1
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Ikuno Y, Takahashi T, Yamaguchi A, Kato T, Kishita M, Fujimoto N. Cutaneous infection by Mycobacterium lentiflavum diagnosed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). J Dermatol 2023; 50:e373-e374. [PMID: 37435717 DOI: 10.1111/1346-8138.16881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/13/2023]
Affiliation(s)
- Yasuaki Ikuno
- Department of Dermatology, Shiga University of Medical Science, Otsu, Japan
| | | | - Akihiko Yamaguchi
- Department of Dermatology, Shiga University of Medical Science, Otsu, Japan
| | - Takeshi Kato
- Department of Dermatology, Shiga University of Medical Science, Otsu, Japan
| | - Megumi Kishita
- Department of Clinical Laboratory, Shiga University of Medical Science, Otsu, Japan
| | - Noriki Fujimoto
- Department of Dermatology, Shiga University of Medical Science, Otsu, Japan
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2
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Rodríguez‐Temporal D, Zvezdánova ME, Benedí P, Marín M, Blázquez‐Sánchez M, Ruiz‐Serrano MJ, Muñoz P, Rodríguez‐Sánchez B. Identification of Nocardia and non-tuberculous Mycobacterium species by MALDI-TOF MS using the VITEK MS coupled to IVD and RUO databases. Microb Biotechnol 2023; 16:778-783. [PMID: 36541026 PMCID: PMC10034632 DOI: 10.1111/1751-7915.14146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/22/2022] [Accepted: 09/01/2022] [Indexed: 12/24/2022] Open
Abstract
Identification of Nocardia and Mycobacterium species by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is still a challenging task that requires both suitable protein extraction procedures and extensive databases. This study aimed to evaluate the VITEK MS Plus system coupled with updated RUO (v4.17) and IVD (v3.2) databases for the identification of Nocardia spp. and Mycobacterium spp. clinical isolates. Sample preparation was carried out using the VITEK MS Mycobacterium/Nocardia kit for protein extraction. From 90 Nocardia spp. isolates analysed, 86 (95.6%) were correctly identified at species or complex level using IVD and 78 (86.7%) using RUO. Only two strains were misidentified as other species pertaining to the same complex. Among the 106 non-tuberculous Mycobacterium clinical isolates tested from a liquid culture medium, VITEK MS identified correctly at species or complex level 96 (90.6%) isolates in the IVD mode and 89 (84.0%) isolates in the RUO mode. No misidentifications were detected. Although the IVD mode was unable to differentiate members of the M. fortuitum complex, the RUO mode correctly discriminated M. peregrinum and M. septicum. The robustness and accuracy showed by this system allow its implementation for routine identification of these microorganisms in clinical laboratories.
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Affiliation(s)
- David Rodríguez‐Temporal
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
| | - Margarita Estreya Zvezdánova
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
| | - Pablo Benedí
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
| | - Mercedes Marín
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
- CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058)MadridSpain
| | - Mario Blázquez‐Sánchez
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
| | - María Jesús Ruiz‐Serrano
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
- CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058)MadridSpain
- Medicine Department, Faculty of MedicineUniversidad Complutense de MadridMadridSpain
| | - Belén Rodríguez‐Sánchez
- Clinical Microbiology and Infectious Diseases DepartmentHospital General Universitario Gregorio MarañónMadridSpain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM)MadridSpain
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3
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Hodges H, Obeng K, Avanzi C, Ausmus AP, Angala SK, Kalera K, Palcekova Z, Swarts BM, Jackson M. Azido Inositol Probes Enable Metabolic Labeling of Inositol-Containing Glycans and Reveal an Inositol Importer in Mycobacteria. ACS Chem Biol 2023; 18:595-604. [PMID: 36856664 PMCID: PMC10071489 DOI: 10.1021/acschembio.2c00912] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Bacteria from the genus Mycobacterium include pathogens that cause serious diseases in humans and remain as difficult infectious agents to treat. Central to these challenges are the composition and organization of the mycobacterial cell envelope, which includes unique and complex glycans. Inositol is an essential metabolite for mycobacteria due to its presence in the structural core of the immunomodulatory cell envelope glycolipids phosphatidylinositol mannoside (PIM) and PIM-anchored lipomannan (LM) and lipoarabinomannan (LAM). Despite their importance to mycobacterial physiology and pathogenesis, many aspects of PIM, LM, and LAM construction and dynamics remain poorly understood. Recently, probes that allow metabolic labeling and detection of specific mycobacterial glycans have been developed to investigate cell envelope assembly and dynamics. However, these tools have been limited to peptidoglycan, arabinogalactan, and mycolic acid-containing glycolipids. Herein, we report the development of synthetic azido inositol (InoAz) analogues as probes that can metabolically label PIMs, LM, and LAM in intact mycobacteria. Additionally, we leverage an InoAz probe to discover an inositol importer and catabolic pathway in Mycobacterium smegmatis. We anticipate that in the future, InoAz probes, in combination with bioorthogonal chemistry, will provide a valuable tool for investigating PIM, LM, and LAM biosynthesis, transport, and dynamics in diverse mycobacterial organisms.
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Affiliation(s)
- Heather Hodges
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523 USA
| | - Kwaku Obeng
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, 48859 USA
| | - Charlotte Avanzi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523 USA
| | - Alex P. Ausmus
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, 48859 USA
| | - Shiva Kumar Angala
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523 USA
| | - Karishma Kalera
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, 48859 USA
- Biochemistry, Cellular, and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI, 48859 USA
| | - Zuzana Palcekova
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523 USA
| | - Benjamin M. Swarts
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, 48859 USA
- Biochemistry, Cellular, and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI, 48859 USA
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523 USA
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4
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Qiu W, Guo Y. Analysis of the oligomeric state of mycobacterial membrane protein large 3 and its interaction with SQ109 with native cell membrane nanoparticles system. Biochim Biophys Acta Biomembr 2022; 1864:183793. [PMID: 34655545 DOI: 10.1016/j.bbamem.2021.183793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 01/24/2023]
Abstract
Mycobacterial membrane protein large 3 (Mmpl3) as a trehalose monomycolate lipid transporter contributes to cell wall biosynthesis. Inhibition of Mmpl3 can suppress cell growth and lead to mycobacterial death. SQ109 is a hydrophobic inhibitor of Mmpl3. We have devised a detergent-free strategy to characterize the SQ109/Mmpl3 interaction using the Native Cell Membrane Nanoparticles (NCMN) system, a new method for extracting membrane proteins that better retains native lipids. The homogeneity of the Mmpl3 NCMN particles was confirmed with electron microscopy. The hydrophobic protein-ligand interaction analysis shown for Mmpl3 using the NCMN system may broadly apply to other membrane proteins.
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Affiliation(s)
- Weihua Qiu
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; Institute for Structural Biology, Drug Discovery, and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23219, USA.
| | - Youzhong Guo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; Institute for Structural Biology, Drug Discovery, and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23219, USA
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5
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Jackson M, Stevens CM, Zhang L, Zgurskaya HI, Niederweis M. Transporters Involved in the Biogenesis and Functionalization of the Mycobacterial Cell Envelope. Chem Rev 2021; 121:5124-5157. [PMID: 33170669 PMCID: PMC8107195 DOI: 10.1021/acs.chemrev.0c00869] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The biology of mycobacteria is dominated by a complex cell envelope of unique composition and structure and of exceptionally low permeability. This cell envelope is the basis of many of the pathogenic features of mycobacteria and the site of susceptibility and resistance to many antibiotics and host defense mechanisms. This review is focused on the transporters that assemble and functionalize this complex structure. It highlights both the progress and the limits of our understanding of how (lipo)polysaccharides, (glyco)lipids, and other bacterial secretion products are translocated across the different layers of the cell envelope to their final extra-cytoplasmic location. It further describes some of the unique strategies evolved by mycobacteria to import nutrients and other products through this highly impermeable barrier.
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Affiliation(s)
- Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA
| | - Casey M. Stevens
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Lei Zhang
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL 35294, USA
| | - Helen I. Zgurskaya
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL 35294, USA
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6
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Oliva E, Arosio M, Mazzola E, Mascheroni M, Cerro A, Cuntró M, Vailati F, Cavallini M, Farina C. Rapid identification of non-tuberculous mycobacteria with MALDI-TOF mass spectrometry. Infez Med 2021; 29:79-84. [PMID: 33664176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Rapid and accurate identification of non-tuberculous mycobacteria (NTM) is important for a prompt start to antibiotic therapy. The aim of this study was to obtain accurate identification of NTM quickly by analyzing the performance of the MALDI-TOF mass spectrometry (MS) system VITEK® MS in identifying various NTM species from solid medium and MGIT 960 liquid medium. The study was performed in two phases: preliminary and perspective. Overall, 41/42 species and 33/34 species were correctly identified from the MGIT medium in the preliminary and perspective phases, respectively. The VITEK® MS system includes in its database part of the mycobacteria from the Mycobacterium fortuitum complex but is unable to discriminate among the various species belonging to the complex. Although the VITEK® MS system does not have the protein spectrum of Mycobacterium chimaera, it is not able to distinguish between Mycobacterium chimaera and Mycobacterium intracellulare. Since the VITEK® MS includes the separate protein spectrum of both M. chelonae and M. abscessus, it can discriminate between the two microorganisms. Thanks to these studies we show that the VITEK® MS system is a reliable method for identification of NTMs directly from MGIT liquid medium, instead of the use of solid media.
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Affiliation(s)
- Ester Oliva
- Microbiology Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Marco Arosio
- Microbiology Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Ester Mazzola
- Microbiology Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | | | - Annarosa Cerro
- Microbiology Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Marina Cuntró
- Microbiology Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
| | | | | | - Claudio Farina
- Microbiology Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
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7
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Angala SK, Joe M, McNeil MR, Liav A, Lowary TL, Jackson M. Use of Synthetic Glycolipids to Probe the Number and Position of Arabinan Chains on Mycobacterial Arabinogalactan. ACS Chem Biol 2021; 16:20-26. [PMID: 33382235 PMCID: PMC7859836 DOI: 10.1021/acschembio.0c00765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The arabinogalactan of Corynebacterianeae is a critical heteropolysaccharide that tethers outer membrane mycolic acids to peptidoglycan thus forming the characteristic cell wall core of these prokaryotes. An essential α-(1→5)-arabinosyltransferase, AftA, is responsible for the transfer of the first arabinofuranosyl (Araf) unit of the arabinan domain to the galactan backbone of arabinogalactan, but the number and precise position at which Araf residue(s) is/are added in mycobacteria remain ill-defined. Using membrane preparations from Mycobacterium smegmatis overexpressing aftA, farnesyl-phospho-arabinose as an Araf donor, and a series of synthetic galactan acceptors of various lengths, we here show that a single priming arabinosyl residue substitutes the C-5 position of a precisely positioned internal 6-linked galactofuranosyl residue of the galactan acceptors, irrespective of their length. This unexpected result suggests that, like the structurally related mycobacterial lipoarabinomannans, the arabinogalactan of mycobacteria may in fact harbor a single arabinan chain.
