1
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Liu Y, Brown CM, Erramilli S, Su YC, Guu SY, Tseng PS, Wang YJ, Duong NH, Tokarz P, Kloss B, Han CR, Chen HY, Rodrigues J, Khoo KH, Archer M, Kossiakoff AA, Lowary TL, Stansfeld PJ, Nygaard R, Mancia F. Structural insights into terminal arabinosylation of mycobacterial cell wall arabinan. Nat Commun 2025; 16:3973. [PMID: 40301320 PMCID: PMC12041299 DOI: 10.1038/s41467-025-58196-5] [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: 08/23/2024] [Accepted: 03/14/2025] [Indexed: 05/01/2025] Open
Abstract
The global challenge of tuberculosis, caused by Mycobacterium tuberculosis (Mtb), is compounded by the emergence of drug-resistant strains. A critical factor in Mtb's pathogenicity is its intricate cell envelope, which acts as a formidable barrier against immune defences and pharmacological interventions. Central to this envelope are arabinogalactan (AG) and lipoarabinomannan (LAM), two complex polysaccharides containing arabinan domains essential for maintaining cell wall structure and function. The arabinofuranosyltransferase AftB plays a pivotal role in the biosynthesis of these arabinan domains by catalyzing the addition of β-(1 → 2)-linked terminal arabinofuranose residues. Here, we present the cryo-EM structures of Mycobacterium chubuense AftB in both its apo form and bound to a donor substrate analog, resolved at 2.9 Å and 3.4 Å resolution, respectively. These structures reveal that AftB has a GT-C fold, with a transmembrane (TM) domain comprised of eleven TM helices and a periplasmic cap domain. AftB has a distinctive irregular, tube-shaped cavity that connects two proposed substrate binding sites. Through an integrated approach combining structural analysis, biochemical assays, and molecular dynamics simulations, we delineate the molecular basis of AftB's reaction mechanism and propose a model for its catalytic function.
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Affiliation(s)
- Yaqi Liu
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Chelsea M Brown
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, UK
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Satchal Erramilli
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL, USA
| | - Yi-Chia Su
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, ROC
| | - Shih-Yun Guu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, ROC
| | - Po-Sen Tseng
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Yu-Jen Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, ROC
| | - Nam Ha Duong
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, ROC
- Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan, ROC
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan, ROC
| | - Piotr Tokarz
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL, USA
| | - Brian Kloss
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Cheng-Ruei Han
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, ROC
| | - Hung-Yu Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, ROC
| | - José Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
| | - Kay-Hooi Khoo
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, ROC
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan, ROC
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL, USA
| | - Todd L Lowary
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, ROC.
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan, ROC.
| | - Phillip J Stansfeld
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, UK.
| | - Rie Nygaard
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, USA.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
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2
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Liu Y, Brown CM, Borges N, Nobre RN, Erramilli S, Belcher Dufrisne M, Kloss B, Giacometti S, Esteves AM, Timóteo CG, Tokarz P, Cater RJ, Lowary TL, Morita YS, Kossiakoff AA, Santos H, Stansfeld PJ, Nygaard R, Mancia F. Mechanistic studies of mycobacterial glycolipid biosynthesis by the mannosyltransferase PimE. Nat Commun 2025; 16:3974. [PMID: 40301322 PMCID: PMC12041525 DOI: 10.1038/s41467-025-57843-1] [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: 08/23/2024] [Accepted: 03/05/2025] [Indexed: 05/01/2025] Open
Abstract
Tuberculosis (TB), a leading cause of death among infectious diseases globally, is caused by Mycobacterium tuberculosis (Mtb). The pathogenicity of Mtb is largely attributed to its complex cell envelope, which includes a class of glycolipids called phosphatidyl-myo-inositol mannosides (PIMs). These glycolipids maintain the integrity of the cell envelope, regulate permeability, and mediate host-pathogen interactions. PIMs comprise a phosphatidyl-myo-inositol core decorated with one to six mannose residues and up to four acyl chains. The mannosyltransferase PimE catalyzes the transfer of the fifth PIM mannose residue from a polyprenyl phosphate-mannose (PPM) donor. This step contributes to the proper assembly and function of the mycobacterial cell envelope; however, the structural basis for substrate recognition and the catalytic mechanism of PimE remain poorly understood. Here, we present the cryo-electron microscopy (cryo-EM) structures of PimE from Mycobacterium abscessus in its apo and product-bound form. The structures reveal a distinctive binding cavity that accommodates both donor and acceptor substrates/products. Key residues involved in substrate coordination and catalysis were identified and validated via in vitro assays and in vivo complementation, while molecular dynamics simulations delineated access pathways and binding dynamics. Our integrated approach provides comprehensive insights into PimE function and informs potential strategies for anti-TB therapeutics.
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Affiliation(s)
- Yaqi Liu
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Chelsea M Brown
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, UK
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh, The Netherlands
| | - Nuno Borges
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
- Marine and Environmental Sciences Centre, Escola Superior de Tecnologia, Instituto Politécnico de Setúbal, Setúbal, Portugal
| | - Rodrigo N Nobre
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Satchal Erramilli
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL, USA
| | - Meagan Belcher Dufrisne
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Brian Kloss
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Sabrina Giacometti
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- School of Medicine, New York University, New York, NY, USA
| | - Ana M Esteves
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cristina G Timóteo
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Piotr Tokarz
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL, USA
| | - Rosemary J Cater
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia
| | - Todd L Lowary
- Institute of Biological Chemistry, Academia Sinica, Nangang, Taipei, Taiwan
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL, USA
| | - Helena Santos
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Phillip J Stansfeld
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, UK.
| | - Rie Nygaard
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, USA.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
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Zinkle AP, Morgan RT, Nygaard R, Mancia F. Structural insights into polyisoprenyl-binding glycosyltransferases. Structure 2025; 33:639-651. [PMID: 39884274 PMCID: PMC11972162 DOI: 10.1016/j.str.2025.01.003] [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: 10/30/2024] [Revised: 12/16/2024] [Accepted: 01/03/2025] [Indexed: 02/01/2025]
Abstract
Glycosyltransferases (GTs) catalyze the addition of sugars to diverse substrates facilitating complex glycoconjugate biosynthesis across all domains of life. When embedded in or associated with the membrane, these enzymes often depend on polyisoprenyl-phosphate or -pyrophosphate (PP) lipid carriers, including undecaprenyl phosphate in bacteria and dolichol phosphate in eukaryotes, to transfer glycan moieties. GTs that bind PP substrates (PP-GTs) are functionally diverse but share some common structural features within their family or subfamily, particularly with respect to how they interact with their cognate PP ligands. Recent advances in single-particle cryo-electron microscopy (cryo-EM) have provided insight into the structures of PP-GTs and the modes by which they bind their PP ligands. Here, we explore the structural landscape of PP-GTs, focusing mainly on those for which there is molecular-level information on liganded states, and highlight how PP coordination modalities may be shared or differ among members of this diverse enzyme class.
