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Shankar G, Akhter Y. Stealing survival: Iron acquisition strategies of Mycobacteriumtuberculosis. Biochimie 2024:S0300-9084(24)00142-1. [PMID: 38901792 DOI: 10.1016/j.biochi.2024.06.006] [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: 05/06/2024] [Revised: 06/07/2024] [Accepted: 06/18/2024] [Indexed: 06/22/2024]
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), faces iron scarcity within the host due to immune defenses. This review explores the importance of iron for Mtb and its strategies to overcome iron restriction. We discuss how the host limits iron as an innate immune response and how Mtb utilizes various iron acquisition systems, particularly the siderophore-mediated pathway. The review illustrates the structure and biosynthesis of mycobactin, a key siderophore in Mtb, and the regulation of its production. We explore the potential of targeting siderophore biosynthesis and uptake as a novel therapeutic approach for TB. Finally, we summarize current knowledge on Mtb's iron acquisition and highlight promising directions for future research to exploit this pathway for developing new TB interventions.
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Affiliation(s)
- Gauri Shankar
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226 025, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226 025, India.
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Bannantine JP, Duffy SC, Colombatti Olivieri MA, Behr MA, Biet F, Price NPJ. Genetic and chemical control of tuberculostearic acid production in Mycobacterium avium subspecies paratuberculosis. Microbiol Spectr 2024; 12:e0050824. [PMID: 38501867 PMCID: PMC11064506 DOI: 10.1128/spectrum.00508-24] [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: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Tuberculostearic acid (TBSA) is a fatty acid unique to mycobacteria and some corynebacteria and has been studied due to its diagnostic value, biofuel properties, and role in membrane dynamics. In this study, we demonstrate that TBSA production can be abrogated either by addition of pivalic acid to mycobacterial growth cultures or by a bfaA gene knockout encoding a flavin adenine dinucleotide (FAD)-binding oxidoreductase. Mycobacterium avium subspecies paratuberculosis (Map) growth and TBSA production were inhibited in 0.5-mg/mL pivalic acid-supplemented cultures, but higher concentrations were needed to have a similar effect in other mycobacteria, including Mycobacterium smegmatis. While Map C-type strains, isolated from cattle and other ruminants, will produce TBSA in the absence of pivalic acid, the S-type Map strains, typically isolated from sheep, do not produce TBSA in any condition. A SAM-dependent methyltransferase encoded by bfaB and FAD-binding oxidoreductase are both required in the two-step biosynthesis of TBSA. However, S-type strains contain a single-nucleotide polymorphism in the bfaA gene, rendering the oxidoreductase enzyme vestigial. This results in the production of an intermediate, termed 10-methylene stearate, which is detected only in S-type strains. Fatty acid methyl ester analysis of a C-type Map bfaA knockout revealed the loss of TBSA production, but the intermediate was present, similar to the S-type strains. Collectively, these results demonstrate the subtle biochemical differences between two primary genetic lineages of Map and other mycobacteria as well as explain the resulting phenotype at the genetic level. These data also suggest that TBSA should not be used as a diagnostic marker for Map.IMPORTANCEBranched-chain fatty acids are a predominant cell wall component among species belonging to the Mycobacterium genus. One of these is TBSA, which is a long-chain middle-branched fatty acid used as a diagnostic marker for Mycobacterium tuberculosis. This fatty acid is also an excellent biolubricant. Control of its production is important for industrial purposes as well as understanding the biology of mycobacteria. In this study, we discovered that a carboxylic acid compound termed pivalic acid inhibits TBSA production in mycobacteria. Furthermore, Map strains from two separate genetic lineages (C-type and S-type) showed differential production of TBSA. Cattle-type strains of Mycobacterium avium subspecies paratuberculosis produce TBSA, while the sheep-type strains do not. This important phenotypic difference is attributed to a single-nucleotide deletion in sheep-type strains of Map. This work sheds further light on the mechanism used by mycobacteria to produce tuberculostearic acid.
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Affiliation(s)
- John P. Bannantine
- National Animal Disease Center, USDA Agricultural Research Service, Ames, Iowa, USA
| | - Shannon C. Duffy
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - María A. Colombatti Olivieri
- National Animal Disease Center, USDA Agricultural Research Service, Ames, Iowa, USA
- ARS Participation Program, Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, Tennessee, USA
| | - Marcel A. Behr
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Franck Biet
- INRAE, ISP, Université de Tours, Nouzilly, France
| | - Neil P. J. Price
- National Center for Agricultural Utilization Research, USDA Agricultural Research Service, Peoria, Illinois, USA
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Thapa S, Rathnaiah G, Zinniel DK, Barletta RG, Bannantine JP, Huebner M, Sreevatsan S. The Fur-like regulatory protein MAP3773c modulates key metabolic pathways in Mycobacterium avium subsp. paratuberculosis under in-vitro iron starvation. Sci Rep 2024; 14:8941. [PMID: 38637716 PMCID: PMC11026511 DOI: 10.1038/s41598-024-59691-3] [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: 02/02/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024] Open
Abstract
Johne's disease (JD) is a chronic enteric infection of dairy cattle worldwide. Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of JD, is fastidious often requiring eight to sixteen weeks to produce colonies in culture-a major hurdle in the diagnosis and therefore in implementation of optimal JD control measures. A significant gap in knowledge is the comprehensive understanding of the metabolic networks deployed by MAP to regulate iron both in-vitro and in-vivo. The genome of MAP carries MAP3773c, a putative metal regulator, which is absent in all other mycobacteria. The role of MAP3773c in intracellular iron regulation is poorly understood. In the current study, a field isolate (K-10) and an in-frame MAP3773c deletion mutant (ΔMAP3773c) derived from K-10, were exposed to iron starvation for 5, 30, 60, and 90 min and RNA-Seq was performed. A comparison of transcriptional profiles between K-10 and ΔMAP3773c showed 425 differentially expressed genes (DEGs) at 30 min time post-iron restriction. Functional analysis of DEGs in ΔMAP3773c revealed that pantothenate (Pan) biosynthesis, polysaccharide biosynthesis and sugar metabolism genes were downregulated at 30 min post-iron starvation whereas ATP-binding cassette (ABC) type metal transporters, putative siderophore biosynthesis, PPE and PE family genes were upregulated. Pathway analysis revealed that the MAP3773c knockout has an impairment in Pan and Coenzyme A (CoA) biosynthesis pathways suggesting that the absence of those pathways likely affect overall metabolic processes and cellular functions, which have consequences on MAP survival and pathogenesis.
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Affiliation(s)
- Sajani Thapa
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, 784 Wilson Road, STEG300, East Lansing, MI, 48824, USA
| | - Govardhan Rathnaiah
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, USA
- University Of Nebraska, Eppley Institute for Cancer Research, Lincoln, USA
| | - Denise K Zinniel
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, USA
| | - Raul G Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, USA
| | | | - Marianne Huebner
- Department of Statistics and Probability, Michigan State University, East Lansing, MI, USA
| | - Srinand Sreevatsan
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, 784 Wilson Road, STEG300, East Lansing, MI, 48824, USA.
