1
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Brenner EP, Sreevatsan S. Global-scale GWAS associates a subset of SNPs with animal-adapted variants in M. tuberculosis complex. BMC Med Genomics 2023; 16:260. [PMID: 37875894 PMCID: PMC10598944 DOI: 10.1186/s12920-023-01695-5] [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: 05/10/2023] [Accepted: 10/11/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND While Mycobacterium tuberculosis complex (MTBC) variants are clonal, variant tuberculosis is a human-adapted pathogen, and variant bovis infects many hosts. Despite nucleotide identity between MTBC variants exceeding 99.95%, it remains unclear what drives these differences. Markers of adaptation into variants were sought by bacterial genome-wide association study of single nucleotide polymorphisms extracted from 6,362 MTBC members from varied hosts and countries. RESULTS The search identified 120 genetic loci associated with MTBC variant classification and certain hosts. In many cases, these changes are uniformly fixed in certain variants while absent in others in this dataset, providing good discriminatory power in distinguishing variants by polymorphisms. Multiple changes were seen in genes for cholesterol and fatty acid metabolism, pathways previously proposed to be important for host adaptation, including Mce4F (part of the fundamental cholesterol intake Mce4 pathway), 4 FadD and FadE genes (playing roles in cholesterol and fatty acid utilization), and other targets like Rv3548c and PTPB, genes shown essential for growth on cholesterol by transposon studies. CONCLUSIONS These findings provide a robust set of genetic loci associated with the split of variant bovis and variant tuberculosis, and suggest that adaptation to new hosts could involve adjustments in uptake and catabolism of cholesterol and fatty acids, like the proposed specialization to different populations in MTB lineages by alterations to host lipid composition. Future studies are required to elucidate how the associations between cholesterol profiles and pathogen utilization differences between hosts and MTBC variants, as well as the investigation of uncharacterized genes discovered in this study. This information will likely provide an understanding on the diversification of MBO away from humans and specialization towards a broad host range.
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Affiliation(s)
- Evan P Brenner
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, 784 Wilson Road, East Lansing, MI, 48824, USA
| | - Srinand Sreevatsan
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, 784 Wilson Road, East Lansing, MI, 48824, USA.
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2
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Wu M, Lai CY, Wang Y, Yuan Z, Guo J. Microbial nitrate reduction in propane- or butane-based membrane biofilm reactors under oxygen-limiting conditions. WATER RESEARCH 2023; 235:119887. [PMID: 36947926 DOI: 10.1016/j.watres.2023.119887] [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: 01/14/2023] [Revised: 03/02/2023] [Accepted: 03/15/2023] [Indexed: 06/18/2023]
Abstract
Nitrate contamination has been commonly detected in water environments and poses serious hazards to human health. Previously methane was proposed as a promising electron donor to remove nitrate from contaminated water. Compared with pure methane, natural gas, which not only contains methane but also other short chain gaseous alkanes (SCGAs), is less expensive and more widely available, representing a more attractive electron source for removing oxidized contaminants. However, it remains unknown if these SCGAs can be utilized as electron donors for nitrate reduction. Here, two lab-scale membrane biofilm reactors (MBfRs) separately supplied with propane and butane were operated under oxygen-limiting conditions to test its feasibility of microbial nitrate reduction. Long-term performance suggested nitrate could be continuously removed at a rate of ∼40-50 mg N/L/d using propane/butane as electron donors. In the absence of propane/butane, nitrate removal rates significantly decreased both in the long-term operation (∼2-10 and ∼4-9 mg N/L/d for propane- and butane-based MBfRs, respectively) and batch tests, indicating nitrate bio-reduction was driven by propane/butane. The consumption rates of nitrate and propane/butane dramatically decreased under anaerobic conditions, but recovered after resupplying limited oxygen, suggesting oxygen was an essential triggering factor for propane/butane-based nitrate reduction. High-throughput sequencing targeting 16S rRNA, bmoX and narG genes indicated Mycobacterium/Rhodococcus/Thauera were the potential microorganisms oxidizing propane/butane, while various denitrifiers (e.g. Dechloromonas, Denitratisoma, Zoogloea, Acidovorax, Variovorax, Pseudogulbenkiania and Rhodanobacter) might perform nitrate reduction in the biofilms. Our findings provide evidence to link SCGA oxidation with nitrate reduction under oxygen-limiting conditions and may ultimately facilitate the design of cost-effective techniques for ex-situ groundwater remediation using natural gas.
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Affiliation(s)
- Mengxiong Wu
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Queensland, Australia
| | - Chun-Yu Lai
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Queensland, Australia
| | - Yulu Wang
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Queensland, Australia
| | - Zhiguo Yuan
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Queensland, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Queensland, Australia.
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3
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Zhang Y, Li D, Yan Q, Xu P, Chen W, Xin H, Wu D, Zhou M, Xu Y, Zhang A, Wei W, Jiang Z. Genome-wide analysis reveals the emergence of multidrug resistant Stenotrophomonas acidaminiphila strain SINDOREI isolated from a patient with sepsis. Front Microbiol 2022; 13:989259. [PMID: 36212813 PMCID: PMC9537462 DOI: 10.3389/fmicb.2022.989259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
Stenotrophomonas acidaminiphila, the most recent reported species in genus Stenotrophomonas, is a relatively rare bacteria and is an aerobic, glucose non-fermentative, Gram-negative bacterium. However, little information of S. acidaminiphila is known to cause human infections. In this research, we firstly reported a multidrug-resistant strain S. acidaminiphila SINDOREI isolated from the blood of a patient with sepsis, who was dead of infection eventually. The whole genome of strain SINDOREI was sequenced, and genome comparisons were performed among six closely related S. acidaminiphila strains. The core genes (2,506 genes) and strain-specific genes were identified, respectively, to know about the strain-level diversity in six S. acidaminiphila stains. The presence of a unique gene (narG) and essential genes involved in biofilm formation in strain SINDOREI are important for the pathogenesis of infections. Strain SINDOREI was resistant to trimethoprim/sulfamethoxazole, ciprofloxacin, ofloxacin, cefepime, ceftazidime, and aztreonam. Several common and specific antibiotic resistance genes were identified in strain SINDOREI. The presence of two sul genes and exclusive determinants GES-1, aadA3, qacL, and cmlA5 is responsible for the resistance to multidrug. The virulence factors and resistance determinants can show the relationship between the phenotype and genotype and afford potential therapeutic strategies for infections.