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Affiliation(s)
- Allen P Zinkle
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ryan T Morgan
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rie Nygaard
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Radiation Oncology, Weill Cornell Medical College, New York, NY 10065, USA.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA.
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4
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Zhang Q. Structural insights into the advancements of mobile colistin resistance enzymes. Microbiol Res 2025; 291:127983. [PMID: 39612773 DOI: 10.1016/j.micres.2024.127983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2024] [Revised: 11/17/2024] [Accepted: 11/23/2024] [Indexed: 12/01/2024]
Abstract
The plasmid-encoded mobile colistin resistance enzyme (MCR) is challenging the clinical efficacy of colistin as a last-resort antibiotic against multidrug-resistant bacteria. This transferase catalyzes the addition of positively charged phosphoethanolamine to lipid A, and its catalytic domain in the periplasm has been elucidated. To date, there are many works on the catalytic domain and function of this enzyme class. However, the roles of unreported soluble or inter-membrane domains remain undefined, which might cause an inaccurate or even incorrect understanding of substrate recognition and binding. In this review, MCR-1 is first compared and analyzed from the perspective of the full-length alpha-fold MCR-1. Specifically, some disputed issues, especially in its architecture and catalytic mechanism are discussed independently. Meanwhile, the structure-based insights into MCRs variants, their evolutions, and the balance between colistin-resistance and survival costs, are also critically analyzed. Importantly, by comparing it with the full-length MCR-1, several potential pockets for drug design have been re-identified. Finally, recent advancements in inhibitors targeting MCR-1 are also in-depth summarized. These details offer a new perspective on MCRs and serve as a valuable foundation for drug development.
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Affiliation(s)
- Qi Zhang
- Centre for Eye and Vision Research, Hong Kong Science Park, Hong Kong.
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5
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Mycroft-West CJ, Leanca MA, Wu L. Structural glycobiology - from enzymes to organelles. Biochem Soc Trans 2025; 53:BST20241119. [PMID: 39889286 DOI: 10.1042/bst20241119] [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: 11/01/2024] [Revised: 12/19/2024] [Accepted: 12/23/2024] [Indexed: 02/02/2025]
Abstract
Biological carbohydrate polymers represent some of the most complex molecules in life, enabling their participation in a huge range of physiological functions. The complexity of biological carbohydrates arises from an extensive enzymatic repertoire involved in their construction, deconstruction and modification. Over the past decades, structural studies of carbohydrate processing enzymes have driven major insights into their mechanisms, supporting associated applications across medicine and biotechnology. Despite these successes, our understanding of how multienzyme networks function to create complex polysaccharides is still limited. Emerging techniques such as super-resolution microscopy and cryo-electron tomography are now enabling the investigation of native biological systems at near molecular resolutions. Here, we review insights from classical in vitro studies of carbohydrate processing, alongside recent in situ studies of glycosylation-related processes. While considerable technical challenges remain, the integration of molecular mechanisms with true biological context promises to transform our understanding of carbohydrate regulation, shining light upon the processes driving functional complexity in these essential biomolecules.
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Affiliation(s)
| | - Miron A Leanca
- The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0QX, Didcot, UK
| | - Liang Wu
- The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0QX, Didcot, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, OX3 7BN, Oxford, UK
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6
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Ashraf KU, Bunoro-Batista M, Ansell TB, Punetha A, Rosario-Garrido S, Firlar E, Kaelber JT, Stansfeld PJ, Petrou VI. Structural basis of undecaprenyl phosphate glycosylation leading to polymyxin resistance in Gram-negative bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.29.634835. [PMID: 39974898 PMCID: PMC11838356 DOI: 10.1101/2025.01.29.634835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
In Gram-negative bacteria, the enzymatic modification of Lipid A with aminoarabinose (L-Ara4N) leads to resistance against polymyxin antibiotics and cationic antimicrobial peptides. ArnC, an integral membrane glycosyltransferase, attaches a formylated form of aminoarabinose to the lipid undecaprenyl phosphate, enabling its association with the bacterial inner membrane. Here, we present cryo-electron microscopy structures of ArnC from S. enterica in apo and nucleotide-bound conformations. These structures reveal a conformational transition that takes place upon binding of the partial donor substrate. Using coarse-grained and atomistic simulations, we provide insights into substrate coordination before and during catalysis, and we propose a catalytic mechanism that may operate on all similar metal-dependent polyprenyl phosphate glycosyltransferases. The reported structures provide a new target for drug design aiming to combat polymyxin resistance.
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Affiliation(s)
- Khuram U Ashraf
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA
| | - Mariana Bunoro-Batista
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, United Kingdom
| | - T. Bertie Ansell
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Ankita Punetha
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA
| | - Stephannie Rosario-Garrido
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA
| | - Emre Firlar
- Rutgers Cryo-EM & Nanoimaging Facility, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jason T. Kaelber
- Rutgers Cryo-EM & Nanoimaging Facility, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Phillip J. Stansfeld
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, United Kingdom
| | - Vasileios I. Petrou
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA
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Liu H, Xia N, Suksawat F, Tengjaroenkul B, Hu Y, Zhou X, Li X, Huang C, Bao Y, Wu Q, Zhang C, Angkititrakul S, Xiang B, Wu X. Prevalence and characterization of IncQ1α-mediated multi-drug resistance in Proteus mirabilis Isolated from pigs in Kunming, Yunnan, China. Front Microbiol 2025; 15:1483633. [PMID: 39850143 PMCID: PMC11754265 DOI: 10.3389/fmicb.2024.1483633] [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: 08/20/2024] [Accepted: 11/07/2024] [Indexed: 01/25/2025] Open
Abstract
Background Proteus mirabilis is a conditionally pathogenic bacterium that is inherently resistant to polymyxin and tigecycline, largely due to antibiotic resistance genes (ARGs). These ARGs can be horizontally transferred to other bacteria, raising concerns about the Inc plasmid-mediated ARG transmission from Proteus mirabilis, which poses a serious public health threat. This study aims to investigate the presence of Inc plasmid types in pig-derived Proteus mirabilis in Kunming, Yunnan, China. Methods Fecal samples were collected from pig farms across six districts of Kunming (Luquan, Jinning, Yiliang, Anning, Songming, and Xundian) from 2022 to 2023. Proteus mirabilis isolates were identified using IDS and 16S rRNA gene sequencing. Then, positive strains underwent antimicrobial susceptibility testing and incompatibility plasmid typing. Multi-drug-resistant isolates with positive incompatibility plasmid genes were selected for whole-genome sequencing. Resistance and Inc group data were then isolated and compared with 126 complete genome sequences from public databases. Whole-genome multi-locus sequence typing, resistance group analysis, genomic island prediction, and plasmid structural gene analysis were performed. Results A total of 30 isolates were obtained from 230 samples, yielding a prevalence of 13.04%. All isolates exhibited multi-drug resistance, with 100% resistance to cotrimoxazole, erythromycin, penicillin G, chloramphenicol, ampicillin, and streptomycin. Among these, 15 isolates tested positive for the IncQ1α plasmid repC gene. The two most multi-drug-resistant and repC-positive strains, NO. 15 and 21, were sequenced to compare genomic features on Inc groups and ARGs with public data. Genome analysis revealed that the repC gene was primarily associated with IncQ1α, with structural genes from other F-type plasmids (TraV, TraU, TraN, TraL, TraK, TraI, TraH, TraG, TraF, TraE/GumN, and TraA) also present. Strain NO. 15 carried 33 ARGs, and strain NO. 21 carried 38 ARGs, conferring resistance to tetracyclines, fluoroquinolones, aminoglycosides, sulfonamides, peptides, chloramphenicol, cephalosporins, lincomycins, macrolides, and 2-aminopyrimidines. Conclusion The repC gene is primarily associated with IncQ1α, with structural genes from other F-type plasmids. A comparison with 126 public genome datasets confirmed this association.