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Vasilatis DM, Christopher MM. Re-examining poikilocytosis in goats: prevalence, type and association with age and disease. Front Vet Sci 2023; 10:1234233. [PMID: 37662982 PMCID: PMC10470038 DOI: 10.3389/fvets.2023.1234233] [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: 06/03/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Background Domestic goats (Capra aegagrus hircus) are a food, fiber and companion animal. Abnormal erythrocyte shapes (poikilocytes) are considered normal in young goats, but their association with disease is not well described. Likewise, there is little information on the significance of poikilocytosis in adult goats. Objective The objective of this study was to investigate the prevalence, severity and type of poikilocytosis in young and adult goats and its association with age, sex, breed, laboratory results, and underlying disease. Methods We retrospectively examined clinical and laboratory data from 1254 goats presented at the University of California-Davis Veterinary Medical Teaching Hospital from 1997 to 2019. We analyzed 313 blood smears from goats with moderate or marked (MOD-MKD) poikilocytosis on initial blood smear evaluation. Number and type of poikilocytes per 1000 red blood cells (RBCs) were enumerated. Laboratory values and primary disease categories were compared with the severity and type of poikilocytosis. Results Kids (<6 mos) and juveniles (>6 mos to <1 year) had a higher prevalence of MOD-MKD poikilocytosis (95/210, 45.2% kids; 27/59, 45.8% juveniles) than adult goats (≥1 year; 190/982, 19.3%) (p < 0.001). Kids had a higher percentage of elliptocytes, dacryocytes, and schistocytes and a lower percentage of polygonal and spiculated RBCs than juvenile and adult goats (p < 0.001). Of goats with MOD-MKD (vs NONE-SLIGHT) poikilocytosis, kids had lower HGB and MCH, and higher RDW (p ≤ 0.02); juveniles and adult goats had lower HCT, MCV, MCH, and albumin concentration (p ≤ 0.01), and all age groups had lower total CO2 concentration and higher PLT counts (p < 0.03). Adult goats with MOD-MKD poikilocytosis also had higher BUN:Cr ratios (p = 0.005). Gastrointestinal parasitism, Johne's disease, diarrhea/enteritis, lice, hepatic disease and renal disease (but not urolithiasis) were significantly associated with MOD-MKD poikilocytosis (p < 0.001). Goats with hepatic and renal disease had a higher prevalence and percentage of spiculated cells (p = 0.001). Goats with Johne's disease had a higher prevalence of polygonal cells (93.3%) and dacryocytes (66.7%) than other diseases, and elliptocytes predominated in a higher proportion (36.0%) of adult goats with GI parasitism vs other diseases (p < 0.05). Conclusion These findings suggest that iron deficiency is an important pathophysiologic mechanism of poikilocytosis in juvenile and adult goats, and possibly in kids, whether due to iron-restricted erythropoiesis, chronic hemorrhage, functional iron deficiency, or a combination of these mechanisms. Further investigation into the detection and monitoring of iron deficiency and the value of poikilocytosis as a diagnostic marker of iron status in goats is warranted.
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Affiliation(s)
- Demitria M. Vasilatis
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Mary M. Christopher
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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Purdie AC, Plain KM, Pooley H, Begg DJ, de Silva K, Whittington RJ. Correlates of vaccine protection against Mycobacterium avium sub-species paratuberculosis infection revealed in a transcriptomic study of responses in Gudair ® vaccinated sheep. Front Vet Sci 2022; 9:1004237. [PMID: 36504842 PMCID: PMC9729357 DOI: 10.3389/fvets.2022.1004237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
A critical hindrance in the development of effective vaccine strategies to combat infectious disease is lack of knowledge about correlates of protection and of the host responses necessary for successful adaptive immunity. Often vaccine formulations are developed by stepwise experimentation, with incomplete investigation of the fundamental mechanisms of protection. Gudair® is a commercially available vaccine registered for use in sheep and goats for controlling spread of Mycobacterium avium sub-species paratuberculosis (MAP) infections and reduces mortality by up to 90%. Here, using an experimental infection model in sheep, we have utilized a transcriptomics approach to identify white blood cell gene expression changes in vaccinated, MAP-exposed Merino sheep with a protective response in comparison to those vaccinated animals that failed to develop immunity to MAP infection. This methodology facilitated an overview of gene-associated functional pathway adaptations using an in-silico analysis approach. We identified a group of genes that were activated in the vaccine-protected animals and confirmed stability of expression in samples obtained from naturally exposed commercially maintained sheep. We propose these genes as correlates of vaccine induced protection.
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Bythrow GV, Farhat MF, Levendosky K, Mohandas P, Germain GA, Yoo B, Quadri LEN. Mycobacterium abscessus Mutants with a Compromised Functional Link between the Type VII ESX-3 System and an Iron Uptake Mechanism Reliant on an Unusual Mycobactin Siderophore. Pathogens 2022; 11:pathogens11090953. [PMID: 36145386 PMCID: PMC9505556 DOI: 10.3390/pathogens11090953] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 11/28/2022] Open
Abstract
The opportunistic pathogen Mycobacterium abscessus subsp. abscessus (Mab) has become an emerging public health threat due to the increasing number of Mab-associated chronic pulmonary disease cases. Treatment requires multiple drug courses and is often combined with surgical resection. Cure rates are only ~50% due to treatment failure and comorbidities. Deeper understanding of the biology of Mab is required to illuminate potential avenues for the development of better therapeutics against Mab infections. The ESX-3 type VII protein secretion system of Mab has an important role in host inflammatory and pathological responses during infection. In this work, we demonstrate a functional link between ESX-3 and an iron uptake system based on an unusual mycobactin-type siderophore (designated MBT Ab) and exploit this link to implement a large screen for transposon mutants with an impaired ESX-3. Most mutants we identified carry insertions in genes encoding predicted ESX-3 secretion machinery components or potential ESX-3 substrates. The mutants overproduce MBT Ab, a trait consistent with an iron uptake defect. Our characterization of MBT Ab revealed structural features reminiscent of nocardial mycobactin-like compounds with cytotoxicity. This finding raises the possibility that MBT Ab may play roles in pathogenesis unlinked to iron homeostasis. The mutants generated herein will facilitate research to better understand the role of ESX-3 and its interplay with the siderophore system.
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Affiliation(s)
- Glennon V. Bythrow
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Manal F. Farhat
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Keith Levendosky
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Poornima Mohandas
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Gabrielle A. Germain
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Barney Yoo
- Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York, NY 10065, USA
| | - Luis E. N. Quadri
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Biochemistry Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Correspondence:
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In Silico and In Vitro Analysis of MAP3773c Protein from Mycobacterium avium subsp. Paratuberculosis. BIOLOGY 2022; 11:biology11081183. [PMID: 36009811 PMCID: PMC9405291 DOI: 10.3390/biology11081183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 12/02/2022]
Abstract
Simple Summary Paratuberculosis is a disease that is caused by Mycobacterium avium subsp. paratuberculosis, a bacterium that survives inside a cell to cause disease. This bacterium therefore needs the nutrients of the cell to survive. Zinc and iron are very important elements in its nutrition and are necessary to carry out many of its survival functions, so the cell develops mechanisms to eliminate these pathogenic bacteria to continue living. One of these mechanisms is the elimination of iron as a strategy to kill the bacteria. In this research, we took on the task of studying one of the proteins of the bacterium called MAP3773c, along with its structure, some of its properties and its particular characteristics. In relation to the affinity for zinc and iron to bind to it, we are interested in discovering and making it known to the scientific community whether MAP3773c is related to the pathology of the disease. Abstract Paratuberculosis is a disease caused by Mycobacterium avium subsp. paratuberculosis (MAP). It is of great interest to better understand the proteins involved in the pathogenicity of this organism in order to be able to identify potential therapeutic targets and design new vaccines. The protein of interest–MAP3773c–was investigated, and molecular modeling in silico, docking, cloning, expression, purification, and partial characterization of the recombinant protein were achieved. In the in silico study, it was shown that MAP3773c of MAP has 34% sequence similarity with Mycobacterium tuberculosis (MTB) FurB, which is a zinc uptake regulator (Zur) protein. The docking data showed that MAP3773c exhibits two metal-binding sites. The presence of structural Zn2+ in the purified protein was confirmed by SDS-PAGE PAR staining. The purification showed one band that corresponded to a monomer, which was confirmed by liquid chromatography–mass spectrometry (LC-MS). The presence of a monomer was verified by analyzing the native protein structure through BN-SDS-PAGE (Native Blue (BN) Two-Dimensional Electrophoresis) and BN–Western blotting. The MAP3773c protein contains structural zinc. In conclusion, our results show that MAP3773c displays the features of a Fur-type protein with two metal-binding sites, one of them coordinating structural Zn2+.
