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Liu Z, Li Y, Shan S, Zhang M, Yang H, Cheng W, Wei X, Wang Y, Wu S. Regulatory roles of APS reductase in Citrobacter sp. XT1-2-2 as a response mechanism to cadmium immobilization in rice. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 284:116892. [PMID: 39153279 DOI: 10.1016/j.ecoenv.2024.116892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/19/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
Citrobacter sp. XT1-2-2, a functional microorganism with potential utilization, has the ability to immobilize soil cadmium. In this study, the regulatory gene cysH, as a rate-limiting enzyme in the sulfur metabolic pathway, was selected for functional analysis affecting cadmium immobilization in soil. To verify the effect of APS reductase on CdS formation, the ΔAPS and ΔAPS-com strains were constructed by conjugation transfer. Through TEM analysis, it was found that the adsorption of Cd2+ was affected by the absence of APS reductase in XT1-2-2 strain. The difference analysis of biofilm formation indicated that APS reductase was necessary for cell aggregation and biofilm formation. The p-XRD, XPS and FT-IR analysis revealed that APS reductase played an important role in the cadmium immobilization process of XT1-2-2 strain and promoting the formation of CdS. According to the pot experiments, the cadmium concentration of roots, culms, leaves and grains inoculated with ΔAPS strain was significantly higher than that of wild-type and ΔAPS-com strains, and the cadmium removal ability of ΔAPS strain was significantly lower than that of wild-type strain. The study provided insights into the exploration of new bacterial assisted technique for the remediation and safe production of rice in cadmium-contaminated paddy soils.
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Affiliation(s)
- Zhudong Liu
- Hunan Institute of Microbiology, Changsha, Hunan 410009, China
| | - Yilu Li
- Hunan Institute of Microbiology, Changsha, Hunan 410009, China
| | - Shiping Shan
- Hunan Institute of Microbiology, Changsha, Hunan 410009, China; Hunan Engineering and Technology Research Center of Agricultural Microbiology Application, Changsha, Hunan 410009, China.
| | - Min Zhang
- Hunan Institute of Microbiology, Changsha, Hunan 410009, China.
| | - Hua Yang
- Hunan Institute of Microbiology, Changsha, Hunan 410009, China.
| | - Wei Cheng
- Hunan Institute of Microbiology, Changsha, Hunan 410009, China
| | - Xiaowu Wei
- Hunan Institute of Microbiology, Changsha, Hunan 410009, China
| | - Yushuang Wang
- Hunan Institute of Microbiology, Changsha, Hunan 410009, China
| | - Shandong Wu
- Hunan Institute of Microbiology, Changsha, Hunan 410009, China
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Nisa A, Pinto R, Britton WJ, Triccas JA, Counoupas C. Immunogenicity and Protective Efficacy of a Multi-Antigen Mycobacterium tuberculosis Subunit Vaccine in Mice. Vaccines (Basel) 2024; 12:997. [PMID: 39340027 PMCID: PMC11435920 DOI: 10.3390/vaccines12090997] [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: 07/10/2024] [Revised: 08/21/2024] [Accepted: 08/28/2024] [Indexed: 09/30/2024] Open
Abstract
There is an urgent need for an effective TB vaccine capable of controlling both acute and chronic Mycobacterium tuberculosis infection in populations with diverse genetic backgrounds. In this study, we characterised the immunogenicity and protective efficacy of a novel protein-in-adjuvant subunit vaccine. The protein component is a fusion protein of three different M. tuberculosis antigens, which we termed CysVac5: CysD, a major component of the M. tuberculosis sulfate activation pathway that is highly expressed during the chronic stage of M. tuberculosis infection, is fused with two major secreted mycobacterial antigens, Ag85B and MPT83. Vaccination of C57BL/6 mice with CysVac5, formulated in a monophosphoryl lipid A (MPLA) and dimethyldioctadecylammonium (DDA) adjuvant combination, resulted in the potent generation of polyfunctional CD4+ T cells secreting multiple cytokines, including IFN-γ, IL-2, TNF and IL-17, against each of the three components of the fusion protein. Furthermore, vaccination with CysVac5-MPLA/DDA conferred significant protection against infection in mouse lungs, which was greater than that afforded by BCG at extended time points post-challenge. The generation of antigen-specific and protective immunity was also observed in CysVac5 vaccinated BALB/c mice, indicating the vaccine could display efficacy across multiple genetic backgrounds. These results indicate that the CysVac5 vaccine has broad immunogenicity, is effective in controlling both acute and chronic phases of M. tuberculosis infection in mice, and warrants further investigation to assess its potential to control pulmonary TB.
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Affiliation(s)
- Annuurun Nisa
- Faculty of Medicine and Health, The University of Sydney Infectious Diseases Institute (Sydney ID), Camperdown, NSW 2050, Australia; (A.N.); (R.P.)
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Rachel Pinto
- Faculty of Medicine and Health, The University of Sydney Infectious Diseases Institute (Sydney ID), Camperdown, NSW 2050, Australia; (A.N.); (R.P.)
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Warwick J. Britton
- Centre for Infection and Immunity, Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia;
- Department of Clinical Immunology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - James A. Triccas
- Faculty of Medicine and Health, The University of Sydney Infectious Diseases Institute (Sydney ID), Camperdown, NSW 2050, Australia; (A.N.); (R.P.)
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
- Centre for Infection and Immunity, Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Claudio Counoupas
- Faculty of Medicine and Health, The University of Sydney Infectious Diseases Institute (Sydney ID), Camperdown, NSW 2050, Australia; (A.N.); (R.P.)
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
- Centre for Infection and Immunity, Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia;
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Khan MZ, Hunt DM, Singha B, Kapoor Y, Singh NK, Prasad DVS, Dharmarajan S, Sowpati DT, de Carvalho LPS, Nandicoori VK. Divergent downstream biosynthetic pathways are supported by <sc>L</sc>-cysteine synthases of Mycobacterium tuberculosis. eLife 2024; 12:RP91970. [PMID: 39207917 PMCID: PMC11361707 DOI: 10.7554/elife.91970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
Mycobacterium tuberculosis's (Mtb) autarkic lifestyle within the host involves rewiring its transcriptional networks to combat host-induced stresses. With the help of RNA sequencing performed under various stress conditions, we identified that genes belonging to Mtb sulfur metabolism pathways are significantly upregulated during oxidative stress. Using an integrated approach of microbial genetics, transcriptomics, metabolomics, animal experiments, chemical inhibition, and rescue studies, we investigated the biological role of non-canonical L-cysteine synthases, CysM and CysK2. While transcriptome signatures of RvΔcysM and RvΔcysK2 appear similar under regular growth conditions, we observed unique transcriptional signatures when subjected to oxidative stress. We followed pool size and labelling (34S) of key downstream metabolites, viz. mycothiol and ergothioneine, to monitor L-cysteine biosynthesis and utilization. This revealed the significant role of distinct L-cysteine biosynthetic routes on redox stress and homeostasis. CysM and CysK2 independently facilitate Mtb survival by alleviating host-induced redox stress, suggesting they are not fully redundant during infection. With the help of genetic mutants and chemical inhibitors, we show that CysM and CysK2 serve as unique, attractive targets for adjunct therapy to combat mycobacterial infection.
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Affiliation(s)
- Mehak Zahoor Khan
- National Institute of ImmunologyNew DelhiIndia
- CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | | | - Biplab Singha
- National Institute of ImmunologyNew DelhiIndia
- CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Yogita Kapoor
- CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | | | - D V Sai Prasad
- Department of Pharmacy, Birla Institute of Technology and Science-PilaniHyderabadIndia
| | - Sriram Dharmarajan
- Department of Pharmacy, Birla Institute of Technology and Science-PilaniHyderabadIndia
| | | | - Luiz Pedro S de Carvalho
- The Francis Crick InstituteLondonUnited Kingdom
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & TechnologyJupiterUnited States
| | - Vinay Kumar Nandicoori
- National Institute of ImmunologyNew DelhiIndia
- CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
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Jia X, Zhu Y, Jia P, Li C, Chu X, Sun T, Liu X, Yu W, Chen F, Xu Y, Yang Q. The key role of iroBCDN-lacking pLVPK-like plasmid in the evolution of the most prevalent hypervirulent carbapenem-resistant ST11-KL64 Klebsiella pneumoniae in China. Drug Resist Updat 2024; 77:101137. [PMID: 39178714 DOI: 10.1016/j.drup.2024.101137] [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: 03/20/2024] [Revised: 07/31/2024] [Accepted: 08/11/2024] [Indexed: 08/26/2024]
Abstract
AIMS Hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP), coharboring hypervirulence and carbapenem-resistance genes mediated by plasmids, causes infections with extremely high mortality and seriously impacts public health. Exploring the transfer mechanisms of virulence/carbapenem-resistance plasmids, as well as the formation and evolution pathway of hv-CRKP is of great significance to the control of hv-CRKP infections. METHODS In this study, we identified the predominant clone of hv-CRKP in China and elucidated its genomic characteristics and formation route based on 239 multicenter clinical K. pneumoniae isolates and 1014 GenBank genomes by using comparative genomic analysis. Further, we revealed the factors affecting the transfer of virulence plasmids, and explained the genetic foundation for the prevalence of Chinese predominant hv-CRKP clone. RESULTS ST11-KL64 is the predominant clone of hv-CRKP in China and primarily evolved from ST11-KL64 CRKP by acquiring the pLVPK-like virulence plasmid from hvKP. Significantly, the virulence gene cluster iroBCDN was lost in the virulence plasmid of ST11-KL64 hv-CRKP but existed in that of hvKP. Moreover, the absence of iroBCDN didn't decrease the virulence of hv-CRKP, which was proved by bacterial test, cell-interaction test and mice infection model. On the contrary, loss of iroBCDN was observed to regulate virulence/carbapenem-resistance plasmid transfer and oxidative stress-related genes in strains and thus promoted the mobilization of nonconjugative virulence plasmid from hvKP into ST11-KL64 CRKP, forming hv-CRKP which finally had elevated antioxidant capacity and enhanced survival capacity in macrophages. The loss of iroBCDN increased the survival ability of hv-CRKP without decreasing its virulence, endowing it with an evolutionary advantage. CONCLUSIONS Our work provides new insights into the key role of iroBCDN loss in convergence of CRKP and hvKP, and the genetic and biological foundation for the widespread prevalence of ST11-KL64 hv-CRKP in China.
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Affiliation(s)
- Xinmiao Jia
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Center for bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Zhu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Peiyao Jia
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Cuidan Li
- China National Center for Bioinformation, Beijing, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xiaobing Chu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Tianshu Sun
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Clinical Biobank, Center for Biomedical Technology, National Science and Technology Key Infrastructure on Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoyu Liu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Yu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Chen
- China National Center for Bioinformation, Beijing, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qiwen Yang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China.
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Yang L, Yu P, Wang J, Zhao T, Zhao Y, Pan Y, Chen L. Genomic and Transcriptomic Analyses Reveal Multiple Strategies for Vibrio parahaemolyticus to Tolerate Sub-Lethal Concentrations of Three Antibiotics. Foods 2024; 13:1674. [PMID: 38890902 PMCID: PMC11171697 DOI: 10.3390/foods13111674] [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: 04/15/2024] [Revised: 05/16/2024] [Accepted: 05/22/2024] [Indexed: 06/20/2024] Open
Abstract
Vibrio parahaemolyticus can cause acute gastroenteritis, wound infections, and septicemia in humans. The overuse of antibiotics in aquaculture may lead to a high incidence of the multidrug-resistant (MDR) pathogen. Nevertheless, the genome evolution of V. parahaemolyticus in aquatic animals and the mechanism of its antibiotic tolerance remain to be further deciphered. Here, we investigated the molecular basis of the antibiotic tolerance of V. parahaemolyticus isolates (n = 3) originated from shellfish and crustaceans using comparative genomic and transcriptomic analyses. The genome sequences of the V. parahaemolyticus isolates were determined (5.0-5.3 Mb), and they contained 4709-5610 predicted protein-encoding genes, of which 823-1099 genes were of unknown functions. Comparative genomic analyses revealed a number of mobile genetic elements (MGEs, n = 69), antibiotic resistance-related genes (n = 7-9), and heavy metal tolerance-related genes (n = 2-4). The V. parahaemolyticus isolates were resistant to sub-lethal concentrations (sub-LCs) of ampicillin (AMP, 512 μg/mL), kanamycin (KAN, 64 μg/mL), and streptomycin (STR, 16 μg/mL) (p < 0.05). Comparative transcriptomic analyses revealed that there were significantly altered metabolic pathways elicited by the sub-LCs of the antibiotics (p < 0.05), suggesting the existence of multiple strategies for antibiotic tolerance in V. parahaemolyticus. The results of this study enriched the V. parahaemolyticus genome database and should be useful for controlling the MDR pathogen worldwide.
