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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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Kelly SD, Duong NH, Nothof JT, Lowary TL, Whitfield C. Three-component systems represent a common pathway for extracytoplasmic addition of pentofuranose sugars into bacterial glycans. Proc Natl Acad Sci U S A 2024; 121:e2402554121. [PMID: 38748580 PMCID: PMC11127046 DOI: 10.1073/pnas.2402554121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/18/2024] [Indexed: 05/27/2024] Open
Abstract
Cell surface glycans are major drivers of antigenic diversity in bacteria. The biochemistry and molecular biology underpinning their synthesis are important in understanding host-pathogen interactions and for vaccine development with emerging chemoenzymatic and glycoengineering approaches. Structural diversity in glycostructures arises from the action of glycosyltransferases (GTs) that use an immense catalog of activated sugar donors to build the repeating unit and modifying enzymes that add further heterogeneity. Classical Leloir GTs incorporate α- or β-linked sugars by inverting or retaining mechanisms, depending on the nucleotide sugar donor. In contrast, the mechanism of known ribofuranosyltransferases is confined to β-linkages, so the existence of α-linked ribofuranose in some glycans dictates an alternative strategy. Here, we use Citrobacter youngae O1 and O2 lipopolysaccharide O antigens as prototypes to describe a widespread, versatile pathway for incorporating side-chain α-linked pentofuranoses by extracytoplasmic postpolymerization glycosylation. The pathway requires a polyprenyl phosphoribose synthase to generate a lipid-linked donor, a MATE-family flippase to transport the donor to the periplasm, and a GT-C type GT (founding the GT136 family) that performs the final glycosylation reaction. The characterized system shares similarities, but also fundamental differences, with both cell wall arabinan biosynthesis in mycobacteria, and periplasmic glucosylation of O antigens first discovered in Salmonella and Shigella. The participation of auxiliary epimerases allows the diversification of incorporated pentofuranoses. The results offer insight into a broad concept in microbial glycobiology and provide prototype systems and bioinformatic guides that facilitate discovery of further examples from diverse species, some in currently unknown glycans.
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Affiliation(s)
- Steven D. Kelly
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ONN1G 2W1, Canada
| | - Nam Ha Duong
- Institute of Biological Chemistry, Academia Sinica, Nangang, Taipei11529, Taiwan
- Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Nangang, Taipei11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu300044, Taiwan
| | - Jeremy T. Nothof
- Department of Chemistry, University of Alberta, Edmonton, ABT6G 2G2, Canada
| | - Todd L. Lowary
- Institute of Biological Chemistry, Academia Sinica, Nangang, Taipei11529, Taiwan
- Department of Chemistry, University of Alberta, Edmonton, ABT6G 2G2, Canada
- Institute of Biochemical Sciences, National Taiwan University, Taipei10617, Taiwan
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ONN1G 2W1, Canada
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The biosynthetic origin of ribofuranose in bacterial polysaccharides. Nat Chem Biol 2022; 18:530-537. [PMID: 35393575 DOI: 10.1038/s41589-022-01006-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/28/2022] [Indexed: 11/08/2022]
Abstract
Bacterial surface polysaccharides are assembled by glycosyltransferase enzymes that typically use sugar nucleotide or polyprenyl-monophosphosugar activated donors. Characterized representatives exist for many monosaccharides but neither the donor nor the corresponding glycosyltransferases have been definitively identified for ribofuranose residues found in some polysaccharides. Klebsiella pneumoniae O-antigen polysaccharides provided prototypes to identify dual-domain ribofuranosyltransferase proteins catalyzing a two-step reaction sequence. Phosphoribosyl-5-phospho-D-ribosyl-α-1-diphosphate serves as the donor for a glycan acceptor-specific phosphoribosyl transferase (gPRT), and a more promiscuous phosphoribosyl-phosphatase (PRP) then removes the residual 5'-phosphate. The 2.5-Å resolution crystal structure of a dual-domain ribofuranosyltransferase ortholog from Thermobacillus composti revealed a PRP domain that conserves many features of the phosphatase members of the haloacid dehalogenase family, and a gPRT domain that diverges substantially from all previously characterized phosphoribosyl transferases. The gPRT represents a new glycosyltransferase fold conserved in the most abundant ribofuranosyltransferase family.