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Mizzi R, Plain KM, Whittington R, Timms VJ. Global Phylogeny of Mycobacterium avium and Identification of Mutation Hotspots During Niche Adaptation. Front Microbiol 2022; 13:892333. [PMID: 35602010 PMCID: PMC9121174 DOI: 10.3389/fmicb.2022.892333] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/06/2022] [Indexed: 12/27/2022] Open
Abstract
Mycobacterium avium is separated into four subspecies: M. avium subspecies avium (MAA), M. avium subspecies silvaticum (MAS), M. avium subspecies hominissuis (MAH), and M. avium subspecies paratuberculosis (MAP). Understanding the mechanisms of host and tissue adaptation leading to their clinical significance is vital to reduce the economic, welfare, and public health concerns associated with diseases they may cause in humans and animals. Despite substantial phenotypic diversity, the subspecies nomenclature is controversial due to high genetic similarity. Consequently, a set of 1,230 M. avium genomes was used to generate a phylogeny, investigate SNP hotspots, and identify subspecies-specific genes. Phylogeny reiterated the findings from previous work and established that Mycobacterium avium is a species made up of one highly diverse subspecies, known as MAH, and at least two clonal pathogens, named MAA and MAP. Pan-genomes identified coding sequences unique to each subspecies, and in conjunction with a mapping approach, mutation hotspot regions were revealed compared to the reference genomes for MAA, MAH, and MAP. These subspecies-specific genes may serve as valuable biomarkers, providing a deeper understanding of genetic differences between M. avium subspecies and the virulence mechanisms of mycobacteria. Furthermore, SNP analysis demonstrated common regions between subspecies that have undergone extensive mutations during niche adaptation. The findings provide insights into host and tissue specificity of this genetically conserved but phenotypically diverse species, with the potential to provide new diagnostic targets and epidemiological and therapeutic advances.
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Affiliation(s)
- Rachel Mizzi
- Farm Animal Health, School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Karren M Plain
- Farm Animal Health, School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia.,Microbiology and Parasitology Research, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Richard Whittington
- Farm Animal Health, School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Verlaine J Timms
- Neilan Laboratory of Microbial and Molecular Diversity, College of Engineering, Science and Environment, The University of Newcastle, Newcastle, NSW, Australia
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Conde C, Price-Carter M, Cochard T, Branger M, Stevenson K, Whittington R, Bannantine JP, Biet F. Whole-Genome Analysis of Mycobacterium avium subsp. paratuberculosis IS 900 Insertions Reveals Strain Type- Specific Modalities. Front Microbiol 2021; 12:660002. [PMID: 34040595 PMCID: PMC8141618 DOI: 10.3389/fmicb.2021.660002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/07/2021] [Indexed: 01/14/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (Map) is the etiological agent of Johne’s disease in ruminants. The IS900 insertion sequence (IS) has been used widely as an epidemiological marker and target for PCR diagnosis. Updated DNA sequencing technologies have led to a rapid increase in available Map genomes, which makes it possible to analyze the distribution of IS900 in this slow-growing bacterium. The objective of this study is to characterize the distribution of the IS900 element and how it affects genomic evolution and gene function of Map. A secondary goal is to develop automated in silico restriction fragment length polymorphism (RFLP) analysis using IS900. Complete genomes from the major phylogenetic lineages known as C-type and S-type (including subtypes I and III), were chosen to represent the genetic diversity of Map. IS900 elements were located in these genomes using BLAST software and the relevant fragments extracted. An in silico RFLP analysis using the BstEII restriction site was performed to obtain exact sizes of the DNA fragments carrying a copy of IS900 and the resulting RFLP profiles were analyzed and compared by digital visualization of the separated restriction fragments. The program developed for this study allowed automated localization of IS900 sequences to identify their position within each genome along with the exact number of copies per genome. The number of IS900 copies ranged from 16 in the C-type isolate to 22 in the S-type subtype I isolate. A loci-by-loci sequence alignment of all IS900 copies within the three genomes revealed new sequence polymorphisms that define three sequevars distinguishing the subtypes. Nine IS900 insertion site locations were conserved across all genomes studied while smaller subsets were unique to a particular lineage. Preferential insertion motif sequences were identified for IS900 along with genes bordering all IS900 insertions. Rarely did IS900 insert within coding sequences as only three genes were disrupted in this way. This study makes it possible to automate IS900 distribution in Map genomes to enrich knowledge on the distribution dynamics of this IS for epidemiological purposes, for understanding Map evolution and for studying the biological implications of IS900 insertions.
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Affiliation(s)
- Cyril Conde
- INRAE, ISP, Université de Tours, Nouzilly, France
| | | | | | | | | | - Richard Whittington
- School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | | | - Franck Biet
- INRAE, ISP, Université de Tours, Nouzilly, France
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Shoyama FM, Janetanakit T, Bannantine JP, Barletta RG, Sreevatsan S. Elucidating the Regulon of a Fur -like Protein in Mycobacterium avium subsp. paratuberculosis ( MAP). Front Microbiol 2020; 11:598. [PMID: 32390963 PMCID: PMC7192006 DOI: 10.3389/fmicb.2020.00598] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/18/2020] [Indexed: 11/13/2022] Open
Abstract
Intracellular iron concentration is tightly regulated to maintain cell viability. Iron plays important roles in electron transport, nucleic acid synthesis, and oxidative stress. A Mycobacterium avium subsp. paratuberculosis (MAP)-specific genomic island carries a putative metal transport operon that includes MAP3773c, which encodes a Fur-like protein. Although well characterized as a global regulator of iron homeostasis in multiple bacteria, the function of Fur (ferric uptake regulator) in MAP is unknown as this organism also carries IdeR (iron dependent regulator), a native iron regulatory protein specific to mycobacteria. Computational analysis using PRODORIC identified 23 different pathways involved in respiration, metabolism, and virulence that were likely regulated by MAP3773c. Thus, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) was performed to confirm the putative regulon of MAP3773c (Fur-like protein) in MAP. ChIP-Seq revealed enriched binding to 58 regions by Fur under iron-replete and -deplete conditions, located mostly within open reading frames (ORFs). Three ChIP peaks were identified in genes that are directly related to iron regulation: MAP3638c (hemophore-like protein), MAP3736c (Fur box), and MAP3776c (ABC transporter). Fur box consensus sequence was identified, and binding specificity and dependence on Mn2+ availability was confirmed by a chemiluminescent electrophoresis mobility shift assay (EMSA). The results confirmed that MAP3773c is a Fur ortholog that recognizes a 19 bp DNA sequence motif (Fur box) and it is involved in metal homeostasis. This work provides a regulatory network of MAP Fur binding sites during iron-replete and -deplete conditions, highlighting unique properties of Fur regulon in MAP.
