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Hart EM, Lyerly E, Bernhardt TG. The conserved σD envelope stress response monitors multiple aspects of envelope integrity in corynebacteria. PLoS Genet 2024; 20:e1011127. [PMID: 38829907 PMCID: PMC11175481 DOI: 10.1371/journal.pgen.1011127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 06/13/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024] Open
Abstract
The cell envelope fortifies bacterial cells against antibiotics and other insults. Species in the Mycobacteriales order have a complex envelope that includes an outer layer of mycolic acids called the mycomembrane (MM) and a cell wall composed of peptidoglycan and arabinogalactan. This envelope architecture is unique among bacteria and contributes significantly to the virulence of pathogenic Mycobacteriales like Mycobacterium tuberculosis. Characterization of pathways that govern envelope biogenesis in these organisms is therefore critical in understanding their biology and for identifying new antibiotic targets. To better understand MM biogenesis, we developed a cell sorting-based screen for mutants defective in the surface exposure of a porin normally embedded in the MM of the model organism Corynebacterium glutamicum. The results revealed a requirement for the conserved σD envelope stress response in porin export and identified MarP as the site-1 protease, respectively, that activate the response by cleaving the membrane-embedded anti-sigma factor. A reporter system revealed that the σD pathway responds to defects in mycolic acid and arabinogalactan biosynthesis, suggesting that the stress response has the unusual property of being induced by activating signals that arise from defects in the assembly of two distinct envelope layers. Our results thus provide new insights into how C. glutamicum and related bacteria monitor envelope integrity and suggest a potential role for members of the σD regulon in protein export to the MM.
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Affiliation(s)
- Elizabeth M. Hart
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Evan Lyerly
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Thomas G. Bernhardt
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
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2
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Banahene N, Peters-Clarke TM, Biegas KJ, Shishkova E, Hart EM, McKitterick AC, Kambitsis NH, Johnson UG, Bernhardt TG, Coon JJ, Swarts BM. Chemical Proteomics Strategies for Analyzing Protein Lipidation Reveal the Bacterial O-Mycoloylome. J Am Chem Soc 2024; 146:12138-12154. [PMID: 38635392 PMCID: PMC11066868 DOI: 10.1021/jacs.4c02278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024]
Abstract
Protein lipidation dynamically controls protein localization and function within cellular membranes. A unique form of protein O-fatty acylation in Corynebacterium, termed protein O-mycoloylation, involves the attachment of mycolic acids─unusually large and hydrophobic fatty acids─to serine residues of proteins in these organisms' outer mycomembrane. However, as with other forms of protein lipidation, the scope and functional consequences of protein O-mycoloylation are challenging to investigate due to the inherent difficulties of enriching and analyzing lipidated peptides. To facilitate the analysis of protein lipidation and enable the comprehensive profiling and site mapping of protein O-mycoloylation, we developed a chemical proteomics strategy integrating metabolic labeling, click chemistry, cleavable linkers, and a novel liquid chromatography-tandem mass spectrometry (LC-MS/MS) method employing LC separation and complementary fragmentation methods tailored to the analysis of lipophilic, MS-labile O-acylated peptides. Using these tools in the model organism Corynebacterium glutamicum, we identified approximately 30 candidate O-mycoloylated proteins, including porins, mycoloyltransferases, secreted hydrolases, and other proteins with cell envelope-related functions─consistent with a role for O-mycoloylation in targeting proteins to the mycomembrane. Site mapping revealed that many of the proteins contained multiple spatially proximal modification sites, which occurred predominantly at serine residues surrounded by conformationally flexible peptide motifs. Overall, this study (i) discloses the putative protein O-mycoloylome for the first time, (ii) yields new insights into the undercharacterized proteome of the mycomembrane, which is a hallmark of important pathogens (e.g., Corynebacterium diphtheriae, Mycobacterium tuberculosis), and (iii) provides generally applicable chemical strategies for the proteomic analysis of protein lipidation.
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Affiliation(s)
- Nicholas Banahene
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
- Biochemistry,
Cell, and Molecular Biology Graduate Programs, Central Michigan University, Mount
Pleasant, Michigan 48859, United States
| | - Trenton M. Peters-Clarke
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53562, United States
- Department
of Biomolecular Chemistry, University of
Wisconsin, Madison, Wisconsin 53562, United States
- National
Center for Quantitative Biology of Complex Systems, University of Wisconsin, Madison, Wisconsin 53562, United States
| | - Kyle J. Biegas
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
- Biochemistry,
Cell, and Molecular Biology Graduate Programs, Central Michigan University, Mount
Pleasant, Michigan 48859, United States
| | - Evgenia Shishkova
- Department
of Biomolecular Chemistry, University of
Wisconsin, Madison, Wisconsin 53562, United States
- National
Center for Quantitative Biology of Complex Systems, University of Wisconsin, Madison, Wisconsin 53562, United States
| | - Elizabeth M. Hart
- Department
of Microbiology, Harvard Medical School, Boston, Massachusetts 02115 United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Amelia C. McKitterick
- Department
of Microbiology, Harvard Medical School, Boston, Massachusetts 02115 United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Nikolas H. Kambitsis
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
| | - Ulysses G. Johnson
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
- Biochemistry,
Cell, and Molecular Biology Graduate Programs, Central Michigan University, Mount
Pleasant, Michigan 48859, United States
| | - Thomas G. Bernhardt
- Department
of Microbiology, Harvard Medical School, Boston, Massachusetts 02115 United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Joshua J. Coon
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53562, United States
- Department
of Biomolecular Chemistry, University of
Wisconsin, Madison, Wisconsin 53562, United States
- National
Center for Quantitative Biology of Complex Systems, University of Wisconsin, Madison, Wisconsin 53562, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53562, United States
| | - Benjamin M. Swarts
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
- Biochemistry,
Cell, and Molecular Biology Graduate Programs, Central Michigan University, Mount
Pleasant, Michigan 48859, United States
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3
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Jeong H, Kim Y, Lee HS. CdbC: a disulfide bond isomerase involved in the refolding of mycoloyltransferases in Corynebacterium glutamicum cells exposed to oxidative conditions. J Biochem 2024; 175:457-470. [PMID: 38227582 DOI: 10.1093/jb/mvae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 01/18/2024] Open
Abstract
In Corynebacterium glutamicum cells, cdbC, which encodes a protein containing the CysXXCys motif, is regulated by the global redox-responsive regulator OsnR. In this study, we assessed the role of the periplasmic protein CdbC in disulfide bond formation and its involvement in mycomembrane biosynthesis. Purified CdbC efficiently refolded scrambled RNaseA, exhibiting prominent disulfide bond isomerase activity. The transcription of cdbC was decreased in cells grown in the presence of the reductant dithiothreitol (DTT). Moreover, unlike wild-type and cdbC-deleted cells, cdbC-overexpressing (P180-cdbC) cells grown in the presence of DTT exhibited retarded growth, abnormal cell morphology, increased cell surface hydrophobicity and altered mycolic acid composition. P180-cdbC cells cultured in a reducing environment accumulated trehalose monocorynomycolate, indicating mycomembrane deformation. Similarly, a two-hybrid analysis demonstrated the interaction of CdbC with the mycoloyltransferases MytA and MytB. Collectively, our findings suggest that CdbC, a periplasmic disulfide bond isomerase, refolds misfolded MytA and MytB and thereby assists in mycomembrane biosynthesis in cells exposed to oxidative conditions.