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Affiliation(s)
- Ying Zhang
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Changsha, China
- Hunan Hematology Oncology Clinical Medical Research Center, Changsha, China
- National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Danhua Li
- Departmant of Scientific Affairs, Hugobiotech Co. Ltd., Beijing, China
| | - Qun Yan
- Department of Laboratory Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Ping Xu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Wei Chen
- Department of Gastroenterology, Changsha Central Hospital, Changsha, China
| | - Hongya Xin
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Changsha, China
- Hunan Hematology Oncology Clinical Medical Research Center, Changsha, China
- National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Dengshu Wu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Changsha, China
- Hunan Hematology Oncology Clinical Medical Research Center, Changsha, China
- National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Mingxiang Zhou
- Department of Laboratory Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Yajing Xu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Changsha, China
- Hunan Hematology Oncology Clinical Medical Research Center, Changsha, China
- National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Ao Zhang
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Changsha, China
- Hunan Hematology Oncology Clinical Medical Research Center, Changsha, China
- National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Wenjia Wei
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Changsha, China
- Hunan Hematology Oncology Clinical Medical Research Center, Changsha, China
- National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhiping Jiang
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Changsha, China
- Hunan Hematology Oncology Clinical Medical Research Center, Changsha, China
- National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Zhiping Jiang,
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4
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Ncube P, Bagheri B, Goosen WJ, Miller MA, Sampson SL. Evidence, Challenges, and Knowledge Gaps Regarding Latent Tuberculosis in Animals. Microorganisms 2022; 10:1845. [PMID: 36144447 PMCID: PMC9503773 DOI: 10.3390/microorganisms10091845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 01/30/2023] Open
Abstract
Mycobacterium bovis and other Mycobacterium tuberculosis complex (MTBC) pathogens that cause domestic animal and wildlife tuberculosis have received considerably less attention than M. tuberculosis, the primary cause of human tuberculosis (TB). Human TB studies have shown that different stages of infection can exist, driven by host-pathogen interactions. This results in the emergence of heterogeneous subpopulations of mycobacteria in different phenotypic states, which range from actively replicating (AR) cells to viable but slowly or non-replicating (VBNR), viable but non-culturable (VBNC), and dormant mycobacteria. The VBNR, VBNC, and dormant subpopulations are believed to underlie latent tuberculosis (LTB) in humans; however, it is unclear if a similar phenomenon could be happening in animals. This review discusses the evidence, challenges, and knowledge gaps regarding LTB in animals, and possible host-pathogen differences in the MTBC strains M. tuberculosis and M. bovis during infection. We further consider models that might be adapted from human TB research to investigate how the different phenotypic states of bacteria could influence TB stages in animals. In addition, we explore potential host biomarkers and mycobacterial changes in the DosR regulon, transcriptional sigma factors, and resuscitation-promoting factors that may influence the development of LTB.
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Affiliation(s)
| | | | | | | | - Samantha Leigh Sampson
- DSI/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Department of Biomedical Sciences, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie Van Zijl Dr, Parow, Cape Town 7505, South Africa
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5
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Romano GE, Silva-Pereira TT, de Melo FM, Sisco MC, Banari AC, Zimpel CK, Soler-Camargo NC, Guimarães AMDS. Unraveling the metabolism of Mycobacterium caprae using comparative genomics. Tuberculosis (Edinb) 2022; 136:102254. [PMID: 36126496 DOI: 10.1016/j.tube.2022.102254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 08/01/2022] [Accepted: 08/25/2022] [Indexed: 11/19/2022]
Abstract
In our laboratory, Mycobacterium caprae has poor growth in standard medium (SM) 7H9-OADC supplemented with pyruvate and Tween-80. Our objectives were to identify mutations affecting M. caprae metabolism and use this information to design a culture medium to improve its growth. We selected 77 M. caprae genomes and sequenced M. caprae NLA000201913 used in our experiments. Mutations present in >95% of the strains compared to Mycobacterium tuberculosis H37Rv were analyzed in silico for their deleterious effects on proteins of metabolic pathways. Apart from the known defect in the pyruvate kinase, M. caprae has important lesions in enzymes of the TCA cycle, methylmalonyl cycle, B12 metabolism, and electron-transport chain. We provide evidence of enzymatic redundancy elimination and epistatic mutations, and possible production of toxic metabolites hindering M. caprae growth in vitro. A newly designed SM supplemented with l-glutamate allowed faster growth and increased final microbial mass of M. caprae. However, possible accumulation of metabolic waste-products and/or nutritional limitations halted M. caprae growth prior to a M. tuberculosis-like stationary phase. Our findings suggest that M. caprae relies on GABA and/or glyoxylate shunts for in vitro growth in routine media. The newly developed medium will improve experiments with this bacterium by allowing faster growth in vitro.
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Affiliation(s)
- Giovanni Emiddio Romano
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil.
| | - Taiana Tainá Silva-Pereira
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil.
| | - Filipe Menegatti de Melo
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil.
| | - Maria Carolina Sisco
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil.
| | - Alexandre Campos Banari
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil; Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, 87 Prof Dr Orlando Marques de Paiva Avenue, São Paulo, SP, 05508-270, Brazil.
| | - Cristina Kraemer Zimpel
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil; Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, 87 Prof Dr Orlando Marques de Paiva Avenue, São Paulo, SP, 05508-270, Brazil.
| | - Naila Cristina Soler-Camargo
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil; Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, 87 Prof Dr Orlando Marques de Paiva Avenue, São Paulo, SP, 05508-270, Brazil.
| | - Ana Marcia de Sá Guimarães
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil; Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University. 625 Harrison Street, West Lafayette, IN, 47907, USA.
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6
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Huang S, Sima M, Long Y, Messenger C, Jaffé PR. Anaerobic degradation of perfluorooctanoic acid (PFOA) in biosolids by Acidimicrobium sp. strain A6. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127699. [PMID: 34799154 DOI: 10.1016/j.jhazmat.2021.127699] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/19/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic incubations were performed with biosolids obtained from an industrial wastewater treatment plant (WWTP) that contained perfluorooctanoic acid (PFOA), and with per- and polyfluoroalkyl substances- (PFAS) free, laboratory-generated, biosolids that were spiked with PFOA. Biosolid slurries were incubated for 150 days as is, after augmenting with either Acidimicrobium sp. Strain A6 or ferrihydrite, or with both, Acidimicrobium sp. Strain A6 and ferrihydrite. Autoclaved controls were run in parallel. Only the biosolids augmented with both, Acidimicrobium sp. Strain A6 and ferrihydrite showed a decrease in the PFOA concentration, in excess of 50% (total, dissolved, and solid associated). Higher concentrations of PFOA in the biosolids spiked with PFOA and no previous PFAS exposure allowed to track the production of fluoride to verify PFOA defluorination. The buildup of fluoride over the incubation time was observed in these biosolid incubations spiked with PFOA. A significant increase in the concentration of perfluoroheptanoic acid (PFHpA) over the incubations of the filter cake samples from the industrial WWTP was observed, indicating the presence of a non-identified precursor in these biosolids. Results show that anaerobic incubation of PFAS contaminated biosolids, after augmentation with Fe(III) and Acidimicrobium sp. Strain A6 can result in PFAS defluorination.