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Affiliation(s)
- Shiva Kumar Angala
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA
| | - Maju Joe
- Department of Chemistry, The University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Michael R. McNeil
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA
| | - Avraham Liav
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA
| | - Todd L. Lowary
- Department of Chemistry, The University of Alberta, Edmonton, AB, T6G 2G2, Canada
- Institute of Biological Chemistry, Academia Sinica, Nangang Taipei 11529, Taiwan
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA
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8
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Abstract
Mass spectrometry-based single-cell proteomic analysis has recently gained momentum and is now an emerging area with established protocols and promising results. Traditional proteomic studies, especially involving bacteria, have been limited to suspension cultures with large protein yields. Such studies, however, remain population centered with the uniqueness of individual responses to environmental challenges becoming diluted. To enable bacterial single-colony proteomics, we describe a quantitative mass spectrometry-based protocol to isolate and analyze the proteome of a single mycobacterial colony from 7H10 media, with growth supplements for optimal growth. Following protein purification and digestion, tryptic peptides are analyzed by UHPLC coupled to a hybrid Q Exactive mass spectrometer. Raw data were analyzed using the MaxQuant Suite, and downstream statistical analysis was performed using Perseus software. A total of 7805 unique peptides and 1387 proteins were identified. Data are available via ProteomeXchange with identifier PXD018168. In this chapter, we identify steps most prone to sample loss and describe measures of alleviation that allows the preservation of protein yield and boosts quantitative power while increasing reproducibility, of "very limiting samples."
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Affiliation(s)
- John Iradukunda
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Tariq Ganief
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jonathan M Blackburn
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease & Molecular Medicine, UCT, Cape Town, South Africa
| | - Nelson C Soares
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah, United Arab Emirates.
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.
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9
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Belcher Dufrisne M, Jorge CD, Timóteo CG, Petrou VI, Ashraf KU, Banerjee S, Clarke OB, Santos H, Mancia F. Structural and Functional Characterization of Phosphatidylinositol-Phosphate Biosynthesis in Mycobacteria. J Mol Biol 2020; 432:5137-5151. [PMID: 32389689 PMCID: PMC7483940 DOI: 10.1016/j.jmb.2020.04.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/23/2020] [Accepted: 04/28/2020] [Indexed: 01/05/2023]
Abstract
In mycobacteria, phosphatidylinositol (PI) acts as a common lipid anchor for key components of the cell wall, including the glycolipids phosphatidylinositol mannoside, lipomannan, and lipoarabinomannan. Glycolipids in Mycobacterium tuberculosis, the causative agent of tuberculosis, are important virulence factors that modulate the host immune response. The identity-defining step in PI biosynthesis in prokaryotes, unique to mycobacteria and few other bacterial species, is the reaction between cytidine diphosphate-diacylglycerol and inositol-phosphate to yield phosphatidylinositol-phosphate, the immediate precursor to PI. This reaction is catalyzed by the cytidine diphosphate-alcohol phosphotransferase phosphatidylinositol-phosphate synthase (PIPS), an essential enzyme for mycobacterial viability. Here we present structures of PIPS from Mycobacterium kansasii with and without evidence of donor and acceptor substrate binding obtained using a crystal engineering approach. PIPS from Mycobacterium kansasii is 86% identical to the ortholog from M. tuberculosis and catalytically active. Functional experiments guided by our structural results allowed us to further characterize the molecular determinants of substrate specificity and catalysis in a new mycobacterial species. This work provides a framework to strengthen our understanding of phosphatidylinositol-phosphate biosynthesis in the context of mycobacterial pathogens.
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Affiliation(s)
- Meagan Belcher Dufrisne
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Carla D Jorge
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República-EAN, 2780-157 Oeiras, Portugal
| | - Cristina G Timóteo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República-EAN, 2780-157 Oeiras, Portugal
| | - Vasileios I Petrou
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Khuram U Ashraf
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Surajit Banerjee
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA; Department of Anesthesiology, Columbia University, New York, NY 10032, USA
| | - Helena Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República-EAN, 2780-157 Oeiras, Portugal
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.
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10
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Matsumoto M, Hayashi K, Araki K, Nakanishi T, Yamamoto A. Availability of culture filtrate protein-10 (CFP-10) secreted from Mycobacterium pseudoshottsii for mycobacteriosis diagnosis in ginbuna crucian carp Carrasius auratus langsdorfii. J Fish Dis 2020; 43:81-89. [PMID: 31701546 DOI: 10.1111/jfd.13108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Abstract
Mycobacteriosis in cultured fish is a challenge for the aquaculture industry worldwide. Treatment by chemical administration is difficult and no effective vaccine has been developed. Therefore, detection and isolation by early diagnosis are important for prevention of the spread of the disease. In mammals, interferon gamma release assays have been established for detection of tuberculosis; these tests are based on the delayed-type hypersensitivity (DTH) response against culture filtrate protein-10 (CFP-10) and the 6-kDa early secreted antigen target (ESAT-6) of Mycobacterium tuberculosis. On the other hand, little is known about the fish immune response against the ESAT-6 and CFP-10 proteins of mycobacteria, although these responses should find application in the diagnosis of mycobacteriosis in fish. In the present study, we identified ESAT-6 and CFP-10 from Mycobacterium pseudoshottsii and cloned the corresponding genes. Intraperitoneal injection of the corresponding DNA plasmid constructs in ginbuna crucian carp yielded increased expression of the fish interferon-γ1-1-encoding gene (IFN-γ1-1). In contrast, IFN-γ1-1 expression accompanied by DTH response was observed only in the CFP-10-DNA plasmid-injected fish. Furthermore, fish that had been prophylactically injected with CFP-10-DNA plasmid exhibited increased survival of M. pseudoshottsii infection. Taken together, these results suggested that CFP-10 may facilitate diagnosis of mycobacteriosis.
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Affiliation(s)
- Megumi Matsumoto
- Department of Marine Bioscience, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Kazuma Hayashi
- Faculty of Fisheries, Kagoshima University, Kagoshima, Japan
| | - Kyosuke Araki
- Department of Marine Bioscience, Tokyo University of Marine Science and Technology, Tokyo, Japan
- Faculty of Fisheries, Kagoshima University, Kagoshima, Japan
| | - Teruyuki Nakanishi
- Department of Veterinary Medicine, Nihon University, Fujisawa, Kanagawa, Japan
| | - Atsushi Yamamoto
- Department of Marine Bioscience, Tokyo University of Marine Science and Technology, Tokyo, Japan
- Faculty of Fisheries, Kagoshima University, Kagoshima, Japan
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11
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Ahmad E, Hegde SR, Nagaraja V. Revisiting intrinsic transcription termination in mycobacteria: U-tract downstream of secondary structure is dispensable for termination. Biochem Biophys Res Commun 2019; 522:226-232. [PMID: 31759631 DOI: 10.1016/j.bbrc.2019.11.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/09/2019] [Indexed: 11/30/2022]
Abstract
In Escherichia coli, G/C-rich hairpin structure followed by a U-tract in the 3' region of the nascent RNA are crucial determinants for intrinsic or factor independent transcription termination. In mycobacteria, there is a scarcity of such intrinsic terminators. However, secondary structures having G/C-rich stem devoid of any U's or with suboptimal U-tracts were identified earlier as terminators and found to be functional both in vitro and in vivo. Two different observations - that a mycobacterial RNA polymerase (RNAP) does not function at intrinsic terminators devoid of U-tracts and the identification of an altogether new motif for termination in mycobacteria necessitated re-examining a number of putative terminators for their function as terminators. When these in silico identified non-canonical terminators were subjected to experimental validation, they were found to dissociate RNA from the elongating RNAP. Termination is observed when the U-tracts were reduced, or totally absent both in vitro and in vivo. Our results, thus indicate that the presence of U-tract following the G/C-rich stem in an intrinsic terminator may not be an essential determinant for transcription termination in mycobacteria.
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Affiliation(s)
- Ezaz Ahmad
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, 560012, India
| | - Shubhada R Hegde
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, 560100, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560100, India.
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12
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Rotcheewaphan S, Lemon JK, Desai UU, Henderson CM, Zelazny AM. Rapid one-step protein extraction method for the identification of mycobacteria using MALDI-TOF MS. Diagn Microbiol Infect Dis 2019; 94:355-360. [PMID: 31053254 DOI: 10.1016/j.diagmicrobio.2019.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/06/2019] [Accepted: 03/10/2019] [Indexed: 11/19/2022]
Abstract
Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry is a quick and accurate method for mycobacterial identification from protein extracts. Our new one-step extraction method successfully reduced routine multistep extraction procedure time from over 60 min to under 10 min and used only 1 μL loopful of mycobacteria while providing clinically acceptable identification scores (≥1.8). Overall, 86.8% and 4.4% of mycobacteria isolates (n = 68) were identified to the species/complex and genus levels, respectively, by one-step loop extraction method, comparable to the routine extraction method. Viability studies confirmed killing of mycobacterial isolates after 5 min in the extraction solution replacing lengthy heat killing step. Retrospective 7-month data analysis showed 100% of rapidly and slowly growing mycobacterial isolates were identified to the species/complex level by rapid extraction methods. Our rapid extraction methods substantially reduced processing time and microbial biomass required for testing without sacrificing quality and accuracy of mycobacterial identification.
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Affiliation(s)
- Suwatchareeporn Rotcheewaphan
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA; Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jamie K Lemon
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Uma U Desai
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Christina M Henderson
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Adrian M Zelazny
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA.