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Affiliation(s)
- Haeri Jeong
- Department of Biotechnology and Bioinformatics, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| | - Younhee Kim
- Department of Korean Medicine, Semyung University, Jecheon, 65, Semyeong-ro, Chungbuk 27136, Republic of Korea
| | - Heung-Shick Lee
- Department of Biotechnology and Bioinformatics, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
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4
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Wang H, Liu D, Zhou X. Effect of Mycolic Acids on Host Immunity and Lipid Metabolism. Int J Mol Sci 2023; 25:396. [PMID: 38203570 PMCID: PMC10778799 DOI: 10.3390/ijms25010396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 01/12/2024] Open
Abstract
Mycolic acids constitute pivotal constituents within the cell wall structure of Mycobacterium tuberculosis. Due to their structural diversity, the composition of mycolic acids exhibits substantial variations among different strains, endowing them with the distinctive label of being the 'signature' feature of mycobacterial species. Within Mycobacterium tuberculosis, the primary classes of mycolic acids include α-, keto-, and methoxy-mycolic acids. While these mycolic acids are predominantly esterified to the cell wall components (such as arabinogalactan, alginate, or glucose) of Mycobacterium tuberculosis, a fraction of free mycolic acids are secreted during in vitro growth of the bacterium. Remarkably, different types of mycolic acids possess varying capabilities to induce foamy macro-phages and trigger immune responses. Additionally, mycolic acids play a regulatory role in the lipid metabolism of host cells, thereby exerting influence over the progression of tuberculosis. Consequently, the multifaceted properties of mycolic acids shape the immune evasion strategy employed by Mycobacterium tuberculosis. A comprehensive understanding of mycolic acids is of paramount significance in the pursuit of developing tuberculosis therapeutics and unraveling the intricacies of its pathogenic mechanisms.
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Affiliation(s)
- Haoran Wang
- College of Veterinary Medicine, China Agricultural University, Beijing 100086, China; (H.W.); (D.L.)
- National Key Laboratory of Veterinary Public Health and Safety, Beijing 100086, China
| | - Dingpu Liu
- College of Veterinary Medicine, China Agricultural University, Beijing 100086, China; (H.W.); (D.L.)
- National Key Laboratory of Veterinary Public Health and Safety, Beijing 100086, China
| | - Xiangmei Zhou
- College of Veterinary Medicine, China Agricultural University, Beijing 100086, China; (H.W.); (D.L.)
- National Key Laboratory of Veterinary Public Health and Safety, Beijing 100086, China
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5
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Gaidhane IV, Biegas KJ, Erickson HE, Agarwal P, Chhonker YS, Ronning DR, Swarts BM. Chemical remodeling of the mycomembrane with chain-truncated lipids sensitizes mycobacteria to rifampicin. Chem Commun (Camb) 2023; 59:13859-13862. [PMID: 37929833 PMCID: PMC10872977 DOI: 10.1039/d3cc02364h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
The outer mycomembrane of Mycobacterium tuberculosis and related pathogens is a robust permeability barrier that protects against antibiotic treatment. Here, we demonstrate that synthetic analogues of the mycomembrane biosynthetic precursor trehalose monomycolate bearing truncated lipid chains increase permeability of Mycobacterium smegmatis cells and sensitize them to treatment with the first-line anti-tubercular drug rifampicin. The reported strategy may be useful for enhancing entry of drugs and other molecules to mycobacterial cells, and represents a new way to study mycomembrane structure and function.
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Affiliation(s)
- Ishani V Gaidhane
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, USA.
| | - Kyle J Biegas
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, USA.
- Biochemistry, Cell, and Molecular Biology Graduate Programs, Central Michigan University, Mount Pleasant, MI, USA
| | - Helen E Erickson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Prachi Agarwal
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yashpal S Chhonker
- Clinical Pharmacology Laboratory, Department of Pharmacy Practice and Science, University of Nebraska Medical Center, Omaha, NE, USA
| | - Donald R Ronning
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Benjamin M Swarts
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, USA.
- Biochemistry, Cell, and Molecular Biology Graduate Programs, Central Michigan University, Mount Pleasant, MI, USA
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6
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Li H, Xu D, Zhang D, Tan X, Huang D, Ma W, Zhao G, Li Y, Liu Z, Wang Y, Hu X, Wang X. Improve L-isoleucine production in Corynebacterium glutamicum WM001 by destructing the biosynthesis of trehalose dicorynomycolate. Microbiol Res 2023; 272:127390. [PMID: 37087971 DOI: 10.1016/j.micres.2023.127390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 04/25/2023]
Abstract
Trehalose dicorynomycolates are structurally important constituents of the cell envelope in Corynebacterium glutamicum. The genes treS, treY, otsA, mytA and mytB are necessary for the biosynthesis of trehalose dicorynomycolates. In this study, the effect of biosynthesis of trehalose dicorynomycolates on L-isoleucine production in C. glutamicum has been investigated by deleting the genes treS, treY, otsA, mytA, and mytB in the L-isoleucine producing C. glutamicum WM001. L-isoleucine production was slightly improved in the mutants ΔtreY, ΔotsA, and ΔtreYA, and not improved in the single deletion mutant ΔtreS , but significantly improved in the triple deletion mutant ΔtreSYA. Deletion of mytA or mytB in ΔtreSYA could further improve L-isoleucine production. However, deletion of both mytA and mytB in ΔtreSYA significantly decreased L-isoleucine production. The final L-isoleucine producing C. glutamicum WL001 was constructed by deletion of treS, treY, otsA, and mytB, insertion of lrp, and replacement of the native promoter of ilvA with the L-isoleucine sensitive promoter PbrnFE7. WL001 grew worse than the control WM001, but produced 36.1% more L-isoleucine after 72 h shake flask cultivation than WM001.