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Affiliation(s)
- Fernanda Miyagaki Shoyama
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Taveesak Janetanakit
- Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - John P. Bannantine
- National Animal Disease Center, USDA-Agricultural Research Service, Ames, IA, United States
| | - Raul G. Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, NE, United States
| | - Srinand Sreevatsan
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
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Thirunavukkarasu S, Khader SA. Advances in Cardiovascular Disease Lipid Research Can Provide Novel Insights Into Mycobacterial Pathogenesis. Front Cell Infect Microbiol 2019; 9:116. [PMID: 31058102 PMCID: PMC6482252 DOI: 10.3389/fcimb.2019.00116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/02/2019] [Indexed: 12/17/2022] Open
Abstract
Cardiovascular disease (CVD) is the leading cause of death in industrialized nations and an emerging health problem in the developing world. Systemic inflammatory processes associated with alterations in lipid metabolism are a major contributing factor that mediates the development of CVDs, especially atherosclerosis. Therefore, the pathways promoting alterations in lipid metabolism and the interplay between varying cellular types, signaling agents, and effector molecules have been well-studied. Mycobacterial species are the causative agents of various infectious diseases in both humans and animals. Modulation of host lipid metabolism by mycobacteria plays a prominent role in its survival strategy within the host as well as in disease pathogenesis. However, there are still several knowledge gaps in the mechanistic understanding of how mycobacteria can alter host lipid metabolism. Considering the in-depth research available in the area of cardiovascular research, this review presents an overview of the parallel areas of research in host lipid-mediated immunological changes that might be extrapolated and explored to understand the underlying basis of mycobacterial pathogenesis.
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Affiliation(s)
- Shyamala Thirunavukkarasu
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO, United States
| | - Shabaana A Khader
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO, United States
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Bannantine JP, Etienne G, Laval F, Stabel JR, Lemassu A, Daffé M, Bayles DO, Ganneau C, Bonhomme F, Branger M, Cochard T, Bay S, Biet F. Cell wall peptidolipids of Mycobacterium avium: from genetic prediction to exact structure of a nonribosomal peptide. Mol Microbiol 2017; 105:525-539. [PMID: 28558126 DOI: 10.1111/mmi.13717] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2017] [Indexed: 10/19/2022]
Abstract
Mycobacteria have a complex cell wall structure that includes many lipids; however, even within a single subspecies of Mycobacterium avium these lipids can differ. Total lipids from an M. avium subsp. paratuberculosis (Map) ovine strain (S-type) contained no identifiable glycopeptidolipids or lipopentapeptide (L5P), yet both lipids are present in other M. avium subspecies. We determined the genetic and phenotypic basis for this difference using sequence analysis as well as biochemical and physico-chemical approaches. This strategy showed that a nonribosomal peptide synthase, encoded by mps1, contains three amino acid specifying modules in ovine strains, compared to five modules in bovine strains (C-type). Sequence analysis predicted these modules would produce the tripeptide Phe-N-Methyl-Val-Ala with a lipid moiety, termed lipotripeptide (L3P). Comprehensive physico-chemical analysis of Map S397 extracts confirmed the structural formula of the native L3P as D-Phe-N-Methyl-L-Val-L-Ala-OMe attached in N-ter to a 20-carbon fatty acid chain. These data demonstrate that S-type strains, which are more adapted in sheep, produce a unique lipid. There is a dose-dependent effect observed for L3P on upregulation of CD25+ CD8 T cells from infected cows, while L5P effects were static. In contrast, L5P demonstrated a significantly stronger induction of CD25+ B cells from infected animals compared to L3P.
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Affiliation(s)
- John P Bannantine
- National Animal Disease Center, USDA-Agricultural Research Service, Ames, IA, 50010, USA
| | - Gilles Etienne
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France.,Université de Toulouse, UPS, IPBS, Toulouse, 31000, France
| | - Françoise Laval
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France.,Université de Toulouse, UPS, IPBS, Toulouse, 31000, France
| | - Judith R Stabel
- National Animal Disease Center, USDA-Agricultural Research Service, Ames, IA, 50010, USA
| | - Anne Lemassu
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France.,Université de Toulouse, UPS, IPBS, Toulouse, 31000, France
| | - Mamadou Daffé
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France.,Université de Toulouse, UPS, IPBS, Toulouse, 31000, France
| | - Darrell O Bayles
- National Animal Disease Center, USDA-Agricultural Research Service, Ames, IA, 50010, USA
| | - Christelle Ganneau
- Institut Pasteur, Unité Chimie des Biomolécules, 75724 Paris Cedex 15, France.,CNRS UMR 3523, 75724 Paris Cedex 15, France
| | - Frédéric Bonhomme
- Institut Pasteur, Unité Chimie des Biomolécules, 75724 Paris Cedex 15, France.,CNRS UMR 3523, 75724 Paris Cedex 15, France
| | - Maxime Branger
- Infectiologie et Santé Publique, INRA, Université de Tours, UMR1282, Nouzilly, F-37380, France
| | - Thierry Cochard
- Infectiologie et Santé Publique, INRA, Université de Tours, UMR1282, Nouzilly, F-37380, France
| | - Sylvie Bay
- Institut Pasteur, Unité Chimie des Biomolécules, 75724 Paris Cedex 15, France.,CNRS UMR 3523, 75724 Paris Cedex 15, France
| | - Franck Biet
- Infectiologie et Santé Publique, INRA, Université de Tours, UMR1282, Nouzilly, F-37380, France
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13
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de Kruijf M, Coffey A, O'Mahony J. The investigation of the truncated mbtA gene within the mycobactin cluster of Mycobacterium avium subspecies paratuberculosis as a novel diagnostic marker for real-time PCR. J Microbiol Methods 2017; 136:40-48. [PMID: 28285167 DOI: 10.1016/j.mimet.2017.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/07/2017] [Accepted: 03/07/2017] [Indexed: 12/20/2022]
Abstract
The inability of Mycobacterium avium subspecies paratuberculosis (MAP) to produce endogenous mycobactin in-vitro is most likely due to the presence of a truncated mbtA gene within the mycobactin cluster of MAP. The main goal of this study was to investigate this unique mbtA truncation as a potential novel PCR diagnostic marker for MAP. Novel primers were designed that were located within the truncated region and the contiguous MAP2179 gene. Primers were evaluated against non-MAP isolates and no amplicons were generated. The detection limit of this mbtA-MAP2179 target was evaluated using a range of MAP DNA concentrations, MAP inoculated faecal material and 20 MAP isolates. The performance of mbtA-MAP2179 was compared to the established f57 target. The detection limits recorded for MAP K-10 DNA and from MAP K-10 inoculated faecal samples were 0.34pg and 104CFU/g respectively for both f57 and mbtA-MAP2179. A detection limit of 103CFU/g was recorded for both targets, but not achieved consistently. The detection limit of MAP from inoculated faecal material was successful at 103CFU/g for mbtA-MAP2179 when FAM probe real-time PCR was used. A MAP cell concentration of 102CFU/g was detected successfully, but again not consistently achieved. All 20 mycobacterial isolates were successfully identified as MAP by f57 and mbtA-MAP2179. Interestingly, the mbtA-MAP2179 real-time PCR assay resulted in the formation of a unique melting curve profile that contained two melting curve peaks rather than one single peak. This melting curve phenomenon was attributed towards the asymmetrical GC% distribution within the mbtA-MAP2179 amplicon. This study investigated the implementation of the mbtA-MAP2179 target as a novel diagnostic marker and the detection limits obtained with mbtA-MAP2179 were comparable to the established f57 target, making the mbtA-MAP2179 an adequate confirmatory target. Moreover, the mbtA-MAP2179 target could be implemented in multiplex real-time PCR assays and with its unique melting curve profile adds increased specificity to MAP diagnostic tests.
