1
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Zhou P, Bu YX, Xu L, Xu XW, Shen HB. Understanding the mechanisms of halotolerance in members of Pontixanthobacter and Allopontixanthobacter by comparative genome analysis. Front Microbiol 2023; 14:1111472. [PMID: 36992937 PMCID: PMC10040529 DOI: 10.3389/fmicb.2023.1111472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/16/2023] [Indexed: 03/14/2023] Open
Abstract
Halotolerant microorganisms have developed versatile mechanisms for coping with saline stress. With the increasing number of isolated halotolerant strains and their genomes being sequenced, comparative genome analysis would help understand the mechanisms of salt tolerance. Six type strains of Pontixanthobacter and Allopontixanthobacter, two phylogenetically close genera, were isolated from diverse salty environments and showed different NaCl tolerances, from 3 to 10% (w/v). Based on the co-occurrence greater than 0.8 between halotolerance and open reading frame (ORF) among the six strains, possible explanations for halotolerance were discussed regarding osmolyte, membrane permeability, transportation, intracellular signaling, polysaccharide biosynthesis, and SOS response, which provided hypotheses for further investigations. The strategy of analyzing genome-wide co-occurrence between genetic diversity and physiological characteristics sheds light on how microorganisms adapt to the environment.
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Affiliation(s)
- Peng Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- *Correspondence: Peng Zhou,
| | - Yu-Xin Bu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China
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2
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Xu X, Dong B, Peng L, Gao C, He Z, Wang C, Zeng J. Anti-tuberculosis drug development via targeting the cell envelope of Mycobacterium tuberculosis. Front Microbiol 2022; 13:1056608. [PMID: 36620019 PMCID: PMC9810820 DOI: 10.3389/fmicb.2022.1056608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis possesses a dynamic cell envelope, which consists of a peptidoglycan layer, a mycolic acid layer, and an arabinogalactan polysaccharide. This envelope possesses a highly complex and unique structure representing a barrier that protects and assists the growth of M. tuberculosis and allows its adaptation to the host. It regulates the immune response of the host cells, causing their damage. Therefore, the cell envelope of M. tuberculosis is an attractive target for vaccine and drug development. The emergence of multidrug-resistant as well as extensively drug resistant tuberculosis and co-infection with HIV prevented an effective control of this disease. Thus, the discovery and development of new drugs is a major keystone for TB treatment and control. This review mainly summarizes the development of drug enzymes involved in the biosynthesis of the cell wall in M. tuberculosis, and other potential drug targets in this pathway, to provide more effective strategies for the development of new drugs.
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Affiliation(s)
- Xinyue Xu
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Baoyu Dong
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Lijun Peng
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chao Gao
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China.,Laboratory of Human Diseases and Immunotherapies, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiqun He
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chuan Wang
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jumei Zeng
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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3
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Characterization of inositol lipid metabolism in gut-associated Bacteroidetes. Nat Microbiol 2022; 7:986-1000. [PMID: 35725777 PMCID: PMC9246714 DOI: 10.1038/s41564-022-01152-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/17/2022] [Indexed: 12/13/2022]
Abstract
Inositol lipids are ubiquitous in eukaryotes and have finely tuned roles in cellular signalling and membrane homoeostasis. In Bacteria, however, inositol lipid production is relatively rare. Recently, the prominent human gut bacterium Bacteroides thetaiotaomicron (BT) was reported to produce inositol lipids and sphingolipids, but the pathways remain ambiguous and their prevalence unclear. Here, using genomic and biochemical approaches, we investigated the gene cluster for inositol lipid synthesis in BT using a previously undescribed strain with inducible control of sphingolipid synthesis. We characterized the biosynthetic pathway from myo-inositol-phosphate (MIP) synthesis to phosphoinositol dihydroceramide, determined the crystal structure of the recombinant BT MIP synthase enzyme and identified the phosphatase responsible for the conversion of bacterially-derived phosphatidylinositol phosphate (PIP-DAG) to phosphatidylinositol (PI-DAG). In vitro, loss of inositol lipid production altered BT capsule expression and antimicrobial peptide resistance. In vivo, loss of inositol lipids decreased bacterial fitness in a gnotobiotic mouse model. We identified a second putative, previously undescribed pathway for bacterial PI-DAG synthesis without a PIP-DAG intermediate, common in Prevotella. Our results indicate that inositol sphingolipid production is widespread in host-associated Bacteroidetes and has implications for symbiosis. The pathways responsible for inositol lipid production in human gut Bacteroides are characterized and these lipids are important for capsule expression and antimicrobial peptide resistance in vitro and colonization in vivo.