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13
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Abstract
Mycobacteria and related bacteria in the Actinobacteria phylum are unusual in that they produce phosphatidylinositol (PI) as a major phospholipid species. PI can be further modified by glycan polymers, leading to the synthesis of PI mannosides (PIMs), lipomannan (LM), and lipoarabinomannan (LAM). Small lipids such as PI and PIMs are extracted with a mixture of chloroform, methanol, and water and analyzed by thin layer chromatography. For larger glycolipids, such as LM and LAM, more hydrophilic solvent is needed for the extraction, and SDS-PAGE is better suited for the analysis. For LM, further structural characterization can be performed by MALDI-TOF mass spectrometry. Precise quantification of PIMs, LM, and LAM can be performed by quantification of glycan staining using analytical software. The metabolic radiolabeling protocol is also described.
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Affiliation(s)
- Kathryn C Rahlwes
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Julia Puffal
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA.
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14
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Liu M, Xiong LB, Tao X, Liu QH, Wang FQ, Wei DZ. Metabolic Adaptation of Mycobacterium neoaurum ATCC 25795 in the Catabolism of Sterols for Producing Important Steroid Intermediates. J Agric Food Chem 2018; 66:12141-12150. [PMID: 30362748 DOI: 10.1021/acs.jafc.8b04777] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
To understand the adaptation of Mycobacterium neoaurum ATCC25795 ( Mn) in sterol catabolism and steroid production, we used integrated transcriptome and proteome analysis to identify the biochemical pathways utilized in this process. Metabolic alterations during sterol catabolism center on propionyl-CoA pools. Generally, enhanced pathways for metabolizing propionyl-CoA were found in Mn, which were tightly coordinated with cell-envelope biosynthesis. The cells responded to sterol substrates and toxic steroid products by changing the composition of the cell envelope. This adaptive mechanism allowed Mn to use minimally water-soluble sterol as a carbon source. Several putative efflux proteins were found to be induced in Mn. They probably transported products to the extracellular environment, protecting the cells against high intracellular levels of toxic intermediates, inhibition of which also influenced sterol uptake. The work provided various targets for rational engineering of robust Mn with powerful sterol-uptake capacity and strong tolerance to toxic products for the steroid industry.
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Affiliation(s)
- Min Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
| | - Liang-Bin Xiong
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
| | - Xinyi Tao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
| | - Qing-Hai Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
| | - Feng-Qing Wang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
| | - Dong-Zhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
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15
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Liu M, Xiong LB, Tao X, Liu QH, Wang FQ, Wei DZ. Integrated Transcriptome and Proteome Studies Reveal the Underlying Mechanisms for Sterol Catabolism and Steroid Production in Mycobacterium neoaurum. J Agric Food Chem 2018; 66:9147-9157. [PMID: 30075077 DOI: 10.1021/acs.jafc.8b02714] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Integrated transcriptome and proteome studies were performed to investigate sterol biotransformation in wild-type Mycobacterium neoaurum ATCC 25795 ( Mn) and the mutant strains producing steroid intermediates. Transcriptome and proteome studies indicated that several metabolic activities were noticeably dynamic, including cholesterol degradation, central carbon metabolism, cell envelope biosynthesis, glycerol metabolism, and transport. Interestingly, a poor overall correlation between mRNA and translation profiles was found, which might contribute to the metabolic adaptation in cholesterol catabolism. A gene cluster covering 111 genes was discovered to encode for cholesterol catabolism in Mn. Generally, transcription and/or translation of the genes in KstR1 regulon was upregulated, and the induction of genes in KstR2 regulon was not as significant as that of KstR1 regulon. Several induced genes showing potential roles for cholesterol catabolism were found. Further identification of these genes and investigation of the correlation among key metabolic activities could help for the development of efficient steroid-producing strains.
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Affiliation(s)
- Min Liu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Liang-Bin Xiong
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Xinyi Tao
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Qing-Hai Liu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Feng-Qing Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Dong-Zhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
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16
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Owens NA, Laurentius LB, Porter MD, Li Q, Wang S, Chatterjee D. Handheld Raman Spectrometer Instrumentation for Quantitative Tuberculosis Biomarker Detection: A Performance Assessment for Point-of-Need Infectious Disease Diagnostics. Appl Spectrosc 2018; 72:1104-1115. [PMID: 29664331 DOI: 10.1177/0003702818770666] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Techniques for the detection of disease biomarkers are key components in the protection of human health. While work over the last few decades has redefined the low-level measurement of disease biomarkers, the translation of these capabilities from the formal clinical setting to point-of-need (PON) usage has been much more limited. This paper presents the results of experiments designed to examine the potential utility of a handheld Raman spectrometer as a PON electronic reader for a sandwich immunoassay based on surface-enhanced Raman scattering (SERS). In so doing, the study herein used a recently developed procedure for the SERS detection of phospho-myo-inositol-capped lipoarabinomannan (PILAM) as a means to compare the performance of laboratory-grade and handheld instrumentation and, therefore, gauge the utility of the handheld instrument for PON deployment. Phospho-myo-inositol-capped lipoarabinomannan is a non-pathogenic simulant for mannose-capped lipoarabinomannan (ManLAM), which is an antigenic marker found in serum and other body fluids of individuals infected with tuberculosis (TB). The results of the measurements with the field-portable spectrometer were then compared to those obtained for the same samples when using a much more sensitive benchtop Raman spectrometer. The results, albeit under different operational settings for the two spectrometers (e.g., signal integration time), are promising in that the limit of detection found for PILAM spiked in human serum when using the handheld system (0.18 ng/mL) approached that of the benchtop instrument (0.032 ng/mL). This work also: (1) identified potential adaptations (e.g., optimization of the plasmonically enhanced response for measurement by the handheld unit through a change in the excitation wavelength) to tighten the gap in performance; and (2) briefly examined the next steps and potential processes required to move this immunoassay platform closer to PON utility.
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Affiliation(s)
- Nicholas A Owens
- 1 Department of Chemistry, University of Utah, Salt Lake City, UT, USA
| | - Lars B Laurentius
- 2 Nano Institute of Utah, University of Utah, Salt Lake City, UT, USA
| | - Marc D Porter
- 1 Department of Chemistry, University of Utah, Salt Lake City, UT, USA
- 2 Nano Institute of Utah, University of Utah, Salt Lake City, UT, USA
- 3 Department of Chemical Engineering, University of Utah, Salt Lake City, UT, USA
| | - Qun Li
- 4 B&W Tek, Inc., Newark, DE, USA
| | | | - Delphi Chatterjee
- 5 Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
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Wanapaisan P, Laothamteep N, Vejarano F, Chakraborty J, Shintani M, Muangchinda C, Morita T, Suzuki-Minakuchi C, Inoue K, Nojiri H, Pinyakong O. Synergistic degradation of pyrene by five culturable bacteria in a mangrove sediment-derived bacterial consortium. J Hazard Mater 2018; 342:561-570. [PMID: 28886568 DOI: 10.1016/j.jhazmat.2017.08.062] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 08/17/2017] [Accepted: 08/23/2017] [Indexed: 05/22/2023]
Abstract
A pyrene-degrading microbial consortium was obtained after enrichment with mangrove sediment collected from Thailand. Five cultivable bacteria (Mycobacterium spp. PO1 and PO2, Novosphingobium pentaromativorans PY1, Ochrobactrum sp. PW1, and Bacillus sp. FW1) were successfully isolated from the consortium. Draft genomes of them showed that two different morphotypes of Mycobacterium (PO1 and PO2), possessed a complete gene set for pyrene degradation. PY1 contained genes for phthalate assimilation via protocatechuate, a central intermediate, by meta-cleavage pathway, and PW1 possessed genes for protocatechuate degradation via ortho-cleavage pathway. The occurrence of biosurfactant-producing genes in FW1 suggests the involvement in enhancing the pyrene bioavailability. Biotransformation experiments revealed that Mycobacterium completely degraded 100mgL-1 pyrene within six days, whereas no significant degradation was observed with the others. Notably, PY1 and PW1 exhibited higher activity for protocatechuate degradation than the others. The artificially reconstructed consortia containing Mycobacterium with the other three strains (PY1, PW1 and FW1) showed three-fold higher degradation rate for pyrene than the individual Mycobacterium. The enhanced pyrene biodegradation achieved in the consortium was due to the cooperative interaction of bacterial mixture. Our findings showing that synergistic degradation of pyrene in the consortium will facilitate the application of the defined bacterial consortium in bioremediation.
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Affiliation(s)
- Pagakrong Wanapaisan
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Natthariga Laothamteep
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Felipe Vejarano
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Joydeep Chakraborty
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masaki Shintani
- Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Chanokporn Muangchinda
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Tomomi Morita
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; Department of Bioscience and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama, Saitama 337-8570, Japan
| | - Chiho Suzuki-Minakuchi
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kengo Inoue
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki, Miyazaki 889-2192, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Onruthai Pinyakong
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand; Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand; Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand.
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18
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Jaén-Luchoro D, Aliaga-Lozano F, Gomila RM, Gomila M, Salvà-Serra F, Lalucat J, Bennasar-Figueras A. First insights into a type II toxin-antitoxin system from the clinical isolate Mycobacterium sp. MHSD3, similar to epsilon/zeta systems. PLoS One 2017; 12:e0189459. [PMID: 29236773 PMCID: PMC5728571 DOI: 10.1371/journal.pone.0189459] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 11/28/2017] [Indexed: 01/21/2023] Open
Abstract
A putative type II toxin-antitoxin (TA) system was found in the clinical isolate Mycobacterium sp. MHSD3, a strain closely related to Mycobacterium chelonae. Further analyses of the protein sequences of the two genes revealed the presence of domains related to a TA system. BLAST analyses indicated the presence of closely related proteins in the genomes of other recently published M. chelonae strains. The functionality of both elements of the TA system was demonstrated when expressed in Escherichia coli cells, and the predicted structure of the toxin is very similar to those of well-known zeta-toxins, leading to the definition of a type II TA system similar to epsilon/zeta TA systems in strains that are closely related to M. chelonae.