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Affiliation(s)
- Lianzhi Yang
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of China, Shanghai 201306, China; (L.Y.); (P.Y.)
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Pan Yu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of China, Shanghai 201306, China; (L.Y.); (P.Y.)
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Juanjuan Wang
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of China, Shanghai 201306, China; (L.Y.); (P.Y.)
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Taixia Zhao
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of China, Shanghai 201306, China; (L.Y.); (P.Y.)
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- College of Tea and Food Science, Wuyi University, Wuyishan 354300, China
| | - Yong Zhao
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of China, Shanghai 201306, China; (L.Y.); (P.Y.)
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Yingjie Pan
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of China, Shanghai 201306, China; (L.Y.); (P.Y.)
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of China, Shanghai 201306, China; (L.Y.); (P.Y.)
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
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Park HE, Kim KM, Shin JI, Choi JG, An WJ, Trinh MP, Kang KM, Yoo JW, Byun JH, Jung MH, Lee KH, Kang HL, Baik SC, Lee WK, Shin MK. Prominent transcriptomic changes in Mycobacterium intracellulare under acidic and oxidative stress. BMC Genomics 2024; 25:376. [PMID: 38632539 PMCID: PMC11022373 DOI: 10.1186/s12864-024-10292-4] [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: 10/20/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Mycobacterium avium complex (MAC), including Mycobacterium intracellulare is a member of slow-growing mycobacteria and contributes to a substantial proportion of nontuberculous mycobacterial lung disease in humans affecting immunocompromised and elderly populations. Adaptation of pathogens in hostile environments is crucial in establishing infection and persistence within the host. However, the sophisticated cellular and molecular mechanisms of stress response in M. intracellulare still need to be fully explored. We aimed to elucidate the transcriptional response of M. intracellulare under acidic and oxidative stress conditions. RESULTS At the transcriptome level, 80 genes were shown [FC] ≥ 2.0 and p < 0.05 under oxidative stress with 10 mM hydrogen peroxide. Specifically, 77 genes were upregulated, while 3 genes were downregulated. In functional analysis, oxidative stress conditions activate DNA replication, nucleotide excision repair, mismatch repair, homologous recombination, and tuberculosis pathways. Additionally, our results demonstrate that DNA replication and repair system genes, such as dnaB, dinG, urvB, uvrD2, and recA, are indispensable for resistance to oxidative stress. On the contrary, 878 genes were shown [FC] ≥ 2.0 and p < 0.05 under acidic stress with pH 4.5. Among these genes, 339 were upregulated, while 539 were downregulated. Functional analysis highlighted nitrogen and sulfur metabolism pathways as the primary responses to acidic stress. Our findings provide evidence of the critical role played by nitrogen and sulfur metabolism genes in the response to acidic stress, including narGHIJ, nirBD, narU, narK3, cysND, cysC, cysH, ferredoxin 1 and 2, and formate dehydrogenase. CONCLUSION Our results suggest the activation of several pathways potentially critical for the survival of M. intracellulare under a hostile microenvironment within the host. This study indicates the importance of stress responses in M. intracellulare infection and identifies promising therapeutic targets.
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Affiliation(s)
- Hyun-Eui Park
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Kyu-Min Kim
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Jeong-Ih Shin
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Jeong-Gyu Choi
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Won-Jun An
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Minh Phuong Trinh
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Kyeong-Min Kang
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Jung-Wan Yoo
- Department of Internal Medicine, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Jung-Hyun Byun
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Myung Hwan Jung
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Kon-Ho Lee
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Hyung-Lyun Kang
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Seung Cheol Baik
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Woo-Kon Lee
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Min-Kyoung Shin
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea.
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea.
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Rakesh S, Aravind L, Krishnan A. Reappraisal of the DNA phosphorothioate modification machinery: uncovering neglected functional modalities and identification of new counter-invader defense systems. Nucleic Acids Res 2024; 52:1005-1026. [PMID: 38163645 PMCID: PMC10853773 DOI: 10.1093/nar/gkad1213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/03/2023] [Accepted: 12/10/2023] [Indexed: 01/03/2024] Open
Abstract
The DndABCDE systems catalysing the unusual phosphorothioate (PT) DNA backbone modification, and the DndFGH systems, which restrict invasive DNA, have enigmatic and paradoxical features. Using comparative genomics and sequence-structure analyses, we show that the DndABCDE module is commonly functionally decoupled from the DndFGH module. However, the modification gene-neighborhoods encode other nucleases, potentially acting as the actual restriction components or suicide effectors limiting propagation of the selfish elements. The modification module's core consists of a coevolving gene-pair encoding the DNA-scanning apparatus - a DndD/CxC-clade ABC ATPase and DndE with two ribbon-helix-helix (MetJ/Arc) DNA-binding domains. Diversification of DndE's DNA-binding interface suggests a multiplicity of target specificities. Additionally, many systems feature DNA cytosine methylase genes instead of PT modification, indicating the DndDE core can recruit other nucleobase modifications. We show that DndFGH is a distinct counter-invader system with several previously uncharacterized domains, including a nucleotide kinase. These likely trigger its restriction endonuclease domain in response to multiple stimuli, like nucleotides, while blocking protective modifications by invader methylases. Remarkably, different DndH variants contain a HerA/FtsK ATPase domain acquired from multiple sources, including cellular genome-segregation systems and mobile elements. Thus, we uncovered novel HerA/FtsK-dependent defense systems that might intercept invasive DNA during replication, conjugation, or packaging.
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Affiliation(s)
- Siuli Rakesh
- Department of Biological Sciences, Indian Institute of Science Education and Research Berhampur (IISER Berhampur), Berhampur 760010, India
| | - L Aravind
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Arunkumar Krishnan
- Department of Biological Sciences, Indian Institute of Science Education and Research Berhampur (IISER Berhampur), Berhampur 760010, India
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Lages MA, do Vale A, Lemos ML, Balado M. Remodulation of bacterial transcriptome after acquisition of foreign DNA: the case of irp-HPI high-pathogenicity island in Vibrio anguillarum. mSphere 2024; 9:e0059623. [PMID: 38078732 PMCID: PMC10826351 DOI: 10.1128/msphere.00596-23] [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: 10/11/2023] [Accepted: 10/27/2023] [Indexed: 01/31/2024] Open
Abstract
The high-pathogenicity island irp-HPI is widespread in Vibrionaceae and encodes the siderophore piscibactin, as well as the regulator PbtA that is essential for its expression. In this work, we aim to study whether PbtA directly interacts with irp-HPI promoters. Furthermore, we hypothesize that PbtA, and thereby the acquisition of irp-HPI island, may also influence the expression of other genes elsewhere in the bacterial genome. To address this question, an RNAseq analysis was conducted to identify differentially expressed genes after pbtA deletion in Vibrio anguillarum RV22 genetic background. The results showed that PbtA not only modulates the irp-HPI genes but also modulates the expression of a plethora of V. anguillarum core genome genes, inducing nitrate, arginine, and sulfate metabolism, T6SS1, and quorum sensing, while repressing lipopolysaccharide (LPS) production, MARTX toxin, and major porins such as OmpV and ChiP. The direct binding of the C-terminal domain of PbtA to piscibactin promoters (PfrpA and PfrpC), quorum sensing (vanT), LPS transporter wza, and T6SS structure- and effector-encoding genes was demonstrated by electrophoretic mobility shift assay (EMSA). The results provide valuable insights into the regulatory mechanisms underlying the expression of irp-HPI island and its impact on Vibrios transcriptome, with implications in pathogenesis.IMPORTANCEHorizontal gene transfer enables bacteria to acquire traits, such as virulence factors, thereby increasing the risk of the emergence of new pathogens. irp-HPI genomic island has a broad dissemination in Vibrionaceae and is present in numerous potentially pathogenic marine bacteria, some of which can infect humans. Previous works showed that certain V. anguillarum strains exhibit an expanded host range plasticity and heightened virulence, a phenomenon linked to the acquisition of the irp-HPI genomic island. The present work shows that this adaptive capability is likely achieved through comprehensive changes in the transcriptome of the bacteria and that these changes are mediated by the master regulator PbtA encoded within the irp-HPI element. Our results shed light on the broad implications of horizontal gene transfer in bacterial evolution, showing that the acquired DNA can directly mediate changes in the expression of the core genome, with profounds implications in pathogenesis.
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Affiliation(s)
- Marta A. Lages
- Department of Microbiology and Parasitology, Institute of Aquaculture, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana do Vale
- Fish Immunology and Vaccinology Group, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Manuel L. Lemos
- Department of Microbiology and Parasitology, Institute of Aquaculture, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Miguel Balado
- Department of Microbiology and Parasitology, Institute of Aquaculture, University of Santiago de Compostela, Santiago de Compostela, Spain
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9
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Limón G, Samhadaneh NM, Pironti A, Darwin KH. Aldehyde accumulation in Mycobacterium tuberculosis with defective proteasomal degradation results in copper sensitivity. mBio 2023; 14:e0036323. [PMID: 37350636 PMCID: PMC10470581 DOI: 10.1128/mbio.00363-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/17/2023] [Indexed: 06/24/2023] Open
Abstract
Mycobacterium tuberculosis is a major human pathogen and the causative agent of tuberculosis disease. M. tuberculosis is able to persist in the face of host-derived antimicrobial molecules nitric oxide (NO) and copper (Cu). However, M. tuberculosis with defective proteasome activity is highly sensitive to NO and Cu, making the proteasome an attractive target for drug development. Previous work linked NO susceptibility with the accumulation of para-hydroxybenzaldehyde (pHBA) in M. tuberculosis mutants with defective proteasomal degradation. In this study, we found that pHBA accumulation was also responsible for Cu sensitivity in these strains. We showed that exogenous addition of pHBA to wild-type M. tuberculosis cultures sensitized bacteria to Cu to a degree similar to that of a proteasomal degradation mutant. We determined that pHBA reduced the production and function of critical Cu resistance proteins of the regulated in copper repressor (RicR) regulon. Furthermore, we extended these Cu-sensitizing effects to an aldehyde that M. tuberculosis may face within the macrophage. Collectively, this study is the first to mechanistically propose how aldehydes can render M. tuberculosis susceptible to an existing host defense and could support a broader role for aldehydes in controlling M. tuberculosis infections. IMPORTANCE M. tuberculosis is a leading cause of death by a single infectious agent, causing 1.5 million deaths annually. An effective vaccine for M. tuberculosis infections is currently lacking, and prior infection does not typically provide robust immunity to subsequent infections. Nonetheless, immunocompetent humans can control M. tuberculosis infections for decades. For these reasons, a clear understanding of how mammalian immunity inhibits mycobacterial growth is warranted. In this study, we show aldehydes can increase M. tuberculosis susceptibility to copper, an established antibacterial metal used by immune cells to control M. tuberculosis and other microbes. Given that activated macrophages produce increased amounts of aldehydes during infection, we propose host-derived aldehydes may help control bacterial infections, making aldehydes a previously unappreciated antimicrobial defense.