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Affiliation(s)
- Hongmei Liu
- Yunnan Joint International R&D Center of Veterinary Public Health, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
- Engineering Research Center for the Prevention and Control of Animal Original Zoonosis of Fujian Province University, College of Life Science, Longyan University, Fujian, China
- Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Na Xia
- Yunnan Joint International R&D Center of Veterinary Public Health, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Fanan Suksawat
- Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand
| | | | - Yue Hu
- Yunnan Joint International R&D Center of Veterinary Public Health, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Xiaofeng Zhou
- Yunnan Joint International R&D Center of Veterinary Public Health, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Xiaojiang Li
- Yunnan Joint International R&D Center of Veterinary Public Health, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Cuiqin Huang
- Engineering Research Center for the Prevention and Control of Animal Original Zoonosis of Fujian Province University, College of Life Science, Longyan University, Fujian, China
| | - Yinli Bao
- Engineering Research Center for the Prevention and Control of Animal Original Zoonosis of Fujian Province University, College of Life Science, Longyan University, Fujian, China
| | - Qiong Wu
- Engineering Research Center for the Prevention and Control of Animal Original Zoonosis of Fujian Province University, College of Life Science, Longyan University, Fujian, China
| | - Chunrong Zhang
- Engineering Research Center for the Prevention and Control of Animal Original Zoonosis of Fujian Province University, College of Life Science, Longyan University, Fujian, China
| | | | - Bin Xiang
- Yunnan Joint International R&D Center of Veterinary Public Health, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Xin Wu
- Yunnan Joint International R&D Center of Veterinary Public Health, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
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8
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Perez C, Szymanski CM. More than one way to add a sugar into bacterial polysaccharides. Proc Natl Acad Sci U S A 2024; 121:e2408556121. [PMID: 38857409 PMCID: PMC11194591 DOI: 10.1073/pnas.2408556121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024] Open
Affiliation(s)
- Camilo Perez
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA30602
| | - Christine M. Szymanski
- Department of Microbiology, University of Georgia, Athens, GA30602
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA30602
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9
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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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Gao X, Han J, Zhu L, Nychas GJE, Mao Y, Yang X, Liu Y, Jiang X, Zhang Y, Dong P. The Effect of the PhoP/PhoQ System on the Regulation of Multi-Stress Adaptation Induced by Acid Stress in Salmonella Typhimurium. Foods 2024; 13:1533. [PMID: 38790833 PMCID: PMC11121531 DOI: 10.3390/foods13101533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Acidic stress in beef cattle slaughtering abattoirs can induce the acid adaptation response of in-plant contaminated Salmonella. This may further lead to multiple resistance responses threatening public health. Therefore, the acid, heat, osmotic and antibiotic resistances of Salmonella typhimurium (ATCC14028) were evaluated after a 90 min adaption in a pH = 5.4 "mild acid" Luria-Bertani medium. Differences in such resistances were also determined between the ∆phoP mutant and wild-type Salmonella strains to confirm the contribution of the PhoP/PhoQ system. The transcriptomic differences between the acid-adapted and ∆phoP strain were compared to explore the role of the PhoP/Q two-component system in regulating multi-stress resistance. Acid adaptation was found to increase the viability of Salmonella to lethal acid, heat and hyperosmotic treatments. In particular, acid adaptation significantly increased the resistance of Salmonella typhimurium to Polymyxin B, and such resistance can last for 21 days when the adapted strain was stored in meat extract medium at 4 °C. Transcriptomics analysis revealed 178 up-regulated and 274 down-regulated genes in the ∆phoP strain. The Salmonella infection, cationic antimicrobial peptide (CAMP) resistance, quorum sensing and two-component system pathways were down-regulated, while the bacterial tricarboxylic acid cycle pathways were up-regulated. Transcriptomics and RT-qPCR analyses revealed that the deletion of the phoP gene resulted in the down-regulation of the expression of genes related to lipid A modification and efflux pumps. These changes in the gene expression result in the change in net negative charge and the mobility of the cell membrane, resulting in enhanced CAMP resistance. The confirmation of multiple stress resistance under acid adaptation and the transcriptomic study in the current study may provide valuable information for the control of multiple stress resistance and meat safety.
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Affiliation(s)
- Xu Gao
- Lab of Beef Processing and Quality Control, Shandong Agricultural University, Taian 271018, China; (X.G.); (L.Z.); (G.-J.E.N.); (Y.M.); (X.Y.); (Y.L.); (X.J.); (Y.Z.)
- International Joint Research Lab (China and Greece) of Digital Transformation as an Enabler for Food Safety and Sustainability, Taian 271018, China
| | - Jina Han
- Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan 250023, China;
| | - Lixian Zhu
- Lab of Beef Processing and Quality Control, Shandong Agricultural University, Taian 271018, China; (X.G.); (L.Z.); (G.-J.E.N.); (Y.M.); (X.Y.); (Y.L.); (X.J.); (Y.Z.)
- International Joint Research Lab (China and Greece) of Digital Transformation as an Enabler for Food Safety and Sustainability, Taian 271018, China
| | - George-John E. Nychas
- Lab of Beef Processing and Quality Control, Shandong Agricultural University, Taian 271018, China; (X.G.); (L.Z.); (G.-J.E.N.); (Y.M.); (X.Y.); (Y.L.); (X.J.); (Y.Z.)