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Affiliation(s)
- Daniel Jaén-Luchoro
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
- * E-mail:
| | - Francisco Aliaga-Lozano
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Laboratorio de Biología Molecular, Clínica Rotger, Palma de Mallorca, Spain
| | - Rosa Maria Gomila
- Serveis Cientifico-Tècnics, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Francisco Salvà-Serra
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Institut Mediterrani d’Estudis Avançats (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Antoni Bennasar-Figueras
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Area de Enfermedades Infecciosas, Instituto Universitario de Investigaciones en Ciencias de la Salud (IUNICS-UIB), Universitat de les Illes Balears, Palma de Mallorca, Spain
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19
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Hanson C, Sieverts M, Vargis E. Effect of Principal Component Analysis Centering and Scaling on Classification of Mycobacteria from Raman Spectra. Appl Spectrosc 2017; 71:1249-1255. [PMID: 27888200 DOI: 10.1177/0003702816678867] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Raman spectroscopy has been used for decades to detect and identify biological substances as it provides specific molecular information. Spectra collected from biological samples are often complex, requiring the aid of data truncation techniques such as principal component analysis (PCA) and multivariate classification methods. Classification results depend on the proper selection of principal components (PCs) and how PCA is performed (scaling and/or centering). There are also guidelines for choosing the optimal number of PCs such as a scree plot, Kaiser criterion, or cumulative percent variance. The goal of this research is to evaluate these methods for best implementation of PCA and PC selection to classify Raman spectra of bacteria. Raman spectra of three different isolates of mycobacteria ( Mycobacterium sp. JLS, Mycobacterium sp. KMS, Mycobacterium sp. MCS) were collected and then passed through PCA and linear discriminant analysis for classification. Principal component analysis implementation as well as PC selection was evaluated by comparing the highest possible classification accuracies against accuracies determined by PC selection methods for each centering and scaling option. Centered and unscaled data provided the best results when selecting PCs based on cumulative percent variance.
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Affiliation(s)
- Cynthia Hanson
- Department of Biological Engineering, Utah State University, UT, USA
| | - Michael Sieverts
- Department of Biological Engineering, Utah State University, UT, USA
| | - Elizabeth Vargis
- Department of Biological Engineering, Utah State University, UT, USA
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20
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Xiong LB, Liu HH, Xu LQ, Wei DZ, Wang FQ. Role Identification and Application of SigD in the Transformation of Soybean Phytosterol to 9α-Hydroxy-4-androstene-3,17-dione in Mycobacterium neoaurum. J Agric Food Chem 2017; 65:626-631. [PMID: 28035826 DOI: 10.1021/acs.jafc.6b05314] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
9α-Hydroxy-4-androstene-3,17-dione (9-OHAD) is a valuable steroid pharmaceutical intermediate which can be produced by the conversion of soybean phytosterols in mycobacteria. However, the unsatisfactory productivity and conversion efficiency of engineered mycobacterial strains hinder their industrial applications. Here, a sigma factor D (sigD) was investigated due to its dramatic downregulation during the conversion of phytosterols to 9-OHAD. It was determined as a negative regulator in the metabolism of phytosterols, and the deletion of sigD in a 9-OHAD-producing strain significantly enhanced the titer of 9-OHAD by 18.9%. Furthermore, a high yielding strain was constructed by the combined modifications of sigD and choM2, a key gene in the phytosterol metabolism pathway. After the modifications, the productivity of 9-OHAD reached 0.071 g/L/h (10.27 g/L from 20 g/L phytosterol), which was 22.5% higher than the original productivity of 0.058 g/L/h (8.37 g/L from 20 g/L phytosterol) in the industrial resting cell biotransformation system.
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Affiliation(s)
- Liang-Bin Xiong
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology , Shanghai, China
| | - Hao-Hao Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology , Shanghai, China
| | - Li-Qin Xu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology , Shanghai, China
| | - Dong-Zhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology , Shanghai, China
| | - Feng-Qing Wang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology , Shanghai, China
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Abstract
The importance of the pathogenic mycobacteria has mainly focused the omic analyses on different aspects of their clinical significance. In contrast, those industrially relevant mycobacteria have received less attention, even though the steroids market sales in 2011, in example, were estimated in $8 billion.The extra-cellular proteome, due to its relevance in the sterols processing and uptake; as well as the intra-cellular proteome, because of its role in steroids bioconversion, are the core of the present chapter. As a proof of concept, the obtaining methods for both sub-proteomes of Mycobacterium neoaurum NRRL B-3805, a relevant industrial strain involved in steroids production, have been developed. Thus, procedures and relevant key points of these proteomes analyses are fully described.
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Affiliation(s)
- Carlos Barreiro
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Avda. Real 1, 24006, León, Spain.
- Área de Microbiología, Departamento de Biología Molecular, Campus de Ponferrada, Universidad de León, Avda. Astorga, s/n, 24400, Ponferrada, Spain.
| | - Alejandro Morales
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Avda. Real 1, 24006, León, Spain
| | - Inés Vázquez-Iglesias
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Avda. Real 1, 24006, León, Spain
| | - Alberto Sola-Landa
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Avda. Real 1, 24006, León, Spain
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Martin-Bertelsen B, Yaghmur A, Franzyk H, Justesen S, Kirkensgaard JJK, Foged C. Conserved Molecular Superlattices in a Series of Homologous Synthetic Mycobacterial Cell-Wall Lipids Forming Interdigitated Bilayers. Langmuir 2016; 32:12693-12701. [PMID: 27934510 DOI: 10.1021/acs.langmuir.6b01720] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Synthetic analogues of the cell-wall lipid monomycoloyl glycerol (MMG) are promising as next-generation vaccine adjuvants. In the present study, the thermotropic phase behavior of an array of synthetic MMG analogues was examined by using simultaneous small- and wide-angle X-ray scattering under excess water conditions. The MMG analogues differed in the alkyl chain lengths and in the stereochemistry of the polar glycerol headgroup or of the lipid tails (native-like versus alternative compounds). All MMG analogues formed poorly hydrated lamellar phases at low temperatures and inverse hexagonal (H2) phases at higher temperatures prior to melting. MMG analogues with a native-like lipid acid configuration self-assembled into noninterdigitated bilayers whereas the analogues displaying an alternative lipid acid configuration formed interdigitated bilayers in a subgel (Lc') state. This is in contrast to previously described interdigitated phases for other lipids, which are usually in a gel (Lβ) state. All investigated MMG analogues displayed an abrupt direct temperature-induced phase transition from Lc' to H2. This transition is ultimately driven by the lipid chain melting and the accompanying change in molecular shape. No intermediate structures were found, but the entire array of MMG analogues displayed phase coexistence during the lamellar to H2 transition. The structural data also showed that the headgroups of the MMG analogues adopting the alternative lipid acid configuration were ordered and formed a two-dimensional molecular superlattice, which was conserved regardless of the lipid tail length. To our knowledge, the MMG analogues with an alternative lipid acid configuration represent the first example of a lipid system showing both interdigitation and superlattice formation, and as such could serve as an interesting model system for future studies. The MMG analogues are also relevant from a subunit vaccine perspective because they are well-tolerated and display promising immunopotentiating activity. The structural characterization described here will serve as a prerequisite for the rational design of nanoparticulate adjuvants with specific and tailored structural features.
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Affiliation(s)
| | | | | | | | - Jacob J K Kirkensgaard
- Niels Bohr Institute, Faculty of Science, University of Copenhagen , Universitetsparken 5, 2100 Copenhagen, Denmark
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Zingue D, Flaudrops C, Drancourt M. Direct matrix-assisted laser desorption ionisation time-of-flight mass spectrometry identification of mycobacteria from colonies. Eur J Clin Microbiol Infect Dis 2016; 35:1983-1987. [PMID: 27549109 DOI: 10.1007/s10096-016-2750-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/03/2016] [Indexed: 11/30/2022]
Abstract
Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) identification of mycobacteria requires a standard acetonitrile/formic acid pre-MALDI-TOF-MS. We prospectively compared this standard protocol with direct deposit with matrix for the identification of mycobacteria cultured on solid media. We first verified that Mycobacterium tuberculosis was killed after it was mixed with matrix. Then, 111 Mycobacterium isolates previously identified by partial rpoB gene sequencing were tested in parallel by the two protocols. An identification score >1.7 was obtained in 86/111 (77.5 %) isolates after protein extraction versus 97/111 (87.4 %) isolates after direct deposit (p = 0.039, Chi-squared test). In a third step, we determined that direct deposit achieved identification for as few as 2.104 M. tuberculosis organisms. In a fourth step, we evaluated direct deposit of one colony for 116 solid medium-cultured clinical isolates finally identified as representative of 12 species (63.8 % M. tuberculosis). For 114/116 (98.3 %) isolates with an identification score >1.2, the MALDI-TOF-MS identification was in complete agreement with the reference rpoB gene sequencing identification. One isolate with a MALDI-TOF-MS identification score of 1.22 for M. fortuitum was identified as M. avium by partial rpoB gene sequencing. One other isolate with a MALDI-TOF-MS identification score of 1.22 for M. tuberculosis was identified as M. tuberculosis by genotyping. All the original MALDI-TOF-MS spectra reported here have been deposited in a public database. Direct deposit of one colony on a MALDI-TOF-MS plate allows for an accurate identification of mycobacteria for an identification score >1.3.
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Affiliation(s)
- D Zingue
- Aix-Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France
| | - C Flaudrops
- Aix-Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France
| | - M Drancourt
- Aix-Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France.
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24
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Xu L, Wang X, Yang H, Yang L, Shi W, Xie Y, Lin S. [Whole-genome sequencing and analysis of a adrostenedione yielding strains Mycobacterium neoaurum MN4]. Wei Sheng Wu Xue Bao 2016; 56:1358-1367. [PMID: 29738205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
OBJECTIVE Mycobaterium neoaurum MN4 is a substrate-resistant mutant strain with high-yield androstenedione. In order to further study MN4 strain substrate-resistant mechanism and androstenedione biosynthetic pathway, it is necessary to decipher the MN4 strain genome. METHODS The genome was sequenced using highthroughput sequencing technology, and analyzed using relevant software for genome assembly, gene prediction and functional annotation, COG cluster analysis and secondary metabolite biosynthesis gene clusters prediction. RESULTS The whole genome is assembled into 33 contigs, and the genome size is 5.39 Mb, GC content of 66.9% with encoding 4920 protein genes. The genome sequence was deposited in the GenBank database under the accession number JXYZ00000000. CONCLUSION This study is the first report of androstenedione producing strain Mycobacterium neoaurum MN4 genome sequence, and provides a theoretical basis for further heterologous expression of secondary metabolites on Mycobacterium neoaurum MN4.