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Affiliation(s)
- Gina Limón
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Nora M. Samhadaneh
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, New York, USA
- Microbial Computational Genomic Core Lab, New York University Grossman School of Medicine, New York, New York, USA
| | - Alejandro Pironti
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, New York, USA
- Microbial Computational Genomic Core Lab, New York University Grossman School of Medicine, New York, New York, USA
| | - K. Heran Darwin
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
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10
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Yang S, Tang R, Xie CJ, Han S, Rensing C, Liu GH, Zhou SG. A novel sulfate-reducing and nitrogen-fixing bacterium Fundidesulfovibrio soli sp. nov., isolated from paddy soils. Arch Microbiol 2023; 205:80. [PMID: 36735086 DOI: 10.1007/s00203-023-03412-3] [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: 12/13/2022] [Accepted: 01/10/2023] [Indexed: 02/04/2023]
Abstract
A strictly anaerobic sulfate-reducing strain, designated SG60T, was isolated from paddy soil collected in Fujian Province, China. Growth of strain SG60T was observed at 20-37 °C, pH 5.5-10.0 and 0-0.7% (w/v) NaCl. Strain SG60T showed the highest 16S rRNA sequence similarities to the type strains of Fundidesulfovibrio magnetotacticus FSS-1T (97.2%) and Fundidesulfovibrio putealis DSM 16056T (96.4%). Phylogenetic trees based on the16S rRNA sequence and genome-based phylogenomic tree constructed using 120 core genes showed that strain SG60T clustered with members of the genus Fundidesulfovibrio. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG60T and the most closely related type strain F. magnetotacticus were 78.2% and 21.6%, respectively. Strain SG60T contained MK-7 as the main respiratory quinone and anteiso-C15:0, anteiso-C17:1 ω9c, iso-C16:0 and iso-C16:1 H as the major fatty acids. Strain SG60T produced desulfoviridin and possessed genes (nifHDK) encoding functions involved in nitrogen fixation. The genomic DNA G + C content was 65.5%. Based on the observed physiological properties, chemotaxonomic characteristics and ANI and dDDH values, strain SG60T represents a novel species of the genus Fundidesulfovibrio, for which the name Fundidesulfovibrio soli sp. nov. is proposed. The type strain is SG60T (= GDMCC 1.3310T = JCM 35676T).
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Affiliation(s)
- Shang Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China
| | - Rong Tang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China
| | - Cheng-Jie Xie
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China
| | - Shuang Han
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China
| | - Guo-Hong Liu
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou City, 350003, Fujian Province, People's Republic of China.
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China.
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11
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Xiong Y, Wei L, Xin S, Min R, Liu F, Li N, Zhang Y. Comprehensive Temporal Protein Dynamics during Postirradiation Recovery in Deinococcus radiodurans. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:1622829. [PMID: 36411759 PMCID: PMC9674996 DOI: 10.1155/2022/1622829] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/19/2022] [Indexed: 10/15/2023]
Abstract
Deinococcus radiodurans (D. radiodurans) is an extremophile that can tolerate ionizing radiation, ultraviolet radiation, and oxidation. How D. radiodurans responds to and survives high levels of ionizing radiation is still not clear. In this study, we performed label-free proteomics to explore the proteome dynamics during postirradiation recovery (PIR). Surprisingly, proteins involved in translation were repressed during the initial hours of PIR. D. radiodurans also showed enhanced DNA repair and antioxidative response after 6 kGy of gamma irradiation. Moreover, proteins involved in sulfur metabolism and phenylalanine metabolism were enriched at 1 h and 12 h, respectively, indicating different energy and material needs during PIR. Furthermore, based on these findings, we proposed a novel model to elucidate the possible molecular mechanisms of robust radioresistance in D. radiodurans, which may serve as a reference for future radiation repair.
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Affiliation(s)
- Yan Xiong
- Analysis & Testing Center, Beijing Institute of Technology, Beijing 102488, China
| | - Linyang Wei
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Shuchen Xin
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Rui Min
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Feng Liu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Nuomin Li
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Yongqian Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
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12
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Sao Emani C, Richter A, Singh A, Bhatt A, Av-Gay Y. The ΔCysK 2 mutant of Mycobacterium tuberculosis is sensitive to vancomycin associated with changes in cell wall phospholipid profile. Biochem Biophys Res Commun 2022; 624:120-126. [PMID: 35940124 DOI: 10.1016/j.bbrc.2022.07.096] [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: 07/05/2022] [Revised: 07/11/2022] [Accepted: 07/25/2022] [Indexed: 11/26/2022]
Abstract
Cysteine plays a versatile role in cellular physiology and has previously been shown to be instrumental to Mycobacterium tuberculosis (M.tb) pathophysiology. In this study, we have generated mutants deficient in CysK2 and CysH, the key Cysteine, biosynthetic enzymes. In contrast to the ΔcysH mutant, the ΔcysK2 mutant is not an auxotroph and as such not essential for cysteine biosynthesis. Interestingly, the ΔcysK2 mutant shows increased sensitivity to cumene hydroperoxide, vitamin C, diamide, rifampicin and Vancomycin and shows alterations in phospholipid profile of Mtb cell wall. Our findings suggest that alteration in phospholipids content of M.tb cell wall by CysK2 may form a mode of defence against selected antibiotics and oxidative stress.
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Affiliation(s)
- Carine Sao Emani
- Division of Infectious Diseases, Department of Medicine/Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Adrian Richter
- Martin-Luther-University of Halle-Wittenberg, Kurt-Mothes-Straße 3, 06120, Halle, Germany
| | - Albel Singh
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Yossef Av-Gay
- Division of Infectious Diseases, Department of Medicine/Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
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13
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Parbhoo T, Mouton JM, Sampson SL. Phenotypic adaptation of Mycobacterium tuberculosis to host-associated stressors that induce persister formation. Front Cell Infect Microbiol 2022; 12:956607. [PMID: 36237425 PMCID: PMC9551238 DOI: 10.3389/fcimb.2022.956607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Mycobacterium tuberculosis exhibits a remarkable ability to interfere with the host antimicrobial response. The pathogen exploits elaborate strategies to cope with diverse host-induced stressors by modulating its metabolism and physiological state to prolong survival and promote persistence in host tissues. Elucidating the adaptive strategies that M. tuberculosis employs during infection to enhance persistence is crucial to understanding how varying physiological states may differentially drive disease progression for effective management of these populations. To improve our understanding of the phenotypic adaptation of M. tuberculosis, we review the adaptive strategies employed by M. tuberculosis to sense and coordinate a physiological response following exposure to various host-associated stressors. We further highlight the use of animal models that can be exploited to replicate and investigate different aspects of the human response to infection, to elucidate the impact of the host environment and bacterial adaptive strategies contributing to the recalcitrance of infection.
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14
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Wang Q, Zhou YM, Xing CY, Li WC, Shen Y, Yan P, Guo JS, Fang F, Chen YP. Encapsulins from Ca. Brocadia fulgida: An effective tool to enhance the tolerance of engineered bacteria (pET-28a-cEnc) to Zn 2. JOURNAL OF HAZARDOUS MATERIALS 2022; 435:128954. [PMID: 35462189 DOI: 10.1016/j.jhazmat.2022.128954] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
Zn2+ is largely discharged from many industries and poses a severe threat to the environment, making its remediation crucial. Encapsulins, proteinaceous nano-compartments, may protect cells against environmental stresses by sequestering toxic substances. To determine whether hemerythrin-containing encapsulins (cEnc) from anammox bacteria Ca. Brocadia fulgida can help cells deal with toxic substances such as Zn2+, we transferred cEnc into E.coli by molecular biology technologies for massive expression and then cultured them in media with increasing Zn2+ levels. The engineered bacteria (with cEnc) grew better and entered the apoptosis phase later, while wild bacteria showed poor survival. Furthermore, tandem mass tag-based quantitative proteomic analysis was used to reveal the underlying regulatory mechanism by which the genetically-engineered bacteria (with cEnc) adapted to Zn2+ stress. When Zn2+ was sequestered in cEnc as a transition, the engineered bacteria presented a complex network of regulatory systems against Zn2+-induced cytotoxicity, including functions related to ribosomes, sulfur metabolism, flagellar assembly, DNA repair, protein synthesis, and Zn2+ efflux. Our findings offer an effective and promising stress control strategy to enhance the Zn2+ tolerance of bacteria for Zn2+ remediation and provide a new application for encapsulins.
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Affiliation(s)
- Que Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Yue-Ming Zhou
- National Base of International Science and Technology Cooperation for Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Chong-Yang Xing
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligence Technology, Chinese Academy of Sciences, Chongqing 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Wen-Chao Li
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Yu Shen
- National Base of International Science and Technology Cooperation for Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Peng Yan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Jin-Song Guo
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Fang Fang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China.
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15
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Bandyopadhyay P, Pramanick I, Biswas R, PS S, Sreedharan S, Singh S, Rajmani RS, Laxman S, Dutta S, Singh A. S-Adenosylmethionine-responsive cystathionine β-synthase modulates sulfur metabolism and redox balance in Mycobacterium tuberculosis. SCIENCE ADVANCES 2022; 8:eabo0097. [PMID: 35749503 PMCID: PMC9232105 DOI: 10.1126/sciadv.abo0097] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/09/2022] [Indexed: 05/10/2023]
Abstract
Methionine and cysteine metabolisms are important for the survival and pathogenesis of Mycobacterium tuberculosis (Mtb). The transsulfuration pathway converts methionine to cysteine and represents an important link between antioxidant and methylation metabolism in diverse organisms. Using a combination of biochemistry and cryo-electron microscopy, we characterized the first enzyme of the transsulfuration pathway, cystathionine β-synthase (MtbCbs) in Mtb. We demonstrated that MtbCbs is a heme-less, pyridoxal-5'-phosphate-containing enzyme, allosterically activated by S-adenosylmethionine (SAM). The atomic model of MtbCbs in its native and SAM-bound conformations revealed a unique mode of SAM-dependent allosteric activation. Further, SAM stabilized MtbCbs by sterically occluding proteasomal degradation, which was crucial for supporting methionine and redox metabolism in Mtb. Genetic deficiency of MtbCbs reduced Mtb survival upon homocysteine overload in vitro, inside macrophages, and in mice coinfected with HIV. Thus, the MtbCbs-SAM axis constitutes an important mechanism of coordinating sulfur metabolism in Mtb.
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Affiliation(s)
- Parijat Bandyopadhyay
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Ishika Pramanick
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Rupam Biswas
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Sabarinath PS
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka 560065, India
| | - Sreesa Sreedharan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka 560065, India
| | - Shalini Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Raju S. Rajmani
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka 560065, India
| | - Somnath Dutta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, Karnataka 560012, India
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16
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Liu H, Hu Z, Zhou M, Zhang H, Zhang X, Yue Y, Yao X, Wang J, Xi C, Zheng P, Xu X, Hu B. PM 2.5 drives bacterial functions for carbon, nitrogen, and sulfur cycles in the atmosphere. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 295:118715. [PMID: 34933062 DOI: 10.1016/j.envpol.2021.118715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 12/06/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Airborne bacteria may absorb the substance from the atmospheric particles and play a role in biogeochemical cycling. However, these studies focused on a few culturable bacteria and the samples were usually collected from one site. The metabolic potential of a majority of airborne bacteria on a regional scale and their driving factors remain unknown. In this study, we collected particulates with aerodynamic diameter ≤2.5 μm (PM2.5) from 8 cities that represent different regions across China and analyzed the samples via high-throughput sequencing of 16S rRNA genes, quantitative polymerase chain reaction (qPCR) analysis, and functional database prediction. Based on the FAPROTAX database, 326 (80.69%), 191 (47.28%) and 45 (11.14%) bacterial genera are possible to conduct the pathways of carbon, nitrogen, and sulfur cycles, respectively. The pathway analysis indicated that airborne bacteria may lead to the decrease in organic carbon while the increase in ammonium and sulfate in PM2.5 samples, all of which are the important components of PM2.5. Among the 19 environmental factors studied including air pollutants, meteorological factors, and geographical conditions, PM2.5 concentration manifested the strongest correlations with the functional genes for the transformation of ammonium and sulfate. Moreover, the PM2.5 concentration rather than the sampling site will drive the distribution of functional genera. Thus, a bi-directional relationship between PM2.5 and bacterial metabolism is suggested. Our findings shed light on the potential bacterial pathway for the biogeochemical cycling in the atmosphere and the important role of PM2.5, offering a new perspective for atmospheric ecology and pollution control.