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4
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Jiang Z, Lu Y, Liu Z, Wu W, Xu X, Dinnyés A, Yu Z, Chen L, Sun Q. Drug resistance prediction and resistance genes identification in Mycobacterium tuberculosis based on a hierarchical attentive neural network utilizing genome-wide variants. Brief Bioinform 2022; 23:6553603. [PMID: 35325021 DOI: 10.1093/bib/bbac041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 01/25/2023] Open
Abstract
Prediction of antimicrobial resistance based on whole-genome sequencing data has attracted greater attention due to its rapidity and convenience. Numerous machine learning-based studies have used genetic variants to predict drug resistance in Mycobacterium tuberculosis (MTB), assuming that variants are homogeneous, and most of these studies, however, have ignored the essential correlation between variants and corresponding genes when encoding variants, and used a limited number of variants as prediction input. In this study, taking advantage of genome-wide variants for drug-resistance prediction and inspired by natural language processing, we summarize drug resistance prediction into document classification, in which variants are considered as words, mutated genes in an isolate as sentences, and an isolate as a document. We propose a novel hierarchical attentive neural network model (HANN) that helps discover drug resistance-related genes and variants and acquire more interpretable biological results. It captures the interaction among variants in a mutated gene as well as among mutated genes in an isolate. Our results show that for the four first-line drugs of isoniazid (INH), rifampicin (RIF), ethambutol (EMB) and pyrazinamide (PZA), the HANN achieves the optimal area under the ROC curve of 97.90, 99.05, 96.44 and 95.14% and the optimal sensitivity of 94.63, 96.31, 92.56 and 87.05%, respectively. In addition, without any domain knowledge, the model identifies drug resistance-related genes and variants consistent with those confirmed by previous studies, and more importantly, it discovers one more potential drug-resistance-related gene.
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Affiliation(s)
- Zhonghua Jiang
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yongmei Lu
- College of Computer Science, Sichuan University, Chengdu, Sichuan 610065, China
| | - Zhuochong Liu
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Wei Wu
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Xinyi Xu
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | | | - Zhonghua Yu
- College of Computer Science, Sichuan University, Chengdu, Sichuan 610065, China
| | - Li Chen
- College of Computer Science, Sichuan University, Chengdu, Sichuan 610065, China
| | - Qun Sun
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
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5
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Sartorio MG, Valguarnera E, Hsu FF, Feldman MF. Lipidomics Analysis of Outer Membrane Vesicles and Elucidation of the Inositol Phosphoceramide Biosynthetic Pathway in Bacteroides thetaiotaomicron. Microbiol Spectr 2022; 10:e0063421. [PMID: 35080445 PMCID: PMC8791184 DOI: 10.1128/spectrum.00634-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 12/19/2021] [Indexed: 12/24/2022] Open
Abstract
Approximately one-third of the human colonic microbiome is formed by bacteria from the genus Bacteroides. These bacteria produce a large amount of uniformly sized outer membrane vesicles (OMVs), which are equipped with hydrolytic enzymes that play a role in the degradation of diet- and host-derived glycans. In this work, we characterize the lipid composition of membranes and OMVs from Bacteroides thetaiotaomicron VPI-5482. Liquid chromatography-mass spectrometry (LC-MS) analysis indicated that OMVs carry sphingolipids, glycerophospholipids, and serine-dipeptide lipids. Sphingolipid species represent more than 50% of the total lipid content of OMVs. The most abundant sphingolipids in OMVs are ethanolamine phosphoceramide (EPC) and inositol phosphoceramide (IPC). Bioinformatics analysis allowed the identification of the BT1522-1526 operon putatively involved in IPC synthesis. Mutagenesis studies revealed that BT1522-1526 is essential for the synthesis of phosphatidylinositol (PI) and IPC, confirming the role of this operon in the biosynthesis of IPC. BT1522-1526 mutant strains lacking IPC produced OMVs that were indistinguishable from the wild-type strain, indicating that IPC sphingolipid species are not involved in OMV biogenesis. Given the known role of sphingolipids in immunomodulation, we suggest that OMVs may act as long-distance vehicles for the delivery of sphingolipids in the human gut. IMPORTANCE Sphingolipids are essential membrane lipid components found in eukaryotes that are also involved in cell signaling processes. Although rare in bacteria, sphingolipids are produced by members of the phylum Bacteroidetes, human gut commensals. Here, we determined that OMVs carry sphingolipids and other lipids of known signaling function. Our results demonstrate that the BT1522-1526 operon is required for IPC biosynthesis in B. thetaiotaomicron.