- International Joint Research Lab (China and Greece) of Digital Transformation as an Enabler for Food Safety and Sustainability, Taian 271018, China
- Department of Food Science and Human Nutrition, Agricultural University of Athens, 11855 Athens, Greece
| | - Yanwei Mao
- Lab of Beef Processing and Quality Control, Shandong Agricultural University, Taian 271018, China; (X.G.); (L.Z.); (G.-J.E.N.); (Y.M.); (X.Y.); (Y.L.); (X.J.); (Y.Z.)
- International Joint Research Lab (China and Greece) of Digital Transformation as an Enabler for Food Safety and Sustainability, Taian 271018, China
| | - Xiaoyin Yang
- Lab of Beef Processing and Quality Control, Shandong Agricultural University, Taian 271018, China; (X.G.); (L.Z.); (G.-J.E.N.); (Y.M.); (X.Y.); (Y.L.); (X.J.); (Y.Z.)
- International Joint Research Lab (China and Greece) of Digital Transformation as an Enabler for Food Safety and Sustainability, Taian 271018, China
| | - Yunge Liu
- Lab of Beef Processing and Quality Control, Shandong Agricultural University, Taian 271018, China; (X.G.); (L.Z.); (G.-J.E.N.); (Y.M.); (X.Y.); (Y.L.); (X.J.); (Y.Z.)
- International Joint Research Lab (China and Greece) of Digital Transformation as an Enabler for Food Safety and Sustainability, Taian 271018, China
| | - Xueqing Jiang
- Lab of Beef Processing and Quality Control, Shandong Agricultural University, Taian 271018, China; (X.G.); (L.Z.); (G.-J.E.N.); (Y.M.); (X.Y.); (Y.L.); (X.J.); (Y.Z.)
- International Joint Research Lab (China and Greece) of Digital Transformation as an Enabler for Food Safety and Sustainability, Taian 271018, China
| | - Yimin Zhang
- Lab of Beef Processing and Quality Control, Shandong Agricultural University, Taian 271018, China; (X.G.); (L.Z.); (G.-J.E.N.); (Y.M.); (X.Y.); (Y.L.); (X.J.); (Y.Z.)
- International Joint Research Lab (China and Greece) of Digital Transformation as an Enabler for Food Safety and Sustainability, Taian 271018, China
| | - Pengcheng Dong
- Lab of Beef Processing and Quality Control, Shandong Agricultural University, Taian 271018, China; (X.G.); (L.Z.); (G.-J.E.N.); (Y.M.); (X.Y.); (Y.L.); (X.J.); (Y.Z.)
- International Joint Research Lab (China and Greece) of Digital Transformation as an Enabler for Food Safety and Sustainability, Taian 271018, China
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11
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Luo XW, Li PL, Zhai YJ, Pan YS, Hu GZ, He DD. Upregulation of outer membrane porin gene ompC contributed to enhancement of azithromycin susceptibility in multidrug-resistant Escherichia coli. Microbiol Spectr 2024; 12:e0391823. [PMID: 38441474 PMCID: PMC10986464 DOI: 10.1128/spectrum.03918-23] [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: 11/10/2023] [Accepted: 02/24/2024] [Indexed: 04/06/2024] Open
Abstract
The outer membrane (OM) in gram-negative bacteria contains proteins that regulate the passive or active uptake of small molecules for growth and cell function, as well as mediate the emergence of antibiotic resistance. This study aims to explore the potential mechanisms for restoring bacteria to azithromycin susceptibility based on transcriptome analysis of bacterial membrane-related genes. Transcriptome sequencing was performed by treating multidrug-resistant Escherichia coli T28R with azithromycin or in combination with colistin and confirmed by reverse transcription-quantitative PCR (RT-qPCR). Azithromycin enzyme-linked immunosorbent assay (ELISA) test, ompC gene overexpression, and molecular docking were utilized to conduct the confirmatory research of the potential mechanisms. We found that colistin combined with azithromycin led to 48 differentially expressed genes, compared to azithromycin alone, such as downregulation of tolA, eptB, lpxP, and opgE and upregulation of ompC gene. Interestingly, the addition of colistin to azithromycin differentially downregulated the mph(A) gene mediating azithromycin resistance, facilitating the intracellular accumulation of azithromycin. Also, overexpression of the ompC elevated azithromycin susceptibility, and colistin contributed to further suppression of the Mph(A) activity in the presence of azithromycin. These findings suggested that colistin firstly enhanced the permeability of bacterial OM, causing intracellular drug accumulation, and then had a repressive effect on the Mph(A) activity along with azithromycin. Our study provides a novel perspective that the improvement of azithromycin susceptibility is related not only to the downregulation of the mph(A) gene and conformational remodeling of the Mph(A) protein but also the upregulation of the membrane porin gene ompC.IMPORTANCEUsually, active efflux via efflux pumps is an important mechanism of antimicrobial resistance, such as the AcrAB-TolC complex and MdtEF. Also, bacterial porins exhibited a substantial fraction of the total number of outer membrane proteins in Enterobacteriaceae, which are involved in mediating the development of the resistance. We found that the upregulation or overexpression of the ompC gene contributed to the enhancement of resistant bacteria to azithromycin susceptibility, probably due to the augment of drug uptakes caused and the opportunity of Mph(A) function suppressed by azithromycin with colistin. Under the combination of colistin and azithromycin treatment, OmpC exhibited an increased selectivity for cationic molecules and played a key role in the restoral of the antibiotic susceptibility. Investigations on the regulation of porin expression that mediated drug resistance would be important in clinical isolates treated with antibiotics.