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Affiliation(s)
- Marcel de Kruijf
- Cork Institute of Technology, Department of Biological Sciences, Rossa Avenue, Bishopstown, Cork, Ireland
| | - Aidan Coffey
- Cork Institute of Technology, Department of Biological Sciences, Rossa Avenue, Bishopstown, Cork, Ireland
| | - Jim O'Mahony
- Cork Institute of Technology, Department of Biological Sciences, Rossa Avenue, Bishopstown, Cork, Ireland.
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Timms VJ, Daskalopoulos G, Mitchell HM, Neilan BA. The Association of Mycobacterium avium subsp. paratuberculosis with Inflammatory Bowel Disease. PLoS One 2016; 11:e0148731. [PMID: 26849125 PMCID: PMC4746060 DOI: 10.1371/journal.pone.0148731] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 12/09/2015] [Indexed: 12/14/2022] Open
Abstract
The association of Mycobacterium avium subspecies paratuberculosis (M. paratuberculosis) with Crohn’s disease is a controversial issue. M. paratuberculosis is detected by amplifying the IS900 gene, as microbial culture is unreliable from humans. We determined the presence of M. paratuberculosis in patients with Crohn’s disease (CD) (n = 22), ulcerative colitis (UC) (n = 20), aphthous ulcers (n = 21) and controls (n = 42) using PCR assays validated on bovine tissue. Culture from human tissue was also performed. M. paratuberculosis prevalence in the CD and UC groups was compared to the prevalence in age and sex matched non-inflammatory bowel disease controls. Patients and controls were determined to be M. paratuberculosis positive if all three PCR assays were positive. A significant association was found between M. paratuberculosis and Crohn’s disease (p = 0.02) that was not related to age, gender, place of birth, smoking or alcohol intake. No significant association was detected between M. paratuberculosis and UC or aphthous ulcers; however, one M. paratuberculosis isolate was successfully cultured from a patient with UC. We report the resistance of this isolate to ethambutol, rifampin, clofazamine and streptomycin. Interestingly this isolate could not only survive but could grow slowly at 5°C. We demonstrate a significant association between M. paratuberculosis and CD using multiple pre-validated PCR assays and that M. paratuberculosis can be isolated from patients with UC.
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Affiliation(s)
- Verlaine J. Timms
- School of Biotechnology and Biomolecular Sciences, Level 3, Biosciences Building, University of New South Wales, Sydney, Australia
| | - George Daskalopoulos
- Inner West Endoscopy Centre, Endoscopy Services Pty. Ltd., Marrickville, Sydney, Australia
| | - Hazel M. Mitchell
- School of Biotechnology and Biomolecular Sciences, Level 3, Biosciences Building, University of New South Wales, Sydney, Australia
| | - Brett A. Neilan
- School of Biotechnology and Biomolecular Sciences, Level 3, Biosciences Building, University of New South Wales, Sydney, Australia
- * E-mail:
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15
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Iron Acquisition in Mycobacterium avium subsp. paratuberculosis. J Bacteriol 2015; 198:857-66. [PMID: 26712939 PMCID: PMC4810606 DOI: 10.1128/jb.00922-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 12/18/2015] [Indexed: 01/26/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis is a host-adapted pathogen that evolved from the environmental bacterium M. avium subsp. hominissuis through gene loss and gene acquisition. Growth of M. avium subsp. paratuberculosis in the laboratory is enhanced by supplementation of the media with the iron-binding siderophore mycobactin J. Here we examined the production of mycobactins by related organisms and searched for an alternative iron uptake system in M. avium subsp. paratuberculosis. Through thin-layer chromatography and radiolabeled iron-uptake studies, we showed that M. avium subsp. paratuberculosis is impaired for both mycobactin synthesis and iron acquisition. Consistent with these observations, we identified several mutations, including deletions, in M. avium subsp. paratuberculosis genes coding for mycobactin synthesis. Using a transposon-mediated mutagenesis screen conditional on growth without myobactin, we identified a potential mycobactin-independent iron uptake system on a M. avium subsp. paratuberculosis-specific genomic island, LSPP15. We obtained a transposon (Tn) mutant with a disruption in the LSPP15 gene MAP3776c for targeted study. The mutant manifests increased iron uptake as well as intracellular iron content, with genes downstream of the transposon insertion (MAP3775c to MAP3772c [MAP3775-2c]) upregulated as the result of a polar effect. As an independent confirmation, we observed the same iron uptake phenotypes by overexpressing MAP3775-2c in wild-type M. avium subsp. paratuberculosis. These data indicate that the horizontally acquired LSPP15 genes contribute to iron acquisition by M. avium subsp. paratuberculosis, potentially allowing the subsequent loss of siderophore production by this pathogen. IMPORTANCE Many microbes are able to scavenge iron from their surroundings by producing iron-chelating siderophores. One exception is Mycobacterium avium subsp. paratuberculosis, a fastidious, slow-growing animal pathogen whose growth needs to be supported by exogenous mycobacterial siderophore (mycobactin) in the laboratory. Data presented here demonstrate that, compared to other closely related M. avium subspecies, mycobactin production and iron uptake are different in M. avium subsp. paratuberculosis, and these phenotypes may be caused by numerous deletions in its mycobactin biosynthesis pathway. Using a genomic approach, supplemented by targeted genetic and biochemical studies, we identified that LSPP15, a horizontally acquired genomic island, may encode an alternative iron uptake system. These findings shed light on the potential physiological consequence of horizontal gene transfer in M. avium subsp. paratuberculosis evolution.
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16
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Timms VJ, Hassan KA, Mitchell HM, Neilan BA. Comparative genomics between human and animal associated subspecies of the Mycobacterium avium complex: a basis for pathogenicity. BMC Genomics 2015; 16:695. [PMID: 26370227 PMCID: PMC4570654 DOI: 10.1186/s12864-015-1889-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 09/01/2015] [Indexed: 12/25/2022] Open
Abstract
Background A human isolate of Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis 43525) was sequenced and compared genomically to other mycobacterial pathogens. M. paratuberculosis 43525 was recently isolated from a patient with ulcerative colitis and belongs to the M. avium complex, a group known to infect both humans and animals. While M. paratuberculosis is a known pathogen of livestock, there are only 20 human isolates from the last 20 years, therefore we took the opportunity to perform a whole genome comparison between human and animal mycobacterial pathogens. We also compared virulence determinants such as the mycobactin cluster, PE/PPE genes and mammalian cell entry (mce) operons between MAC subspecies that infect animals and those that infect humans. M. tuberculosis was also included in these analyses given its predominant role as a human pathogen. Results This genome comparison showed the PE/PPE profile of M. paratuberculosis 43525 to be largely the same as other M. paratuberculosis isolates, except that it had one PPE and one PE_PGRS protein that are only present in human MAC strains and M. tuberculosis. PE/PPE proteins that were unique to M. paratuberculosis 43525, M. avium subsp. hominissuis and a caprine M. paratuberculosis isolate, were also identified. In addition, the mycobactin cluster differed between human and animal isolates and a unique mce operon flanked by two mycobactin genes, mbtA and mbtJ, was identified in all available M. paratuberculosis genomes. Conclusions Despite the whole genome comparison placing M. paratuberculosis 43525 as closely related to bovine M. paratuberculosis, key virulence factors were similar to human mycobacterial pathogens. This study highlights key factors of mycobacterial pathogenesis in humans and forms the basis for future functional studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1889-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Verlaine J Timms
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia. .,Centre for Infectious Diseases and Microbiology, Institute of Clinical Microbiology and Medical Research, Westmead Hospital, Sydney, NSW, Australia.