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Affiliation(s)
- Hedan Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Daqing Xu
- College of Life Sciences, Hebei Agricultural University, Baoding 071000, China
| | - Dezhi Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xin Tan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Danyang Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Wenjian Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Guihong Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Ying Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Ziwei Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yang Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiaoqing Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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7
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Gu H, Hao X, Liu R, Shi Z, Zhao Z, Chen F, Wang W, Wang Y, Shen X. Small protein Cgl2215 enhances phenolic tolerance by promoting MytA activity in Corynebacterium glutamicum. STRESS BIOLOGY 2022; 2:49. [PMID: 37676548 PMCID: PMC10441969 DOI: 10.1007/s44154-022-00071-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/24/2022] [Indexed: 09/08/2023]
Abstract
Corynebacterium glutamicum is a promising chassis microorganism for the bioconversion of lignocellulosic biomass owing to its good tolerance and degradation of the inhibitors generated in lignocellulosic pretreatments. Among the identified proteins encoded by genes within the C. glutamicum genome, nearly 400 are still functionally unknown. Based on previous transcriptome analysis, we found that the hypothetical protein gene cgl2215 was highly upregulated in response to phenol, ferulic acid, and vanillin stress. The cgl2215 deletion mutant was shown to be more sensitive than the parental strain to phenolic compounds as well as other environmental factors such as heat, ethanol, and oxidative stresses. Cgl2215 interacts with C. glutamicum mycoloyltransferase A (MytA) and enhances its in vitro esterase activity. Sensitivity assays of the ΔmytA and Δcgl2215ΔmytA mutants in response to phenolic stress established that the role of Cgl2215 in phenolic tolerance was mediated by MytA. Furthermore, transmission electron microscopy (TEM) results showed that cgl2215 and mytA deletion both led to defects in the cell envelope structure of C. glutamicum, especially in the outer layer (OL) and electron-transparent layer (ETL). Collectively, these results indicate that Cgl2215 can enhance MytA activity and affect the cell envelope structure by directly interacting with MytA, thus playing an important role in resisting phenolic and other environmental stresses.
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Affiliation(s)
- Huawei Gu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinwei Hao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruirui Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhenkun Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Zehua Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Fu Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenqiang Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xihui Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
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8
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de Sousa-d'Auria C, Constantinesco F, Bayan N, Constant P, Tropis M, Daffé M, Graille M, Houssin C. Cg1246, a new player in mycolic acid biosynthesis in Corynebacterium glutamicum. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35394419 DOI: 10.1099/mic.0.001171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mycolic acids are key components of the complex cell envelope of Corynebacteriales. These fatty acids, conjugated to trehalose or to arabinogalactan form the backbone of the mycomembrane. While mycolic acids are essential to the survival of some species, such as Mycobacterium tuberculosis, their absence is not lethal for Corynebacterium glutamicum, which has been extensively used as a model to depict their biosynthesis. Mycolic acids are first synthesized on the cytoplasmic side of the inner membrane and transferred onto trehalose to give trehalose monomycolate (TMM). TMM is subsequently transported to the periplasm by dedicated transporters and used by mycoloyltransferase enzymes to synthesize all the other mycolate-containing compounds. Using a random transposition mutagenesis, we recently identified a new uncharacterized protein (Cg1246) involved in mycolic acid metabolism. Cg1246 belongs to the DUF402 protein family that contains some previously characterized nucleoside phosphatases. In this study, we performed a functional and structural characterization of Cg1246. We showed that absence of the protein led to a significant reduction in the pool of TMM in C. glutamicum, resulting in a decrease in all other mycolate-containing compounds. We found that, in vitro, Cg1246 has phosphatase activity on organic pyrophosphate substrates but is most likely not a nucleoside phosphatase. Using a computational approach, we identified important residues for phosphatase activity and constructed the corresponding variants in C. glutamicum. Surprisingly complementation with these non-functional proteins fully restored the defect in TMM of the Δcg1246 mutant strain, suggesting that in vivo, the phosphatase activity is not involved in mycolic acid biosynthesis.
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Affiliation(s)
- Célia de Sousa-d'Auria
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Florence Constantinesco
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Nicolas Bayan
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Patricia Constant
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Maryelle Tropis
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Mamadou Daffé
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, F-91128 Palaiseau Cedex, Paris, France
| | - Christine Houssin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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9
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Carlier M, Lesur E, Baron A, Lemétais A, Guitot K, Roupnel L, Dietrich C, Doisneau G, Urban D, Bayan N, Beau JM, Guianvarc'h D, Vauzeilles B, Bourdreux Y. Synthesis of chemical tools to label the mycomembrane of corynebacteria using a modified Iron (III) chloride-mediated protection of trehalose. Org Biomol Chem 2022; 20:1974-1981. [DOI: 10.1039/d2ob00107a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trehalose-based probes are useful tools allowing the detection of the mycomembrane of Mycobacteria through the metabolic labeling approach. Some of them are trehalose analogues conjugated to fluorescent probes and others...