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Hao N, Chen X, Jayawardana KW, Wu B, Sundhoro M, Yan M. Shape control of mesoporous silica nanomaterials templated with dual cationic surfactants and their antibacterial activities. Biomater Sci 2016; 4:87-91. [PMID: 26364920 PMCID: PMC4679464 DOI: 10.1039/c5bm00197h] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mesoporous silica nanomaterials of different shapes (film, platelet, sphere, rod) were synthesized simply by tuning the mole ratio of dual cationic surfactant templates, cetyltrimethylammonium bromide (CTAB) and tetrabutylammonium iodine (TBAI). The film showed the most potent antibacterial activity against mycobacteria.
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Affiliation(s)
- Nanjing Hao
- Department of Chemistry, University of Massachusetts, 1 University Ave., Lowell, MA 01854, USA.
| | - Xuan Chen
- Department of Chemistry, University of Massachusetts, 1 University Ave., Lowell, MA 01854, USA.
| | - Kalana W Jayawardana
- Department of Chemistry, University of Massachusetts, 1 University Ave., Lowell, MA 01854, USA.
| | - Bin Wu
- Department of Chemistry, University of Massachusetts, 1 University Ave., Lowell, MA 01854, USA.
| | - Madanodaya Sundhoro
- Department of Chemistry, University of Massachusetts, 1 University Ave., Lowell, MA 01854, USA.
| | - Mingdi Yan
- Department of Chemistry, University of Massachusetts, 1 University Ave., Lowell, MA 01854, USA.
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Shao M, Zhang X, Rao Z, Xu M, Yang T, Li H, Xu Z. Enhanced Production of Androst-1,4-Diene-3,17-Dione by Mycobacterium neoaurum JC-12 Using Three-Stage Fermentation Strategy. PLoS One 2015; 10:e0137658. [PMID: 26352898 PMCID: PMC4564235 DOI: 10.1371/journal.pone.0137658] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 08/19/2015] [Indexed: 11/30/2022] Open
Abstract
To improve the androst-1,4-diene-3,17-dione (ADD) production from phytosterol by Mycobacterium neoaurum JC-12, fructose was firstly found favorable as the initial carbon source to increase the biomass and eliminate the lag phase of M. neoaurum JC-12 in the phytosterol transformation process. Based on this phenomenon, two-stage fermentation by using fructose as the initial carbon source and feeding glucose to maintain strain metabolism was designed. By applying this strategy, the fermentation duration was decreased from 168 h to 120 h with the ADD productivity increased from 0.071 g/(L·h) to 0.108 g/(L·h). Further, three-stage fermentation by adding phytosterol to improve ADD production at the end of the two-stage fermentation was carried out and the final ADD production reached 18.6 g/L, which is the highest reported ADD production using phytosterol as substrate. Thus, this strategy provides a possible way in enhancing the ADD production in pharmaceutical industry.
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Affiliation(s)
- Minglong Shao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province, 214122, P. R. China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province, 214122, P. R. China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province, 214122, P. R. China
- * E-mail:
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province, 214122, P. R. China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province, 214122, P. R. China
| | - Hui Li
- Laboratory of Pharmaceutical Engineering, School of Pharmaceutical Science, Jiangnan University, Wuxi, Jiangsu Province, 214122, P. R. China
| | - Zhenghong Xu
- Laboratory of Pharmaceutical Engineering, School of Pharmaceutical Science, Jiangnan University, Wuxi, Jiangsu Province, 214122, P. R. China
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27
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Hanashima S, Götze S, Liu Y, Ikeda A, Kojima-Aikawa K, Taniguchi N, Varón Silva D, Feizi T, Seeberger PH, Yamaguchi Y. Defining the Interaction of Human Soluble Lectin ZG16p and Mycobacterial Phosphatidylinositol Mannosides. Chembiochem 2015; 16:1502-11. [PMID: 25919894 PMCID: PMC5896728 DOI: 10.1002/cbic.201500103] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Indexed: 11/11/2022]
Abstract
ZG16p is a soluble mammalian lectin that interacts with mannose and heparan sulfate. Here we describe detailed analysis of the interaction of human ZG16p with mycobacterial phosphatidylinositol mannosides (PIMs) by glycan microarray and NMR. Pathogen-related glycan microarray analysis identified phosphatidylinositol mono- and di-mannosides (PIM1 and PIM2) as novel ligand candidates of ZG16p. Saturation transfer difference (STD) NMR and transferred NOE experiments with chemically synthesized PIM glycans indicate that PIMs preferentially interact with ZG16p by using the mannose residues. The binding site of PIM was identified by chemical-shift perturbation experiments with uniformly (15)N-labeled ZG16p. NMR results with docking simulations suggest a binding mode of ZG16p and PIM glycan; this will help to elucidate the physiological role of ZG16p.
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Affiliation(s)
- Shinya Hanashima
- Structural Glycobiology Team, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama 351-0198 (Japan)
| | - Sebastian Götze
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam (Germany)
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin (Germany)
| | - Yan Liu
- Glycosciences Laboratory, Department of Medicine, Imperial College London, Du Cane Road, London W12 0NN (UK)
| | - Akemi Ikeda
- Structural Glycobiology Team, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama 351-0198 (Japan)
| | - Kyoko Kojima-Aikawa
- The Glycoscience Institute, Ochanomizu University, Otsuka, Bunkyo-ku, Tokyo 112-8610 (Japan)
| | - Naoyuki Taniguchi
- Disease Glycomics Team, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama 351-0198 (Japan)
| | - Daniel Varón Silva
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam (Germany)
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin (Germany)
| | - Ten Feizi
- Glycosciences Laboratory, Department of Medicine, Imperial College London, Du Cane Road, London W12 0NN (UK)
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam (Germany)
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin (Germany)
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama 351-0198 (Japan).
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Abstract
Mycobacteria are microorganisms that contain a very high content of structurally diverse lipids, some of them being biologically active substances. As such the lipid composition is commonly used to characterize mycobacterial strains at the species and type-species level. This chapter describes the methods that allow the purification of the most commonly isolated biologically active lipids and those used for analyzing extractable lipids and their constituents, cell wall-linked mycolic acids and lipoarabinomannan (LAM). The latter involve simple chromatographic and analytical techniques, such as thin-layer chromatography and gas chromatography coupled to mass spectrometry.
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Affiliation(s)
- Marie-Antoinette Lanéelle
- Tuberculosis & Infection Biology Department, Institut de Pharmacologie et de BiologieStructurale (IPBS), Centre National de la Recherche Scientifique (CNRS), BP 64182, 205 route de Narbonne, 31077, Toulouse, France
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Amlerová J, Studentová V, Hrabák J. [Identification of Mycobacterium spp. isolates using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS)]. Epidemiol Mikrobiol Imunol 2014; 63:196-199. [PMID: 25412483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
STUDY OBJECTIVE Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has recently been widely used in diagnostic microbiological laboratories. It is a cheap and rapid method for the identification of bacteria and micromycetes. Apart from this purpose, it is also used for the detection of antibiotic resistance mechanisms. It has the potential to be extended for other purposes in microbiology. The aim of this study was to validate MALDI-TOF MS for the identification of mycobacteria. MATERIAL AND METHODS Thirty isolates of Mycobacterium spp. isolated in the Laboratory of Mycobacteriology of the Plzeň University Hospital were included in the study. The isolates were identified to the species level using biochemical tests, gene probes, and sequencing of the gene encoding 16S rRNA. The identification by MALDI-TOF MS was performed with the use of silica beads. Strain identification by sequencing the gene encoding 16S rRNA was considered as the reference method. RESULTS MALDI-TOF MS correctly identified all isolates of Mycobacterium spp. (score range 1.461 - 2.168). The species identified were Mycobacterium tuberculosis (n= 5), Mycobacterium kansasii (n=5), Mycobacterium avium (n=6), Mycobacterium intracelullare (n=3), Mycobacterium xenopi (n=3), Mycobacterium gordonae (n=1), Mycobacterium abscessus (n=1), Mycobacterium kumamotonense (n=2), Mycobacterium mantenii (n=1), Mycobacterium lentiflavum (n=1), Mycobacterium fortuitum (n=1), and Mycobacterium scrofulaceum (n=1). CONCLUSION MALDI-TOF MS is a suitable tool for the routine identification of Mycobacterium spp. in laboratories using this method for the conventional identification of microbes.
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Abstract
Capuramycin and its congeners are considered to be important lead molecules for the development of a new drug for multidrug-resistant (MDR) Mycobacterium tuberculosis infections. Extensive structure-activity relationship studies of capuramycin to improve the efficacy have been limited because of difficulties in selectively chemically modifying the desired position(s) of the natural product with biologically interesting functional groups. We have developed efficient syntheses of capuramycin and its analogues by using new protecting groups, derived from the chiral (chloro-4-methoxyphenyl)(chlorophenyl)methanols, for the uridine ureido nitrogen and primary alcohol. The chiral nonracemic (2,6-dichloro-4-methoxyphenyl)(2,4-dichlorophenyl)methanol derivative is a useful reagent to resolve rac-3-amino-1,3-dihydro-5-phenyl-2H-1,4-benzodiazepin-2-one, the (S)-configuration isomer of which plays a significant role in improving the mycobactericidal activity of capuramycin.
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Affiliation(s)
| | | | | | - Michio Kurosu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison, Memphis, TN 38163-0001 (USA), FAX: (+1) 901-448-6940
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31
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Ulea I, Stavri H. Thin layer chromatography characterization of ELISA specific glycolipids antigens immunomagnetically purified from environmental mycobacteria. Roum Arch Microbiol Immunol 2013; 72:105-120. [PMID: 24187809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Thin layer chromatography (TLC) could easily and rapidly evidentiate the qualitative differences between glycolipids (GLs). Different immunomagnetically purified mycobacterial GLs have been compared using TLC, in order to choose the most appropriate antigens to be utilized in ELISA. The GLs were purified from environmental mycobacteria (EM) (M. avium-intracellulare, M. kansasii, M. xenopi, M. scrofulaceum and M. gordonae) and from M. tuberculosis H37Rv. BioMag Amine and BioMag Carboxyl terminated superparamagnetic microparticles were utilized in the magnetic separation of glycolipids from mycobacterial species. TLC of GLs before and after magnetic purification, corroborated with ELISA results, shows that COOH-terminated particles allow a better purification for M. kansasii, M. xenopi and M. scrofulaceum, while NH2-terminated particles act better on MAI and M. gordonae GLs. The use of GL purified antigens in ELISA could fulfill the criteria of high levels of both sensitivity and specificity of serologic assays in EM diagnosis.