| | - Karl A Hassan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia.
| | - Hazel M Mitchell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
| | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
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17
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Genetic diversity of Mycobacterium avium subspecies paratuberculosis and the influence of strain type on infection and pathogenesis: a review. Vet Res 2015; 46:64. [PMID: 26092160 PMCID: PMC4473831 DOI: 10.1186/s13567-015-0203-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 01/16/2015] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (Map) is an important pathogen that causes a chronic, progressive granulomatous enteritis known as Johne's disease or paratuberculosis. The disease is endemic in many parts of the world and responsible for considerable losses to the livestock and associated industries. Diagnosis and control are problematic, due mostly to the long incubation period of the disease when infected animals show no clinical signs and are difficult to detect, and the ability of the organism to survive and persist in the environment. The existence of phenotypically distinct strains of Map has been known since the 1930s but the genetic differentiation of Map strain types has been challenging and only recent technologies have proven sufficiently discriminative for strain comparisons, tracing the sources of infection and epidemiological studies. It is important to understand the differences that exist between Map strains and how they influence both development and transmission of disease. This information is required to develop improved diagnostics and effective vaccines for controlling Johne's disease. Here I review the current classification of Map strain types, the sources of the genetic variability within strains, growth characteristics and epidemiological traits associated with strain type and the influence of strain type on infection and pathogenicity.
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18
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Eckelt E, Meißner T, Meens J, Laarmann K, Nerlich A, Jarek M, Weiss S, Gerlach GF, Goethe R. FurA contributes to the oxidative stress response regulation of Mycobacterium avium ssp. paratuberculosis. Front Microbiol 2015; 6:16. [PMID: 25705205 PMCID: PMC4319475 DOI: 10.3389/fmicb.2015.00016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 01/07/2015] [Indexed: 11/13/2022] Open
Abstract
The ferric uptake regulator A (FurA) is known to be involved in iron homeostasis and stress response in many bacteria. In mycobacteria the precise role of FurA is still unclear. In the presented study, we addressed the functional role of FurA in the ruminant pathogen Mycobacterium avium ssp. paratuberculosis (MAP) by construction of a furA deletion strain (MAPΔfurA). RNA deep sequencing revealed that the FurA regulon consists of repressed and activated genes associated to stress response or intracellular survival. Not a single gene related to metal homeostasis was affected by furA deletion. A decisive role of FurA during intracellular survival in macrophages was shown by significantly enhanced survival of MAPΔfurA compared to the wildtype, indicating that a principal task of mycobacterial FurA is oxidative stress response regulation in macrophages. This resistance was not associated with altered survival of mice after long term infection with MAP. Our results demonstrate for the first time, that mycobacterial FurA is not involved in the regulation of iron homeostasis. However, they provide strong evidence that FurA contributes to intracellular survival as an oxidative stress sensing regulator.
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Affiliation(s)
- Elke Eckelt
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover Hannover, Germany
| | - Thorsten Meißner
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover Hannover, Germany
| | - Jochen Meens
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover Hannover, Germany
| | - Kristin Laarmann
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover Hannover, Germany
| | - Andreas Nerlich
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover Hannover, Germany
| | - Michael Jarek
- Genome Analytics, Helmholtz Centre for Infection Research Braunschweig, Germany
| | - Siegfried Weiss
- Molecular Immunology, Helmholtz Centre for Infection Research Braunschweig, Germany
| | - Gerald-F Gerlach
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover Hannover, Germany
| | - Ralph Goethe
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover Hannover, Germany
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19
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Dow CT. M. paratuberculosis and Parkinson's disease--is this a trigger. Med Hypotheses 2014; 83:709-12. [PMID: 25459140 DOI: 10.1016/j.mehy.2014.09.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/04/2014] [Accepted: 09/30/2014] [Indexed: 12/14/2022]
Abstract
Genetic linkage studies and genome wide analysis have provided insights into complex medical diseases. Mycobacterium avium ss. paratuberculosis (MAP) causes Johne's disease, an important enteric inflammatory disease mostly studied in ruminant animals. MAP is also the putative cause of Crohn's disease. Moreover, MAP has been linked to other inflammatory diseases: sarcoidosis, Blau syndrome, autoimmune diabetes, autoimmune thyroiditis and multiple sclerosis. Genetic studies reveal an association between Parkinson's disease (PD), leprosy and Crohn's disease and since discovered, these findings have been considered "surprising". Autophagy and ubiquitin-proteosome systems are cellular systems that both fight intracellular pathogens (xenophagy) and maintain cellular protein quality control. PD is a common neurodegenerative disease that manifests clinically as a profound movement disorder. The recognized genetic defects of PD create disruption of cellular homeostasis that result in protein folding abnormalities of PD called Lewy bodies. Those same genetic defects are associated with susceptibility to intracellular pathogens, including mycobacteria. It is now understood that PD Lewy body pathology starts in the enteric nervous system and "spreads" to the brain in a retrograde fashion via the vagus nerve. This is the same process by which prions affect the brain. Lewy body pathology of the enteric nervous system predates the Lewy body pathology of the central nervous system (CNS) by years or even decades. This article proposes that genetic defects associated with PD also result in a permissive environment for MAP infection--ineffective xenophagy. It postulates that beginning as an enteric infection, MAP--via the vagus nerve--initiates a pathologic process that results in a targeted neuroinvasion of the CNS. The article proposes that MAP infection and resultant PD pathology are due, in the genetically at-risk and age dependant, to the consumptive exhaustion of the protein quality control systems.
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Affiliation(s)
- Coad Thomas Dow
- McPherson Eye Research Institute, University of Wisconsin-Madison, 9431 WIMR, 1111 Highland Avenue, Madison, WI 53705, United States; Chippewa Valley Eye Clinic, 2715 Damon Street, Eau Claire, WI 54701, United States.
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20
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Lamont EA, Xu WW, Sreevatsan S. Host-Mycobacterium avium subsp. paratuberculosis interactome reveals a novel iron assimilation mechanism linked to nitric oxide stress during early infection. BMC Genomics 2013; 14:694. [PMID: 24112552 PMCID: PMC3832399 DOI: 10.1186/1471-2164-14-694] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 10/02/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The initial interaction between host cell and pathogen sets the stage for the ensuing infection and ultimately determine the course of disease. However, there is limited knowledge of the transcripts utilized by host and pathogen and how they may impact one another during this critical step. The purpose of this study was to create a host-Mycobacterium avium subsp. paratuberculosis (MAP) interactome for early infection in an epithelium-macrophage co-culture system using RNA-seq. RESULTS Establishment of the host-MAP interactome revealed a novel iron assimilation system for carboxymycobactin. Iron assimilation is linked to nitric oxide synthase-2 production by the host and subsequent nitric oxide buildup. Iron limitation as well as nitric oxide is a prompt for MAP to enter into an iron sequestration program. This new iron sequestration program provides an explanation for mycobactin independence in some MAP strains grown in vitro as well as during infection within the host cell. Utilization of such a pathway is likely to aid MAP establishment and long-term survival within the host. CONCLUSIONS The host-MAP interactome identified a number of metabolic, DNA repair and virulence genes worthy for consideration as novel drug targets as well as future pathogenesis studies. Reported interactome data may also be utilized to conduct focused, hypothesis-driven research. Co-culture of uninfected bovine epithelial cells (MAC-T) and primary bovine macrophages creates a tolerant genotype as demonstrated by downregulation of inflammatory pathways. This co-culture system may serve as a model to investigate other bovine enteric pathogens.