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Affiliation(s)
- Xing-Wei Luo
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Peng-Liang Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Ya-Jun Zhai
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Yu-Shan Pan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Gong-Zheng Hu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Dan-Dan He
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
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12
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Bhattacharje G, Ghosh A, Das AK. Deciphering the mannose transfer mechanism of mycobacterial PimE by molecular dynamics simulations. Glycobiology 2024; 34:cwad096. [PMID: 38039077 DOI: 10.1093/glycob/cwad096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023] Open
Abstract
Phosphatidyl-myo-inositol mannosides (PIMs), Lipomannan (LM), and Lipoarabinomannan (LAM) are essential components of the cell envelopes of mycobacteria. At the beginning of the biosynthesis of these compounds, phosphatidylinositol (PI) is mannosylated and acylated by various enzymes to produce Ac1/2PIM4, which is used to synthesize either Ac1/2PIM6 or LM/LAM. The protein PimE, a membrane-bound glycosyltransferase (GT-C), catalyzes the addition of a mannose group to Ac1PIM4 to produce Ac1PIM5, using polyprenolphosphate mannose (PPM) as the mannose donor. PimE-deleted Mycobacterium smegmatis (Msmeg) showed structural deformity and increased antibiotic and copper sensitivity. Despite knowing that the mutation D58A caused inactivity in Msmeg, how PimE catalyzes the transfer of mannose from PPM to Ac1/2PIM4 remains unknown. In this study, analyzing the AlphaFold structure of PimE revealed the presence of a tunnel through the D58 residue with two differently charged gates. Molecular docking suggested PPM binds to the hydrophobic tunnel gate, whereas Ac1PIM4 binds to the positively charged tunnel gate. Molecular dynamics (MD) simulations further demonstrated the critical roles of the residues N55, F87, L89, Y163, Q165, K197, L198, R251, F277, W324, H326, and I375 in binding PPM and Ac1PIM4. The mutation D58A caused a faster release of PPM from the catalytic tunnel, explaining the loss of PimE activity. Along with a hypothetical mechanism of mannose transfer by PimE, we also observe the presence of tunnels through a negatively charged aspartate or glutamate with two differently-charged gates among most GT-C enzymes. Common hydrophobic gates of GT-C enzymes probably harbor sugar donors, whereas, differently-charged tunnel gates accommodate various sugar-acceptors.
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Affiliation(s)
- Gourab Bhattacharje
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Midnapore, WB 721302, India
| | - Amit Ghosh
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Midnapore, WB 721302, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Midnapore, WB 721302, India
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13
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Li D. Structure and Function of the Glycosylphosphatidylinositol Transamidase, a Transmembrane Complex Catalyzing GPI Anchoring of Proteins. Subcell Biochem 2024; 104:425-458. [PMID: 38963495 DOI: 10.1007/978-3-031-58843-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Glycosylphosphatidylinositol (GPI) anchoring of proteins is a ubiquitous posttranslational modification in eukaryotic cells. GPI-anchored proteins (GPI-APs) play critical roles in enzymatic, signaling, regulatory, and adhesion processes. Over 20 enzymes are involved in GPI synthesis, attachment to client proteins, and remodeling after attachment. The GPI transamidase (GPI-T), a large complex located in the endoplasmic reticulum membrane, catalyzes the attachment step by replacing a C-terminal signal peptide of proproteins with GPI. In the last three decades, extensive research has been conducted on the mechanism of the transamidation reaction, the components of the GPI-T complex, the role of each subunit, and the substrate specificity. Two recent studies have reported the three-dimensional architecture of GPI-T, which represent the first structures of the pathway. The structures provide detailed mechanisms for assembly that rationalizes previous biochemical results and subunit-dependent stability data. While the structural data confirm the catalytic role of PIGK, which likely uses a caspase-like mechanism to cleave the proproteins, they suggest that unlike previously proposed, GPAA1 is not a catalytic subunit. The structures also reveal a shared cavity for GPI binding. Somewhat unexpectedly, PIGT, a single-pass membrane protein, plays a crucial role in GPI recognition. Consistent with the assembly mechanisms and the active site architecture, most of the disease mutations occur near the active site or the subunit interfaces. Finally, the catalytic dyad is located ~22 Å away from the membrane interface of the GPI-binding site, and this architecture may confer substrate specificity through topological matching between the substrates and the elongated active site. The research conducted thus far sheds light on the intricate processes involved in GPI anchoring and paves the way for further mechanistic studies of GPI-T.
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Affiliation(s)
- Dianfan Li
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China.
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14
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Géraud N, Falcou C, Parra J, Froment C, Rengel D, Burlet-Schiltz O, Marcoux J, Nigou J, Rivière M, Fabre E. Development of a novel target-based cell assay, reporter of the activity of Mycobacterium tuberculosis protein-O-mannosyltransferase. Glycobiology 2023; 33:1139-1154. [PMID: 37698262 DOI: 10.1093/glycob/cwad072] [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: 07/12/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/13/2023] Open
Abstract
The Protein-O-mannosyltransferase is crucial for the virulence of Mycobacterium tuberculosis, the etiological agent of tuberculosis. This enzyme, called MtPMT (Rv1002c), is responsible for the post-translational O-mannosylation of mycobacterial proteins. It catalyzes the transfer of a single mannose residue from a polyprenol phospho-mannosyl lipidic donor to the hydroxyl groups of selected Ser/Thr residues in acceptor proteins during their translocation across the membrane. Previously, we provided evidence that the loss of MtPMT activity causes the absence of mannoproteins in Mycobacterium tuberculosis, severely impacting its intracellular growth, as well as a strong attenuation of its pathogenicity in immunocompromised mice. Therefore, it is of interest to develop specific inhibitors of this enzyme to better understand mycobacterial infectious diseases. Here we report the development of a "target-based" phenotypic assay for this enzyme, assessing its O-mannosyltransferase activity in bacteria, in the non-pathogenic Mycobacterium smegmatis strain. Robustness of the quantitative contribution of this assay was evaluated by intact protein mass spectrometry, using a panel of control strains, overexpressing the MtPMT gene, carrying different key point-mutations. Then, screening of a limited library of 30 compounds rationally chosen allowed us to identify 2 compounds containing pyrrole analogous rings, as significant inhibitors of MtPMT activity, affecting neither the growth of the mycobacterium nor its secretion of mannoproteins. These molecular cores could therefore serve as scaffold for the design of new pharmaceutical agents that could improve treatment of mycobacterial diseases. We report here the implementation of a miniaturized phenotypic activity assay for a glycosyltransferase of the C superfamily.