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10
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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] [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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11
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Yan W, Hamid N, Deng S, Jia PP, Pei DS. Individual and combined toxicogenetic effects of microplastics and heavy metals (Cd, Pb, and Zn) perturb gut microbiota homeostasis and gonadal development in marine medaka (Oryzias melastigma). JOURNAL OF HAZARDOUS MATERIALS 2020; 397:122795. [PMID: 32388101 DOI: 10.1016/j.jhazmat.2020.122795] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/02/2020] [Accepted: 04/19/2020] [Indexed: 05/21/2023]
Abstract
Currently, microplastics (MPs) attracted increased attention for their ubiquity and toxic properties. In this study, marine medaka was used to explore the individual and combined toxicity of heavy metals (HMs) and MPs on intestinal bacteria and gonadal development. After exposure to environmentally relevant concentrations of MPs and HMs, significant alterations of intestinal microbiota were found. The MPs treatment reduced the diversity and abundance of intestinal microbiota, while the HMs and MPs-HMs treatments increased them, which were confirmed by the abundance changes of Proteobacteria. According to the KEGG analysis, the metabolism and environmental information processing (EIP) pathways in the microbial community were significantly affected. This study showed that the MPs-HMs treatment caused a higher pollution load on the gut of the marine medaka, and triggered more significant changes of specific bacterial species and gut function in the males. However, during the gonadal development, HMs and MPs-HMs treatments resulted in empty follicles (EF) and follicular atresia (FA), and altered the gene expression levels related to hypothalamic-pituitary-gonadal (HPG) axis. In short, this study demonstrated that the reproductive disturbance was mainly due to HMs, but the combination of MPs and HMs did not strengthen the risk to the gonad development of the marine medaka.
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Affiliation(s)
- Wang Yan
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Naima Hamid
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shun Deng
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pan-Pan Jia
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - De-Sheng Pei
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China; College of Life Science, Henan Normal University, Xinxiang 453007, China.
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12
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Kalera K, Stothard AI, Woodruff PJ, Swarts BM. The role of chemoenzymatic synthesis in advancing trehalose analogues as tools for combatting bacterial pathogens. Chem Commun (Camb) 2020; 56:11528-11547. [PMID: 32914793 PMCID: PMC7919099 DOI: 10.1039/d0cc04955g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trehalose, a disaccharide of glucose, is increasingly recognized as an important contributor to virulence in major bacterial pathogens, such as Mycobacterium tuberculosis, Clostridioides difficile, and Burkholderia pseudomallei. Accordingly, bacterial trehalose metabolic pathways that are not present in humans have gained traction as targets for antibiotic and diagnostic development. Toward this goal, trehalose can be modified through a combination of rational design and synthesis to produce functionalized trehalose analogues, which can be deployed to probe or inhibit bacterial trehalose metabolism. However, the unique α,α-1,1-glycosidic bond and C2 symmetry of trehalose make analogue synthesis via traditional chemical methods very challenging. We and others have turned to the creation of chemoenzymatic synthesis methods, which in principle allow the use of nature's trehalose-synthesizing enzymes to stereo- and regioselectively couple simple, unprotected substrates to efficiently and conveniently generate trehalose analogues. Here, we provide a contextual account of our team's development of a trehalose analogue synthesis method that employs a highly substrate-tolerant, thermostable trehalose synthase enzyme, TreT from Thermoproteus tenax. Then, in three vignettes, we highlight how chemoenzymatic synthesis has accelerated the development of trehalose-based imaging probes and inhibitors that target trehalose-utilizing bacterial pathogens. We describe the role of TreT catalysis and related methods in the development of (i) tools for in vitro and in vivo imaging of mycobacteria, (ii) anti-biofilm compounds that sensitize drug-tolerant mycobacteria to clinical anti-tubercular compounds, and (iii) degradation-resistant trehalose analogues that block trehalose metabolism in C. difficile and potentially other trehalose-utilizing bacteria. We conclude by recapping progress and discussing priorities for future research in this area, including improving the scope and scale of chemoenzymatic synthesis methods to support translational research and expanding the functionality and applicability of trehalose analogues to study and target diverse bacterial pathogens.
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Affiliation(s)
- Karishma Kalera
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, USA.
| | - Alicyn I Stothard
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, USA.
| | - Peter J Woodruff
- Department of Chemistry, University of Southern Maine, Portland, ME, USA
| | - Benjamin M Swarts
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, USA.
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13
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Kavunja HW, Biegas KJ, Banahene N, Stewart JA, Piligian BF, Groenevelt JM, Sein CE, Morita YS, Niederweis M, Siegrist MS, Swarts BM. Photoactivatable Glycolipid Probes for Identifying Mycolate-Protein Interactions in Live Mycobacteria. J Am Chem Soc 2020; 142:7725-7731. [PMID: 32293873 PMCID: PMC7949286 DOI: 10.1021/jacs.0c01065] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mycobacteria have a distinctive glycolipid-rich outer membrane, the mycomembrane, which is a critical target for tuberculosis drug development. However, proteins that associate with the mycomembrane, or that are involved in its metabolism and host interactions, are not well-characterized. To facilitate the study of mycomembrane-related proteins, we developed photoactivatable trehalose monomycolate analogues that metabolically incorporate into the mycomembrane in live mycobacteria, enabling in vivo photo-cross-linking and click-chemistry-mediated analysis of mycolate-interacting proteins. When deployed in Mycobacterium smegmatis with quantitative proteomics, this strategy enriched over 100 proteins, including the mycomembrane porin (MspA), several proteins with known mycomembrane synthesis or remodeling functions (CmrA, MmpL3, Ag85, Tdmh), and numerous candidate mycolate-interacting proteins. Our approach is highly versatile, as it (i) enlists click chemistry for flexible protein functionalization; (ii) in principle can be applied to any mycobacterial species to identify endogenous bacterial proteins or host proteins that interact with mycolates; and (iii) can potentially be expanded to investigate protein interactions with other mycobacterial lipids. This tool is expected to help elucidate fundamental physiological and pathological processes related to the mycomembrane and may reveal novel diagnostic and therapeutic targets.