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Affiliation(s)
- Huan Liu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China; School of Civil Engineering, Chongqing University, Chongqing, 400044, China
| | - Zhichao Hu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Meng Zhou
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hao Zhang
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaole Zhang
- Institute of Environmental Engineering (IfU), ETH Zürich, Zürich, CH-8093, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Dübendorf, CH-8600, Switzerland
| | - Yang Yue
- Institute of Environmental Engineering (IfU), ETH Zürich, Zürich, CH-8093, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Dübendorf, CH-8600, Switzerland
| | - Xiangwu Yao
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jing Wang
- Institute of Environmental Engineering (IfU), ETH Zürich, Zürich, CH-8093, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Dübendorf, CH-8600, Switzerland
| | - Chuanwu Xi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, 48109-2029, USA
| | - Ping Zheng
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiangyang Xu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Baolan Hu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, 310058, China.
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17
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Mycobacterium tuberculosis VapC4 toxin engages small ORFs to initiate an integrated oxidative and copper stress response. Proc Natl Acad Sci U S A 2021; 118:2022136118. [PMID: 34362841 DOI: 10.1073/pnas.2022136118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Mycobacterium tuberculosis (Mtb) VapBC4 toxin-antitoxin system is essential for the establishment of Mtb infection. Using a multitier, systems-level approach, we uncovered the sequential molecular events triggered by the VapC4 toxin that activate a circumscribed set of critical stress survival pathways which undoubtedly underlie Mtb virulence. VapC4 exclusively inactivated the sole transfer RNACys (tRNACys) through cleavage at a single site within the anticodon sequence. Depletion of the pool of tRNACys led to ribosome stalling at Cys codons within actively translating messenger RNAs. Genome mapping of these Cys-stalled ribosomes unexpectedly uncovered several unannotated Cys-containing open reading frames (ORFs). Four of these are small ORFs (sORFs) encoding Cys-rich proteins of fewer than 50 amino acids that function as Cys-responsive attenuators that engage ribosome stalling at tracts of Cys codons to control translation of downstream genes. Thus, VapC4 mimics a state of Cys starvation, which then activates Cys attenuation at sORFs to globally redirect metabolism toward the synthesis of free Cys. The resulting newly enriched pool of Cys feeds into the synthesis of mycothiol, the glutathione counterpart in this pathogen that is responsible for maintaining cellular redox homeostasis during oxidative stress, as well as into a circumscribed subset of cellular pathways that enable cells to defend against oxidative and copper stresses characteristically endured by Mtb within macrophages. Our ability to pinpoint activation or down-regulation of pathways that collectively align with Mtb virulence-associated stress responses and the nonreplicating persistent state brings to light a direct and vital role for the VapC4 toxin in mediating these critical pathways.
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18
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Dong K, Li Y, Luo S, Zhang F, Pan H, Zhao L, Wang Y, Liao X. Hydrostatic pressure boost rate and mode to enhance sterilization mediated by GroEL-interacting proteins. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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19
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Verma D, Gupta V. New insights into the structure and function of an emerging drug target CysE. 3 Biotech 2021; 11:373. [PMID: 34367865 DOI: 10.1007/s13205-021-02891-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 06/09/2021] [Indexed: 11/24/2022] Open
Abstract
The antimicrobial resistant strains of several pathogens are major culprits of hospital-acquired nosocomial infections. An active and urgent action is necessary against these pathogens for the development of unique therapeutics. The cysteine biosynthetic pathway or genes (that are absent in humans) involved in the production of L-cysteine appear to be an attractive target for developing novel antibiotics. CysE, a Serine Acetyltransferase (SAT), catalyzes the first step of cysteine synthesis and is reported to be essential for the survival of persistence in several microbes including Mycobacterium tuberculosis. Structure determination provides fundamental insight into structure and function of protein and aid in drug design/discovery efforts. This review focuses on the overview of current knowledge of structure function, regulatory mechanism, and potential inhibitors (active site as well as allosteric site) of CysE. Despite having conserved structure, slight modification in CysE structure lead to altered the regulatory mechanism and hence affects the cysteine production. Due to its possible role in virulence and vital metabolism of pathogens makes it a potential target in the quest to develop novel therapeutics to treat multi-drug-resistant bacteria.
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Affiliation(s)
- Deepali Verma
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, Uttar Pradesh 201309 India
| | - Vibha Gupta
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, Uttar Pradesh 201309 India
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20
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Ingale P, Lad B, Kabra R, Singh S. Dissecting druggability of ABC transporter proteins in Mycobacterium species through network modeling. J Biomol Struct Dyn 2021; 40:8365-8374. [PMID: 33890552 DOI: 10.1080/07391102.2021.1911856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is an infectious disease that affects nearly 9.6 million people every year. Metals are important determinants of growth and pathogenicity of mycobacterium. In the present study, we have analyzed protein-protein interaction networks belonging to the iron, sulfur and molybdenum metabolism of Mycobacterium. Our analysis has identified some of the important target proteins one among them being irtA. Iron taken up by siderophores from the host is transported to irtA through which iron enters Mycobacterium. Thus, irtA plays a major role as an iron transporter in Mycobacterium. As irtA protein structure was not solved experimentally, we have predicted 3D structure of irtA. After successful model evaluation, we have identified thiosemicarbazones as possible drug candidates for irtA. Henceforth, we have designed five analogues of thiosemicarbazones and tested in silico for their efficacy against irtA using molecular docking, among them analogue 1 showed a very good efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prajakta Ingale
- Department of Pathogenesis and Cellular Response, National Centre for Cell Science, NCCS Complex, Pune, India
| | - Bhagwat Lad
- Department of Pathogenesis and Cellular Response, National Centre for Cell Science, NCCS Complex, Pune, India
| | - Ritika Kabra
- Department of Pathogenesis and Cellular Response, National Centre for Cell Science, NCCS Complex, Pune, India
| | - Shailza Singh
- Department of Pathogenesis and Cellular Response, National Centre for Cell Science, NCCS Complex, Pune, India
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21
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Kim M, Lee BH, Lee KE, Park W. Flavobacterium phycosphaerae sp. nov. isolated from the phycosphere of Microcystis aeruginosa. Int J Syst Evol Microbiol 2021; 71. [PMID: 33709898 DOI: 10.1099/ijsem.0.004735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel aerobic bacterial strain, designated MK012T, was isolated from the phycosphere of Microcystis aeruginosa. MK012T appears to be Gram-stain-negative, non-motile and rod-shaped and has yellow pigments. Phylogenetic analysis using 16S rRNA revealed that this bacterium was most closely related to Flavobacterium buctense T7T (=JCM 30750T; 97.5 %), Flavobacterium dankookense ARSA-19T (=KCTC 23179T; 97.5 %) and Flavobacterium macrobrachii an-8T (=DSM 22219T; 97.3 %). The genome size and genomic DNA G+C content of MK012T were estimated at 3.3 Mbp and 37.6 mol%, respectively. The average nucleotide identity (ANI), average amino acid identity (AAI) and in silico DNA-DNA hybridization (dDDH) values of MK012T and the members of the genus Flavobacterium were found to be 71.8-78.3 %, 65.1-79.6% and 19.1-21.5 %, respectively. MK012T exhibited oxidase but no catalase activity. The cells grew at 14-36 °C (optimum, 25 °C), pH 5-10 (optimum, pH 7) and 0-0.4 % (w/v) NaCl (optimum, 0 % NaCl) in R2A medium. MK012T did not produce flexirubin-type pigments. The predominant cellular fatty acids of MK012T were determined to be iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH, and summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1ω9c); MK-6 was identified as its only respiratory quinone. Its major polar lipids were determined to be phosphatidylethanolamine, two unidentified aminolipids, and two unidentified polar lipids. The genotypic and phenotypic characteristics indicate that MK012T (=KACC 21509T=JCM 33879T) represents a novel species of the genus Flavobacterium; therefore, the name Flavobacterium phycosphaerae sp. nov. is proposed.
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Affiliation(s)
- Minkyung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Byoung-Hee Lee
- National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Ki-Eun Lee
- National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
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22
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Young AT, Carette X, Helmel M, Steen H, Husson RN, Quackenbush J, Platig J. Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis. NPJ Syst Biol Appl 2021; 7:8. [PMID: 33514755 PMCID: PMC7846781 DOI: 10.1038/s41540-020-00164-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 12/07/2020] [Indexed: 11/30/2022] Open
Abstract
The ability of Mycobacterium tuberculosis (Mtb) to adapt to diverse stresses in its host environment is crucial for pathogenesis. Two essential Mtb serine/threonine protein kinases, PknA and PknB, regulate cell growth in response to environmental stimuli, but little is known about their downstream effects. By combining RNA-Seq data, following treatment with either an inhibitor of both PknA and PknB or an inactive control, with publicly available ChIP-Seq and protein–protein interaction data for transcription factors, we show that the Mtb transcription factor (TF) regulatory network propagates the effects of kinase inhibition and leads to widespread changes in regulatory programs involved in cell wall integrity, stress response, and energy production, among others. We also observe that changes in TF regulatory activity correlate with kinase-specific phosphorylation of those TFs. In addition to characterizing the downstream regulatory effects of PknA/PknB inhibition, this demonstrates the need for regulatory network approaches that can incorporate signal-driven transcription factor modifications.
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Affiliation(s)
- Albert T Young
- School of Medicine, University of California, San Francisco, USA
| | - Xavier Carette
- Division of Infectious Diseases, Boston Children's Hospital, Boston, USA.,Harvard Medical School, Boston, USA
| | - Michaela Helmel
- Harvard Medical School, Boston, USA.,Department of Pathology, Boston Children's Hospital, Boston, USA
| | - Hanno Steen
- Division of Infectious Diseases, Boston Children's Hospital, Boston, USA.,Harvard Medical School, Boston, USA.,Department of Pathology, Boston Children's Hospital, Boston, USA
| | - Robert N Husson
- Division of Infectious Diseases, Boston Children's Hospital, Boston, USA.,Harvard Medical School, Boston, USA
| | - John Quackenbush
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, USA
| | - John Platig
- Harvard Medical School, Boston, USA. .,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, USA.