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Affiliation(s)
- Shan Huang
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Matthew Sima
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Ying Long
- The Chemours Company, Chemours Discovery Hub, 201 Discovery Blvd, Newark, DE 19713, USA
| | - Courtney Messenger
- The Chemours Company, Chemours Discovery Hub, 201 Discovery Blvd, Newark, DE 19713, USA
| | - Peter R Jaffé
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ 08544, USA.
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7
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Gibson AJ, Passmore IJ, Faulkner V, Xia D, Nobeli I, Stiens J, Willcocks S, Clark TG, Sobkowiak B, Werling D, Villarreal-Ramos B, Wren BW, Kendall SL. Probing Differences in Gene Essentiality Between the Human and Animal Adapted Lineages of the Mycobacterium tuberculosis Complex Using TnSeq. Front Vet Sci 2021; 8:760717. [PMID: 35004921 PMCID: PMC8739905 DOI: 10.3389/fvets.2021.760717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/29/2021] [Indexed: 12/11/2022] Open
Abstract
Members of the Mycobacterium tuberculosis complex (MTBC) show distinct host adaptations, preferences and phenotypes despite being >99% identical at the nucleic acid level. Previous studies have explored gene expression changes between the members, however few studies have probed differences in gene essentiality. To better understand the functional impacts of the nucleic acid differences between Mycobacterium bovis and Mycobacterium tuberculosis, we used the Mycomar T7 phagemid delivery system to generate whole genome transposon libraries in laboratory strains of both species and compared the essentiality status of genes during growth under identical in vitro conditions. Libraries contained insertions in 54% of possible TA sites in M. bovis and 40% of those present in M. tuberculosis, achieving similar saturation levels to those previously reported for the MTBC. The distributions of essentiality across the functional categories were similar in both species. 527 genes were found to be essential in M. bovis whereas 477 genes were essential in M. tuberculosis and 370 essential genes were common in both species. CRISPRi was successfully utilised in both species to determine the impacts of silencing genes including wag31, a gene involved in peptidoglycan synthesis and Rv2182c/Mb2204c, a gene involved in glycerophospholipid metabolism. We observed species specific differences in the response to gene silencing, with the inhibition of expression of Mb2204c in M. bovis showing significantly less growth impact than silencing its orthologue (Rv2182c) in M. tuberculosis. Given that glycerophospholipid metabolism is a validated pathway for antimicrobials, our observations suggest that target vulnerability in the animal adapted lineages cannot be assumed to be the same as the human counterpart. This is of relevance for zoonotic tuberculosis as it implies that the development of antimicrobials targeting the human adapted lineage might not necessarily be effective against the animal adapted lineage. The generation of a transposon library and the first reported utilisation of CRISPRi in M. bovis will enable the use of these tools to further probe the genetic basis of survival under disease relevant conditions.
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Affiliation(s)
- Amanda J. Gibson
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Ian J. Passmore
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Valwynne Faulkner
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Dong Xia
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Irene Nobeli
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Jennifer Stiens
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Sam Willcocks
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Taane G. Clark
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ben Sobkowiak
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Dirk Werling
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | | | - Brendan W. Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sharon L. Kendall
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom,*Correspondence: Sharon L. Kendall
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8
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Hamidieh F, Farnia P, Nowroozi J, Farnia P, Velayati AA. An Overview of Genetic Information of Latent Mycobacterium tuberculosis. Tuberc Respir Dis (Seoul) 2020; 84:1-12. [PMID: 33121230 PMCID: PMC7801807 DOI: 10.4046/trd.2020.0116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/30/2020] [Indexed: 11/24/2022] Open
Abstract
Mycobacterium tuberculosis has infected more than two billion individuals worldwide, of whom 5%–10% have clinically active disease and 90%–95% remain in the latent stage with a reservoir of viable bacteria in the macrophages for extended periods of time. The tubercle bacilli at this stage are usually called dormant, non-viable, and/or non-culturable microorganisms. The patients with latent bacilli will not have clinical pictures and are not infectious. The infections in about 2%–23% of the patients with latent status become reactivated for various reasons such as cancer, human immunodeficiency virus infection, diabetes, and/or aging. Many studies have examined the mechanisms involved in the latent state of Mycobacterium and showed that latency modified the expression of many genes. Therefore, several mechanisms will change in this bacterium. Hence, this study aimed to briefly examine the genes involved in the latent state as well as the changes that are caused by Mycobacterium tuberculosis. The study also evaluated the relationship between the functions of these genes.
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Affiliation(s)
- Faezeh Hamidieh
- Departement of Microbiology, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Parissa Farnia
- Mycobacteriology Research (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jamileh Nowroozi
- Departement of Microbiology, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Poopak Farnia
- Mycobacteriology Research (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Biotechnology, School of Advanced Technology in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Akbar Velayati
- Mycobacteriology Research (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
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9
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Campos PC, Gomes MTR, Marinho FAV, Guimarães ES, de Moura Lodi Cruz MGF, Oliveira SC. Brucella abortus nitric oxide metabolite regulates inflammasome activation and IL-1β secretion in murine macrophages. Eur J Immunol 2019; 49:1023-1037. [PMID: 30919410 DOI: 10.1002/eji.201848016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/20/2019] [Accepted: 03/25/2019] [Indexed: 11/07/2022]
Abstract
NLRP3 inflammasome is a protein complex crucial to caspase-1 activation and IL-1β and IL-18 maturation. This receptor participates in innate immune responses to different pathogens, including the bacteria of genus Brucella. Our group recently demonstrated that Brucella abortus-induced IL-1β secretion involves NLRP3 inflammasome and it is partially dependent on mitochondrial ROS production. However, other factors could be involved, such as P2X7-dependent potassium efflux, membrane destabilization, and cathepsin release. Moreover, there is increasing evidence that nitric oxide acts as a modulator of NLRP3 inflammasome. The aim of this study was to unravel the mechanism of NLRP3 inflammasome activation induced by B. abortus, as well as the involvement of bacterial nitric oxide (NO) as a modulator of this inflammasome pathway. We demonstrated that NO produced by B. abortus can be used by the bacteria to modulate IL-1β secretion in infected murine macrophages. Additionally, our results suggest that B. abortus-induced IL-1β secretion depends on a P2X7-independent potassium efflux, lysosomal acidification, cathepsin release, mechanisms clearly associated to NLRP3 inflammasome. In summary, our results help to elucidate the molecular mechanisms of NLRP3 activation and regulation during an intracellular bacterial infection.