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Affiliation(s)
- Herbert W Kavunja
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Kyle J Biegas
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Nicholas Banahene
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Jessica A Stewart
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Brent F Piligian
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Jessica M Groenevelt
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Caralyn E Sein
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - M Sloan Siegrist
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Benjamin M Swarts
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, Michigan 48859, United States
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14
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Dietrich C, Li de la Sierra-Gallay I, Masi M, Girard E, Dautin N, Constantinesco-Becker F, Tropis M, Daffé M, van Tilbeurgh H, Bayan N. The C-terminal domain of Corynebacterium glutamicum mycoloyltransferase A is composed of five repeated motifs involved in cell wall binding and stability. Mol Microbiol 2020; 114:1-16. [PMID: 32073722 DOI: 10.1111/mmi.14492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/07/2020] [Indexed: 12/29/2022]
Abstract
The genomes of Corynebacteriales contain several genes encoding mycoloyltransferases (Myt) that are specific cell envelope enzymes essential for the biogenesis of the outer membrane. MytA is a major mycoloyltransferase of Corynebacterium glutamicum, displaying an N-terminal domain with esterase activity and a C-terminal extension containing a conserved repeated Leu-Gly-Phe-Pro (LGFP) sequence motif of unknown function. This motif is highly conserved in Corynebacteriales and found associated with cell wall hydrolases and with proteins of unknown function. In this study, we determined the crystal structure of MytA and found that its C-terminal domain is composed of five LGFP motifs and forms a long stalk perpendicular to the N-terminal catalytic α/β-hydrolase domain. The LGFP motifs are composed of a 4-stranded β-fold and occupy alternating orientations along the axis of the stalk. Multiple acetate binding pockets were identified in the stalk, which could correspond to putative ligand-binding sites. By using various MytA mutants and complementary in vitro and in vivo approaches, we provide evidence that the C-terminal LGFP domain interacts with the cell wall peptidoglycan-arabinogalactan polymer. We also show that the C-terminal LGFP domain is not required for the activity of MytA but rather contributes to the overall integrity of the cell envelope.
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Affiliation(s)
- Christiane Dietrich
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Muriel Masi
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Eric Girard
- University of Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Nathalie Dautin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | | | - Maryelle Tropis
- Institut de Pharmacologie et de Biologie Structurale, CNRS UMR 5089, Toulouse Cedex, France
| | - Mamadou Daffé
- Institut de Pharmacologie et de Biologie Structurale, CNRS UMR 5089, Toulouse Cedex, France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Nicolas Bayan
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
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15
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Zheng Y, Zhou Z, Ye X, Huang J, Jiang L, Chen G, Chen L, Wang Z. Identifying microbial community evolution in membrane bioreactors coupled with anaerobic side-stream reactor, packing carriers and ultrasonication for sludge reduction by linear discriminant analysis. BIORESOURCE TECHNOLOGY 2019; 291:121920. [PMID: 31382094 DOI: 10.1016/j.biortech.2019.121920] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
An anoxic/oxic membrane bioreactor (AO-MBR), an anaerobic side-stream reactor (ASSR) coupled MBRs (A-MBRs), an A-MBR with carriers packed in ASSR (AP-MBR) and an AP-MBR with sludge ultrasonicated before ASSR (AUP-MBR) were operated for 261 d to investigate effects of ASSR, packing carriers and ultrasonication on sludge reduction and microbial population. Sludge reduction efficiencies of A-MBR, AP-MBR and AUP-MBR were 36.2%, 46.4% and 51.4%, respectively. Packing carriers and ultrasonication both enhanced hydrolysis by stimulating activities of α-glucosidase and protease, while uncoupling metabolism was enhanced greatly by packing carriers but slightly by ultrasonication. Linear discriminant analysis of effect size (LEfSe) results showed that packing carriers promoted the growth of hydrolytic and fermentative bacteria in bulk sludge, and enriched anaerobes and fermentative bacteria on the surface of carriers. Ultrasonication screened ultrasonication-resistant bacteria, and created an anaerobic environment beneficial to hydrolytic and fermentative bacteria.
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Affiliation(s)
- Yue Zheng
- Shanghai Engineering Research Center of Energy - Saving in Heat Exchange Systems, College of Environmental and Chemical Engineering, Shanghai University of Electric Power, Shanghai 200090, China
| | - Zhen Zhou
- Shanghai Engineering Research Center of Energy - Saving in Heat Exchange Systems, College of Environmental and Chemical Engineering, Shanghai University of Electric Power, Shanghai 200090, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
| | - Xiaofang Ye
- Shanghai Engineering Research Center of Energy - Saving in Heat Exchange Systems, College of Environmental and Chemical Engineering, Shanghai University of Electric Power, Shanghai 200090, China
| | - Jing Huang
- Shanghai Engineering Research Center of Energy - Saving in Heat Exchange Systems, College of Environmental and Chemical Engineering, Shanghai University of Electric Power, Shanghai 200090, China
| | - Lingyan Jiang
- Shanghai Chengtou Wastewater Treatment Co Ltd, Shanghai 201203, China
| | - Guang Chen
- Shanghai Chengtou Wastewater Treatment Co Ltd, Shanghai 201203, China
| | - Liuyu Chen
- Shanghai Engineering Research Center of Energy - Saving in Heat Exchange Systems, College of Environmental and Chemical Engineering, Shanghai University of Electric Power, Shanghai 200090, China
| | - Zhiwei Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
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16
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Rastogi R, Kaur G, Maan P, Bhatnagar A, Narang T, Dogra S, Kaur J. Molecular characterization and immunogenic function of ML1899 (LipG) of Mycobacterium leprae. J Med Microbiol 2019; 68:1629-1640. [PMID: 31553301 DOI: 10.1099/jmm.0.001080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. ML1899 is conserved in all mycobacterium sp. and is a middle member of mle-ML1898 operon involved in mycolic acid modification.Aim. In the present study attempts were made to characterize ML1899 in detail.Methodology. Bioinformatics tools were used for prediction of active-site residues, antigenic epitopes and a three-dimensional model of protein. The gene was cloned, expressed and purified as His-tagged protein in Escherichia coli for biophysical/biochemical characterization. Recombinant protein was used to treat THP-1 cells to study change in production of nitric oxide (NO), reactive oxygen species (ROS), cytokines and chemokines using flowcytometry/ELISA.Results. In silico analysis predicted ML1899 as a member of α/β hydrolase family with GXSXG-motif and Ser126, His282, Asp254 as active-site residues that were confirmed by site-directed mutagensis. ML1899 exhibited esterase activity. It hydrolysed pNP-butyrate as optimum substrate at pH 8.0 and 50 °C with 5.56 µM-1 min-1 catalytic efficiency. The enzyme exhibited stability up to 60 °C temperature and between pH 6.0 to 9.0. K m, V max and specific activity of ML1899 were calculated to be 400 µM, 40 µmoles min-1 ml-1 and 27 U mg- 1, respectively. ML1899 also exhibited phospholipase activity. The protein affected the survival of macrophages when treated at higher concentration. ML1899 enhanced ROS/NO production and up-regulated pro-inflammatory cytokines and chemokine including TNF-α, IFN-γ, IL-6 and IL-8 in macrophages. ML1899 was also observed to elicit humoral response in 69 % of leprosy patients.Conclusion. These results suggested that ML1899, an esterase could up-regulate the immune responses in favour of macrophages at a low concentration but kills the THP-1 macrophages cells at a higher concentration.