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23
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Independent genomic polymorphisms in the PknH serine threonine kinase locus during evolution of the Mycobacterium tuberculosis Complex affect virulence and host preference. PLoS Pathog 2020; 16:e1009061. [PMID: 33347499 PMCID: PMC7785237 DOI: 10.1371/journal.ppat.1009061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/05/2021] [Accepted: 10/09/2020] [Indexed: 12/15/2022] Open
Abstract
Species belonging to the Mycobacterium tuberculosis Complex (MTBC) show more than 99% genetic identity but exhibit distinct host preference and virulence. The molecular genetic changes that underly host specificity and infection phenotype within MTBC members have not been fully elucidated. Here, we analysed RD900 genomic region across MTBC members using whole genome sequences from 60 different MTBC strains so as to determine its role in the context of MTBC evolutionary history. The RD900 region comprises two homologous genes, pknH1 and pknH2, encoding a serine/threonine protein kinase PknH flanking the tbd2 gene. Our analysis revealed that RD900 has been independently lost in different MTBC lineages and different strains, resulting in the generation of a single pknH gene. Importantly, all the analysed M. bovis and M. caprae strains carry a conserved deletion within a proline rich-region of pknH, independent of the presence or absence of RD900. We hypothesized that deletion of pknH proline rich-region in M. bovis may affect PknH function, having a potential role in its virulence and evolutionary adaptation. To explore this hypothesis, we constructed two M. bovis ‘knock-in’ strains containing the M. tuberculosis pknH gene. Evaluation of their virulence phenotype in mice revealed a reduced virulence of both M. bovis knock-in strains compared to the wild type, suggesting that PknH plays an important role in the differential virulence phenotype of M. bovis vs M. tuberculosis. Tuberculosis is caused in humans and animals by organisms from the Mycobacterium tuberculosis Complex (MTBC), that share more than 99% genetic identity but exhibit distinct host preference and virulence. While Mycobacterium tuberculosis is the main causative agent of human TB, Mycobacterium bovis is responsible for bovine TB disease, that exacts a tremendous economic burden worldwide, as well as being a zoonotic threat. Unlike the human restriction of M. tuberculosis, M. bovis has a broader host range and it has been found to be more virulent than M. tuberculosis in different animal models. However, the molecular basis for host preference and virulence divergence between M. tuberculosis and M. bovis is not fully elucidated. Here we study the genetic variations of the genomic region RD900 in the context of MTBC phylogeny. RD900 contains two genes encoding orthologues of the serine/threonine kinase PknH, which is linked to the regulation of several bacterial processes including virulence. We found that M. bovis pknH genes show a conserved deletion that is not present in M. tuberculosis strains, and we evaluated the potential impact of these variations in the regulation of M. bovis vs M. tuberculosis virulence through the construction and in vivo characterization of M. bovis pknH mutant strains.
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24
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Harnagel A, Lopez Quezada L, Park SW, Baranowski C, Kieser K, Jiang X, Roberts J, Vaubourgeix J, Yang A, Nelson B, Fay A, Rubin E, Ehrt S, Nathan C, Lupoli TJ. Nonredundant functions of Mycobacterium tuberculosis chaperones promote survival under stress. Mol Microbiol 2020; 115:272-289. [PMID: 32996193 DOI: 10.1111/mmi.14615] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022]
Abstract
Bacterial chaperones ClpB and DnaK, homologs of the respective eukaryotic heat shock proteins Hsp104 and Hsp70, are essential in the reactivation of toxic protein aggregates that occur during translation or periods of stress. In the pathogen Mycobacterium tuberculosis (Mtb), the protective effect of chaperones extends to survival in the presence of host stresses, such as protein-damaging oxidants. However, we lack a full understanding of the interplay of Hsps and other stress response genes in mycobacteria. Here, we employ genome-wide transposon mutagenesis to identify the genes that support clpB function in Mtb. In addition to validating the role of ClpB in Mtb's response to oxidants, we show that HtpG, a homolog of Hsp90, plays a distinct role from ClpB in the proteotoxic stress response. While loss of neither clpB nor htpG is lethal to the cell, loss of both through genetic depletion or small molecule inhibition impairs recovery after exposure to host-like stresses, especially reactive nitrogen species. Moreover, defects in cells lacking clpB can be complemented by overexpression of other chaperones, demonstrating that Mtb's stress response network depends upon finely tuned chaperone expression levels. These results suggest that inhibition of multiple chaperones could work in concert with host immunity to disable Mtb.
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Affiliation(s)
- Alexa Harnagel
- Department of Chemistry, New York University, New York, NY, USA
| | - Landys Lopez Quezada
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Catherine Baranowski
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Karen Kieser
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Xiuju Jiang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Julia Roberts
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Julien Vaubourgeix
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Amy Yang
- Department of Chemistry, New York University, New York, NY, USA
| | - Brock Nelson
- Department of Chemistry, New York University, New York, NY, USA
| | - Allison Fay
- Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | - Eric Rubin
- Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Carl Nathan
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Tania J Lupoli
- Department of Chemistry, New York University, New York, NY, USA.,Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
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25
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Dragset MS, Ioerger TR, Zhang YJ, Mærk M, Ginbot Z, Sacchettini JC, Flo TH, Rubin EJ, Steigedal M. Genome-wide Phenotypic Profiling Identifies and Categorizes Genes Required for Mycobacterial Low Iron Fitness. Sci Rep 2019; 9:11394. [PMID: 31388080 PMCID: PMC6684656 DOI: 10.1038/s41598-019-47905-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/18/2019] [Indexed: 11/26/2022] Open
Abstract
Iron is vital for nearly all living organisms, but during infection, not readily available to pathogens. Infectious bacteria therefore depend on specialized mechanisms to survive when iron is limited. These mechanisms make attractive targets for new drugs. Here, by genome-wide phenotypic profiling, we identify and categorize mycobacterial genes required for low iron fitness. Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), can scavenge host-sequestered iron by high-affinity iron chelators called siderophores. We take advantage of siderophore redundancy within the non-pathogenic mycobacterial model organism M. smegmatis (Msmeg), to identify genes required for siderophore dependent and independent fitness when iron is low. In addition to genes with a potential function in recognition, transport or utilization of mycobacterial siderophores, we identify novel putative low iron survival strategies that are separate from siderophore systems. We also identify the Msmeg in vitro essential gene set, and find that 96% of all growth-required Msmeg genes have a mutual ortholog in Mtb. Of these again, nearly 90% are defined as required for growth in Mtb as well. Finally, we show that a novel, putative ferric iron ABC transporter contributes to low iron fitness in Msmeg, in a siderophore independent manner.
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Affiliation(s)
- Marte S Dragset
- NTNU Norwegian University of Science and Technology, Centre of Molecular Inflammation Research and Department of Clinical and Molecular Medicine, Trondheim, 7491, Norway. .,Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA, 02115, USA. .,Germans Trias i Pujol Research Institute, Tuberculosis Research Unit, Badalona, 80916, Spain.
| | - Thomas R Ioerger
- Texas A&M University, Department of Computer Science, College Station, TX, 77843, USA
| | - Yanjia J Zhang
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA, 02115, USA
| | - Mali Mærk
- NTNU Norwegian University of Science and Technology, Centre of Molecular Inflammation Research and Department of Clinical and Molecular Medicine, Trondheim, 7491, Norway
| | - Zekarias Ginbot
- NTNU Norwegian University of Science and Technology, Centre of Molecular Inflammation Research and Department of Clinical and Molecular Medicine, Trondheim, 7491, Norway
| | - James C Sacchettini
- Texas A&M University, Department of Biochemistry and Biophysics, College Station, TX, 77843, USA
| | - Trude H Flo
- NTNU Norwegian University of Science and Technology, Centre of Molecular Inflammation Research and Department of Clinical and Molecular Medicine, Trondheim, 7491, Norway
| | - Eric J Rubin
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA, 02115, USA
| | - Magnus Steigedal
- NTNU Norwegian University of Science and Technology, Centre of Molecular Inflammation Research and Department of Clinical and Molecular Medicine, Trondheim, 7491, Norway.,Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA, 02115, USA.,St. Olavs University Hospital, Department of Medical Microbiology, Trondheim, 7030, Norway
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26
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Gample SP, Agrawal S, Sarkar D. Evidence of nitrite acting as a stable and robust inducer of non-cultivability in Mycobacterium tuberculosis with physiological relevance. Sci Rep 2019; 9:9261. [PMID: 31239517 PMCID: PMC6593118 DOI: 10.1038/s41598-019-45652-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/30/2019] [Indexed: 11/21/2022] Open
Abstract
Tuberculosis (TB) is the ninth leading cause of death worldwide, ranking above human immunodeficiency virus. Latency is the major obstacle in the eradication of this disease. How the physiology of the pathogen changes in transition to the latent stage needs to be understood. The latent bacteria extracted from animal hosts exist in a nonculturable (NC) phase, whereas bacteria extracted from most in vitro models are culture-positive. In the present study, we observed that nitrite, up to a concentration of 5 mM, shows the growth of Mycobacterium tuberculosis (MTB) in liquid media, but this effect starts reversing at higher concentrations. At a concentration of 10 mM, nitrite induces rapid nonculturability of MTB at the aerobic stage. This noncultivable dormancy was confirmed by analyzing the characteristics of NC bacteria. Further differential gene expression analyses clearly supported the formation of a dormancy phenotype. This study will be helpful for the use of this bacillus as a dormancy model in future studies on TB latency.
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Affiliation(s)
- Suwarna P Gample
- CSIR-National Chemical Laboratory, Organic Chemistry Division, Pune, 411008, Maharashtra, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sonia Agrawal
- CSIR-National Chemical Laboratory, Organic Chemistry Division, Pune, 411008, Maharashtra, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Dhiman Sarkar
- CSIR-National Chemical Laboratory, Organic Chemistry Division, Pune, 411008, Maharashtra, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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27
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León-Sobrino C, Ramond JB, Maggs-Kölling G, Cowan DA. Nutrient Acquisition, Rather Than Stress Response Over Diel Cycles, Drives Microbial Transcription in a Hyper-Arid Namib Desert Soil. Front Microbiol 2019; 10:1054. [PMID: 31139170 PMCID: PMC6527771 DOI: 10.3389/fmicb.2019.01054] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 04/26/2019] [Indexed: 11/13/2022] Open
Abstract
Hot desert surface soils are characterized by extremely low water activities for large parts of any annual cycle. It is widely assumed that microbial processes in such soils are very limited. Here we present the first metatranscriptomic survey of microbial community function in a low water activity hyperarid desert soil. Sequencing of total mRNA revealed a diverse and active community, dominated by Actinobacteria. Metatranscriptomic analysis of samples taken at different times over 3 days indicated that functional diel variations were limited at the whole community level, and mostly affected the eukaryotic subpopulation which was induced during the cooler night hours. High levels of transcription of chemoautotrophic carbon fixation genes contrasted with limited expression of photosynthetic genes, indicating that chemoautotrophy is an important alternative to photosynthesis for carbon cycling in desiccated desert soils. Analysis of the transcriptional levels of key N-cycling genes provided strong evidence that soil nitrate was the dominant nitrogen input source. Transcriptional network analyses and taxon-resolved functional profiling suggested that nutrient acquisition processes, and not diurnal environmental variation, were the main drivers of community activity in hyperarid Namib Desert soil. While we also observed significant levels of expression of common stress response genes, these genes were not dominant hubs in the co-occurrence network.
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Affiliation(s)
- Carlos León-Sobrino
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | | | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
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28
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Afzal M, Manzoor I, Kuipers OP, Shafeeq S. Cysteine-Mediated Gene Expression and Characterization of the CmbR Regulon in Streptococcus pneumoniae. Front Microbiol 2016; 7:1929. [PMID: 27990139 PMCID: PMC5131005 DOI: 10.3389/fmicb.2016.01929] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/16/2016] [Indexed: 11/13/2022] Open
Abstract
In this study, we investigated the transcriptomic response of Streptococcus pneumoniae D39 to cysteine. Transcriptome comparison of the D39 wild-type grown at a restricted concentration of cysteine (0.03 mM) to one grown at a high concentration of cysteine (50 mM) in chemically-defined medium (CDM) revealed elevated expression of various genes/operons, i.e., spd-0150, metQ, spd-0431, metEF, gshT, spd-0618, fhs, tcyB, metB-csd, metA, spd-1898, yvdE, and cysK, likely to be involved in the transport and utilization of cysteine and/or methionine. Microarray-based data were further confirmed by quantitative RT-PCR. Promoter lacZ-fusion studies and quantitative RT-PCR data showed that the transcriptional regulator CmbR acts as a transcriptional repressor of spd-0150, metEF, gshT, spd-0618, tcyB, metA, and yvdE, putatively involved in cysteine uptake and utilization. The operator site of CmbR in the promoter regions of CmbR-regulated genes is predicted and confirmed by mutating or deleting CmbR operator sites from the promoter regions of these genes.