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Affiliation(s)
- Mariana G. Sartorio
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Ezequiel Valguarnera
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Fong-Fu Hsu
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Mario F. Feldman
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States
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6
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Xiao Y, Wang P, Zhu X, Xie Z. Pseudomonas donghuensis HYS gtrA/ B/ II Gene Cluster Contributes to Its Pathogenicity toward Caenorhabditis elegans. Int J Mol Sci 2021; 22:ijms221910741. [PMID: 34639082 PMCID: PMC8509367 DOI: 10.3390/ijms221910741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 12/11/2022] Open
Abstract
Pseudomonas donghuensis HYS is more virulent than P. aeruginosa toward Caenorhabditis elegans but the mechanism underlying virulence is unclear. This study is the first to report that the specific gene cluster gtrA/B/II in P. donghuensis HYS is involved in the virulence of this strain toward C. elegans, and there are no reports of GtrA, GtrB and GtrII in any Pseudomonas species. The pathogenicity of P. donghuensis HYS was evaluated using C. elegans as a host. Based on the prediction of virulence factors and comparative genomic analysis of P. donghuensis HYS, we identified 42 specific virulence genes in P. donghuensis HYS. Slow-killing assays of these genes showed that the gtrAB mutation had the greatest effect on the virulence of P. donghuensis HYS, and GtrA, GtrB and GtrII all positively affected P. donghuensis HYS virulence. Two critical GtrII residues (Glu47 and Lys480) were identified in P. donghuensis HYS. Transmission electron microscopy (TEM) showed that GtrA, GtrB and GtrII were involved in the glucosylation of lipopolysaccharide (LPS) O-antigen in P. donghuensis HYS. Furthermore, colony-forming unit (CFU) assays showed that GtrA, GtrB and GtrII significantly enhanced P. donghuensis HYS colonization in the gut of C. elegans, and glucosylation of LPS O-antigen and colonization in the host intestine contributed to the pathogenicity of P. donghuensis HYS. In addition, experiments using the worm mutants ZD101, KU4 and KU25 revealed a correlation between P. donghuensis HYS virulence and the TIR-1/SEK-1/PMK-1 pathways of the innate immune p38 MAPK pathway in C. elegans. In conclusion, these results reveal that the specific virulence gene cluster gtrA/B/II contributes to the unique pathogenicity of HYS compared with other pathogenic Pseudomonas, and that this process also involves C. elegans innate immunity. These findings significantly increase the available information about GtrA/GtrB/GtrII-based virulence mechanisms in the genus Pseudomonas.