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Affiliation(s)
- Priscila Carneiro Campos
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marco Túlio Ribeiro Gomes
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fábio Antônio Vitarelli Marinho
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Erika Sousa Guimarães
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Sergio Costa Oliveira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais (INCT-DT), Conselho Nacional de Desenvolvimento Científico e Tecnológico, Ministério de Ciência, Tecnologia e Inovação, Salvador, Bahia, Brazil
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Mycobacterium tuberculosis Complex Members Adapted to Wild and Domestic Animals. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1019:135-154. [PMID: 29116633 DOI: 10.1007/978-3-319-64371-7_7] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Mycobacterium tuberculosis complex (MTBC) is composed of several highly genetically related species that can be broadly classified into those that are human-host adapted and those that possess the ability to propagate and transmit in a variety of wild and domesticated animals. Since the initial description of the bovine tubercle bacillus, now known as Mycobacterium bovis, by Theobald Smith in the late 1800's, isolates originating from a wide range of animal hosts have been identified and characterized as M. microti, M. pinnipedii, the Dassie bacillus, M. mungi, M. caprae, M. orygis and M. suricattae. This chapter outlines the events resulting in the identification of each of these animal-adapted species, their close genetic relationships, and how genome-based phylogenetic analyses of species-specific variation amongst MTBC members is beginning to unravel the events that resulted in the evolution of the MTBC and the observed host tropism between the human- and animal-adapted member species.
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Malone KM, Rue-Albrecht K, Magee DA, Conlon K, Schubert OT, Nalpas NC, Browne JA, Smyth A, Gormley E, Aebersold R, MacHugh DE, Gordon SV. Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli. Microb Genom 2018; 4:e000163. [PMID: 29557774 PMCID: PMC5885015 DOI: 10.1099/mgen.0.000163] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 02/26/2018] [Indexed: 01/30/2023] Open
Abstract
Members of the Mycobacterium tuberculosis complex (MTBC) are the causative agents of tuberculosis in a range of mammals, including humans. A key feature of MTBC pathogens is their high degree of genetic identity yet distinct host tropism. Notably, while Mycobacterium bovis is highly virulent and pathogenic for cattle, the human pathogen M. tuberculosis is attenuated in cattle. Previous research also suggests that host preference amongst MTBC members has a basis in host innate immune responses. To explore MTBC host tropism, we present in-depth profiling of the MTBC reference strains M. bovis AF2122/97 and M. tuberculosis H37Rv at both the global transcriptional and the translational level via RNA-sequencing and SWATH MS. Furthermore, a bovine alveolar macrophage infection time course model was used to investigate the shared and divergent host transcriptomic response to infection with M. tuberculosis H37Rv or M. bovis AF2122/97. Significant differential expression of virulence-associated pathways between the two bacilli was revealed, including the ESX-1 secretion system. A divergent transcriptional response was observed between M. tuberculosis H37Rv and M. bovis AF2122/97 infection of bovine alveolar macrophages, in particular cytosolic DNA-sensing pathways at 48 h post-infection, and highlights a distinct engagement of M. bovis with the bovine innate immune system. The work presented here therefore provides a basis for the identification of host innate immune mechanisms subverted by virulent host-adapted mycobacteria to promote their survival during the early stages of infection.
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Affiliation(s)
- Kerri M. Malone
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Present address: European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kévin Rue-Albrecht
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
- Present address: Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Headington, Oxford OX3 7FY, UK
| | - David A. Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kevin Conlon
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Olga T. Schubert
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093, Switzerland
- Present address: Department of Human Genetics, University of California, Los Angeles, USA
| | - Nicolas C. Nalpas
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
- Present address: Quantitative Proteomics and Proteome Centre Tübingen, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - John A. Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Alicia Smyth
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Eamonn Gormley
- Tuberculosis Diagnostics and Immunology Research Centre, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093, Switzerland
| | - David E. MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Stephen V. Gordon
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
- UCD School of Medicine, University College Dublin, Dublin 4, Ireland
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
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12
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Hards K, Cook GM. Targeting bacterial energetics to produce new antimicrobials. Drug Resist Updat 2018; 36:1-12. [DOI: 10.1016/j.drup.2017.11.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/25/2017] [Accepted: 10/31/2017] [Indexed: 12/31/2022]
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13
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Bigi MM, Blanco FC, Araújo FR, Thacker TC, Zumárraga MJ, Cataldi AA, Soria MA, Bigi F. Polymorphisms of 20 regulatory proteins between Mycobacterium tuberculosis and Mycobacterium bovis. Microbiol Immunol 2017; 60:552-60. [PMID: 27427512 DOI: 10.1111/1348-0421.12402] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/21/2016] [Accepted: 07/13/2016] [Indexed: 12/21/2022]
Abstract
Mycobacterium tuberculosis and Mycobacterium bovis are responsible for tuberculosis in humans and animals, respectively. Both species are closely related and belong to the Mycobacterium tuberculosis complex (MTC). M. tuberculosis is the most ancient species from which M. bovis and other members of the MTC evolved. The genome of M. bovis is over >99.95% identical to that of M. tuberculosis but with seven deletions ranging in size from 1 to 12.7 kb. In addition, 1200 single nucleotide mutations in coding regions distinguish M. bovis from M. tuberculosis. In the present study, we assessed 75 M. tuberculosis genomes and 23 M. bovis genomes to identify non-synonymous mutations in 202 coding sequences of regulatory genes between both species. We identified species-specific variants in 20 regulatory proteins and confirmed differential expression of hypoxia-related genes between M. bovis and M. tuberculosis.