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Madani A, Ridenour JN, Martin BP, Paudel RR, Abdul Basir A, Le Moigne V, Herrmann JL, Audebert S, Camoin L, Kremer L, Spilling CD, Canaan S, Cavalier JF. Cyclipostins and Cyclophostin Analogues as Multitarget Inhibitors That Impair Growth of Mycobacterium abscessus. ACS Infect Dis 2019; 5:1597-1608. [PMID: 31299146 DOI: 10.1021/acsinfecdis.9b00172] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Twelve new Cyclophostin and Cyclipostins analogues (CyC19-30) were synthesized, thus extending our series to 38 CyCs. Their antibacterial activities were evaluated against four pathogenic mycobacteria (Mycobacterium abscessus, Mycobacterium marinum, Mycobacterium bovis BCG, and Mycobacterium tuberculosis) and two Gram negative bacteria. The CyCs displayed very low toxicity toward host cells and were only active against mycobacteria. Importantly, several CyCs were active against extracellular M. abscessus (CyC17/CyC18β/CyC25/CyC26) or intramacrophage residing mycobacteria (CyC7(α,β)/CyC8(α,β)) with minimal inhibitory concentrations (MIC50) values comparable to or better than those of amikacin or imipenem, respectively. An activity-based protein profiling combined with mass spectrometry allowed identification of the potential target enzymes of CyC17/CyC26, mostly being involved in lipid metabolism and/or in cell wall biosynthesis. Overall, these results strengthen the selective activity of the CyCs against mycobacteria, including the most drug-resistant M. abscessus, through the cumulative inhibition of a large number of Ser- and Cys-enzymes participating in key physiological processes.
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Affiliation(s)
- Abdeldjalil Madani
- Aix-Marseille Université, CNRS, LISM, Institut de Microbiologie de la Méditerranée, Marseille, France 13402 Cedex 20
| | - Jeremy N. Ridenour
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Benjamin P. Martin
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Rishi R. Paudel
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Anosha Abdul Basir
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Vincent Le Moigne
- APHP, GHU PIFO, Hôpital Raymond-Poincaré−Hôpital Ambroise-Paré, 92100 Boulogne-Billancourt, France
| | - Jean-Louis Herrmann
- APHP, GHU PIFO, Hôpital Raymond-Poincaré−Hôpital Ambroise-Paré, 92100 Boulogne-Billancourt, France
- 2I, UVSQ, INSERM UMR 1173, Université Paris-Saclay, 78035 Versailles, France
| | - Stéphane Audebert
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, 13273 Marseille Cedex 09, France
| | - Luc Camoin
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, 13273 Marseille Cedex 09, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, 34293 Montpellier, France
- IRIM, INSERM, 34293 Montpellier, France
| | - Christopher D. Spilling
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Stéphane Canaan
- Aix-Marseille Université, CNRS, LISM, Institut de Microbiologie de la Méditerranée, Marseille, France 13402 Cedex 20
| | - Jean-François Cavalier
- Aix-Marseille Université, CNRS, LISM, Institut de Microbiologie de la Méditerranée, Marseille, France 13402 Cedex 20
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Kavvas ES, Seif Y, Yurkovich JT, Norsigian C, Poudel S, Greenwald WW, Ghatak S, Palsson BO, Monk JM. Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. BMC SYSTEMS BIOLOGY 2018; 12:25. [PMID: 29499714 PMCID: PMC5834885 DOI: 10.1186/s12918-018-0557-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 02/21/2018] [Indexed: 11/10/2022]
Abstract
BACKGROUND The efficacy of antibiotics against M. tuberculosis has been shown to be influenced by experimental media conditions. Investigations of M. tuberculosis growth in physiological conditions have described an environment that is different from common in vitro media. Thus, elucidating the interplay between available nutrient sources and antibiotic efficacy has clear medical relevance. While genome-scale reconstructions of M. tuberculosis have enabled the ability to interrogate media differences for the past 10 years, recent reconstructions have diverged from each other without standardization. A unified reconstruction of M. tuberculosis H37Rv would elucidate the impact of different nutrient conditions on antibiotic efficacy and provide new insights for therapeutic intervention. RESULTS