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7
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Harvey DJ. ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016. MASS SPECTROMETRY REVIEWS 2021; 40:408-565. [PMID: 33725404 DOI: 10.1002/mas.21651] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/24/2020] [Indexed: 06/12/2023]
Abstract
This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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8
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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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9
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Batt SM, Burke CE, Moorey AR, Besra GS. Antibiotics and resistance: the two-sided coin of the mycobacterial cell wall. Cell Surf 2020; 6:100044. [PMID: 32995684 PMCID: PMC7502851 DOI: 10.1016/j.tcsw.2020.100044] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/26/2020] [Accepted: 08/26/2020] [Indexed: 01/07/2023] Open
Abstract
Mycobacterium tuberculosis, the bacterium responsible for tuberculosis, is the global leading cause of mortality from an infectious agent. Part of this success relies on the unique cell wall, which consists of a thick waxy coat with tightly packed layers of complexed sugars, lipids and peptides. This coat provides a protective hydrophobic barrier to antibiotics and the host's defences, while enabling the bacterium to spread efficiently through sputum to infect and survive within the macrophages of new hosts. However, part of this success comes at a cost, with many of the current first- and second-line drugs targeting the enzymes involved in cell wall biosynthesis. The flip side of this coin is that resistance to these drugs develops either in the target enzymes or the activation pathways of the drugs, paving the way for new resistant clinical strains. This review provides a synopsis of the structure and synthesis of the cell wall and the major current drugs and targets, along with any mechanisms of resistance.
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Affiliation(s)
- Sarah M. Batt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Christopher E. Burke
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alice R. Moorey
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Gurdyal S. Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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10
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Shao M, McNeil M, Cook GM, Lu X. MmpL3 inhibitors as antituberculosis drugs. Eur J Med Chem 2020; 200:112390. [DOI: 10.1016/j.ejmech.2020.112390] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022]
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11
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Abriata LA, Dal Peraro M. State-of-the-art web services for de novo protein structure prediction. Brief Bioinform 2020; 22:5870389. [PMID: 34020540 DOI: 10.1093/bib/bbaa139] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 02/06/2023] Open
Abstract
Residue coevolution estimations coupled to machine learning methods are revolutionizing the ability of protein structure prediction approaches to model proteins that lack clear homologous templates in the Protein Data Bank (PDB). This has been patent in the last round of the Critical Assessment of Structure Prediction (CASP), which presented several very good models for the hardest targets. Unfortunately, literature reporting on these advances often lacks digests tailored to lay end users; moreover, some of the top-ranking predictors do not provide webservers that can be used by nonexperts. How can then end users benefit from these advances and correctly interpret the predicted models? Here we review the web resources that biologists can use today to take advantage of these state-of-the-art methods in their research, including not only the best de novo modeling servers but also datasets of models precomputed by experts for structurally uncharacterized protein families. We highlight their features, advantages and pitfalls for predicting structures of proteins without clear templates. We present a broad number of applications that span from driving forward biochemical investigations that lack experimental structures to actually assisting experimental structure determination in X-ray diffraction, cryo-EM and other forms of integrative modeling. We also discuss issues that must be considered by users yet still require further developments, such as global and residue-wise model quality estimates and sources of residue coevolution other than monomeric tertiary structure.
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Affiliation(s)
- Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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12
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Rismondo J, Haddad TFM, Shen Y, Loessner MJ, Gründling A. GtcA is required for LTA glycosylation in Listeria monocytogenes serovar 1/2a and Bacillus subtilis. ACTA ACUST UNITED AC 2020; 6:100038. [PMID: 32743150 PMCID: PMC7389260 DOI: 10.1016/j.tcsw.2020.100038] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/16/2020] [Accepted: 02/11/2020] [Indexed: 11/26/2022]
Abstract
The cell wall polymers wall teichoic acid (WTA) and lipoteichoic acid (LTA) are often modified with glycosyl and D-alanine residues. Recent studies have shown that a three-component glycosylation system is used for the modification of LTA in several Gram-positive bacteria including Bacillus subtilis and Listeria monocytogenes. In the L. monocytogenes 1/2a strain 10403S, the cytoplasmic glycosyltransferase GtlA is thought to use UDP-galactose to produce the C55-P-galactose lipid intermediate, which is transported across the membrane by an unknown flippase. Next, the galactose residue is transferred onto the LTA backbone on the outside of the cell by the glycosyltransferase GtlB. Here we show that GtcA is necessary for the glycosylation of LTA in L. monocytogenes 10403S and B. subtilis 168 and we hypothesize that these proteins act as C55-P-sugar flippases. With this we revealed that GtcA is involved in the glycosylation of both teichoic acid polymers in L. monocytogenes 10403S, namely WTA with N-acetylglucosamine and LTA with galactose residues. These findings indicate that the L. monocytogenes GtcA protein can act on different C55-P-sugar intermediates. Further characterization of GtcA in L. monocytogenes led to the identification of residues essential for its overall function as well as residues, which predominately impact WTA or LTA glycosylation.