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Affiliation(s)
- María M Bigi
- School of Agronomy, UBA, Buenos Aires 1417, Argentina
| | - Federico Carlos Blanco
- Biotechnology Institute, National Institute of Agricultural Technology (INTA), Hurlingham 1686, Argentina
| | | | - Tyler C Thacker
- United States Department of Agriculture, Agricultural Research Service, National Animal Disease Center, 1920 Dayton Ave, Ames, Iowa 50010, USA
| | - Martín J Zumárraga
- Biotechnology Institute, National Institute of Agricultural Technology (INTA), Hurlingham 1686, Argentina
| | - Angel A Cataldi
- Biotechnology Institute, National Institute of Agricultural Technology (INTA), Hurlingham 1686, Argentina
| | | | - Fabiana Bigi
- Biotechnology Institute, National Institute of Agricultural Technology (INTA), Hurlingham 1686, Argentina
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14
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Iona E, Pardini M, Mustazzolu A, Piccaro G, Nisini R, Fattorini L, Giannoni F. Mycobacterium tuberculosis gene expression at different stages of hypoxia-induced dormancy and upon resuscitation. J Microbiol 2016; 54:565-72. [PMID: 27480637 DOI: 10.1007/s12275-016-6150-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/01/2016] [Accepted: 06/27/2016] [Indexed: 11/25/2022]
Abstract
The physiology of dormant Mycobacterium tuberculosis was studied in detail by examining the gene expression of 51 genes using quantitative Reverse-Transcription Polymerase Chain Reaction. A forty-day period of dormancy in the Wayne culture model depicted four major transcription patterns. Some sigma factors and many metabolic genes were constant, whereas genes belonging to the dormancy regulon were activated on day 9. In particular, alpha-crystallin mRNA showed more than a 1,000-fold increase compared to replicating bacilli. Genes belonging to the enduring hypoxic response were up-regulated at day 16, notably, transcription factors sigma B and E. Early genes typical of log-phase bacilli, esat-6 and fbpB, were uniformly down-regulated during dormancy. Late stages of dormancy showed a drop in gene expression likely due to a lack of substrates in anaerobic respiration as demonstrated by the transcriptional activation observed following nitrates addition. Among genes involved in nitrate metabolism, narG was strongly up-regulated by nitrates addition. Dormant bacilli responded very rapidly when exposed to oxygen and fresh medium, showing a transcriptional activation of many genes, including resuscitation-promoting factors, within one hour. Our observations extend the current knowledge on dormant M. tuberculosis gene expression and its response to nutrients and to aerobic and anaerobic respiration.
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Affiliation(s)
- Elisabetta Iona
- Dipartimento di Malattie Infettive, Parassitarie e Immunomediate, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy
| | - Manuela Pardini
- Dipartimento di Malattie Infettive, Parassitarie e Immunomediate, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy
| | - Alessandro Mustazzolu
- Dipartimento di Malattie Infettive, Parassitarie e Immunomediate, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy
| | - Giovanni Piccaro
- Dipartimento di Malattie Infettive, Parassitarie e Immunomediate, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy
| | - Roberto Nisini
- Dipartimento di Malattie Infettive, Parassitarie e Immunomediate, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy
| | - Lanfranco Fattorini
- Dipartimento di Malattie Infettive, Parassitarie e Immunomediate, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy
| | - Federico Giannoni
- Dipartimento di Malattie Infettive, Parassitarie e Immunomediate, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy.
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15
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Sohaskey CD, Voskuil MI. In vitro models that utilize hypoxia to induce non-replicating persistence in Mycobacteria. Methods Mol Biol 2015; 1285:201-13. [PMID: 25779317 DOI: 10.1007/978-1-4939-2450-9_11] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The Wayne model and Rapid Anaerobic Dormancy model are widely used methods to analyze the response of Mycobacterium tuberculosis to hypoxia and anaerobiosis. In these models tubercle bacilli are grown in sealed tubes in which bacilli aerobic respiration produces a temporal oxygen gradient. The gradual depletion of oxygen results in a non-replicating persistent culture capable of extended microaerobic and anaerobic survival. Here we describe both models used to induce hypoxic non-replicating persistence in M. tuberculosis. Additional techniques such as the isolation of RNA, the detection of nitrate reductase activity and ATP levels, and the determination of the NAD(+)/NADH ratio are described.
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Affiliation(s)
- Charles D Sohaskey
- Department of Veterans Affairs Medical Center, Long Beach, CA, 90822, USA,
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16
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Da Silva MLB, Cantão ME, Mezzari MP, Ma J, Nossa CW. Assessment of bacterial and archaeal community structure in Swine wastewater treatment processes. MICROBIAL ECOLOGY 2015; 70:77-87. [PMID: 25432577 DOI: 10.1007/s00248-014-0537-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/12/2014] [Indexed: 05/27/2023]
Abstract
Microbial communities from two field-scale swine wastewater treatment plants (WWTPs) were assessed by pyrosequencing analyses of bacterial and archaeal 16S ribosomal DNA (rDNA) fragments. Effluent samples from secondary (anaerobic covered lagoons and upflow anaerobic sludge blanket [UASB]) and tertiary treatment systems (open-pond natural attenuation lagoon and air-sparged nitrification-denitrification tank followed by alkaline phosphorus precipitation process) were analyzed. A total of 56,807 and 48,859 high-quality reads were obtained from bacterial and archaeal libraries, respectively. Dominant bacterial communities were associated with the phylum Firmicutes, Bacteroidetes, Proteobacteria, or Actinobacteria. Bacteria and archaea diversity were highest in UASB effluent sample. Escherichia, Lactobacillus, Bacteroides, and/or Prevotella were used as indicators of putative pathogen reduction throughout the WWTPs. Satisfactory pathogen reduction was observed after the open-pond natural attenuation lagoon but not after the air-sparged nitrification/denitrification followed by alkaline phosphorus precipitation treatment processes. Among the archaeal communities, 80% of the reads was related to hydrogeno-trophic methanogens Methanospirillum. Enrichment of hydrogenotrophic methanogens detected in effluent samples from the anaerobic covered lagoons and UASB suggested that CO2 reduction with H2 was the dominant methanogenic pathway in these systems. Overall, the results served to improve our current understanding of major microbial communities' changes downgradient from the pen and throughout swine WWTP as a result of different treatment processes.
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17
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Huang Q, Abdalla AE, Xie J. Phylogenomics of Mycobacterium Nitrate Reductase Operon. Curr Microbiol 2015; 71:121-8. [PMID: 25980349 DOI: 10.1007/s00284-015-0838-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/13/2015] [Indexed: 11/24/2022]
Abstract
NarGHJI operon encodes a nitrate reductase that can reduce nitrate to nitrite. This process enhances bacterial survival by nitrate respiration under anaerobic conditions. NarGHJI operon exists in many bacteria, especially saprophytic bacteria living in soil which play a key role in the nitrogen cycle. Most actinomycetes, including Mycobacterium tuberculosis, possess NarGHJI operons. M. tuberculosis is a facultative intracellular pathogen that expands in macrophages and has the ability to persist in a non-replicative form in granuloma lifelong. Nitrogen and nitrogen compounds play crucial roles in the struggle between M. tuberculosis and host. M. tuberculosis can use nitrate as a final electron acceptor under anaerobic conditions to enhance its survival. In this article, we reviewed the mechanisms regulating nitrate reductase expression and affecting its activity. Potential genes involved in regulating the nitrate reductase expression in M. tuberculosis were identified. The conserved NarG might be an alternative mycobacterium taxonomic marker.