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Affiliation(s)
- Irina Ulea
- Cantacuzino National Institute of Research-Development for Microbiology and Immunology, Mycobacterial Antigens Department, Bucharest, Romania
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32
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Kuban M, Öngen G, Khan IA, Bedir E. Microbial transformation of cycloastragenol. Phytochemistry 2013; 88:99-104. [PMID: 23357596 DOI: 10.1016/j.phytochem.2012.12.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 12/11/2012] [Accepted: 12/17/2012] [Indexed: 06/01/2023]
Abstract
The microbial transformation of cycloastragenol by the fungi Cunninghamella blakesleeana NRRL 1369 and Glomerella fusarioides ATCC 9552, and the bacterium Mycobacterium sp. NRRL 3805 were investigated. Both fungi mainly provided hydroxylated metabolites together with products formed by cyclization, dehydrogenation and Baeyer-Villiger oxidation resulting in a ring cleavage. The bacteria yielded only a single oxidation product, namely, 3-oxo-cycloastragenol. Structures of the metabolites were elucidated by 1-D ((1)H,(13)C), 2-D NMR (COSY, HMBC, HMQC) and HRMS analyses.
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Affiliation(s)
- Melis Kuban
- Ege University, Faculty of Engineering, Department of Bioengineering, 35100 Bornova, İzmir, Turkey
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Brambilla C, Sánchez-Chardi A, Pérez-Trujillo M, Julián E, Luquin M. Cyclopropanation of α-mycolic acids is not required for cording in Mycobacterium brumae and Mycobacterium fallax. Microbiology (Reading) 2012; 158:1615-1621. [PMID: 22493302 DOI: 10.1099/mic.0.057919-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The capacity to form microscopic cords (cording) of Mycobacterium species has been related to their virulence. The compounds responsible for cording are unknown, but a recent study has shown that cording could be related to the fine structure of α-mycolic acids. This investigation attributes the need for a proximal cyclopropane in α-mycolic acids for cording in Mycobacterium tuberculosis and Mycobacterium bovis BCG and proposes cyclopropanases as good targets for new chemotherapeutic agents. As other Mycobacterium species in addition to M. tuberculosis and M. bovis form microscopic cords, it would be of major interest to know whether the relationship between proximal cyclopropanation of α-mycolic acids and cording could be extended to non-tuberculous mycobacteria. In this study, we have examined the correlation between the cording and cyclopropanation of α-mycolic acids in two species, Mycobacterium brumae and Mycobacterium fallax. Scanning electron microscopy images showed, for the first time to our knowledge, the fine structure of microscopic cords of M. brumae and M. fallax, confirming that these two species form true cords. Furthermore, NMR analysis performed on the same cording cultures corroborates the absence of cyclopropane rings in their α-mycolic acids. Therefore, we can conclude that the correlation between cording and cyclopropanation of α-mycolic acids cannot be extended to all mycobacteria. As M. brumae and M. fallax grow rapidly and have a simple pattern of mycolic acids (only α-unsaturated mycolic acids), we propose these two species as suitable models for the study of the role of mycolic acids in cording.
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Affiliation(s)
- Cecilia Brambilla
- Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | | | - Míriam Pérez-Trujillo
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Esther Julián
- Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Marina Luquin
- Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
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Hattori Y, Sugita M. [Molecular and cellular biology of mycobacteria]. Nihon Rinsho 2011; 69:1356-1360. [PMID: 21838029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The cell wall of mycobacteria contains mycobacteria-specific long-chain fatty acids, called mycolic acids, and mycolic acid-containing glycolipids. This highly hydrophobic structure of the cell wall of mycobacteria is critical not only for their acid-fast properties but also for their resistance to a variety of chemical attacks from the host cells, supporting their ability to survive for years within the host. On the other hand, the host T cells are capable of recognizing these critical lipid components of the cell wall of mycobacteria, such as glucose monomycolates, that are captured by group 1 CD1 molecules. These T cells are able to eliminate mycobacteria-infected cells. This opens the possibility for a new type of lipid-based vaccines against tuberculosis.
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Affiliation(s)
- Yuki Hattori
- Laboratory of Cell Regulation, Institute for Virus Research, Kyoto University
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35
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Akhtar S, Sarkar S, Mishra A, Sarkar D. A method to extract intact and pure RNA from mycobacteria. Anal Biochem 2011; 417:286-8. [PMID: 21767523 DOI: 10.1016/j.ab.2011.06.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2011] [Revised: 06/20/2011] [Accepted: 06/21/2011] [Indexed: 11/19/2022]
Abstract
We describe a high-yielding, simple, and aerosol-free protocol for the isolation of RNA from mycobacteria that does not require sophisticated instruments. The method yielded 50 μg of RNA from 10(7) cells, 50 times more than a recently reported method. Our method can extract total RNA from aerobically grown bacteria and from in vitro hypoxia-induced dormant bacilli and mycobacteria residing within infected macrophages.
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Affiliation(s)
- Shamim Akhtar
- Combi Chem Bio Resource Center, Organic Chemical Division, National Chemical Laboratory, Pune, Maharashtra 411008, India
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36
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Abstract
Accurate and rapid cell counts of mycobacterial species in culture are difficult to obtain. Here, a method using modified Kinyoun acid-fast staining was adapted for use with a Petroff-Hausser sperm and bacteria cell-counting chamber by using a liquid suspension staining technique. Cell counts obtained by this method were compared to viable cell counts by agar plate counting, revealing accurate correlation.
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Affiliation(s)
- Robin Treuer
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Shelley E. Haydel
- School of Life Sciences, Arizona State University, Tempe, AZ
- The Biodesign Institute Center for Infectious Diseases and Vaccinology, Arizona State University, Tempe, AZ
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Kateete DP, Okee M, Katabazi FA, Okeng A, Asiimwe J, Boom HW, Eisenach KD, Joloba ML. Rhomboid homologs in mycobacteria: insights from phylogeny and genomic analysis. BMC Microbiol 2010; 10:272. [PMID: 21029479 PMCID: PMC2989971 DOI: 10.1186/1471-2180-10-272] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Accepted: 10/29/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rhomboids are ubiquitous proteins with diverse functions in all life kingdoms, and are emerging as important factors in the biology of some pathogenic apicomplexa and Providencia stuartii. Although prokaryotic genomes contain one rhomboid, actinobacteria can have two or more copies whose sequences have not been analyzed for the presence putative rhomboid catalytic signatures. We report detailed phylogenetic and genomic analyses devoted to prokaryotic rhomboids of an important genus, Mycobacterium. RESULTS Many mycobacterial genomes contained two phylogenetically distinct active rhomboids orthologous to Rv0110 (rhomboid protease 1) and Rv1337 (rhomboid protease 2) of Mycobacterium tuberculosis H37Rv, which were acquired independently. There was a genome-wide conservation and organization of the orthologs of Rv1337 arranged in proximity with glutamate racemase (mur1), while the orthologs of Rv0110 appeared evolutionary unstable and were lost in Mycobacterium leprae and the Mycobacterium avium complex. The orthologs of Rv0110 clustered with eukaryotic rhomboids and contained eukaryotic motifs, suggesting a possible common lineage. A novel nonsense mutation at the Trp73 codon split the rhomboid of Mycobacterium avium subsp. Paratuberculosis into two hypothetical proteins (MAP2425c and MAP2426c) that are identical to MAV_1554 of Mycobacterium avium. Mycobacterial rhomboids contain putative rhomboid catalytic signatures, with the protease active site stabilized by Phenylalanine. The topology and transmembrane helices of the Rv0110 orthologs were similar to those of eukaryotic secretase rhomboids, while those of Rv1337 orthologs were unique. Transcription assays indicated that both mycobacterial rhomboids are possibly expressed. CONCLUSIONS Mycobacterial rhomboids are active rhomboid proteases with different evolutionary history. The Rv0110 (rhomboid protease 1) orthologs represent prokaryotic rhomboids whose progenitor may be the ancestors of eukaryotic rhomboids. The Rv1337 (rhomboid protease 2) orthologs appear more stable and are conserved nearly in all mycobacteria, possibly alluding to their importance in mycobacteria. MAP2425c and MAP2426c provide the first evidence for a split homologous rhomboid, contrasting whole orthologs of genetically related species. Although valuable insights to the roles of rhomboids are provided, the data herein only lays a foundation for future investigations for the roles of rhomboids in mycobacteria.
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Affiliation(s)
- David P Kateete
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Moses Okee
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Fred A Katabazi
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Alfred Okeng
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Jeniffer Asiimwe
- Department of Veterinary Parasitology & Microbiology, Faculty of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Henry W Boom
- Case Western Reserve University, Cleveland, OH, USA
| | - Kathleen D Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Moses L Joloba
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
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Splain RA, Kiessling LL. Synthesis of galactofuranose-based acceptor substrates for the study of the carbohydrate polymerase GlfT2. Bioorg Med Chem 2010; 18:3753-9. [PMID: 20513638 PMCID: PMC2888036 DOI: 10.1016/j.bmc.2010.04.068] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2010] [Revised: 04/20/2010] [Accepted: 04/21/2010] [Indexed: 11/23/2022]
Abstract
Despite the prevalence and importance of carbohydrate polymers, the molecular details of their biosynthesis remain elusive. Many enzymes responsible for the synthesis of carbohydrate polymers require a 'primer' or 'initiator' carbohydrate sequence. One example of such an enzyme is the mycobacterial galactofuranosyltransferase GlfT2 (Rv3808c), which generates an essential cell wall building block. We recently demonstrated that recombinant GlfT2 is capable of producing a polymer composed of alternating beta-(1,5) and beta-(1,6)-linked galactofuranose (Galf) residues. Intriguingly, the length of the polymers produced from a synthetic glycosyl acceptor is consistent with those found in the cell wall. To probe the mechanism by which polymer length is controlled, a collection of initiator substrates has been assembled. The central feature of the synthetic route is a ruthenium-catalyzed cross-metathesis as the penultimate transformation. Access to synthetic substrates has led us to postulate a new mechanism for length control in this template-independent polymerization. Moreover, our investigations indicate that lipids possessing but a single galactofuranose residue can act as substrates for GlfT2.