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Affiliation(s)
- Jeanine Rismondo
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Talal F M Haddad
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Yang Shen
- Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Angelika Gründling
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
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13
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Sommer R, Neres J, Piton J, Dhar N, van der Sar A, Mukherjee R, Laroche T, Dyson PJ, McKinney JD, Bitter W, Makarov V, Cole ST. Fluorescent Benzothiazinone Analogues Efficiently and Selectively Label Dpre1 in Mycobacteria and Actinobacteria. ACS Chem Biol 2018; 13:3184-3192. [PMID: 30289689 DOI: 10.1021/acschembio.8b00790] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Benzothiazinones (BTZ) are highly potent bactericidal inhibitors of mycobacteria and the lead compound, BTZ043, and the optimized drug candidate, PBTZ169, have potential for the treatment of tuberculosis. Here, we exploited the tractability of the BTZ scaffold by attaching a range of fluorophores to the 2-substituent of the BTZ ring via short linkers. We show by means of fluorescence imaging that the most advanced derivative, JN108, is capable of efficiently labeling its target, the essential flavoenzyme DprE1, both in cell-free extracts and after purification as well as in growing cells of different actinobacterial species. DprE1 displays a polar localization in Mycobacterium tuberculosis, M. marinum, M. smegmatis, and Nocardia farcinica but not in Corynebacterium glutamicum. Finally, mutation of the cysteine residue in DprE1 in these species, to which BTZ covalently binds, abolishes completely the interaction with JN108, thereby highlighting the specificity of this fluorescent probe.
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Affiliation(s)
- Raphael Sommer
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - João Neres
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- More Medicines for Tuberculosis (MM4TB) Consortium (www.mm4tb.org), EPFL, 1015 Lausanne, Switzerland
| | - Jérémie Piton
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- More Medicines for Tuberculosis (MM4TB) Consortium (www.mm4tb.org), EPFL, 1015 Lausanne, Switzerland
| | - Neeraj Dhar
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- More Medicines for Tuberculosis (MM4TB) Consortium (www.mm4tb.org), EPFL, 1015 Lausanne, Switzerland
| | - Astrid van der Sar
- Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Raju Mukherjee
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- More Medicines for Tuberculosis (MM4TB) Consortium (www.mm4tb.org), EPFL, 1015 Lausanne, Switzerland
| | - Thierry Laroche
- Faculty of Life Sciences (SV), BioImaging and Optics Platform (BIOP), Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 15, 1015, Lausanne, Switzerland
| | - Paul J. Dyson
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - John D. McKinney
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- More Medicines for Tuberculosis (MM4TB) Consortium (www.mm4tb.org), EPFL, 1015 Lausanne, Switzerland
| | - Wilbert Bitter
- Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Vadim Makarov
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- More Medicines for Tuberculosis (MM4TB) Consortium (www.mm4tb.org), EPFL, 1015 Lausanne, Switzerland
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14
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Chikhale RV, Barmade MA, Murumkar PR, Yadav MR. Overview of the Development of DprE1 Inhibitors for Combating the Menace of Tuberculosis. J Med Chem 2018; 61:8563-8593. [PMID: 29851474 DOI: 10.1021/acs.jmedchem.8b00281] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Decaprenylphosphoryl-β-d-ribose 2'-epimerase (DprE1), a vital enzyme for cell wall synthesis, plays a crucial role in the formation of lipoarabinomannan and arabinogalactan. It was first reported as a druggable target on the basis of inhibitors discovered in high throughput screening of a drug library. Since then, inhibitors with different types of chemical scaffolds have been reported for their activity against this enzyme. Formation of a covalent or noncovalent bond by the interacting ligand with the enzyme causes loss of its catalytic activity which ultimately leads to the death of the mycobacterium. This Perspective describes various DprE1 inhibitors as anti-TB agents reported to date.