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Affiliation(s)
- Nicolas Géraud
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UT3), 31400 Toulouse, France
| | - Camille Falcou
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UT3), 31400 Toulouse, France
| | - Julien Parra
- Infrastructure nationale de protéomique, ProFI, 205 Rte de Narbonne, 31400 Toulouse, France
| | - Carine Froment
- Infrastructure nationale de protéomique, ProFI, 205 Rte de Narbonne, 31400 Toulouse, France
| | - David Rengel
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UT3), 31400 Toulouse, France
| | - Odile Burlet-Schiltz
- Infrastructure nationale de protéomique, ProFI, 205 Rte de Narbonne, 31400 Toulouse, France
| | - Julien Marcoux
- Infrastructure nationale de protéomique, ProFI, 205 Rte de Narbonne, 31400 Toulouse, France
| | - Jérôme Nigou
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UT3), 31400 Toulouse, France
| | - Michel Rivière
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UT3), 31400 Toulouse, France
| | - Emeline Fabre
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UT3), 31400 Toulouse, France
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15
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Vergoz D, Le H, Bernay B, Schaumann A, Barreau M, Nilly F, Desriac F, Tahrioui A, Giard JC, Lesouhaitier O, Chevalier S, Brunel JM, Muller C, Dé E. Antibiofilm and Antivirulence Properties of 6-Polyaminosteroid Derivatives against Antibiotic-Resistant Bacteria. Antibiotics (Basel) 2023; 13:8. [PMID: 38275318 PMCID: PMC10812528 DOI: 10.3390/antibiotics13010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
The emergence of multi-drug resistant pathogens is a major public health problem, leading us to rethink and innovate our bacterial control strategies. Here, we explore the antibiofilm and antivirulence activities of nineteen 6-polyaminosterol derivatives (squalamine-based), presenting a modulation of their polyamine side chain on four major pathogens, i.e., carbapenem-resistant A. baumannii (CRAB) and P. aeruginosa (CRPA), methicillin-resistant S. aureus (MRSA), and vancomycin-resistant E. faecium (VRE) strains. We screened the effect of these derivatives on biofilm formation and eradication. Derivatives 4e (for CRAB, VRE, and MRSA) and 4f (for all the strains) were the most potent ones and displayed activities as good as those of conventional antibiotics. We also identified 11 compounds able to decrease by more than 40% the production of pyocyanin, a major virulence factor of P. aeruginosa. We demonstrated that 4f treatment acts against bacterial infections in Galleria mellonella and significantly prolonged larvae survival (from 50% to 80%) after 24 h of CRAB, VRE, and MRSA infections. As shown by proteomic studies, 4f triggered distinct cellular responses depending on the bacterial species but essentially linked to cell envelope. Its interesting antibiofilm and antivirulence properties make it a promising a candidate for use in therapeutics.
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Affiliation(s)
- Delphine Vergoz
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, PBS UMR 6270, F-76000 Rouen, France; (D.V.); (H.L.); (A.S.)
| | - Hung Le
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, PBS UMR 6270, F-76000 Rouen, France; (D.V.); (H.L.); (A.S.)
| | - Benoit Bernay
- Univ Caen Normandie, Proteogen Platform, US EMERODE, F-14000 Caen, France;
| | - Annick Schaumann
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, PBS UMR 6270, F-76000 Rouen, France; (D.V.); (H.L.); (A.S.)
| | - Magalie Barreau
- Univ Rouen Normandie, Univ Caen Normandie, Normandie Univ, Communication Bactérienne et Stratégies Anti-Infectieuses, CBSA UR4312, F-76000 Rouen, France; (M.B.); (F.N.); (F.D.); (A.T.); (O.L.); (S.C.)
| | - Flore Nilly
- Univ Rouen Normandie, Univ Caen Normandie, Normandie Univ, Communication Bactérienne et Stratégies Anti-Infectieuses, CBSA UR4312, F-76000 Rouen, France; (M.B.); (F.N.); (F.D.); (A.T.); (O.L.); (S.C.)
| | - Florie Desriac
- Univ Rouen Normandie, Univ Caen Normandie, Normandie Univ, Communication Bactérienne et Stratégies Anti-Infectieuses, CBSA UR4312, F-76000 Rouen, France; (M.B.); (F.N.); (F.D.); (A.T.); (O.L.); (S.C.)
| | - Ali Tahrioui
- Univ Rouen Normandie, Univ Caen Normandie, Normandie Univ, Communication Bactérienne et Stratégies Anti-Infectieuses, CBSA UR4312, F-76000 Rouen, France; (M.B.); (F.N.); (F.D.); (A.T.); (O.L.); (S.C.)
| | | | - Olivier Lesouhaitier
- Univ Rouen Normandie, Univ Caen Normandie, Normandie Univ, Communication Bactérienne et Stratégies Anti-Infectieuses, CBSA UR4312, F-76000 Rouen, France; (M.B.); (F.N.); (F.D.); (A.T.); (O.L.); (S.C.)
| | - Sylvie Chevalier
- Univ Rouen Normandie, Univ Caen Normandie, Normandie Univ, Communication Bactérienne et Stratégies Anti-Infectieuses, CBSA UR4312, F-76000 Rouen, France; (M.B.); (F.N.); (F.D.); (A.T.); (O.L.); (S.C.)
| | | | - Cécile Muller
- Univ Rouen Normandie, Univ Caen Normandie, Normandie Univ, Communication Bactérienne et Stratégies Anti-Infectieuses, CBSA UR4312, F-76000 Rouen, France; (M.B.); (F.N.); (F.D.); (A.T.); (O.L.); (S.C.)
| | - Emmanuelle Dé
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, PBS UMR 6270, F-76000 Rouen, France; (D.V.); (H.L.); (A.S.)
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16
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Muñoz-Escudero D, Breazeale SD, Lee M, Guan Z, Raetz CRH, Sousa MC. Structure and Function of ArnD. A Deformylase Essential for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance. Biochemistry 2023; 62:2970-2981. [PMID: 37782650 PMCID: PMC10914315 DOI: 10.1021/acs.biochem.3c00293] [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] [Indexed: 10/04/2023]
Abstract
Covalent modification of lipid A with 4-deoxy-4-amino-l-arabinose (Ara4N) mediates resistance to cationic antimicrobial peptides and polymyxin antibiotics in Gram-negative bacteria. The proteins required for Ara4N biosynthesis are encoded in the pmrE and arnBCADTEF loci, with ArnT ultimately transferring the amino sugar from undecaprenyl-phospho-4-deoxy-4-amino-l-arabinose (C55P-Ara4N) to lipid A. However, Ara4N is N-formylated prior to its transfer to undecaprenyl-phosphate by ArnC, requiring a deformylase activity downstream in the pathway to generate the final C55P-Ara4N donor. Here, we show that deletion of the arnD gene in an Escherichia coli mutant that constitutively expresses the arnBCADTEF operon leads to accumulation of the formylated ArnC product undecaprenyl-phospho-4-deoxy-4-formamido-l-arabinose (C55P-Ara4FN), suggesting that ArnD is the downstream deformylase. Purification of Salmonella typhimurium ArnD (stArnD) shows that it is membrane-associated. We present the crystal structure of stArnD revealing a NodB homology domain structure characteristic of the metal-dependent carbohydrate esterase family 4 (CE4). However, ArnD displays several distinct features: a 44 amino acid insertion, a C-terminal extension in the NodB fold, and sequence divergence in the five motifs that define the CE4 family, suggesting that ArnD represents a new family of carbohydrate esterases. The insertion is responsible for membrane association as its deletion results in a soluble ArnD variant. The active site retains a metal coordination H-H-D triad, and in the presence of Co2+ or Mn2+, purified stArnD efficiently deformylates C55P-Ara4FN confirming its role in Ara4N biosynthesis. Mutations D9N and H233Y completely inactivate stArnD implicating these two residues in a metal-assisted acid-base catalytic mechanism.