We present a new genome-scale model of M. tuberculosis H37Rv, named iEK1011, that unifies and updates previous M. tuberculosis H37Rv genome-scale reconstructions. We functionally assess iEK1011 against previous models and show that the model increases correct gene essentiality predictions on two different experimental datasets by 6% (53% to 60%) and 18% (60% to 71%), respectively. We compared simulations between in vitro and approximated in vivo media conditions to examine the predictive capabilities of iEK1011. The simulated differences recapitulated literature defined characteristics in the rewiring of TCA metabolism including succinate secretion, gluconeogenesis, and activation of both the glyoxylate shunt and the methylcitrate cycle. To assist efforts to elucidate mechanisms of antibiotic resistance development, we curated 16 metabolic genes related to antimicrobial resistance and approximated evolutionary drivers of resistance. Comparing simulations of these antibiotic resistance features between in vivo and in vitro media highlighted condition-dependent differences that may influence the efficacy of antibiotics. CONCLUSIONS iEK1011 provides a computational knowledge base for exploring the impact of different environmental conditions on the metabolic state of M. tuberculosis H37Rv. As more experimental data and knowledge of M. tuberculosis H37Rv become available, a unified and standardized M. tuberculosis model will prove to be a valuable resource to the research community studying the systems biology of M. tuberculosis.
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Affiliation(s)
- Erol S. Kavvas
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA
| | - Yara Seif
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA
| | - James T. Yurkovich
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA
| | - Charles Norsigian
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA
| | - Saugat Poudel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA
| | - William W. Greenwald
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA
| | - Sankha Ghatak
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark
| | - Jonathan M. Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA
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Parmar KM, Hathi ZJ, Dafale NA. Control of Multidrug-Resistant Gene Flow in the Environment Through Bacteriophage Intervention. Appl Biochem Biotechnol 2016; 181:1007-1029. [PMID: 27723009 DOI: 10.1007/s12010-016-2265-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/23/2016] [Indexed: 02/06/2023]
Abstract
The spread of multidrug-resistant (MDR) bacteria is an emerging threat to the environment and public wellness. Inappropriate use and indiscriminate release of antibiotics in the environment through un-metabolized form create a scenario for the emergence of virulent pathogens and MDR bugs in the surroundings. Mechanisms underlying the spread of resistance include horizontal and vertical gene transfers causing the transmittance of MDR genes packed in different host, which pass across different food webs. Several controlling agents have been used for combating pathogens; however, the use of lytic bacteriophages proves to be one of the most eco-friendly due to their specificity, killing only target bacteria without damaging the indigenous beneficial flora of the habitat. Phages are part of the natural microflora present in different environmental niches and are remarkably stable in the environment. Diverse range of phage products, such as phage enzymes, phage peptides having antimicrobial properties, and phage cocktails also have been used to eradicate pathogens along with whole phages. Recently, the ability of phages to control pathogens has extended from the different areas of medicine, agriculture, aquaculture, food industry, and into the environment. To avoid the arrival of pre-antibiotic epoch, phage intervention proves to be a potential option to eradicate harmful pathogens generated by the MDR gene flow which are uneasy to cure by conventional treatments.
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Affiliation(s)
- Krupa M Parmar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India
| | - Zubeen J Hathi
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India
| | - Nishant A Dafale
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India.