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Affiliation(s)
- Ruchi Rastogi
- Department of Biochemistry, BMS Block 2, South Campus, Panjab University, Sector 25, Chandigarh 160014, India
| | - Gurkamaljit Kaur
- Department of Biotechnology, BMS Block 1, South Campus, Panjab University, Sector 25, Chandigarh 160014, India
| | - Pratibha Maan
- Present address: Department of Experimental Medicine and Biotechnology, PGIMER, Chandigarh, 160012, India.,Department of Biotechnology, BMS Block 1, South Campus, Panjab University, Sector 25, Chandigarh 160014, India
| | - Archana Bhatnagar
- Department of Biochemistry, BMS Block 2, South Campus, Panjab University, Sector 25, Chandigarh 160014, India
| | - Tarun Narang
- Department of Dermatology, Veberology and Leprology, PGIMER, Chandigarh, 160012, India
| | - Sunil Dogra
- Department of Dermatology, Veberology and Leprology, PGIMER, Chandigarh, 160012, India
| | - Jagdeep Kaur
- Department of Biotechnology, BMS Block 1, South Campus, Panjab University, Sector 25, Chandigarh 160014, India
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17
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Fiolek TJ, Banahene N, Kavunja HW, Holmes NJ, Rylski AK, Pohane AA, Siegrist MS, Swarts BM. Engineering the Mycomembrane of Live Mycobacteria with an Expanded Set of Trehalose Monomycolate Analogues. Chembiochem 2019; 20:1282-1291. [PMID: 30589191 PMCID: PMC6614877 DOI: 10.1002/cbic.201800687] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Indexed: 01/20/2023]
Abstract
Mycobacteria and related organisms in the Corynebacterineae suborder are characterized by a distinctive outer membrane referred to as the mycomembrane. Biosynthesis of the mycomembrane occurs through an essential process called mycoloylation, which involves antigen 85 (Ag85)-catalyzed transfer of mycolic acids from the mycoloyl donor trehalose monomycolate (TMM) to acceptor carbohydrates and, in some organisms, proteins. We recently described an alkyne-modified TMM analogue (O-AlkTMM-C7) which, in conjunction with click chemistry, acted as a chemical reporter for mycoloylation in intact cells and allowed metabolic labeling of mycoloylated components of the mycomembrane. Here, we describe the synthesis and evaluation of a toolbox of TMM-based reporters bearing alkyne, azide, trans-cyclooctene, and fluorescent tags. These compounds gave further insight into the substrate tolerance of mycoloyltransferases (e.g., Ag85s) in a cellular context and they provide significantly expanded experimental versatility by allowing one- or two-step cell labeling, live cell labeling, and rapid cell labeling via tetrazine ligation. Such capabilities will facilitate research on mycomembrane composition, biosynthesis, and dynamics. Moreover, because TMM is exclusively metabolized by Corynebacterineae, the described probes may be valuable for the specific detection and cell-surface engineering of Mycobacterium tuberculosis and related pathogens. We also performed experiments to establish the dependence of probe incorporation on mycoloyltransferase activity, results from which suggested that cellular labeling is a function not only of metabolic incorporation (and likely removal) pathway(s), but also accessibility across the envelope. Thus, whole-cell labeling experiments with TMM reporters should be carefully designed and interpreted when envelope permeability may be compromised. On the other hand, this property of TMM reporters can potentially be exploited as a convenient way to probe changes in envelope integrity and permeability, facilitating drug development studies.
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Affiliation(s)
- Taylor J Fiolek
- Department of Chemistry and Biochemistry, Central Michigan University, 1200 S. Franklin St., Mount Pleasant, MI, 48859, USA
| | - Nicholas Banahene
- Department of Chemistry and Biochemistry, Central Michigan University, 1200 S. Franklin St., Mount Pleasant, MI, 48859, USA
| | - Herbert W Kavunja
- Department of Chemistry and Biochemistry, Central Michigan University, 1200 S. Franklin St., Mount Pleasant, MI, 48859, USA
| | - Nathan J Holmes
- Department of Chemistry and Biochemistry, Central Michigan University, 1200 S. Franklin St., Mount Pleasant, MI, 48859, USA
| | - Adrian K Rylski
- Department of Chemistry and Biochemistry, Central Michigan University, 1200 S. Franklin St., Mount Pleasant, MI, 48859, USA
| | - Amol Arunrao Pohane
- Department of Microbiology, University of Massachusetts, 639 N. Pleasant Street, Amherst, MA, 01003, USA
| | - M Sloan Siegrist
- Department of Microbiology, University of Massachusetts, 639 N. Pleasant Street, Amherst, MA, 01003, USA
| | - Benjamin M Swarts
- Department of Chemistry and Biochemistry, Central Michigan University, 1200 S. Franklin St., Mount Pleasant, MI, 48859, USA
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18
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Holmes N, Kavunja HW, Yang Y, Vannest BD, Ramsey CN, Gepford DM, Banahene N, Poston AW, Piligian BF, Ronning DR, Ojha AK, Swarts BM. A FRET-Based Fluorogenic Trehalose Dimycolate Analogue for Probing Mycomembrane-Remodeling Enzymes of Mycobacteria. ACS OMEGA 2019; 4:4348-4359. [PMID: 30842987 PMCID: PMC6396954 DOI: 10.1021/acsomega.9b00130] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/12/2019] [Indexed: 05/17/2023]
Abstract
The mycobacterial outer membrane, or mycomembrane, is essential for the viability and virulence of Mycobacterium tuberculosis and related pathogens. The mycomembrane is a dynamic structure, whose chemical composition and biophysical properties can change during stress to give an advantage to the bacterium. However, the mechanisms that govern mycomembrane remodeling and their significance to mycobacterial pathogenesis are still not well characterized. Recent studies have shown that trehalose dimycolate (TDM), a major glycolipid of the mycomembrane, is broken down by the mycobacteria-specific enzyme TDM hydrolase (Tdmh) in response to nutrient deprivation, a process which appears to modulate the mycomembrane to increase nutrient acquisition, but at the expense of stress tolerance. Tdmh activity thus balances the growth of M. tuberculosis during infection in a manner that is contingent upon host immunity. Current methods to probe Tdmh activity are limited, impeding the development of inhibitors and the investigation of the role of Tdmh in bacterial growth and persistence. Here, we describe the synthesis and evaluation of FRET-TDM, which is a fluorescence-quenched analogue of TDM that is designed to fluoresce upon hydrolysis by Tdmh and potentially other trehalose ester-degrading hydrolases involved in mycomembrane remodeling. We found that FRET-TDM was efficiently activated in vitro by recombinant Tdmh, generating a 100-fold increase in fluorescence. FRET-TDM was also efficiently activated in the presence of whole cells of Mycobacterium smegmatis and M. tuberculosis, but the observed signal was predominantly Tdmh-independent, suggesting that physiological levels of Tdmh are low and that other mycobacterial enzymes also hydrolyze the probe. The latter notion was confirmed by employing a native protein gel-based fluorescence assay to profile FRET-TDM-activating enzymes from M. smegmatis lysates. On the other hand, FRET-TDM was capable of detecting the activity of Tdmh in cells when it was overexpressed. Together, our data demonstrate that FRET-TDM is a convenient and sensitive in vitro probe of Tdmh activity, which will be beneficial for Tdmh enzymatic characterization and inhibitor screening. In more complex samples, for example, live cells or cell lysates, FRET-TDM can serve as a tool to probe Tdmh activity at elevated enzyme levels, and it may facilitate the identification and characterization of related hydrolases that are involved in mycomembrane remodeling. Our study also provides insights as to how the structure of FRET-TDM or related fluorogenic probes can be optimized to achieve improved specificity and sensitivity for detecting mycobacteria.