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Affiliation(s)
- Rupesh V Chikhale
- Faculty of Pharmacy, Kalabhavan Campus , The Maharaja Sayajirao University of Baroda , Vadodara 390 001 , India.,School of Health Sciences, Division of Pharmacy and Optometry , University of Manchester , Manchester M13 9PL , U.K
| | - Mahesh A Barmade
- Faculty of Pharmacy, Kalabhavan Campus , The Maharaja Sayajirao University of Baroda , Vadodara 390 001 , India
| | - Prashant R Murumkar
- Faculty of Pharmacy, Kalabhavan Campus , The Maharaja Sayajirao University of Baroda , Vadodara 390 001 , India
| | - Mange Ram Yadav
- Faculty of Pharmacy, Kalabhavan Campus , The Maharaja Sayajirao University of Baroda , Vadodara 390 001 , India
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15
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Rismondo J, Percy MG, Gründling A. Discovery of genes required for lipoteichoic acid glycosylation predicts two distinct mechanisms for wall teichoic acid glycosylation. J Biol Chem 2018; 293:3293-3306. [PMID: 29343515 PMCID: PMC5836110 DOI: 10.1074/jbc.ra117.001614] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/13/2018] [Indexed: 12/20/2022] Open
Abstract
The bacterial cell wall is an important and highly complex structure that is essential for bacterial growth because it protects bacteria from cell lysis and environmental insults. A typical Gram-positive bacterial cell wall is composed of peptidoglycan and the secondary cell wall polymers, wall teichoic acid (WTA) and lipoteichoic acid (LTA). In many Gram-positive bacteria, LTA is a polyglycerol-phosphate chain that is decorated with d-alanine and sugar residues. However, the function of and proteins responsible for the glycosylation of LTA are either unknown or not well-characterized. Here, using bioinformatics, genetic, and NMR spectroscopy approaches, we found that the Bacillus subtilis csbB and yfhO genes are essential for LTA glycosylation. Interestingly, the Listeria monocytogenes gene lmo1079, which encodes a YfhO homolog, was not required for LTA glycosylation, but instead was essential for WTA glycosylation. LTA is polymerized on the outside of the cell and hence can only be glycosylated extracellularly. Based on the similarity of the genes coding for YfhO homologs that are required in B. subtilis for LTA glycosylation or in L. monocytogenes for WTA glycosylation, we hypothesize that WTA glycosylation might also occur extracellularly in Listeria species. Finally, we discovered that in L. monocytogenes, lmo0626 (gtlB) was required for LTA glycosylation, indicating that the encoded protein has a function similar to that of YfhO, although the proteins are not homologous. Together, our results enable us to propose an updated model for LTA glycosylation and also indicate that glycosylation of WTA might occur through two different mechanisms in Gram-positive bacteria.