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Affiliation(s)
- Rebecca A. Splain
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706, U.S.A
| | - Laura L. Kiessling
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706, U.S.A
- Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706, U.S.A
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Toney N, Adekambi T, Toney S, Yakrus M, Butler WR. Revival and emended description of 'Mycobacterium paraffinicum' Davis, Chase and Raymond 1956 as Mycobacterium paraffinicum sp. nov., nom. rev. Int J Syst Evol Microbiol 2009; 60:2307-2313. [PMID: 19915104 DOI: 10.1099/ijs.0.016972-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The omission of the name 'Mycobacterium paraffinicum' from the Approved Lists of Bacterial Names was due to phenotypic confusion surrounding a close relationship with Mycobacterium scrofulaceum. Correspondingly, 'M. paraffinicum' strains grew slowly in > 7 days, stained acid-alcohol-fast and produced yellow-pigmented, smooth, waxy colonies in the dark at an optimal temperature of 35°C. However, 'M. paraffinicum' strains demonstrated no activity for urease, nicotinamidase or pyrazinamidase and lacked growth at 42°C, unlike M. scrofulaceum. The mycolic acid pattern, as determined by HPLC, clustered 'M. paraffinicum' with M. scrofulaceum, Mycobacterium avium and Mycobacterium parascrofulaceum. Strains were fully susceptible to linezolid, rifabutin, clarithromycin and amikacin. Examination of the historical reference strain of 'M. paraffinicum', ATCC 12670, and five additional isolates using comparative studies with 16S rRNA, hsp65 and rpoB gene and concatenated sequences showed that they formed a tight taxonomic group that was distinct from similar non-tuberculous mycobacteria. Multilocus enzyme electrophoresis (MEE) analysis confirmed a close association of the five additional isolates with the reference strain of 'M. paraffinicum' with a genetic distance of 0.12 and showed that all six strains were distinct from other closely related species. These genetic results provided unambiguous evidence of the uniqueness of this slowly growing, scotochromogenic species and supported the revival of the name as Mycobacterium paraffinicum (ex Davis, Chase and Raymond 1956) sp. nov., nom. rev. We propose the previously deposited reference strain ATCC 12670(T) =DSM 44181(T) =NCIMB 10420(T), located in collections worldwide, as the type strain.
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Affiliation(s)
- Nadege Toney
- Mycobacteriology Branch, Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Toidi Adekambi
- Mycobacteriology Branch, Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sean Toney
- Mycobacteriology Branch, Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mitchell Yakrus
- Mycobacteriology Branch, Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - W Ray Butler
- Mycobacteriology Branch, Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Chimara E, Ferrazoli L, Ueky SYM, Martins MC, Durham AM, Arbeit RD, Leão SC. Reliable identification of mycobacterial species by PCR-restriction enzyme analysis (PRA)-hsp65 in a reference laboratory and elaboration of a sequence-based extended algorithm of PRA-hsp65 patterns. BMC Microbiol 2008; 8:48. [PMID: 18366704 PMCID: PMC2323382 DOI: 10.1186/1471-2180-8-48] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Accepted: 03/20/2008] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Identification of nontuberculous mycobacteria (NTM) based on phenotypic tests is time-consuming, labor-intensive, expensive and often provides erroneous or inconclusive results. In the molecular method referred to as PRA-hsp65, a fragment of the hsp65 gene is amplified by PCR and then analyzed by restriction digest; this rapid approach offers the promise of accurate, cost-effective species identification. The aim of this study was to determine whether species identification of NTM using PRA-hsp65 is sufficiently reliable to serve as the routine methodology in a reference laboratory. RESULTS A total of 434 NTM isolates were obtained from 5019 cultures submitted to the Institute Adolpho Lutz, Sao Paulo Brazil, between January 2000 and January 2001. Species identification was performed for all isolates using conventional phenotypic methods and PRA-hsp65. For isolates for which these methods gave discordant results, definitive species identification was obtained by sequencing a 441 bp fragment of hsp65. Phenotypic evaluation and PRA-hsp65 were concordant for 321 (74%) isolates. These assignments were presumed to be correct. For the remaining 113 discordant isolates, definitive identification was based on sequencing a 441 bp fragment of hsp65. PRA-hsp65 identified 30 isolates with hsp65 alleles representing 13 previously unreported PRA-hsp65 patterns. Overall, species identification by PRA-hsp65 was significantly more accurate than by phenotype methods (392 (90.3%) vs. 338 (77.9%), respectively; p < .0001, Fisher's test). Among the 333 isolates representing the most common pathogenic species, PRA-hsp65 provided an incorrect result for only 1.2%. CONCLUSION PRA-hsp65 is a rapid and highly reliable method and deserves consideration by any clinical microbiology laboratory charged with performing species identification of NTM.
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Affiliation(s)
| | | | | | | | - Alan Mitchel Durham
- Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, Brazil
| | - Robert D Arbeit
- Tufts University School of Medicine, Division of Geographic Medicine and Infectious Diseases, Boston, Massachusetts, USA
| | - Sylvia Cardoso Leão
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
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Donova MV, Nikolayeva VM, Dovbnya DV, Gulevskaya SA, Suzina NE. Methyl-beta-cyclodextrin alters growth, activity and cell envelope features of sterol-transforming mycobacteria. Microbiology (Reading) 2007; 153:1981-1992. [PMID: 17526855 DOI: 10.1099/mic.0.2006/001636-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Modified beta-cyclodextrins have been shown previously to enhance sterol conversion to 4-androstene-3,17-dione (AD) and 1,4-androstadiene-3,17-dione (ADD) by growing Mycobacterium spp. The enhancement effect was mainly attributed to steroid solubilization by the formation of inclusion complexes with modified cyclodextrins. In this work, the influence of randomly methylated beta-cyclodextrin (MCD) on the growth, AD- and ADD-producing activity, cell wall (CW) composition and ultrastructure of sterol-transforming Mycobacterium sp. VKM Ac-1816D was studied. The specific growth rate of the strain on glycerol increased in the presence of MCD (20-100 mM). Washed cells grown in the presence of MCD (20-40 mM) expressed 1.6-fold higher ADD-producing activity than did the cells grown without MCD, and their adhesiveness differed. Electron microscopy showed MCD-mediated CW exfoliation and accumulation of membrane-like structures outside the cells, while preserving cells intact. The analysis of CW composition revealed both a decrease in the proportion of extractable lipids and a considerable shift in fatty acid profile resulting from MCD action. The MCD-mediated enhancement of mycolic and fatty acids content was observed outside the cells. The total secreted protein level rose 2.4-fold, and the extracellular 3-hydroxysteroid oxidase activity 3.2-fold. The composition of the CW polysaccharide was not altered, while the overall proportion of the carbohydrates in the CW of the MCD-exposed mycobacteria increased. The results showed that the multiple mechanisms of MCD-mediated intensification of sterol to AD(D) conversion by mycobacteria include not only solubilization of steroids, but also the increase of CW permeability for both steroids and soluble nutrients, disorganization of the lipid bilayer and the release of steroid-transforming enzymes weakly associated with the CW.
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Affiliation(s)
- M V Donova
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia
| | - V M Nikolayeva
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia
| | - D V Dovbnya
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia
| | - S A Gulevskaya
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia
| | - N E Suzina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia
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Abstract
Strategies for the stereoselective synthesis of mycobacterial arabinan were explored. Arabinofuranosyl donors with various protective groups were screened in terms of suitability for beta-(1,2-cis)-selective glycosylation. The protective group was found to affect the stereoselectivity of arabinofuranosylation. Beta-selectivity was drastically enhanced by using donors protected with 3,5-TIDPS, possibly due to conformational constraints on the furanose ring. Synthesis of heptaarabinofuranoside was then performed to demonstrate the practicality of this methodology. [reaction: see text].
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Affiliation(s)
- Akihiro Ishiwata
- RIKEN (Institute of Physical and Chemical Research), Wako-shi, Saitama 351-0198, Japan
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Silva RA, Grossi V, Alvarez HM. Biodegradation of phytane (2,6,10,14-tetramethylhexadecane) and accumulation of related isoprenoid wax esters byMycobacterium ratisbonensestrain SD4 under nitrogen-starved conditions. FEMS Microbiol Lett 2007; 272:220-8. [PMID: 17521403 DOI: 10.1111/j.1574-6968.2007.00770.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The accumulation of storage lipids during the biodegradation of 2,6,10,14-tetramethylhexadecane (phytane) by Mycobacterium ratisbonense strain SD4 grown under nitrogen-starved conditions was investigated. Detailed chemical analysis of intracellular metabolites revealed the existence of (at least) three different pathways for the catabolism of phytane, and the accumulation of significant proportions (39% of the total lipids) of several isoprenoid wax esters formed by condensation of oxidation products of the hydrocarbon. In contrast, triacylglycerols but no wax esters were accumulated by strain SD4 grown on hexadecane, the unbranched homologue of phytane.
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Affiliation(s)
- Roxana A Silva
- Centro Regional de Investigación y Desarrollo Científico--Tecnológico (CRIDECIT), Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco, Chubut, Argentina
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Ramakrishnan C, Lakshmi B, Kurien A, Devipriya D, Srinivasan N. Structural Compromise of Disallowed Conformations in Peptide and Protein Structures. Protein Pept Lett 2007; 14:672-82. [PMID: 17897093 DOI: 10.2174/092986607781483921] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Using a data set of 454 crystal structures of peptides and 80 crystal structures of non-homologous proteins solved at ultra high resolution of 1.2 A or better we have analyzed the occurrence of disallowed Ramachandran (phi, psi) angles. Out of 1492 and 13508 non-glycyl residues in peptides and proteins respectively 12 and 76 residues in the two datasets adopt clearly disallowed combinations of Ramachandran angles. These examples include a number of conformational points which are far away from any of the allowed regions in the Ramachandran map. According to the Ramachandran map a given (phi, psi) combination is considered disallowed when two non-bonded atoms in a system of two-linked peptide units with ideal geometry are prohibitively proximal in space. However, analysis of the disallowed conformations in peptide and protein structures reveals that none of the observations of disallowed conformations in the crystal structures correspond to a short contact between non-bonded atoms. A further analysis of deviations of bond lengths and angles, from the ideal peptide geometry, at the residue positions of disallowed conformations in the crystal structures suggest that individual bond lengths and angles are all within acceptable limits. Thus, it appears that the rare tolerance of disallowed conformations is possible by gentle and acceptable deviations in a number of bond lengths and angles, from ideal geometry, over a series of bonds resulting in a net gross effect of acceptable non-bonded inter-atomic distances.