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Affiliation(s)
- Muhammad Afzal
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands; Department of Bioinformatics and Biotechnology, Government College UniversityFaisalabad, Pakistan
| | - Irfan Manzoor
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands; Department of Bioinformatics and Biotechnology, Government College UniversityFaisalabad, Pakistan
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Groningen, Netherlands
| | - Sulman Shafeeq
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Stockholm, Sweden
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29
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Counoupas C, Pinto R, Nagalingam G, Hill-Cawthorne GA, Feng CG, Britton WJ, Triccas JA. Mycobacterium tuberculosis components expressed during chronic infection of the lung contribute to long-term control of pulmonary tuberculosis in mice. NPJ Vaccines 2016; 1:16012. [PMID: 29263854 PMCID: PMC5707878 DOI: 10.1038/npjvaccines.2016.12] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/27/2016] [Accepted: 07/05/2016] [Indexed: 11/09/2022] Open
Abstract
Tuberculosis (TB) remains a major cause of mortality and morbidity worldwide, yet current control strategies, including the existing BCG vaccine, have had little impact on disease control. The tubercle bacillus modifies protein expression to adapt to chronic infection of the host, and this can potentially be exploited to develop novel therapeutics. We identified the gene encoding the first step of the Mycobacterium tuberculosis sulphur assimilation pathway, cysD, as highly induced during chronic infection in the mouse lung, suggesting therapies based on CysD could be used to target infection. Vaccination with the composite vaccine CysVac2, a fusion of CysD and the immunogenic Ag85B of M. tuberculosis, resulted in the generation of multifunctional CD4+ T cells (interferon (IFN)-γ+TNF+IL-2+IL-17+) in the lung both pre- and post-aerosol challenge with M. tuberculosis. CysVac2 conferred significant protection against pulmonary M. tuberculosis challenge and was particularly effective at controlling late-stage infection, a property not shared by BCG. CysVac2 delivered as a booster following BCG vaccination afforded greater protection against M. tuberculosis challenge than BCG alone. The antigenic components of CysVac2 were conserved amongst M. tuberculosis strains, and protective efficacy afforded by CysVac2 was observed across varying murine MHC haplotypes. Strikingly, administration of CysVac2 to mice previously infected with M. tuberculosis reduced bacterial load and immunopathology in the lung compared with BCG-vaccinated mice. These results indicate that CysVac2 warrants further investigation to assess its potential to control pulmonary TB in humans.
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Affiliation(s)
- Claudio Counoupas
- Microbial Pathogenesis and Immunity Group, Department of Infectious Diseases and Immunology, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Tuberculosis Research Program, Centenary Institute, University of Sydney, Sydney, NSW, Australia
| | - Rachel Pinto
- Microbial Pathogenesis and Immunity Group, Department of Infectious Diseases and Immunology, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Tuberculosis Research Program, Centenary Institute, University of Sydney, Sydney, NSW, Australia
| | - Gayathri Nagalingam
- Microbial Pathogenesis and Immunity Group, Department of Infectious Diseases and Immunology, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Tuberculosis Research Program, Centenary Institute, University of Sydney, Sydney, NSW, Australia
| | - Grant A Hill-Cawthorne
- Sydney Medical School and The Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia
- School of Public Health, University of Sydney, Sydney, NSW, Australia
| | - Carl G Feng
- Tuberculosis Research Program, Centenary Institute, University of Sydney, Sydney, NSW, Australia
- Sydney Medical School and The Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia
- Immunology and Host Defense Group, Department of Infectious Diseases and Immunology, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Warwick J Britton
- Tuberculosis Research Program, Centenary Institute, University of Sydney, Sydney, NSW, Australia
- Sydney Medical School and The Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia
| | - James A Triccas
- Microbial Pathogenesis and Immunity Group, Department of Infectious Diseases and Immunology, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Tuberculosis Research Program, Centenary Institute, University of Sydney, Sydney, NSW, Australia
- Sydney Medical School and The Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia
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30
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Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis. Sci Rep 2016; 6:23440. [PMID: 27000948 PMCID: PMC4802306 DOI: 10.1038/srep23440] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/07/2016] [Indexed: 12/25/2022] Open
Abstract
Robustness of metabolic networks is accomplished by gene regulation, modularity, re-routing of metabolites and plasticity. Here, we probed robustness against perturbations of biochemical reactions of M. tuberculosis in the form of predicting compensatory trends. In order to investigate the transcriptional programming of genes associated with correlated fluxes, we integrated with gene co-expression network. Knock down of the reactions NADH2r and ATPS responsible for producing the hub metabolites, and Central carbon metabolism had the highest proportion of their associated genes under transcriptional co-expression with genes of their flux correlated reactions. Reciprocal gene expression correlations were observed among compensatory routes, fresh activation of alternative routes and in the multi-copy genes of Cysteine synthase and of Phosphate transporter. Knock down of 46 reactions caused the activation of Isocitrate lyase or Malate synthase or both reactions, which are central to the persistent state of M. tuberculosis. A total of 30 new freshly activated routes including Cytochrome c oxidase, Lactate dehydrogenase, and Glycine cleavage system were predicted, which could be responsible for switching into dormant or persistent state. Thus, our integrated approach of exploring transcriptional programming of flux correlated reactions has the potential to unravel features of system architecture conferring robustness.
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31
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Wang D, Xu S, Song D, Knight S, Mao X. A gene encoding a potential adenosine 5'-phosphosulphate kinase is necessary for timely development of Myxococcus xanthus. MICROBIOLOGY-SGM 2016; 162:672-683. [PMID: 26860640 DOI: 10.1099/mic.0.000254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A Myxococcus xanthus gene, MXAN3487, was identified by transposon mutagenesis to be required for the expression of mcuABC, an operon coding for part of the chaperone-usher (CU) system in this bacterium. The MXAN3487 protein displays sequence and structural homology to adenosine 5'-phosphosulphate (APS) kinase family members and contains putative motifs for ATP and APS binding. Although the MXAN3487 locus is not linked to other sulphate assimilation genes, its protein product may have APS kinase activity in vivo and the importance of the ATP-binding site for activity was demonstrated. Expression of MXAN3487 was not affected by sulphate availability, suggesting that MXAN3487 may not function in a reductive sulphate assimilation pathway. Deletion of MXAN3487 significantly delayed fruiting body formation and the production of McuA, a spore coat protein secreted by the M. xanthus Mcu CU system. Based on these observations and data from our previous studies, we propose that MXAN3487 may phosphorylate molecules structurally related to APS, generating metabolites necessary for M. xanthus development, and that MXAN3487 exerts a positive effect on the mcuABC operon whose expression is morphogenesis dependent.
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Affiliation(s)
- Daoyong Wang
- Department of Biochemistry, School of Medicine, Key Laboratory of Ministry of Education for Developmental Genes and Human Diseases, Southeast University, Nanjing, Jiangsu 210009, PR China
| | - Shihui Xu
- Department of Biochemistry, School of Medicine, Key Laboratory of Ministry of Education for Developmental Genes and Human Diseases, Southeast University, Nanjing, Jiangsu 210009, PR China
| | - Dan Song
- Department of Biochemistry, School of Medicine, Key Laboratory of Ministry of Education for Developmental Genes and Human Diseases, Southeast University, Nanjing, Jiangsu 210009, PR China
| | - Stefan Knight
- Department of Cell and Molecular Biology, Uppsala University, Uppsala Biomedical Centre, 75124 Uppsala, Sweden
| | - Xiaohua Mao
- Department of Biochemistry, School of Medicine, Key Laboratory of Ministry of Education for Developmental Genes and Human Diseases, Southeast University, Nanjing, Jiangsu 210009, PR China
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Palde PB, Bhaskar A, Pedrό Rosa LE, Madoux F, Chase P, Gupta V, Spicer T, Scampavia L, Singh A, Carroll KS. First-in-Class Inhibitors of Sulfur Metabolism with Bactericidal Activity against Non-Replicating M. tuberculosis. ACS Chem Biol 2016; 11:172-84. [PMID: 26524379 PMCID: PMC4729198 DOI: 10.1021/acschembio.5b00517] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Development of effective therapies to eradicate persistent, slowly replicating M. tuberculosis (Mtb) represents a significant challenge to controlling the global TB epidemic. To develop such therapies, it is imperative to translate information from metabolome and proteome adaptations of persistent Mtb into the drug discovery screening platforms. To this end, reductive sulfur metabolism is genetically and pharmacologically implicated in survival, pathogenesis, and redox homeostasis of persistent Mtb. Therefore, inhibitors of this pathway are expected to serve as powerful tools in its preclinical and clinical validation as a therapeutic target for eradicating persisters. Here, we establish a first functional HTS platform for identification of APS reductase (APSR) inhibitors, a critical enzyme in the assimilation of sulfate for the biosynthesis of cysteine and other essential sulfur-containing molecules. Our HTS campaign involving 38 350 compounds led to the discovery of three distinct structural classes of APSR inhibitors. A class of bioactive compounds with known pharmacology displayed potent bactericidal activity in wild-type Mtb as well as MDR and XDR clinical isolates. Top compounds showed markedly diminished potency in a conditional ΔAPSR mutant, which could be restored by complementation with Mtb APSR. Furthermore, ITC studies on representative compounds provided evidence for direct engagement of the APSR target. Finally, potent APSR inhibitors significantly decreased the cellular levels of key reduced sulfur-containing metabolites and also induced an oxidative shift in mycothiol redox potential of live Mtb, thus providing functional validation of our screening data. In summary, we have identified first-in-class inhibitors of APSR that can serve as molecular probes in unraveling the links between Mtb persistence, antibiotic tolerance, and sulfate assimilation, in addition to their potential therapeutic value.
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Affiliation(s)
- Prakash B. Palde
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Ashima Bhaskar
- Department of Microbiology and Cell Biology (MCBL), Center for Infectious Disease Research (CIDR), Indian Institute of Science (IISc.), Bangalore 560012, India
| | - Laura E. Pedrό Rosa
- Lead Identification Division, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Franck Madoux
- Lead Identification Division, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Peter Chase
- Lead Identification Division, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Vinayak Gupta
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Timothy Spicer
- Lead Identification Division, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Louis Scampavia
- Lead Identification Division, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Amit Singh
- Department of Microbiology and Cell Biology (MCBL), Center for Infectious Disease Research (CIDR), Indian Institute of Science (IISc.), Bangalore 560012, India
| | - Kate S. Carroll
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
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Erickson AI, Sarsam RD, Fisher AJ. Crystal Structures of Mycobacterium tuberculosis CysQ, with Substrate and Products Bound. Biochemistry 2015; 54:6830-41. [PMID: 26512869 DOI: 10.1021/acs.biochem.5b01000] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In many organisms, 3'-phosphoadenosine 5'-phosphate (PAP) is a product of two reactions in the sulfur activation pathway. The sulfurylation of biomolecules, catalyzed by sulfotransferases, uses 3'-phosphoadenosine 5'-phosphosulfate (PAPS) as a sulfate donor, producing the sulfated biomolecule and PAP product. Additionally, the first step in sulfate reduction for many bacteria and fungi reduces the sulfate moiety of PAPS, producing PAP and sulfite, which is subsequently reduced to sulfide. PAP is removed by the phosphatase activity of CysQ, a 3',5'-bisphosphate nucleotidase, yielding AMP and phosphate. Because excess PAP alters the equilibrium of the sulfur pathway and inhibits sulfotransferases, PAP concentrations can affect the levels of sulfur-containing metabolites. Therefore, CysQ, a divalent cation metal-dependent phosphatase, is a major regulator of this pathway. CysQ (Rv2131c) from Mycobacterium tuberculosis (Mtb) was successfully expressed, purified, and crystallized in a variety of ligand-bound states. Here we report six crystal structures of Mtb CysQ, including a ligand-free structure, a lithium-inhibited state with substrate PAP bound, and a product-bound complex with AMP, phosphate, and three Mg(2+) ions bound. Comparison of these structures together with homologues of the superfamily has provided insight into substrate specificity, metal coordination, and catalytic mechanism.