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Affiliation(s)
- Elise A Lamont
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Avenue, Saint Paul, MN 55108, USA
| | - Wayne W Xu
- Minnesota Supercomputing Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Srinand Sreevatsan
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Avenue, Saint Paul, MN 55108, USA
- Department of Veterinary Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
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Key role for the alternative sigma factor, SigH, in the intracellular life of Mycobacterium avium subsp. paratuberculosis during macrophage stress. Infect Immun 2013; 81:2242-57. [PMID: 23569115 DOI: 10.1128/iai.01273-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis causes Johne's disease, an enteric infection in cattle and other ruminants, greatly afflicting the dairy industry worldwide. Once inside the cell, M. avium subsp. paratuberculosis is known to survive harsh microenvironments, especially those inside activated macrophages. To improve our understanding of M. avium subsp. paratuberculosis pathogenesis, we examined phagosome maturation associated with transcriptional responses of M. avium subsp. paratuberculosis during macrophage infection. Monitoring cellular markers, only live M. avium subsp. paratuberculosis bacilli were able to prevent phagosome maturation and reduce its acidification. On the transcriptional level, over 300 M. avium subsp. paratuberculosis genes were significantly and differentially regulated in both naive and IFN-γ-activated macrophages. These genes include the sigma factor H (sigH) that was shown to be important for M. avium subsp. paratuberculosis survival inside gamma interferon (IFN-γ)-activated bovine macrophages. Interestingly, an sigH-knockout mutant showed increased sensitivity to a sustained level of thiol-specific oxidative stress. Large-scale RNA sequence analysis revealed that a large number of genes belong to the sigH regulon, especially following diamide stress. Genes involved in oxidative stress and virulence were among the induced genes in the sigH regulon with a putative consensus sequence for SigH binding that was recognized in a subset of these genes (n = 30), suggesting direct regulation by SigH. Finally, mice infections showed a significant attenuation of the ΔsigH mutant compared to its parental strain, suggesting a role for sigH in M. avium subsp. paratuberculosis virulence. Such analysis could identify potential targets for further testing as vaccine candidates against Johne's disease.
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22
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Phenotypic and transcriptomic response of auxotrophic Mycobacterium avium subsp. paratuberculosis leuD mutant under environmental stress. PLoS One 2012; 7:e37884. [PMID: 22675497 PMCID: PMC3366959 DOI: 10.1371/journal.pone.0037884] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 04/30/2012] [Indexed: 01/26/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of severe gastroenteritis in cattle. To gain a better understanding of MAP virulence, we investigated the role of leuD gene in MAP metabolism and stress response. For this, we have constructed an auxotrophic strain of MAP by deleting the leuD gene using allelic exchange. The wildtype and mutant strains were then compared for metabolic phenotypic changes using Biolog phenotype microarrays. The responses of both strains to physiologically relevant stress conditions were assessed using DNA microarrays. Transcriptomic data was then analyzed in the context of cellular metabolic pathways and gene networks. Our results showed that deletion of leuD gene has a global effect on both MAP phenotypic and transcriptome response. At the metabolic level, the mutant strain lost the ability to utilize most of the carbon, nitrogen, sulphur, phosphorus and nutrient supplements as energy source. At the transcriptome level, more than 100 genes were differentially expressed in each of the stress condition tested. Systems level network analysis revealed that the differentially expressed genes were distributed throughout the gene network, thus explaining the global impact of leuD deletion in metabolic phenotype. Further, we find that leuD deletion impacted metabolic pathways associated with fatty acids. We verified this by experimentally estimating the total fatty acid content of both mutant and wildtype. The mutant strain had 30% less fatty acid content when compared to wildtype, thus supporting the results from transcriptional and computational analyses. Our results therefore reveal the intricate connection between the metabolism and virulence in MAP.
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23
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Bannantine JP, Wu CW, Hsu C, Zhou S, Schwartz DC, Bayles DO, Paustian ML, Alt DP, Sreevatsan S, Kapur V, Talaat AM. Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association. BMC Genomics 2012; 13:89. [PMID: 22409516 PMCID: PMC3337245 DOI: 10.1186/1471-2164-13-89] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 03/12/2012] [Indexed: 01/09/2023] Open
Abstract
Background The genome of Mycobacterium avium subspecies paratuberculosis (MAP) is remarkably homogeneous among the genomes of bovine, human and wildlife isolates. However, previous work in our laboratories with the bovine K-10 strain has revealed substantial differences compared to sheep isolates. To systematically characterize all genomic differences that may be associated with the specific hosts, we sequenced the genomes of three U.S. sheep isolates and also obtained an optical map. Results Our analysis of one of the isolates, MAP S397, revealed a genome 4.8 Mb in size with 4,700 open reading frames (ORFs). Comparative analysis of the MAP S397 isolate showed it acquired approximately 10 large sequence regions that are shared with the human M. avium subsp. hominissuis strain 104 and lost 2 large regions that are present in the bovine strain. In addition, optical mapping defined the presence of 7 large inversions between the bovine and ovine genomes (~ 2.36 Mb). Whole-genome sequencing of 2 additional sheep strains of MAP (JTC1074 and JTC7565) further confirmed genomic homogeneity of the sheep isolates despite the presence of polymorphisms on the nucleotide level. Conclusions Comparative sequence analysis employed here provided a better understanding of the host association, evolution of members of the M. avium complex and could help in deciphering the phenotypic differences observed among sheep and cattle strains of MAP. A similar approach based on whole-genome sequencing combined with optical mapping could be employed to examine closely related pathogens. We propose an evolutionary scenario for M. avium complex strains based on these genome sequences.
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Affiliation(s)
- John P Bannantine
- National Animal Disease Center, USDA-Agricultural Research Service, Ames, Iowa, USA.
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Genomic and transcriptomic studies in Mycobacterium avium subspecies paratuberculosis. Vet Immunol Immunopathol 2010; 138:303-11. [PMID: 21047690 DOI: 10.1016/j.vetimm.2010.10.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Microarray technology is an important tool in functional genomic research. It has enabled a deeper analysis of genomic diversity among bacteria belonging to the Mycobacterium avium complex (MAC). In addition, the expression of thousands of genes can be studied simultaneously in a single experiment. With the complete genome sequence of a bovine isolate of M. avium subspecies paratuberculosis, and the independent construction of DNA microarrays in our laboratories, transcriptomic studies for this veterinary pathogen are now possible. Furthermore, the bovine genome sequence project is completed and bovine arrays have been developed to examine host responses to infection with M. avium subsp. paratuberculosis. Collectively, genomic and transcriptomic data has yielded novel insights surrounding the genetic regulation and biology of Johne's disease.