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Affiliation(s)
- Daniel Muñoz-Escudero
- Department of Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309
| | - Steven D. Breazeale
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710
| | - Myeongseon Lee
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710
| | | | - Marcelo C. Sousa
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309
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17
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Abban MK, Ayerakwa EA, Mosi L, Isawumi A. The burden of hospital acquired infections and antimicrobial resistance. Heliyon 2023; 9:e20561. [PMID: 37818001 PMCID: PMC10560788 DOI: 10.1016/j.heliyon.2023.e20561] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/21/2023] [Accepted: 09/29/2023] [Indexed: 10/12/2023] Open
Abstract
The burden of Hospital care-associated infections (HCAIs) is becoming a global concern. This is compounded by the emergence of virulent and high-risk bacterial strains such as "ESKAPE" pathogens - (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species), especially within Intensive care units (ICUs) that house high-risk and immunocompromised patients. In this review, we discuss the contributions of AMR pathogens to the increasing burden of HCAIs and provide insights into AMR mechanisms, with a particular focus on last-resort antibiotics like polymyxins. We extensively discuss how structural modifications of surface-membrane lipopolysaccharides and cationic interactions influence and inform AMR, and subsequent severity of HCAIs. We highlight some bacterial phenotypic survival mechanisms against polymyxins. Lastly, we discuss the emergence of plasmid-mediated resistance as a phenomenon making mitigation of AMR difficult, especially within the ICUs. This review provides a balanced perspective on the burden of HCAIs, associated pathogens, implication of AMR and factors influencing emerging AMR mechanisms.
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Affiliation(s)
- Molly Kukua Abban
- West African Centre for Cell Biology of Infectious Pathogens, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
| | - Eunice Ampadubea Ayerakwa
- West African Centre for Cell Biology of Infectious Pathogens, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
| | - Lydia Mosi
- West African Centre for Cell Biology of Infectious Pathogens, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
| | - Abiola Isawumi
- West African Centre for Cell Biology of Infectious Pathogens, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
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18
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Yang H, Sherman ME, Koo CJ, Treaster LM, Smith JP, Gallaher SG, Goodlett DR, Sweet CR, Ernst RK. Structure Determination of Lipid A with Multiple Glycosylation Sites by Tandem MS of Lithium-Adducted Negative Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1047-1055. [PMID: 37184080 DOI: 10.1021/jasms.3c00014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
FLATn is a tandem mass spectrometric technique that can be used to rapidly generate spectral information applicable for structural elucidation of lipids like lipid A from Gram-negative bacterial species from a single bacterial colony. In this study, we extend the scope and capability of FLATn by tandem MS fragmentation of lithium-adducted molecular lipid A anions and fragments (FLATn-Li) that provides additional structural and diagnostic data from FLATn samples allowing for the discrimination of terminal phosphate modifications in a variety of pathogenic and environmental species. Using FLATn-Li, we elucidated the lipid A structure from several bacterial species, including novel structures from arctic bacterioplankton of the Duganella and Massilia genera that favor 4-amino-4-deoxy-l-arabinopyranose (Ara4N) modification at the 1-phosphate position and that demonstrate double glycosylation with Ara4N at the 1 and 4' phosphate positions simultaneously. The structures characterized in this work demonstrate that some environmental psychrophilic species make extensive use of this structural lipid A modification previously characterized as a pathogenic adaptation and the structural basis of resistance to cationic antimicrobial peptides. This observation extends the role of phosphate modification(s) in environmental species adaptation and suggests that Ara4N modification can functionally replace the positive charge of the phosphoethanolamine modification that is more typically found attached to the 1-phosphate position of modified lipid A.
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Affiliation(s)
- Hyojik Yang
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States of America
| | - Matthew E Sherman
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States of America
| | - Caitlyn J Koo
- Chemistry Department, United States Naval Academy, Annapolis, Maryland 21402, United States of America
- School of Medicine, Uniformed Services University, Bethesda, Maryland 20814, United States of America
| | - Logan M Treaster
- Chemistry Department, United States Naval Academy, Annapolis, Maryland 21402, United States of America
- School of Medicine, University of Kansas, Kansas City, Kansas 66160, United States of America
| | - Joseph P Smith
- Oceanography Department, United States Naval Academy, Annapolis, Maryland 21402, United States of America
| | - Shawn G Gallaher
- Oceanography Department, United States Naval Academy, Annapolis, Maryland 21402, United States of America
| | - David R Goodlett
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
- Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7Z8, Canada
| | - Charles R Sweet
- Chemistry Department, United States Naval Academy, Annapolis, Maryland 21402, United States of America
| | - Robert K Ernst
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States of America
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19
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Bloch JS, John A, Mao R, Mukherjee S, Boilevin J, Irobalieva RN, Darbre T, Scott NE, Reymond JL, Kossiakoff AA, Goddard-Borger ED, Locher KP. Structure, sequon recognition and mechanism of tryptophan C-mannosyltransferase. Nat Chem Biol 2023; 19:575-584. [PMID: 36604564 PMCID: PMC10154233 DOI: 10.1038/s41589-022-01219-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/28/2022] [Indexed: 01/07/2023]
Abstract
C-linked glycosylation is essential for the trafficking, folding and function of secretory and transmembrane proteins involved in cellular communication processes. The tryptophan C-mannosyltransferase (CMT) enzymes that install the modification attach a mannose to the first tryptophan of WxxW/C sequons in nascent polypeptide chains by an unknown mechanism. Here, we report cryogenic-electron microscopy structures of Caenorhabditis elegans CMT in four key states: apo, acceptor peptide-bound, donor-substrate analog-bound and as a trapped ternary complex with both peptide and a donor-substrate mimic bound. The structures indicate how the C-mannosylation sequon is recognized by this CMT and its paralogs, and how sequon binding triggers conformational activation of the donor substrate: a process relevant to all glycosyltransferase C superfamily enzymes. Our structural data further indicate that the CMTs adopt an unprecedented electrophilic aromatic substitution mechanism to enable the C-glycosylation of proteins. These results afford opportunities for understanding human disease and therapeutic targeting of specific CMT paralogs.