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Affiliation(s)
- Anna I Erickson
- Department of Chemistry, ‡Department of Molecular and Cellular Biology, and §Graduate Program in Biochemistry and Molecular, Cellular and Developmental Biology, University of California , One Shields Avenue, Davis, California 95616, United States
| | - Reta D Sarsam
- Department of Chemistry, ‡Department of Molecular and Cellular Biology, and §Graduate Program in Biochemistry and Molecular, Cellular and Developmental Biology, University of California , One Shields Avenue, Davis, California 95616, United States
| | - Andrew J Fisher
- Department of Chemistry, ‡Department of Molecular and Cellular Biology, and §Graduate Program in Biochemistry and Molecular, Cellular and Developmental Biology, University of California , One Shields Avenue, Davis, California 95616, United States
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Paritala H, Suzuki Y, Carroll KS. Design, synthesis and evaluation of Fe-S targeted adenosine 5'-phosphosulfate reductase inhibitors. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:199-220. [PMID: 25710356 DOI: 10.1080/15257770.2014.978012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Adenosine 5'-phosphosulfate reductase (APR) is an iron-sulfur enzyme that is vital for survival of Mycobacterium tuberculosis during dormancy and is an attractive target for the treatment of latent tuberculosis (TB) infection. The 4Fe-4S cluster is coordinated to APR by sulfur atoms of four cysteine residues, is proximal to substrate, adenosine 5'-phopsphosulfate (APS), and is essential for catalytic activity. Herein, we present an approach for the development of a new class of APR inhibitors. As an initial step, we have employed an improved solid-phase chemistry method to prepare a series of N(6)-substituted adenosine analogues and their 5'-phosphates as well as adenosine 5'-phosphate diesters bearing different Fe and S binding groups, such as thiols or carboxylic and hydroxamic acid moieties. Evaluation of the resulting compounds indicates a clearly defined spacing requirement between the Fe-S targeting group and adenosine scaffold and that smaller Fe-S targeting groups are better tolerated. Molecular docking analysis suggests that the S atom of the most potent inhibitor may establish a favorable interaction with an S atom in the cluster. In summary, this study showcases an improved solid-phase method that expedites the preparation of adenosine and related 5'-phosphate derivatives and presents a unique Fe-S targeting strategy for the development of APR inhibitors.
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Gopinath V, Raghunandanan S, Gomez RL, Jose L, Surendran A, Ramachandran R, Pushparajan AR, Mundayoor S, Jaleel A, Kumar RA. Profiling the Proteome of Mycobacterium tuberculosis during Dormancy and Reactivation. Mol Cell Proteomics 2015; 14:2160-76. [PMID: 26025969 DOI: 10.1074/mcp.m115.051151] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Indexed: 11/06/2022] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis, still remains a major global health problem. The main obstacle in eradicating this disease is the ability of this pathogen to remain dormant in macrophages, and then reactivate later under immuno-compromised conditions. The physiology of hypoxic nonreplicating M. tuberculosis is well-studied using many in vitro dormancy models. However, the physiological changes that take place during the shift from dormancy to aerobic growth (reactivation) have rarely been subjected to a detailed investigation. In this study, we developed an in vitro reactivation system by re-aerating the virulent laboratory strain of M. tuberculosis that was made dormant employing Wayne's dormancy model, and compared the proteome profiles of dormant and reactivated bacteria using label-free one-dimensional LC/MS/MS analysis. The proteome of dormant bacteria was analyzed at nonreplicating persistent stage 1 (NRP1) and stage 2 (NRP2), whereas that of reactivated bacteria was analyzed at 6 and 24 h post re-aeration. Proteome of normoxially grown bacteria served as the reference. In total, 1871 proteins comprising 47% of the M. tuberculosis proteome were identified, and many of them were observed to be expressed differentially or uniquely during dormancy and reactivation. The number of proteins detected at different stages of dormancy (764 at NRP1, 691 at NRP2) and reactivation (768 at R6 and 983 at R24) was very low compared with that of the control (1663). The number of unique proteins identified during normoxia, NRP1, NRP2, R6, and R24 were 597, 66, 56, 73, and 94, respectively. We analyzed various biological functions during these conditions. Fluctuation in the relative quantities of proteins involved in energy metabolism during dormancy and reactivation was the most significant observation we made in this study. Proteins that are up-regulated or uniquely expressed during reactivation from dormancy offer to be attractive targets for therapeutic intervention to prevent reactivation of latent tuberculosis.
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Affiliation(s)
- Vipin Gopinath
- From the ‡Mycobacterium Research Group, Rajiv Gandhi Centre for Biotechnology, Thycaud P.O., Thiruvananthapuram 695014, India
| | - Sajith Raghunandanan
- From the ‡Mycobacterium Research Group, Rajiv Gandhi Centre for Biotechnology, Thycaud P.O., Thiruvananthapuram 695014, India
| | - Roshna Lawrence Gomez
- From the ‡Mycobacterium Research Group, Rajiv Gandhi Centre for Biotechnology, Thycaud P.O., Thiruvananthapuram 695014, India
| | - Leny Jose
- From the ‡Mycobacterium Research Group, Rajiv Gandhi Centre for Biotechnology, Thycaud P.O., Thiruvananthapuram 695014, India
| | - Arun Surendran
- §Mass Spectrometry and Proteomic Core Facility, Rajiv Gandhi Centre for Biotechnology, Thycaud P.O., Thiruvananthapuram 695014, India
| | - Ranjit Ramachandran
- From the ‡Mycobacterium Research Group, Rajiv Gandhi Centre for Biotechnology, Thycaud P.O., Thiruvananthapuram 695014, India
| | - Akhil Raj Pushparajan
- From the ‡Mycobacterium Research Group, Rajiv Gandhi Centre for Biotechnology, Thycaud P.O., Thiruvananthapuram 695014, India
| | - Sathish Mundayoor
- From the ‡Mycobacterium Research Group, Rajiv Gandhi Centre for Biotechnology, Thycaud P.O., Thiruvananthapuram 695014, India
| | - Abdul Jaleel
- §Mass Spectrometry and Proteomic Core Facility, Rajiv Gandhi Centre for Biotechnology, Thycaud P.O., Thiruvananthapuram 695014, India
| | - Ramakrishnan Ajay Kumar
- From the ‡Mycobacterium Research Group, Rajiv Gandhi Centre for Biotechnology, Thycaud P.O., Thiruvananthapuram 695014, India;
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Sikri K, Kumari P, Tyagi JS, Nandi M, Taneja NK, Batra SD. The pleiotropic transcriptional response of Mycobacterium tuberculosis to vitamin C is robust and overlaps with the bacterial response to multiple intracellular stresses. Microbiology (Reading) 2015; 161:739-53. [DOI: 10.1099/mic.0.000049] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/28/2015] [Indexed: 11/18/2022] Open
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Poyraz Ö, Brunner K, Lohkamp B, Axelsson H, Hammarström LGJ, Schnell R, Schneider G. Crystal structures of the kinase domain of the sulfate-activating complex in Mycobacterium tuberculosis. PLoS One 2015; 10:e0121494. [PMID: 25807013 PMCID: PMC4373884 DOI: 10.1371/journal.pone.0121494] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/01/2015] [Indexed: 11/25/2022] Open
Abstract
In Mycobacterium tuberculosis the sulfate activating complex provides a key branching point in sulfate assimilation. The complex consists of two polypeptide chains, CysD and CysN. CysD is an ATP sulfurylase that, with the energy provided by the GTPase activity of CysN, forms adenosine-5'-phosphosulfate (APS) which can then enter the reductive branch of sulfate assimilation leading to the biosynthesis of cysteine. The CysN polypeptide chain also contains an APS kinase domain (CysC) that phosphorylates APS leading to 3'-phosphoadenosine-5'-phosphosulfate, the sulfate donor in the synthesis of sulfolipids. We have determined the crystal structures of CysC from M. tuberculosis as a binary complex with ADP, and as ternary complexes with ADP and APS and the ATP mimic AMP-PNP and APS, respectively, to resolutions of 1.5 Å, 2.1 Å and 1.7 Å, respectively. CysC shows the typical APS kinase fold, and the structures provide comprehensive views of the catalytic machinery, conserved in this enzyme family. Comparison to the structure of the human homolog show highly conserved APS and ATP binding sites, questioning the feasibility of the design of specific inhibitors of mycobacterial CysC. Residue Cys556 is part of the flexible lid region that closes off the active site upon substrate binding. Mutational analysis revealed this residue as one of the determinants controlling lid closure and hence binding of the nucleotide substrate.
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Affiliation(s)
- Ömer Poyraz
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Katharina Brunner
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Bernhard Lohkamp
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hanna Axelsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory Stockholm, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Lars G. J. Hammarström
- Chemical Biology Consortium Sweden, Science for Life Laboratory Stockholm, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Robert Schnell
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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Erickson AI, Sarsam RD, Fisher AJ. Expression, purification and preliminary crystallographic analysis of Mycobacterium tuberculosis CysQ, a phosphatase involved in sulfur metabolism. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:750-3. [PMID: 24915085 DOI: 10.1107/s2053230x14008619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/16/2014] [Indexed: 11/10/2022]
Abstract
CysQ is part of the sulfur-activation pathway that dephosphorylates 3'-phosphoadenosine 5'-monophosphate (PAP) to regenerate adenosine 5'-monophosphate (AMP) and free phosphate. PAP is the product of sulfate-transfer reactions from sulfotransferases that use the universal sulfate donor 3'-phosphoadenosine 5'-phosphosulfate (PAPS). In some organisms PAP is also the product of PAPS reductases that reduce sulfate from PAPS to sulfite. CysQ from Mycobacterium tuberculosis, which plays an important role in the biosynthesis of sulfated glycoconjugates, was successfully purified and crystallized in 24% PEG 1500, 20% glycerol. X-ray diffraction data were collected to 1.7 Å resolution using a synchrotron-radiation source. Crystals grew in the orthorhombic space group P2₁2₁2₁, with unit-cell parameters a=40.3, b=57.9, c=101.7 Å and with one monomer per asymmetric unit.
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Affiliation(s)
- Anna I Erickson
- Graduate Program in Biochemistry, Molecular, Cellular and Developmental Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Reta D Sarsam
- Department of Molecular and Cellular Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Andrew J Fisher
- Graduate Program in Biochemistry, Molecular, Cellular and Developmental Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
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Krisko A, Copic T, Gabaldón T, Lehner B, Supek F. Inferring gene function from evolutionary change in signatures of translation efficiency. Genome Biol 2014; 15:R44. [PMID: 24580753 PMCID: PMC4054840 DOI: 10.1186/gb-2014-15-3-r44] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 03/03/2014] [Indexed: 11/13/2022] Open
Abstract
Background The genetic code is redundant, meaning that most amino acids can be encoded by more than one codon. Highly expressed genes tend to use optimal codons to increase the accuracy and speed of translation. Thus, codon usage biases provide a signature of the relative expression levels of genes, which can, uniquely, be quantified across the domains of life. Results Here we describe a general statistical framework to exploit this phenomenon and to systematically associate genes with environments and phenotypic traits through changes in codon adaptation. By inferring evolutionary signatures of translation efficiency in 911 bacterial and archaeal genomes while controlling for confounding effects of phylogeny and inter-correlated phenotypes, we linked 187 gene families to 24 diverse phenotypic traits. A series of experiments in Escherichia coli revealed that 13 of 15, 19 of 23, and 3 of 6 gene families with changes in codon adaptation in aerotolerant, thermophilic, or halophilic microbes. Respectively, confer specific resistance to, respectively, hydrogen peroxide, heat, and high salinity. Further, we demonstrate experimentally that changes in codon optimality alone are sufficient to enhance stress resistance. Finally, we present evidence that multiple genes with altered codon optimality in aerobes confer oxidative stress resistance by controlling the levels of iron and NAD(P)H. Conclusions Taken together, these results provide experimental evidence for a widespread connection between changes in translation efficiency and phenotypic adaptation. As the number of sequenced genomes increases, this novel genomic context method for linking genes to phenotypes based on sequence alone will become increasingly useful.