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Affiliation(s)
- Nathan
J. Holmes
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
| | - Herbert W. Kavunja
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
| | - Yong Yang
- Division
of Genetics, Wadsworth Center, New York
State Department of Health, Albany, New York 12208, United States
| | - B. Dillon Vannest
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
| | - Claudia N. Ramsey
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
| | - Dana M. Gepford
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
| | - Nicholas Banahene
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
| | - Anne W. Poston
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
| | - Brent F. Piligian
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
| | - Donald R. Ronning
- Department
of Chemistry and Biochemistry, University
of Toledo, Toledo, Ohio 43606-3390, United States
| | - Anil K. Ojha
- Division
of Genetics, Wadsworth Center, New York
State Department of Health, Albany, New York 12208, United States
- Department
of Biomedical Sciences, University at Albany, New York 12208, United States
| | - Benjamin M. Swarts
- Department
of Chemistry and Biochemistry, Central Michigan
University, Mount
Pleasant, Michigan 48859, United States
- E-mail:
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19
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Sequential assembly of the septal cell envelope prior to V snapping in Corynebacterium glutamicum. Nat Chem Biol 2019; 15:221-231. [PMID: 30664686 DOI: 10.1038/s41589-018-0206-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/27/2018] [Indexed: 12/11/2022]
Abstract
Members of the Corynebacterineae, including Corynebacterium and Mycobacterium, have an atypical cell envelope characterized by an additional mycomembrane outside of the peptidoglycan layer. How this multilayered cell envelope is assembled remains unclear. Here, we tracked the assembly dynamics of different envelope layers in Corynebacterium glutamicum and Mycobacterium smegmatis by using metabolic labeling and found that the septal cell envelope is assembled sequentially in both species. Additionally, we demonstrate that in C. glutamicum, the peripheral peptidoglycan layer at the septal junction remains contiguous throughout septation, forming a diffusion barrier for the fluid mycomembrane. This diffusion barrier is resolved through perforations in the peripheral peptidoglycan, thus leading to the confluency of the mycomembrane before daughter cell separation (V snapping). Furthermore, the same junctional peptidoglycan also serves as a mechanical link holding the daughter cells together and undergoes mechanical fracture during V snapping. Finally, we show that normal V snapping in C. glutamicum depends on complete assembly of the septal cell envelope.
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20
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Lesur E, Baron A, Dietrich C, Buchotte M, Doisneau G, Urban D, Beau JM, Bayan N, Vauzeilles B, Guianvarc’h D, Bourdreux Y. First access to a mycolic acid-based bioorthogonal reporter for the study of the mycomembrane and mycoloyltransferases in Corynebacteria. Chem Commun (Camb) 2019; 55:13074-13077. [DOI: 10.1039/c9cc05754d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study we describe the first synthesis of an alkyne-based trehalose monomycolate probe closely mimicking the complex pattern of mycolic acids and its utility for the study of mycomembrane and mycoloyltransferases in Corynebacteria.
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Maan P, Kumar A, Kaur J, Kaur J. Rv1288, a Two Domain, Cell Wall Anchored, Nutrient Stress Inducible Carboxyl-Esterase of Mycobacterium tuberculosis, Modulates Cell Wall Lipid. Front Cell Infect Microbiol 2018; 8:421. [PMID: 30560095 PMCID: PMC6287010 DOI: 10.3389/fcimb.2018.00421] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/16/2018] [Indexed: 01/29/2023] Open
Abstract
Rv1288, a conserved hypothetical protein of M. tuberculosis (M.tb), was recently characterized as two-domain esterase enzyme by in silico study. In the present study, Rv1288 and its domains (Est and Lyt) were cloned individually from M.tb into E. coli for expression and purification. The purified rRv1288 and rEst proteins exhibited lipolytic activity with medium chain length esters as optimum substrates, while Lyt domain did not show enzymatic activity. However, presence of Lyt domain resulted in enhanced rate of protein aggregation at higher temperature. Both rRv1288 and rEst followed the similar patterns of substrate specificity, temperature and pH activity. Site directed mutagenesis confirmed the Ser-294, Asp-391 and His-425 as catalytic site residues. Rv1288 was found to be present in cell wall fraction of M.tb H37Ra. Peptidoglycan binding activity of Rv1288 and its domains demonstrated that the Lyt domain is essential for anchoring protein to the cell wall. Expression of rv1288 was up regulated in M.tb under nutrient starved condition. Over expression of rv1288 in surrogate host M. smegmatis led to change in colony morphology, enhanced pellicle and aggregate formation that might be linked with the changed lipid composition of bacterial cell wall. Cell wall of M. smegmatis expressing rv1288 had higher amount of lipids, with a significant increase in trehalose dimycolate content. Rv1288 also leads to increase in drug resistance of M. smegmatis. Rv1288 also enhanced the intracellular survival of M. smegmatis in Raw264.7 cell line. Overall, this study suggested that Rv1288, a cell wall localized carboxyl hydrolase with mycolyl-transferase activity, modulated the cell wall lipids to favor the survival of bacteria under stress condition.
