of omeprazole oxidation by BoBVMO was developed, indicating that this enzyme is a promising biocatalyst for the synthesis of bulky and pharmaceutically relevant chiral sulfoxide drugs. These results demonstrate that the newly identified enzymes are suitable templates for the discovery of more and better thioether-converting BVMOs.
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17
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Puffal J, García-Heredia A, Rahlwes KC, Siegrist MS, Morita YS. Spatial control of cell envelope biosynthesis in mycobacteria. Pathog Dis 2018; 76:4953754. [DOI: 10.1093/femspd/fty027] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/25/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Julia Puffal
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Alam García-Heredia
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Kathryn C Rahlwes
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - M Sloan Siegrist
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
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18
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He X, Jiang HW, Chen H, Zhang HN, Liu Y, Xu ZW, Wu FL, Guo SJ, Hou JL, Yang MK, Yan W, Deng JY, Bi LJ, Zhang XE, Tao SC. Systematic Identification of Mycobacterium tuberculosis Effectors Reveals that BfrB Suppresses Innate Immunity. Mol Cell Proteomics 2017; 16:2243-2253. [PMID: 29018126 DOI: 10.1074/mcp.ra117.000296] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Indexed: 12/14/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) has evolved multiple strategies to counter the human immune system. The effectors of Mtb play important roles in the interactions with the host. However, because of the lack of highly efficient strategies, there are only a handful of known Mtb effectors, thus hampering our understanding of Mtb pathogenesis. In this study, we probed Mtb proteome microarray with biotinylated whole-cell lysates of human macrophages, identifying 26 Mtb membrane proteins and secreted proteins that bind to macrophage proteins. Combining GST pull-down with mass spectroscopy then enabled the specific identification of all binders. We refer to this proteome microarray-based strategy as SOPHIE (Systematic unlOcking of Pathogen and Host Interacting Effectors). Detailed investigation of a novel effector identified here, the iron storage protein BfrB (Rv3841), revealed that BfrB inhibits NF-κB-dependent transcription through binding and reducing the nuclear abundance of the ribosomal protein S3 (RPS3), which is a functional subunit of NF- κB. The importance of this interaction was evidenced by the promotion of survival in macrophages of the mycobacteria, Mycobacterium smegmatis, by overexpression of BfrB. Thus, beyond demonstrating the power of SOPHIE in the discovery of novel effectors of human pathogens, we expect that the set of Mtb effectors identified in this work will greatly facilitate the understanding of the pathogenesis of Mtb, possibly leading to additional potential molecular targets in the battle against tuberculosis.
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Affiliation(s)
- Xiang He
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China.,§School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - He-Wei Jiang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong Chen
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Nan Zhang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yin Liu
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhao-Wei Xu
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan-Lin Wu
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shu-Juan Guo
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing-Li Hou
- ¶Instrumental Analysis Center of Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ming-Kun Yang
- ‖Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wei Yan
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiao-Yu Deng
- **State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Li-Jun Bi
- ‡‡National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding; RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,§§School of Stomatology and Medicine, Foshan University, Foshan 528000, Guangdong Province, China
| | - Xian-En Zhang
- ‡‡National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding; RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sheng-Ce Tao
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China; .,§School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.,¶¶State Key Laboratory of Oncogenes and Related Genes, Shanghai 200240, China
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Bhat ZS, Rather MA, Maqbool M, Lah HU, Yousuf SK, Ahmad Z. Cell wall: A versatile fountain of drug targets in Mycobacterium tuberculosis. Biomed Pharmacother 2017; 95:1520-1534. [PMID: 28946393 DOI: 10.1016/j.biopha.2017.09.036] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/07/2017] [Accepted: 09/10/2017] [Indexed: 12/18/2022] Open
Abstract
Tuberculosis is the leading infectious disease responsible for an estimated one and a half million human deaths each year around the globe. HIV-TB coinfection and rapid increase in the emergence of drug resistant forms of TB is a dangerous scenario. This underlines the urgent need for new drugs with novel mechanism of action. A plethora of literature exist that highlight the importance of enzymes involved in the biosynthesis of mycobacterial cell wall responsible for its survival, growth, permeability, virulence and resistance to antibiotics. Therefore, assembly of cell wall components is an attractive target for the development of chemotherapeutics against Mycobacterium tuberculosis. The aim of this review is to highlight novel sets of enzyme inhibitors that disrupt its cell wall biosynthetic pathway. These include the currently approved first and second line drugs, candidates in clinical trials and current structure activity guided endeavors of scientific community to identify new potent inhibitors with least cytotoxicity and better efficacy against emergence of drug resistance till date.
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Affiliation(s)
- Zubair Shanib Bhat
- Clinical Microbiology and PK/PD Division, Indian Institute of Integrative Medicine (IIIM), Campus, Sanat Nagar, Srinagar, Jammu & Kashmir 190005, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Indian Institute of Integrative Medicine (IIIM), Campus, Sanat Nagar, Srinagar, Jammu & Kashmir 190005, India.
| | - Muzafar Ahmad Rather
- Clinical Microbiology and PK/PD Division, Indian Institute of Integrative Medicine (IIIM), Campus, Sanat Nagar, Srinagar, Jammu & Kashmir 190005, India; Department of Biochemistry, University of Kashmir, Srinagar, Jammu & Kashmir 190006, India
| | - Mubashir Maqbool
- Clinical Microbiology and PK/PD Division, Indian Institute of Integrative Medicine (IIIM), Campus, Sanat Nagar, Srinagar, Jammu & Kashmir 190005, India; Department of Zoology, University of Kashmir, Srinagar, Jammu & Kashmir 190006, India
| | - Hafiz Ul Lah
- Medicinal Chemistry Division, Indian Institute of Integrative Medicine (IIIM), Campus, Sanat Nagar, Srinagar, Jammu & Kashmir 190005, India
| | - Syed Khalid Yousuf
- Academy of Scientific and Innovative Research (AcSIR), CSIR- Indian Institute of Integrative Medicine (IIIM), Campus, Sanat Nagar, Srinagar, Jammu & Kashmir 190005, India; Medicinal Chemistry Division, Indian Institute of Integrative Medicine (IIIM), Campus, Sanat Nagar, Srinagar, Jammu & Kashmir 190005, India
| | - Zahoor Ahmad
- Clinical Microbiology and PK/PD Division, Indian Institute of Integrative Medicine (IIIM), Campus, Sanat Nagar, Srinagar, Jammu & Kashmir 190005, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Indian Institute of Integrative Medicine (IIIM), Campus, Sanat Nagar, Srinagar, Jammu & Kashmir 190005, India.
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