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Affiliation(s)
- Jeanine Rismondo
- From the Section of Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Matthew G Percy
- From the Section of Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Angelika Gründling
- From the Section of Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
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16
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Abriata LA, Tamò GE, Monastyrskyy B, Kryshtafovych A, Dal Peraro M. Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods. Proteins 2017; 86 Suppl 1:97-112. [DOI: 10.1002/prot.25423] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Luciano A. Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB); Lausanne Switzerland
| | - Giorgio E. Tamò
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB); Lausanne Switzerland
| | | | | | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB); Lausanne Switzerland
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17
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Abriata LA, Kinch LN, Tamò GE, Monastyrskyy B, Kryshtafovych A, Dal Peraro M. Definition and classification of evaluation units for tertiary structure prediction in CASP12 facilitated through semi-automated metrics. Proteins 2017; 86 Suppl 1:16-26. [DOI: 10.1002/prot.25403] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/03/2017] [Accepted: 10/11/2017] [Indexed: 01/31/2023]
Affiliation(s)
- Luciano A. Abriata
- Institute of Bioengineering, School of Life Sciences; École Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
| | - Lisa N. Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas; Dallas Texas
| | - Giorgio E. Tamò
- Institute of Bioengineering, School of Life Sciences; École Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
| | | | | | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences; École Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
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18
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Abstract
Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis (TB), is recognized as a global health emergency as promoted by the World Health Organization. Over 1 million deaths per year, along with the emergence of multi- and extensively-drug resistant strains of Mtb, have triggered intensive research into the pathogenicity and biochemistry of this microorganism, guiding the development of anti-TB chemotherapeutic agents. The essential mycobacterial cell wall, sharing some common features with all bacteria, represents an apparent ‘Achilles heel’ that has been targeted by TB chemotherapy since the advent of TB treatment. This complex structure composed of three distinct layers, peptidoglycan, arabinogalactan and mycolic acids, is vital in supporting cell growth, virulence and providing a barrier to antibiotics. The fundamental nature of cell wall synthesis and assembly has rendered the mycobacterial cell wall as the most widely exploited target of anti-TB drugs. This review provides an overview of the biosynthesis of the prominent cell wall components, highlighting the inhibitory mechanisms of existing clinical drugs and illustrating the potential of other unexploited enzymes as future drug targets.
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19
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Mann E, Whitfield C. A widespread three-component mechanism for the periplasmic modification of bacterial glycoconjugates. CAN J CHEM 2016. [DOI: 10.1139/cjc-2015-0594] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The diverse structures of bacterial glycoconjugates are generally established during the early stages of synthesis by the activities of nucleotide sugar-dependent glycosyltransferases active in the cytoplasm. However, in some cases, further modifications of varying complexity occur after the glycoconjugate is exported to the periplasm. These processes are distinguished by the involvement of polyprenyl monosphosphoryl donors and require glycosyltransferases possessing GT-C folds. Established prototypes are found in modifications of some bacterial lipopolysaccharides, where 4-amino-4-deoxy-l-arabinose is added to lipid A and glucose side branches are used to modify O-antigens. Here we review the current understanding of these systems and describe similarities to other periplasmic glycan modifications in bacteria and the N-glycosylation pathway for assembly of eukaryotic glycoproteins.
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Affiliation(s)
- Evan Mann
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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20
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Characterization of DprE1-Mediated Benzothiazinone Resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2016; 60:6451-6459. [PMID: 27527085 DOI: 10.1128/aac.01523-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 08/07/2016] [Indexed: 12/12/2022] Open
Abstract
Benzothiazinones (BTZs) are a class of compounds found to be extremely potent against both drug-susceptible and drug-resistant Mycobacterium tuberculosis strains. The potency of BTZs is explained by their specificity for their target decaprenylphosphoryl-d-ribose oxidase (DprE1), in particular by covalent binding of the activated form of the compound to the critical cysteine 387 residue of the enzyme. To probe the role of C387, we used promiscuous site-directed mutagenesis to introduce other codons at this position into dprE1 of M. tuberculosis The resultant viable BTZ-resistant mutants were characterized in vitro, ex vivo, and biochemically to gain insight into the effects of these mutations on DprE1 function and on M. tuberculosis Five different mutations (C387G, C387A, C387S, C387N, and C387T) conferred various levels of resistance to BTZ and exhibited different phenotypes. The C387G and C387N mutations resulted in a lower growth rate of the mycobacterium on solid medium, which could be attributed to the significant decrease in the catalytic efficiency of the DprE1 enzyme. All five mutations rendered the mycobacterium less cytotoxic to macrophages. Finally, differences in the potencies of covalent and noncovalent DprE1 inhibitors in the presence of C387 mutations were revealed by enzymatic assays. As expected from the mechanism of action, the covalent inhibitor PBTZ169 only partially inhibited the mutant DprE1 enzymes compared to the near-complete inhibition with a noncovalent DprE1 inhibitor, Ty38c. This study emphasizes the importance of the C387 residue for DprE1 activity and for the killing action of covalent inhibitors such as BTZs and other recently identified nitroaromatic inhibitors.
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