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Affiliation(s)
- Qinqin Huang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, 1 Rd Tiansheng, Beibei, Chongqing, 400715, People's Republic of China
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18
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Singh S, Kumar M, Singh P. Evolution of M. bovis BCG Vaccine: Is Niacin Production Still a Valid Biomarker? Tuberc Res Treat 2015; 2015:957519. [PMID: 25694828 PMCID: PMC4324913 DOI: 10.1155/2015/957519] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 12/15/2014] [Accepted: 01/06/2015] [Indexed: 02/07/2023] Open
Abstract
BCG vaccine is usually considered to be safe though rarely serious complications have also been reported, often incriminating contamination of the seed strain with pathogenic Mycobacterium tuberculosis. In such circumstances, it becomes prudent to rule out the contamination of the vaccine seed. M. bovis BCG can be confirmed by the absence of nitrate reductase, negative niacin test, and resistance to pyrazinamide and cycloserine. Recently in India, some stocks were found to be niacin positive which led to a national controversy and closer of a vaccine production plant. This prompted us to write this review and the comparative biochemical and genotypic studies were carried out on the these contentious vaccine stocks at the Indian vaccine plant and other seeds and it was found that some BCG vaccine strains and even some strains of M. bovis with eugenic-growth characteristics mainly old laboratory strains may give a positive niacin reaction. Most probably, the repeated subcultures lead to undefined changes at the genetic level in these seed strains. These changing biological characteristics envisage reevaluation of biochemical characters of existing BCG vaccine seeds and framing of newer guidelines for manufacturing, production, safety, and effectiveness of BCG vaccine.
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Affiliation(s)
- Sarman Singh
- 1Division of Clinical Microbiology & Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi 110029, India
- *Sarman Singh:
| | - Manoj Kumar
- 1Division of Clinical Microbiology & Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Pragati Singh
- 2National Polio Surveillance Project, Country Office for India, World Health Organization, Mathura 281001, India
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19
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bis-Molybdopterin guanine dinucleotide is required for persistence of Mycobacterium tuberculosis in guinea pigs. Infect Immun 2014; 83:544-50. [PMID: 25404027 DOI: 10.1128/iai.02722-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mycobacterium tuberculosis is able to synthesize molybdopterin cofactor (MoCo), which is utilized by numerous enzymes that catalyze redox reactions in carbon, nitrogen, and sulfur metabolism. In bacteria, MoCo is further modified through the activity of a guanylyltransferase, MobA, which converts MoCo to bis-molybdopterin guanine dinucleotide (bis-MGD), a form of the cofactor that is required by the dimethylsulfoxide (DMSO) reductase family of enzymes, which includes the nitrate reductase NarGHI. In this study, the functionality of the mobA homolog in M. tuberculosis was confirmed by demonstrating the loss of assimilatory and respiratory nitrate reductase activity in a mobA deletion mutant. This mutant displayed no survival defects in human monocytes or mouse lungs but failed to persist in the lungs of guinea pigs. These results implicate one or more bis-MGD-dependent enzymes in the persistence of M. tuberculosis in guinea pig lungs and underscore the applicability of this animal model for assessing the role of molybdoenzymes in this pathogen.
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Lofthouse EK, Wheeler PR, Beste DJV, Khatri BL, Wu H, Mendum T, Kierzek AM, McFadden J. Systems-based approaches to probing metabolic variation within the Mycobacterium tuberculosis complex. PLoS One 2013; 8:e75913. [PMID: 24098743 PMCID: PMC3783153 DOI: 10.1371/journal.pone.0075913] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 08/16/2013] [Indexed: 01/11/2023] Open
Abstract
The Mycobacterium tuberculosis complex includes bovine and human strains of the tuberculosis bacillus, including Mycobacterium tuberculosis, Mycobacterium bovis and the Mycobacterium bovis BCG vaccine strain. M. bovis has evolved from a M. tuberculosis-like ancestor and is the ancestor of the BCG vaccine. The pathogens demonstrate distinct differences in virulence, host range and metabolism, but the role of metabolic differences in pathogenicity is poorly understood. Systems biology approaches have been used to investigate the metabolism of M. tuberculosis, but not to probe differences between tuberculosis strains. In this study genome scale metabolic networks of M. bovis and M. bovis BCG were constructed and interrogated, along with a M. tuberculosis network, to predict substrate utilisation, gene essentiality and growth rates. The models correctly predicted 87-88% of high-throughput phenotype data, 75-76% of gene essentiality data and in silico-predicted growth rates matched measured rates. However, analysis of the metabolic networks identified discrepancies between in silico predictions and in vitro data, highlighting areas of incomplete metabolic knowledge. Additional experimental studies carried out to probe these inconsistencies revealed novel insights into the metabolism of these strains. For instance, that the reduction in metabolic capability observed in bovine tuberculosis strains, as compared to M. tuberculosis, is not reflected by current genetic or enzymatic knowledge. Hence, the in silico networks not only successfully simulate many aspects of the growth and physiology of these mycobacteria, but also provide an invaluable tool for future metabolic studies.