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Two-Year Follow-up Study of Mycobacterium tuberculosis Antigen-Driven IFN-γ Responses and Macrophage sCD14 Levels After Tuberculosis Contact. Indian J Microbiol 2016; 56:205-13. [PMID: 27570313 DOI: 10.1007/s12088-016-0571-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 02/16/2016] [Indexed: 02/07/2023] Open
Abstract
Clinical data regarding the prediction of active tuberculosis (TB) development in close TB contacts are scarce. To address this problem, we performed a 2-year follow-up study of Mycobacterium tuberculosis (M.tb) antigen-driven IFN-gamma responses and serum levels of soluble macrophage CD14 receptor in individuals with recent or prolonged M.tb exposure. Between June 2011 and June 2013, we studied 60 healthy Polish adults with recent household or long-term work TB contact and individuals without known M.tb exposure. All of them underwent baseline and repeated testing with IGRA (IFN-gamma release assay) and serum sCD14 ELISA quantification. Frequencies of IGRA results differed at the baseline and follow-up testing. IGRA reversions were noticed in almost one-third of Work TB Contacts and no participants from the Household TB Contact group. IGRA conversions were found in 40 % of Household TB Contacts. No correlation between the IGRA result and the sCD14 level was observed. IFN-γ variability has important implications for clinical practice and requires caution in interpreting the results to distinguish new infections from nonspecific inter-individual variations in cytokine responses. The impairment of IFN-γ response in some individuals with prolonged M.tb exposure representing a resistant immune status does not allow considering IGRA results as reliable and credible. Monitoring the serum sCD14 level can reduce the likelihood of a false prediction of active TB development in close TB contacts showing an M.tb-specific increase in the IFN-gamma production in repeated IGRA testing.
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Jiang T, Cai L, Zhao X, He L, Ma Y, Zang S, Zhang C, Li X, Xin Y. Functional identification of MSMEG_6402 protein from Mycobacterium smegmatis in decaprenylphosphoryl-D-arabinose biosynthesis. Microb Pathog 2014; 76:44-50. [PMID: 25223716 DOI: 10.1016/j.micpath.2014.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 08/18/2014] [Accepted: 09/11/2014] [Indexed: 11/24/2022]
Abstract
The arabinogalactan (AG) of the mycobacterial cell wall consists of an arabinan region, a galactan region and a disaccharide linker. Decaprenylphosphoryl-D-arabinose (DPA) is the donor for arabinofuran residues, which are formed from phosphoribose diphosphate (PRPP) and decaprenyl phosphate (DP). DP is sequentially catalyzed by a three-step process that involves a transferase, a phosphatase and an epimerase. Rv3807c is a putative phospholipid phosphatase that might generate the intermediate product of decaprenyl-phosphoryl-ribose (DPR) in DPA biosynthesis. Mycobacterium smegmatis MSMEG_6402 is a homolog gene of Mycobacterium tuberculosis Rv3807c and was substituted for the functional identification of Rv3807c. Previously, we generated a conditional MSMEG_6402 gene knockout strain (M. sm-ΔM_6402) that exhibited significantly affected cell wall structure. To understand the function of MSMEG_6402 in DPA biosynthesis, this gene was amplified and expressed, and the resulting protein was identified and purified using a His-tagged approach. A MSMEG_6402 enzymatic reaction system with PRPP and DP as substrates was utilized, and the reaction products were separated using thin layer chromatography (TLC). The results revealed a specific lipid-linked sugar band that appeared in the reaction with the addition of MSMEG_6402. Furthermore, ESI-MS detection was utilized in this study, and the results revealed that the enzymatic reaction products involving MSMEG_6402 included DPPR and a sodium ion adduct of DPR. Additionally, the phosphatase activity of MSMEG_6402 was also determined through phosphate group detection using the colorimetric method. Based on our results together with the results of previous studies, including the functional identification and bioinformatics analysis of M. tuberculosis Rv3807c, we propose that MSMEG_6402, as a phosphatase, has an intimate relationship with DPA biosynthesis.
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Affiliation(s)
- Tao Jiang
- Department of Biotechnology, Dalian Medical University, Dalian 116044, China
| | - Lina Cai
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China
| | - Xiaojiao Zhao
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China
| | - Lianqi He
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China
| | - Yufang Ma
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China
| | - Shizhu Zang
- Department of Biotechnology, Dalian Medical University, Dalian 116044, China
| | - Cuili Zhang
- Department of Biotechnology, Dalian Medical University, Dalian 116044, China
| | - Xinli Li
- Department of Biotechnology, Dalian Medical University, Dalian 116044, China
| | - Yi Xin
- Department of Biotechnology, Dalian Medical University, Dalian 116044, China.
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