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Baharoglu Z, Babosan A, Mazel D. Identification of genes involved in low aminoglycoside-induced SOS response in Vibrio cholerae: a role for transcription stalling and Mfd helicase. Nucleic Acids Res 2013; 42:2366-79. [PMID: 24319148 PMCID: PMC3936754 DOI: 10.1093/nar/gkt1259] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Sub-inhibitory concentrations (sub-MIC) of antibiotics play a very important role in selection and development of resistances. Unlike Escherichia coli, Vibrio cholerae induces its SOS response in presence of sub-MIC aminoglycosides. A role for oxidized guanine residues was observed, but the mechanisms of this induction remained unclear. To select for V. cholerae mutants that do not induce low aminoglycoside-mediated SOS induction, we developed a genetic screen that renders induction of SOS lethal. We identified genes involved in this pathway using two strategies, inactivation by transposition and gene overexpression. Interestingly, we obtained mutants inactivated for the expression of proteins known to destabilize the RNA polymerase complex. Reconstruction of the corresponding mutants confirmed their specific involvement in induction of SOS by low aminoglycoside concentrations. We propose that DNA lesions formed on aminoglycoside treatment are repaired through the formation of single-stranded DNA intermediates, inducing SOS. Inactivation of functions that dislodge RNA polymerase leads to prolonged stalling on these lesions, which hampers SOS induction and repair and reduces viability under antibiotic stress. The importance of these mechanisms is illustrated by a reduction of aminoglycoside sub-MIC. Our results point to a central role for transcription blocking at DNA lesions in SOS induction, so far underestimated.
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Affiliation(s)
- Zeynep Baharoglu
- Département Génomes et Génétique, Unité Plasticité du Génome Bactérien, Institut Pasteur, 75015 Paris, France and Centre National de la Recherche Scientifique, CNRS, UMR3525 Paris, France
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Visualization of imbalances in sulfur assimilation and synthesis of sulfur-containing amino acids at the single-cell level. Appl Environ Microbiol 2013; 79:6730-6. [PMID: 23995919 DOI: 10.1128/aem.01804-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe genetically encoded sensors which transmit elevated cytosolic concentrations of O-acetyl serine (OAS) and O-acetyl homoserine (OAH)-intermediates of l-cysteine and l-methionine synthesis-into an optical output. The sensor pSenOAS3 elicits 7.5-fold-increased fluorescence in cultures of a Corynebacterium glutamicum strain that excrete l-cysteine. Determination of the cytosolic OAS concentration revealed an increase to 0.13 mM, whereas the concentration in the reference strain was below the detection limit, indicating that incorporation of assimilatory sulfur is limited in the strain studied. In another strain, overexpression of metX encoding homoserine acetyltransferase resulted in an 8-fold increase in culture fluorescence at a cytosolic OAH concentration of 0.76 mM. We also assayed for consequences of extracellular sulfur supply and observed a graded fluorescence increase at decreasing sulfur concentrations below 400 μM. Overall, this demonstrates the usefulness of the sensors for monitoring intracellular sulfur availability. The sensors also enable monitoring at the single-cell level, and since related and close homologs of the transcription factor used in the constructed sensors are widespread among bacteria, this technology offers a new possibility of assaying in vivo for sulfur limitation and of doing this at the single-cell level.
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Paritala H, Carroll KS. New targets and inhibitors of mycobacterial sulfur metabolism. Infect Disord Drug Targets 2013; 13:85-115. [PMID: 23808874 PMCID: PMC4332622 DOI: 10.2174/18715265113139990022] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 05/08/2013] [Indexed: 11/22/2022]
Abstract
The identification of new antibacterial targets is urgently needed to address multidrug resistant and latent tuberculosis infection. Sulfur metabolic pathways are essential for survival and the expression of virulence in many pathogenic bacteria, including Mycobacterium tuberculosis. In addition, microbial sulfur metabolic pathways are largely absent in humans and therefore, represent unique targets for therapeutic intervention. In this review, we summarize our current understanding of the enzymes associated with the production of sulfated and reduced sulfur-containing metabolites in Mycobacteria. Small molecule inhibitors of these catalysts represent valuable chemical tools that can be used to investigate the role of sulfur metabolism throughout the Mycobacterial lifecycle and may also represent new leads for drug development. In this light, we also summarize recent progress made in the development of inhibitors of sulfur metabolism enzymes.
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Affiliation(s)
| | - Kate S. Carroll
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, 33458, USA
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Pinto R, Leotta L, Shanahan ER, West NP, Leyh TS, Britton W, Triccas JA. Host cell-induced components of the sulfate assimilation pathway are major protective antigens of Mycobacterium tuberculosis. J Infect Dis 2012; 207:778-85. [PMID: 23225904 DOI: 10.1093/infdis/jis751] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
New therapies to control tuberculosis are urgently required because of the inability of the only available vaccine, BCG, to adequately protect against tuberculosis. Here we demonstrate that proteins of the Mycobacterium tuberculosis sulfate-assimilation pathway (SAP) represent major immunogenic targets of the bacillus, as defined by strong T-cell recognition by both mice and humans infected with M. tuberculosis. SAP proteins displayed increased expression when M. tuberculosis was resident within host cells, which may account in part for their ability to stimulate anti-M. tuberculosis host immunity. Vaccination with the first enzyme in this pathway, adenosine-5'-triphosphate sulfurylase, conferred significant protection against murine tuberculosis and boosted BCG-induced protective immunity in the lung. Therefore, we have identified SAP components as a new family of M. tuberculosis antigens, and we have demonstrated that these components are promising candidate for inclusion in new vaccines to control tuberculosis in humans.
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Affiliation(s)
- Rachel Pinto
- Mycobacterial Research Program, Centenary Institute, Newtown, Australia
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Fischer M, Schmidt C, Falke D, Sawers RG. Terminal reduction reactions of nitrate and sulfate assimilation in Streptomyces coelicolor A3(2): identification of genes encoding nitrite and sulfite reductases. Res Microbiol 2012; 163:340-8. [DOI: 10.1016/j.resmic.2012.05.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/27/2012] [Accepted: 04/19/2012] [Indexed: 11/15/2022]
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Zheng F, Xie J. The interaction topology of Mycobacterium tuberculosis genes response to capreomycin and novel clues for more drug targets. J Cell Biochem 2012; 112:2716-20. [PMID: 21678479 DOI: 10.1002/jcb.23232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The resurgence of tuberculosis (TB) and emergence of multidrug-resistant TB (MDR-TB) are significant obstacles to stop TB treatment. Capreomycin (CPM) is regarded as an ideal second-line treatment for TB as well as for MDR-TB. However, the inexorable emergence of capreomycin resistant TB cases accentuates the urgent need for more detailed characterization of CPM targets. Most of these are single gene mutation, such as those involved in the complex formation of ribosomal 30S initiation, inhibit protein synthesis, affect 50S ribosomal protein L10, control transcription and translation of operon rpIJL-rpoBC. A new paradigm integrating gene, small metabolites, protein and underlying signaling pathway to shed light on the physiology, pathogenesis, and network of pathogen response is emerging. This model holds great promise to unravel the intricacy of drug action. However, to our knowledge, no such work regarding Mycobacterium tuberculosis response to capreomycin exposure was ever reported. We employed the data mining to construct an interaction topology of M. tuberculosis genes response to capreomycin. Most valuable genes were summarized for further experimental validation based on this topology. Dampening the virulence factors and respiratory of M. tuberculosis might be the new targets of CPM beyond Rv1364c, pe_pgrs38, pe_pgrs51 which are the salient nodes of the network and represent most promising new capreomycin targets meriting further exploration. This work will facilitate further investigation of capreomycin targets against M. tuberculosis and be conducive to novel TB drug discovery.
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Affiliation(s)
- Fei Zheng
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three GorgesArea, School of Life Sciences, Southwest University, Chongqing 400715, China
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Global transcriptome analysis of the E. coli O157 response to Agrimonia pilosa extract. Mol Cell Toxicol 2011. [DOI: 10.1007/s13273-011-0036-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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48
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Kataria J, Rukmangadachar LA, Hariprasad G, O J, Tripathi M, Srinivasan A. Two dimensional difference gel electrophoresis analysis of cerebrospinal fluid in tuberculous meningitis patients. J Proteomics 2011; 74:2194-203. [DOI: 10.1016/j.jprot.2011.06.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 06/01/2011] [Accepted: 06/18/2011] [Indexed: 12/14/2022]
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Abstract
Mycobacterium tuberculosis (Mtb) has evolved into a highly successful human pathogen. It deftly subverts the bactericidal mechanisms of alveolar macrophages, ultimately inducing granuloma formation and establishing long-term residence in the host. These hallmarks of Mtb infection are facilitated by the metabolic adaptation of the pathogen to its surrounding environment and the biosynthesis of molecules that mediate its interactions with host immune cells. The sulfate assimilation pathway of Mtb produces a number of sulfur-containing metabolites with important contributions to pathogenesis and survival. This pathway is regulated by diverse environmental cues and regulatory proteins that mediate sulfur transactions in the cell. Here, we discuss the transcriptional and biochemical mechanisms of sulfur metabolism regulation in Mtb and potential small molecule regulators of the sulfate assimilation pathway that are collectively poised to aid this intracellular pathogen in its expert manipulation of the host. From this global analysis, we have identified a subset of sulfur-metabolizing enzymes that are sensitive to multiple regulatory cues and may be strong candidates for therapeutic intervention.
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Affiliation(s)
- Stavroula K. Hatzios
- Department of Chemistry, University of California, Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, United States of America
| | - Carolyn R. Bertozzi
- Department of Chemistry, University of California, Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, United States of America
- * E-mail:
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Voskuil MI, Bartek IL, Visconti K, Schoolnik GK. The response of mycobacterium tuberculosis to reactive oxygen and nitrogen species. Front Microbiol 2011; 2:105. [PMID: 21734908 PMCID: PMC3119406 DOI: 10.3389/fmicb.2011.00105] [Citation(s) in RCA: 216] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 04/27/2011] [Indexed: 02/06/2023] Open
Abstract
The bacteriostatic and bactericidal effects and the transcriptional response of Mycobacterium tuberculosis to representative oxidative and nitrosative stresses were investigated by growth and survival studies and whole genome expression analysis. The M. tuberculosis reaction to a range of hydrogen peroxide (H2O2) concentrations fell into three distinct categories: (1) low level exposure resulted in induction of a few highly sensitive H2O2-responsive genes, (2) intermediate exposure resulted in massive transcriptional changes without an effect on growth or survival, and (3) high exposure resulted in a muted transcriptional response and eventual death. M. tuberculosis appears highly resistant to DNA damage-dependent, mode-one killing caused by low millimolar levels of H2O2 and only succumbs to overwhelming levels of oxidative stress observed in mode-two killing. Nitric oxide (NO) exposure initiated much the same transcriptional response as H2O2. However, unlike H2O2 exposure, NO exposure induced dormancy-related genes and caused dose-dependent bacteriostatic activity without killing. Included in the large shared response to H2O2 and NO was the induction of genes encoding iron–sulfur cluster repair functions including iron acquisition. Stress regulons controlled by IdeR, Sigma H, Sigma E, and FurA comprised a large portion of the response to both stresses. Expression of several oxidative stress defense genes was constitutive, or increased moderately from an already elevated constitutive level, suggesting that bacilli are continually primed for oxidative stress defense.
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Affiliation(s)
- Martin I Voskuil
- Department of Microbiology, School of Medicine, University of Colorado Denver Aurora, CO, USA
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