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Affiliation(s)
- Emma K. Lofthouse
- Animal Health and Veterinary Laboratories Agency (Weybridge), Department for Bovine Tuberculosis, New Haw, Surrey, United Kingdom
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Stag Hill, Guildford, Surrey, United Kingdom
| | - Paul R. Wheeler
- Animal Health and Veterinary Laboratories Agency (Weybridge), Department for Bovine Tuberculosis, New Haw, Surrey, United Kingdom
| | - Dany J. V. Beste
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Stag Hill, Guildford, Surrey, United Kingdom
| | - Bhagwati L. Khatri
- Animal Health and Veterinary Laboratories Agency (Weybridge), Department for Bovine Tuberculosis, New Haw, Surrey, United Kingdom
| | - Huihai Wu
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Stag Hill, Guildford, Surrey, United Kingdom
| | - Tom A. Mendum
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Stag Hill, Guildford, Surrey, United Kingdom
| | - Andrzej M. Kierzek
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Stag Hill, Guildford, Surrey, United Kingdom
| | - Johnjoe McFadden
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Stag Hill, Guildford, Surrey, United Kingdom
- * E-mail:
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Jung JY, Madan-Lala R, Georgieva M, Rengarajan J, Sohaskey CD, Bange FC, Robinson CM. The intracellular environment of human macrophages that produce nitric oxide promotes growth of mycobacteria. Infect Immun 2013; 81:3198-209. [PMID: 23774601 PMCID: PMC3754229 DOI: 10.1128/iai.00611-13] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 06/11/2013] [Indexed: 11/20/2022] Open
Abstract
Nitric oxide (NO) is a diffusible radical gas produced from the activity of nitric oxide synthase (NOS). NOS activity in murine macrophages has a protective role against mycobacteria through generation of reactive nitrogen intermediates (RNIs). However, the production of NO by human macrophages has remained unclear due to the lack of sensitive reagents to detect NO directly. The purpose of this study was to investigate NO production and the consequence to mycobacteria in primary human macrophages. We found that Mycobacterium bovis BCG or Mycobacterium tuberculosis infection of human macrophages induced expression of NOS2 and NOS3 that resulted in detectable production of NO. Treatment with gamma interferon (IFN-γ), l-arginine, and tetrahydrobiopterin enhanced expression of NOS2 and NOS3 isoforms, as well as NO production. Both of these enzymes were shown to contribute to NO production. The maximal level of NO produced by human macrophages was not bactericidal or bacteriostatic to M. tuberculosis or BCG. The number of viable mycobacteria was increased in macrophages that produced NO, and this requires expression of nitrate reductase. An narG mutant of M. tuberculosis persisted but was unable to grow in human macrophages. Taken together, these data (i) enhance our understanding of primary human macrophage potential to produce NO, (ii) demonstrate that the level of RNIs produced in response to IFN-γ in vitro is not sufficient to limit intracellular mycobacterial growth, and (iii) suggest that mycobacteria may use RNIs to enhance their survival in human macrophages.
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Affiliation(s)
- Joo-Yong Jung
- Department of Pathology, Microbiology, and Immunology, University of South Carolina, School of Medicine, Columbia, South Carolina, USA
| | | | | | - Jyothi Rengarajan
- Emory Vaccine Center
- Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
| | - Charles D. Sohaskey
- Tuberculosis Research Laboratory, Department of Veterans Affairs Medical Center, Long Beach, California, USA
| | | | - Cory M. Robinson
- Department of Pathology, Microbiology, and Immunology, University of South Carolina, School of Medicine, Columbia, South Carolina, USA
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22
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Williams M, Mizrahi V, Kana BD. Molybdenum cofactor: a key component of Mycobacterium tuberculosis pathogenesis? Crit Rev Microbiol 2013; 40:18-29. [PMID: 23317461 DOI: 10.3109/1040841x.2012.749211] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mycobacterium tuberculosis (Mtb) and other members of the Mtb complex possess an expanded complement of genes for the biosynthesis of molybdenum cofactor (MoCo), a tricyclic pterin molecule that is covalently attached to molybdate. This cofactor allows the redox properties of molybdenum to be harnessed by enzymes in order to catalyze redox reactions in carbon, nitrogen and sulfur metabolism. In this article, we summarize recent advances in elucidating the MoCo biosynthetic pathway in Mtb and highlight the evidence implicating the biosynthesis of this cofactor, as well as the enzymes that depend upon it for activity, in Mtb pathogenesis.
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Affiliation(s)
- Monique Williams
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Division of Medical Microbiology, Faculty of Health Sciences , University of Cape Town
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Giffin MM, Raab RW, Morganstern M, Sohaskey CD. Mutational analysis of the respiratory nitrate transporter NarK2 of Mycobacterium tuberculosis. PLoS One 2012; 7:e45459. [PMID: 23029022 PMCID: PMC3445494 DOI: 10.1371/journal.pone.0045459] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 08/22/2012] [Indexed: 11/24/2022] Open
Abstract
Mycobacterium tuberculosis induces nitrate reductase activity in response to decreasing oxygen levels. This is due to regulation of both the transcription and the activity of the nitrate transporter NarK2. A model of NarK2 structure is proposed containing 12 membrane spanning regions consistent with other members of the major facilitator superfamily. The role of the proton gradient was determined by exposing M. tuberculosis to uncouplers. Nitrite production decreased indicating that the importation of nitrate involved an H+/nitrate symporter. The addition of nitrite before nitrate had no effect, suggesting no role for a nitrate/nitrite antiporter. In addition the NarK2 knockout mutant showed no defect in nitrite export. NarK2 is proposed to be a Type I H+/nitrate symporter. Site directed mutagenesis was performed changing 23 amino acids of NarK2. This allowed the identification of important regions and amino acids of this transporter. Five of these mutants were inactive for nitrate transport, seven produced reduced activity and eleven mutants retained wild type activity. NarK2 is inactivated in the presence of oxygen by an unknown mechanism. However none of the mutants, including those with mutated cysteines, were altered in their response to oxygen levels. The assimilatory nitrate transporter NasA of Bacillus subtilis was expressed in the M. tuberculosis NarK2 mutant. It remained active during aerobic incubation showing that the point of oxygen control is NarK2.
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Sarkar S, Sarkar D. Potential use of nitrate reductase as a biomarker for the identification of active and dormant inhibitors of Mycobacterium tuberculosis in a THP1 infection model. ACTA ACUST UNITED AC 2012; 17:966-73. [PMID: 22573731 DOI: 10.1177/1087057112445485] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The development of a macrophage-based, antitubercular high-throughput screening system could expedite discovery programs for identifying novel inhibitors. In this study, the kinetics of nitrate reduction (NR) by Mycobacterium tuberculosis during growth in Thp1 macrophages was found to be almost parallel to viable bacilli count. NR in the culture medium containing 50 mM of nitrate was found to be optimum on the fifth day after infection with M. tuberculosis. The signal-to-noise (S/N) ratio and Z-factor obtained from this macrophage-based assay were 5.4 and 0.965, respectively, which confirms the robustness of the assay protocol. The protocol was further validated by using standard antitubercular inhibitors such as rifampicin, isoniazid, streptomycin, ethambutol, and pyrazinamide, added at their IC(90) value, on the day of infection. These inhibitors were not able to kill the bacilli when added to the culture on the fifth day after infection. Interestingly, pentachlorophenol and rifampicin killed the bacilli immediately after addition on the fifth day of infection. Altogether, this assay protocol using M. tuberculosis-infected Thp-1 macrophages provides a novel, cost-efficient, robust, and easy-to-perform screening platform for the identification of both active and hypoxic stage-specific inhibitors against tuberculosis.