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Janagama HK, Senthilkumar, Bannantine JP, Kugadas A, Jagtap P, Higgins L, Witthuhn B, Sreevatsan S. Iron-sparing response of Mycobacterium avium subsp. paratuberculosis is strain dependent. BMC Microbiol 2010; 10:268. [PMID: 20969756 PMCID: PMC2975660 DOI: 10.1186/1471-2180-10-268] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2010] [Accepted: 10/22/2010] [Indexed: 01/05/2023] Open
Abstract
Background Two genotypically and microbiologically distinct strains of Mycobacterium avium subsp. paratuberculosis (MAP) exist - S and C MAP strains that primarily infect sheep and cattle, respectively. Concentration of iron in the cultivation medium has been suggested as one contributing factor for the observed microbiologic differences. We recently demonstrated that S strains have defective iron storage systems, leading us to propose that these strains might experience iron toxicity when excess iron is provided in the medium. To test this hypothesis, we carried out transcriptional and proteomic profiling of these MAP strains under iron-replete or -deplete conditions. Results We first complemented M. smegmatisΔideR with IdeR of C MAP or that derived from S MAP and compared their transcription profiles using M. smegmatis mc2155 microarrays. In the presence of iron, sIdeR repressed expression of bfrA and MAP2073c, a ferritin domain containing protein suggesting that transcriptional control of iron storage may be defective in S strain. We next performed transcriptional and proteomic profiling of the two strain types of MAP under iron-deplete and -replete conditions. Under iron-replete conditions, C strain upregulated iron storage (BfrA), virulence associated (Esx-5 and antigen85 complex), and ribosomal proteins. In striking contrast, S strain downregulated these proteins under iron-replete conditions. iTRAQ (isobaric tag for relative and absolute quantitation) based protein quantitation resulted in the identification of four unannotated proteins. Two of these were upregulated by a C MAP strain in response to iron supplementation. The iron-sparing response to iron limitation was unique to the C strain as evidenced by repression of non-essential iron utilization enzymes (aconitase and succinate dehydrogenase) and upregulation of proteins of essential function (iron transport, [Fe-S] cluster biogenesis and cell division). Conclusions Taken together, our study revealed that C and S strains of MAP utilize divergent metabolic pathways to accommodate in vitro iron stress. The knowledge of the metabolic pathways these divergent responses play a role in are important to 1) advance our ability to culture the two different strains of MAP efficiently, 2) aid in diagnosis and control of Johne's disease, and 3) advance our understanding of MAP virulence.
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Affiliation(s)
- Harish K Janagama
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, USA
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Janagama HK, Lamont EA, George S, Bannantine JP, Xu WW, Tu ZJ, Wells SJ, Schefers J, Sreevatsan S. Primary transcriptomes of Mycobacterium avium subsp. paratuberculosis reveal proprietary pathways in tissue and macrophages. BMC Genomics 2010; 11:561. [PMID: 20939887 PMCID: PMC3091710 DOI: 10.1186/1471-2164-11-561] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Accepted: 10/12/2010] [Indexed: 12/15/2022] Open
Abstract
Background Mycobacterium avium subsp. paratuberculosis (MAP) persistently infects intestines and mesenteric lymph nodes leading to a prolonged subclinical disease. The MAP genome sequence was published in 2005, yet its transcriptional organization in natural infection is unknown. While prior research analyzed regulated gene sets utilizing defined, in vitro stress related or advanced surgical methods with various animal species, we investigated the intracellular lifestyle of MAP in the intestines and lymph nodes to understand the MAP pathways that function to govern this persistence. Results Our transcriptional analysis shows that 21%, 8% and 3% of the entire MAP genome was represented either inside tissues, macrophages or both, respectively. Transcripts belonging to latency and cell envelope biogenesis were upregulated in the intestinal tissues whereas those belonging to intracellular trafficking and secretion were upregulated inside the macrophages. Transcriptomes of natural infection and in vitro macrophage infection shared genes involved in transcription and inorganic ion transport and metabolism. MAP specific genes within large sequence polymorphisms of ancestral M. avium complex were downregulated exclusively in natural infection. Conclusions We have unveiled common and unique MAP pathways associated with persistence, cell wall biogenesis and virulence in naturally infected cow intestines, lymph nodes and in vitro infected macrophages. This dichotomy also suggests that in vitro macrophage models may be insufficient in providing accurate information on the events that transpire during natural infection. This is the first report to examine the primary transcriptome of MAP at the local infection site (i.e. intestinal tissue). Regulatory pathways that govern the lifecycle of MAP appear to be specified by tissue and cell type. While tissues show a "shut-down" of major MAP metabolic genes, infected macrophages upregulate several MAP specific genes along with a putative pathogenicity island responsible for iron acquisition. Many of these regulatory pathways rely on the advanced interplay of host and pathogen and in order to decipher their message, an interactome must be established using a systems biology approach. Identified MAP pathways place current research into direct alignment in meeting the future challenge of creating a MAP-host interactome.
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Affiliation(s)
- Harish K Janagama
- Department of Veterinary Population Medicine, University of Minnesota, 1365 Gortner Avenue, Saint Paul, MN 55108, USA
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DR2539 is a novel DtxR-like regulator of Mn/Fe ion homeostasis and antioxidant enzyme in Deinococcus radiodurans. Biochem Biophys Res Commun 2010; 396:413-8. [PMID: 20417183 DOI: 10.1016/j.bbrc.2010.04.106] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 04/17/2010] [Indexed: 11/22/2022]
Abstract
Transcriptional regulators of the diphtheria toxin repressor (DtxR) family control the expression of genes involved in the uptake of iron and manganese, which is not only necessitous nutrients but also was suggested to be essential for intracellular redox cycling of microorganisms. We identified a unique DtxR homologue (DR2539) with special characteristics from Deinococcus radiodurans, which is known for its extreme resistance to radiation and oxidants. The dr2539 mutant showed higher resistance to hydrogen peroxide than the wild-type strain R1. Intracellular catalase activity assay and semiquantitative PCR analysis demonstrated that this DtxR is a negative regulator of catalase (katE). Furthermore, quantitative real-time PCR, global transcription profile and inductively coupled plasma-mass spectrometry analysis showed that the DtxR is involved in the regulation of antioxidant system by maintaining the intracellular Mn/Fe ion homeostasis of D. radiodurans. However, unlike the other DtxR homologues, the DtxR of D. radiodurans acts as a negative regulator of a Mn transporter gene (dr2283) and as a positive regulator of Fe-dependent transporter genes (dr1219, drb0125) in D. radiodurans.
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Bannantine JP, Stabel JR, Bayles DO, Geisbrecht BV. Characteristics of an extensive Mycobacterium avium subspecies paratuberculosis recombinant protein set. Protein Expr Purif 2010; 72:223-33. [PMID: 20359537 DOI: 10.1016/j.pep.2010.03.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 03/17/2010] [Accepted: 03/25/2010] [Indexed: 12/16/2022]
Abstract
In the first step of a comprehensive large-scale antigen discovery project, 651 genes of Mycobacterium avium subspecies paratuberculosis were expressed in Escherichia coli. All of these were purified by affinity chromatography, dialyzed in phosphate buffered saline, and analyzed on SDS-PAGE gels. Collectively, these purified recombinant proteins represent 14.9% of the total M. avium subsp. paratuberculosis proteome. This volume of protein expression and purification has yielded unique observations that may be missed in smaller scale expression and purification projects. For example, the 252 putative membrane proteins predicted by PSORTb analysis, resulted in lower average expression yields (3.51mg/l culture) than the 176 predicted cytoplasmic proteins (7.27mg/l culture). A few proteins (MAP0107c, MAP3169c and MAP3640) appear to promote lysis of E. coli since there was a drop in optical density of the growth culture minutes after the inducing agent was added. Certain M. avium subsp. paratuberculosis proteins, when expressed in E. coli changed the color of the column resin or appearance of harvested cell pellets. Finally, 19 proteins showed an absorbance maximum at 260nm rather than 280nm that was attributed to binding of nucleic acid during purification. This extensive recombinant protein repository provides a powerful tool for proteome- and genome-scale research of this organism.
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Affiliation(s)
- John P Bannantine
- National Animal Disease Center, USDA-ARS, Ames, IA 50010, United States.
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