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Affiliation(s)
- Pratibha Maan
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Arbind Kumar
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Jashandeep Kaur
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Jagdeep Kaur
- Department of Biotechnology, Panjab University, Chandigarh, India
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Abstract
Control and manipulation of bacterial populations requires an understanding of the factors that govern growth, division, and antibiotic action. Fluorescent and chemically reactive small molecule probes of cell envelope components can visualize these processes and advance our knowledge of cell envelope biosynthesis (e.g., peptidoglycan production). Still, fundamental gaps remain in our understanding of the spatial and temporal dynamics of cell envelope assembly. Previously described reporters require steps that limit their use to static imaging. Probes that can be used for real-time imaging would advance our understanding of cell envelope construction. To this end, we synthesized a fluorogenic probe that enables continuous live cell imaging in mycobacteria and related genera. This probe reports on the mycolyltransferases that assemble the mycolic acid membrane. This peptidoglycan-anchored bilayer-like assembly functions to protect these cells from antibiotics and host defenses. Our probe, quencher-trehalose-fluorophore (QTF), is an analog of the natural mycolyltransferase substrate. Mycolyltransferases process QTF by diverting their normal transesterification activity to hydrolysis, a process that unleashes fluorescence. QTF enables high contrast continuous imaging and the visualization of mycolyltransferase activity in cells. QTF revealed that mycolyltransferase activity is augmented before cell division and localized to the septa and cell poles, especially at the old pole. This observed localization suggests that mycolyltransferases are components of extracellular cell envelope assemblies, in analogy to the intracellular divisomes and polar elongation complexes. We anticipate QTF can be exploited to detect and monitor mycobacteria in physiologically relevant environments.
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Toyoda K, Inui M. Extracytoplasmic function sigma factor σDconfers resistance to environmental stress by enhancing mycolate synthesis and modifying peptidoglycan structures inCorynebacterium glutamicum. Mol Microbiol 2017; 107:312-329. [DOI: 10.1111/mmi.13883] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Koichi Toyoda
- Research institute of Innovative Technology for the Earth (RITE), 9-2 Kizugawa; Kyoto 619-0292 Japan
| | - Masayuki Inui
- Research institute of Innovative Technology for the Earth (RITE), 9-2 Kizugawa; Kyoto 619-0292 Japan
- Graduate School of Biological Sciences; Nara Institute of Science and Technology, 8916-5; Takayama, Ikoma, Nara 630-0101 Japan
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Dissecting the mycobacterial cell envelope and defining the composition of the native mycomembrane. Sci Rep 2017; 7:12807. [PMID: 28993692 PMCID: PMC5634507 DOI: 10.1038/s41598-017-12718-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/18/2017] [Indexed: 11/20/2022] Open
Abstract
The mycobacterial envelope is unique, containing the so-called mycomembrane (MM) composed of very-long chain fatty acids, mycolic acids (MA). Presently, the molecular composition of the MM remains unproven, due to the diversity of methods used for determining its composition. The plasma membranes (PM) and the native MM-containing cell walls (MMCW) of two rapid-growing mycobacterial species, Mycobacterium aurum and M. smegmatis, were isolated from their cell lysates by differential ultracentrifugation. Transmission electron microscopy and biochemical analyses demonstrated that the two membranes were virtually pure. Bottom-up quantitative proteomics study indicated a different distribution of more than 2,100 proteins between the PM and MMCW. Among these, the mannosyltransferase PimB, galactofuranosyltransferase GlfT2, Cytochrome p450 and ABC transporter YjfF, were most abundant in the PM, which also contain lipoglycans, phospholipids, including phosphatidylinositol mannosides, and only a tiny amount of other glycolipids. Antigen85 complex proteins, porins and the putative transporters MCE protein family were mostly found in MMCW fraction that contains MA esterifying arabinogalactan, constituting the inner leaflet of MM. Glycolipids, phospholipids and lipoglycans, together with proteins, presumably composed the outer leaflet of the MM, a lipid composition that differs from that deduced from the widely used extraction method of mycobacterial cells with dioctylsulfosuccinate sodium.
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25
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Angell CA, Magazù S, Migliardo F. Science for life - Recent advances in biochemical and biophysical methods. Biochim Biophys Acta Gen Subj 2016; 1861:3501-3503. [PMID: 27657805 DOI: 10.1016/j.bbagen.2016.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- C Austen Angell
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Salvatore Magazù
- Department of Mathematical and Informatics Sciences, Physical Sciences and Earth Sciences, University of Messina, Viale D'Alcontres 31, 98166 Messina, Italy
| | - Federica Migliardo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale D'Alcontres 31, 98166 Messina, Italy.
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Kavunja HW, Piligian BF, Fiolek TJ, Foley HN, Nathan TO, Swarts BM. A chemical reporter strategy for detecting and identifying O-mycoloylated proteins in Corynebacterium. Chem Commun (Camb) 2016; 52:13795-13798. [DOI: 10.1039/c6cc07143k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A trehalose monomycolate (TMM)-mimicking chemical reporter facilitated the investigation of a recently discovered class of lipidated proteins in the Corynebacterineae.
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Affiliation(s)
- Herbert W. Kavunja
- Department of Chemistry and Biochemistry, Central Michigan University
- Mount Pleasant
- USA
| | - Brent F. Piligian
- Department of Chemistry and Biochemistry, Central Michigan University
- Mount Pleasant
- USA
| | - Taylor J. Fiolek
- Department of Chemistry and Biochemistry, Central Michigan University
- Mount Pleasant
- USA
| | - Hannah N. Foley
- Department of Chemistry and Biochemistry, Central Michigan University
- Mount Pleasant
- USA
| | - Temitope O. Nathan
- Department of Chemistry and Biochemistry, Central Michigan University
- Mount Pleasant
- USA
| | - Benjamin M. Swarts
- Department of Chemistry and Biochemistry, Central Michigan University
- Mount Pleasant
- USA
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