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Affiliation(s)
- Sampa Sarkar
- Combichem Bioresource Center, CSIR-National Chemical Laboratory, Pune, India.
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Khan A, Sarkar D. Nitrate reduction pathways in mycobacteria and their implications during latency. MICROBIOLOGY-SGM 2011; 158:301-307. [PMID: 22174380 DOI: 10.1099/mic.0.054759-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Mycobacterial persistence has gained a lot of attention with respect to developing novel antitubercular drugs, which could drastically reduce the duration of tuberculosis (TB) therapy. A better understanding of the physiology of Mycobacterium tuberculosis, and of the metabolic state of the bacillus during the latent period, is a primary need in finding drug targets against persistent TB. Recent biochemical and genetic studies of nitrate reduction in mycobacteria have revealed the roles of distinct proteins and enzymes involved in the pathway. The differential degree of nitrate reduction among pathogenic and non-pathogenic mycobacterial species, and its regulation during oxygen and nutrient limitation, suggest a link between nitrate reduction pathways and latency. The respiratory and assimilatory reduction of nitrate in mycobacteria may be interconnected to facilitate rapid adaptation to changing oxygen and/or nitrogen conditions, increasing metabolic flexibility for survival in the hostile host environment. This review summarizes the nitrate metabolic pathways operative in mycobacteria to provide an insight into the mechanisms that M. tuberculosis has evolved to adapt successfully to the host environment.
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Affiliation(s)
- Arshad Khan
- Department of Pathology and Laboratory Medicine, University of Texas, Health Science Center at Houston, Medical School, Houston, TX 77030, USA
| | - Dhiman Sarkar
- Combi Chem-Bio Resource Center, National Chemical Laboratory, Dr Homi Bhabha Road, Pune, Maharashtra 411008, India
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Genes and regulatory networks involved in persistence of Mycobacterium tuberculosis. SCIENCE CHINA-LIFE SCIENCES 2011; 54:300-10. [PMID: 21267668 DOI: 10.1007/s11427-011-4134-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 09/06/2010] [Indexed: 10/18/2022]
Abstract
The causative agent of tuberculosis, Mycobacterium tuberculosis, is one of the most successful of human pathogens. It can evade the host immune response and establish a persistent infection or enter a dormant state within the host which can be reactivated if the host becomes immuno-compromised. Both of these features are major obstacles to tuberculosis eradication. Dormancy and reactivation of M. tuberculosis are tightly coordinated dynamic processes involving numerous genes and their products. Molecular mechanisms underlying M. tuberculosis persistence may provide an opportunity for the discovery of effective drug targets for tuberculosis control. Here, we review the genes required for M. tuberculosis persistence and propose a regulatory network for the action of these genes using text mining. This should provide fresh insights into the persistence mechanisms of M. tuberculosis and suggest candidates for new drug targets and immune intervention.
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Fischer M, Alderson J, van Keulen G, White J, Sawers RG. The obligate aerobe Streptomyces coelicolor A3(2) synthesizes three active respiratory nitrate reductases. MICROBIOLOGY-SGM 2010; 156:3166-3179. [PMID: 20595262 DOI: 10.1099/mic.0.042572-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Streptomyces coelicolor A3(2) synthesizes three membrane-associated respiratory nitrate reductases (Nars). During aerobic growth in liquid medium the bacterium was able to reduce 50 mM nitrate stoichiometrically to nitrite. Construction and analysis of a mutant in which all three narGHJI operons were deleted showed that it failed to reduce nitrate. Deletion of the gene encoding MoaA, which catalyses the first step in molybdenum cofactor biosynthesis, also prevented nitrate reduction, consistent with the Nars being molybdoenzymes. In contrast to the triple narGHJI mutant, the moaA mutant was also unable to use nitrate as sole nitrogen source, which indicates that the assimilatory nitrate reductases in S. coelicolor are also molybdenum-dependent. Analysis of S. coelicolor growth on solid medium demonstrated that Nar activity is present in both spores and mycelium (hypha). Development of a survival assay with the nitrate analogue chlorate revealed that wild-type S. coelicolor spores and mycelium were sensitive to chlorate after anaerobic incubation, independent of the presence of nitrate, while both the moaA and triple nar mutants were chlorate-resistant. Complementation of the triple nar mutant with the individual narGHJI operons delivered on cosmids revealed that each operon encoded an enzyme that was synthesized and active in nitrate or chlorate reduction. The data obtained from these studies allow a tentative assignment of Nar1 activity to spores, Nar2 to spores and mycelium, and Nar3 exclusively to mycelium.
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Affiliation(s)
- Marco Fischer
- Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Jesse Alderson
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Geertje van Keulen
- Institute of Life Sciences, School of Medicine, Swansea University, Swansea, UK
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Janet White
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - R Gary Sawers
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
- Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
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Hayashi D, Takii T, Mukai T, Makino M, Yasuda E, Horita Y, Yamamoto R, Fujiwara A, Kanai K, Kondo M, Kawarazaki A, Yano I, Yamamoto S, Onozaki K. Biochemical characteristics amongMycobacterium bovisBCG substrains. FEMS Microbiol Lett 2010; 306:103-9. [DOI: 10.1111/j.1574-6968.2010.01947.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Flores Valdez MA, Schoolnik GK. DosR-regulon genes induction in Mycobacterium bovis BCG under aerobic conditions. Tuberculosis (Edinb) 2010; 90:197-200. [PMID: 20421176 DOI: 10.1016/j.tube.2010.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 03/31/2010] [Accepted: 04/01/2010] [Indexed: 11/18/2022]
Abstract
In this report we demonstrated that under aerobic conditions, Mycobacterium bovis BCG expressing an hsp60-driven second copy of the hypoxia-related transcriptional regulator DosR increased 2-fold or greater the expression of 38 out of the 48 genes belonging to the DosR regulon, including the latency antigens Rv1733c, Rv2029, Rv2627, and Rv2628. Expression of DosR under these conditions slightly delayed in vitro growth, but did not promote a non-replicating state as opposed to microaerobic and hypoxic adaptation. Our results suggest BCG producing DosR can be cultured under standard in vitro conditions, allowing evaluation of this strain as a latency-specific vaccine candidate.
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Chauhan S, Singh A, Tyagi JS. A single-nucleotide mutation in the −10 promoter region inactivates thenarK2Xpromoter inMycobacterium bovisandMycobacterium bovisBCG and has an application in diagnosis. FEMS Microbiol Lett 2010; 303:190-6. [DOI: 10.1111/j.1574-6968.2009.01876.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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