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Affiliation(s)
- C Ramakrishnan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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Fujita Y, Okamoto Y, Uenishi Y, Sunagawa M, Uchiyama T, Yano I. Molecular and supra-molecular structure related differences in toxicity and granulomatogenic activity of mycobacterial cord factor in mice. Microb Pathog 2007; 43:10-21. [PMID: 17434713 DOI: 10.1016/j.micpath.2007.02.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2006] [Revised: 02/19/2007] [Accepted: 02/19/2007] [Indexed: 11/16/2022]
Abstract
To establish the structure biological activity relationship of cord factor (trehalose 6,6'-dimycolate, TDM), we compared the molecular or supra-molecular structure of TDM micelles with toxicity, thymic atrophy and granulomatogenicity in lungs and spleen of BALB/c mice. According to the difference in the mycolyl subclass composition, TDM was divided into two groups, one possessing alpha-, methoxy- and keto-mycolates in M. tuberculosis H37Rv, M. bovis BCG and M. kansasii (group A) and the other having alpha-, keto- and wax ester-mycolates in M. avium serotype 4, M. phlei and M. flavescens (group B), although mycolic acid molecular species composition differed in each group considerably. Supra-molecular structure of TDM micelle differed species to species substantially and the micelle size of TDM from M. bovis BCG Connaught was the largest. The highest toxicity was shown with TDM from M. tuberculosis H37Rv which possessed the highest amount of alpha- (47.3%) and methoxy-mycolates (40.8%), while TDM from M. phlei having the low amount of alpha-mycolate (11.6%) showed almost no toxicity with the given doses. The thymic atrophy was observed with TDM from group A, but not with TDM from group B. On the other hand, TDM from group B showed massive lung granulomatogenic activity based on the histological observations and organ indices. Taken together, group A TDM showed a wide variety of micelle sizes and specific surface areas, high to low toxicity and marked to moderate granulomatogenicity, while group B TDM showed smaller sizes of micelles and larger specific surface areas, lower toxicity but higher granulomatogenicity in lungs. Existence of higher amount of longer chain alpha-mycolates in TDM appeared to be essential for high toxicity and thymic apoptotic activity, whereas TDM possessing wax ester-mycolate with smaller sized micelles seemed to be less toxic, but more granulomatogenic in lungs in mice. Thus, the mycolic acid subclass and molecular species composition of TDM affect critically the micelle forms, toxicity and granulomatogenicity in mice, while the relative abundances and carbon chain length of alpha-mycolate affected the toxicity in mice.
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Affiliation(s)
- Yukiko Fujita
- Japan BCG Central Laboratory, 3-1-5 Matsuyama, Kiyose-shi, Tokyo 204-0022, Japan.
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Santora K, Rasa C, Visco D, Steinetz BG, Bagnell CA. Antiarthritic Effects of Relaxin, in Combination with Estrogen, in Rat Adjuvant-Induced Arthritis. J Pharmacol Exp Ther 2007; 322:887-93. [PMID: 17526806 DOI: 10.1124/jpet.107.122903] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The incidence and severity of rheumatoid arthritis (RA) are reduced during pregnancy. Estradiol-17beta and relaxin (RLX), hormones of pregnancy, are implicated in decreased immune responsiveness. The aim of this study was to determine the effects of estrogen and RLX, alone or in combination, on the development of adjuvant-induced arthritis (AIA) in ovariectomized (OVX) Lewis rats. Arthritis was induced on day 0 by adjuvant injection in the left hind paw. Rats were treated with estradiol valerate (E), porcine RLX, E + RLX, or vehicle. Healthy OVX control animals were used for comparison. Treatment with RLX or E alone decreased adjuvant-induced inflammation in both the injected (primary) and noninjected (secondary) hind paws. Combined treatment with E and RLX was more effective than either hormone alone in blocking secondary paw inflammation. Furthermore, E plus RLX reduced changes to spleen and thymus weights induced by adjuvant injection. Both E and RLX alone decreased circulating tumor necrosis factor (TNF) alpha. The combination of E and RLX resulted in a greater decline in TNFalpha than treatment with either hormone alone. There was no effect of hormones on the proinflammatory cytokine, interleukin (IL)-1beta. The anti-inflammatory cytokine IL-10 increased in response to E and E plus RLX. In conclusion, combined therapy with E and RLX was more effective than either hormone alone in reducing chronic inflammation, joint changes, and high circulating TNFalpha associated with AIA in rats. Accordingly, these hormones could play a role in reducing RA-induced inflammation during pregnancy by an effect on the immune system.
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Affiliation(s)
- Karen Santora
- Department of Animal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
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Hettick JM, Kashon ML, Slaven JE, Ma Y, Simpson JP, Siegel PD, Mazurek GN, Weissman DN. Discrimination of intact mycobacteria at the strain level: a combined MALDI-TOF MS and biostatistical analysis. Proteomics 2007; 6:6416-25. [PMID: 17109381 DOI: 10.1002/pmic.200600335] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
New methodologies for surveillance and identification of Mycobacterium tuberculosis are required to stem the spread of disease worldwide. In addition, the ability to discriminate mycobacteria at the strain level may be important to contact or source case investigations. To this end, we are developing MALDI-TOF MS methods for the identification of M. tuberculosis in culture. In this report, we describe the application of MALDI-TOF MS, as well as statistical analysis including linear discriminant and random forest analysis, to 16 medically relevant strains from four species of mycobacteria, M. tuberculosis, M. avium, M. intracellulare, and M. kansasii. Although species discrimination can be accomplished on the basis of unique m/z values observed in the MS fingerprint spectrum, discrimination at the strain level is predicted on the relative abundance of shared m/z values among strains within a species. For the 16 mycobacterial strains investigated in the present study, it is possible to unambiguously identify strains within a species on the basis of MALDI-TOF MS data. The error rate for classification of individual strains using linear discriminant analysis was 0.053 using 37 m/z variables, whereas the error rate for classification of individual strains using random forest analysis was 0.023 using only 18 m/z variables. In addition, using random forest analysis of MALDI-TOF MS data, it was possible to correctly classify bacterial strains as either M. tuberculosis or non-tuberculous with 100% accuracy.
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Affiliation(s)
- Justin M Hettick
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Health Effects Laboratory Division, Morgantown, WV, USA.
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Puissegur MP, Lay G, Gilleron M, Botella L, Nigou J, Marrakchi H, Mari B, Duteyrat JL, Guerardel Y, Kremer L, Barbry P, Puzo G, Altare F. Mycobacterial Lipomannan Induces Granuloma Macrophage Fusion via a TLR2-Dependent, ADAM9- and β1Integrin-Mediated Pathway. J Immunol 2007; 178:3161-9. [PMID: 17312164 DOI: 10.4049/jimmunol.178.5.3161] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Tuberculous granulomas are the sites of interaction between the host response and the tubercle bacilli within infected individuals. They mainly consist of organized aggregations of lymphocytes and macrophages (Mf). A predominant role of mycobacterial envelope glycolipids in granulomas formation has been recently emphasized, yet the signaling events interfering with granuloma cell differentiation remain elusive. To decipher this molecular machinery, we have recently developed an in vitro human model of mycobacterial granulomas. In this study, we provide evidence that the mycobacterial proinflammatory phosphatidyl-myo-inositol mannosides and lipomannans (LM), as well as the anti-inflammatory lipoarabinomannan induce granuloma formation, yet only the proinflammatory glycolipids induce the fusion of granuloma Mf into multinucleated giant cells (MGC). We also demonstrate that LM induces large MGC resembling those found in vivo within the granulomas of tuberculosis patients, and that this process is mediated by TLR2 and is dependent on the beta(1) integrin/ADAM9 cell fusion machinery. Our results demonstrate for the first time that the Mf differentiation stage specifically occurring within granulomatous structures (i.e., MGC formation) is triggered by mycobacterial envelope glycolipids, which are capable of inducing the cell fusion machinery. This provides the first characterization of the ontogeny of human granuloma MGC, thus resulting in a direct modulation by a particular mycobacterial envelope glycolipid of the differentiation process of granuloma Mf.
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Affiliation(s)
- Marie-Pierre Puissegur
- Laboratory of Molecular Physiology of Mycobacterial Granulomas, Department of Molecular Mechanisms of Mycobacterial Infections, Institut de Pharmacologie et Biologie Structurale, CNRS/UMR 5089, 205 Route de Narbonne, Toulouse, France
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Gilleron M, Lindner B, Puzo G. MS/MS approach for characterization of the fatty acid distribution on mycobacterial phosphatidyl-myo-inositol mannosides. Anal Chem 2007; 78:8543-8. [PMID: 17165851 DOI: 10.1021/ac061574a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphatidyl-myo-inositol mannosides (PIM) are not only important structural components of the mycobacterial envelope but also are major non-peptidic antigens of the host innate and acquired immune responses. Indeed, they are ligands of TLR-2 and they activate CD1-restricted T lymphocytes. In addition, PIM constitute the basic structure of the lipidic anchor of two lipoglycans, lipomannans and lipoarabinomannans, which are important immunomodulators in the course of tuberculosis. The fatty acyl substituents present on PIM molecules play a crucial role for both their physical properties and biological activities. PIM contain four acylation sites, two on the glycerol, one on a mannose, and one on the myo-inositol units. We propose here an analytical procedure, based on mass spectrometry, to determine the structure of the fatty acids present on each of these different acylation sites. We show that the nature of the fatty acids located on both positions of glycerol can be deduced from IRMPD analysis of negative precursor ions from native PIM species, while the fatty acids located on myo-inositol and mannose units can be identified by MALDI-TOF CID MS of protonated and cationized molecular ions. Thus, the combination of MS/MS data obtained from positive and negative pseudomolecular ions generated by ESI or MALDI appears as a powerful approach for the structural characterization of the PIM acyl form structure.
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Affiliation(s)
- Martine Gilleron
- Institut de Pharmacologie et de Biologie Structurale du Centre National de la Recherche Scientifique, 205 route de Narbonne, 31077 Toulouse Cedex 4, France.
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