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Affiliation(s)
- Joël S Bloch
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
- Laboratory of Molecular Neurobiology and Biophysics and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Alan John
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Runyu Mao
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Somnath Mukherjee
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Jérémy Boilevin
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | | | - Tamis Darbre
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Jean-Louis Reymond
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Ethan D Goddard-Borger
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
| | - Kaspar P Locher
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
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20
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Alexander JAN, Locher KP. Emerging structural insights into C-type glycosyltransferases. Curr Opin Struct Biol 2023; 79:102547. [PMID: 36827761 DOI: 10.1016/j.sbi.2023.102547] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/19/2022] [Accepted: 01/11/2023] [Indexed: 02/24/2023]
Abstract
Glycosyltransferases of the C superfamily (GT-Cs) are enzymes found in all domains of life. They catalyse the stepwise synthesis of oligosaccharides or the transfer of assembled glycans from lipid-linked donor substrates to acceptor proteins. The processes mediated by GT-Cs are required for C-, N- and O-linked glycosylation, all of which are essential post-translational modifications in higher-order eukaryotes. Until recently, GT-Cs were thought to share a conserved structural module of 7 transmembrane helices; however, recently determined GT-C structures revealed novel folds. Here we analyse the growing diversity of GT-C folds and discuss the emergence of two subclasses, termed GT-CA and GT-CB. Further substrate-bound structures are needed to facilitate a molecular understanding of glycan recognition and catalysis in these two subclasses.
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Affiliation(s)
| | - Kaspar P Locher
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
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21
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Gao Z, Jiang S, Zhong W, Liu T, Guo J. Linalool controls the viability of Escherichia coli by regulating the synthesis and modification of lipopolysaccharide, the assembly of ribosome, and the expression of substrate transporting proteins. Food Res Int 2023; 164:112337. [PMID: 36737930 DOI: 10.1016/j.foodres.2022.112337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/08/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
Escherichia coli (E. coli) is a Gram-negative bacterium and some pathogenic types may cause serious diseases, foods or food environments were the primary routes for its infection. Citrus aurantium L. var. amara Engl., a variety of sour orange, were used as a kind of non-conventional edible plant in China, but its antimicrobial activity and mechanisms were not well studied. Thus, in this study, EO from the flower of Citrus aurantium L. var. amara Engl. (CAEO) were studied as a kind of natural antimicrobial agent to control E. coli, our results showed that both of CAEO and its main component (linalool) exhibited strong antibacterial efficacy. Further, transcriptomic and proteomic analysis were carried out to explore cell response under linalool treatment and the main results included: (1) The synthesis and modification of lipopolysaccharide (LPS) was significantly influenced. (2) Ribosomal assembly and protein synthesis were significantly inhibited. (3) The expression of proteins related to the uptake of several essential substances was significantly changed. In all, our results would supply a theoretical basis for the proper use of CAEO and linalool as a promising antimicrobial agent to prevent and control E. coli infection in the future.
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Affiliation(s)
- Zhipeng Gao
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, Hunan Province, China.
| | - Sifan Jiang
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, Hunan Province, China
| | - Weiming Zhong
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, Hunan Province, China
| | - Ting Liu
- Hunan Agriculture Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China
| | - Jiajing Guo
- Hunan Agriculture Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China.
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22
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Rapid, direct, visualized and antibody-free bacterial detection with extra species identification and susceptibility evaluation capabilities. Biosens Bioelectron 2022; 221:114902. [DOI: 10.1016/j.bios.2022.114902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/26/2022] [Accepted: 11/07/2022] [Indexed: 11/14/2022]
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23
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Panda G, Dash S, Sahu SK. Harnessing the Role of Bacterial Plasma Membrane Modifications for the Development of Sustainable Membranotropic Phytotherapeutics. MEMBRANES 2022; 12:914. [PMID: 36295673 PMCID: PMC9612325 DOI: 10.3390/membranes12100914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/08/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Membrane-targeted molecules such as cationic antimicrobial peptides (CAMPs) are amongst the most advanced group of antibiotics used against drug-resistant bacteria due to their conserved and accessible targets. However, multi-drug-resistant bacteria alter their plasma membrane (PM) lipids, such as lipopolysaccharides (LPS) and phospholipids (PLs), to evade membrane-targeted antibiotics. Investigations reveal that in addition to LPS, the varying composition and spatiotemporal organization of PLs in the bacterial PM are currently being explored as novel drug targets. Additionally, PM proteins such as Mla complex, MPRF, Lpts, lipid II flippase, PL synthases, and PL flippases that maintain PM integrity are the most sought-after targets for development of new-generation drugs. However, most of their structural details and mechanism of action remains elusive. Exploration of the role of bacterial membrane lipidome and proteome in addition to their organization is the key to developing novel membrane-targeted antibiotics. In addition, membranotropic phytochemicals and their synthetic derivatives have gained attractiveness as popular herbal alternatives against bacterial multi-drug resistance. This review provides the current understanding on the role of bacterial PM components on multidrug resistance and their targeting with membranotropic phytochemicals.
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Affiliation(s)
- Gayatree Panda
- Department of Biotechnology, Maharaja Sriram Chandra Bhanjadeo University (Erstwhile: North Orissa University), Baripada 757003, India
| | - Sabyasachi Dash
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Santosh Kumar Sahu
- Department of Biotechnology, Maharaja Sriram Chandra Bhanjadeo University (Erstwhile: North Orissa University), Baripada 757003, India
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24
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Valvano MA. Remodelling of the Gram-negative bacterial Kdo 2-lipid A and its functional implications. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35394417 DOI: 10.1099/mic.0.001159] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The lipopolysaccharide (LPS) is a characteristic molecule of the outer leaflet of the Gram-negative bacterial outer membrane, which consists of lipid A, core oligosaccharide, and O antigen. The lipid A is embedded in outer membrane and provides an efficient permeability barrier, which is particularly important to reduce the permeability of antibiotics, toxic cationic metals, and antimicrobial peptides. LPS, an important modulator of innate immune responses ranging from localized inflammation to disseminated sepsis, displays a high level of structural and functional heterogeneity, which arise due to regulated differences in the acylation of the lipid A and the incorporation of non-stoichiometric modifications in lipid A and the core oligosaccharide. This review focuses on the current mechanistic understanding of the synthesis and assembly of the lipid A molecule and its most salient non-stoichiometric modifications.
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Affiliation(s)
- Miguel A Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, UK
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25
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Ashraf KU, Nygaard R, Vickery ON, Erramilli SK, Herrera CM, McConville TH, Petrou VI, Giacometti SI, Dufrisne MB, Nosol K, Zinkle AP, Graham CLB, Loukeris M, Kloss B, Skorupinska-Tudek K, Swiezewska E, Roper DI, Clarke OB, Uhlemann AC, Kossiakoff AA, Trent MS, Stansfeld PJ, Mancia F. Structural basis of lipopolysaccharide maturation by the O-antigen ligase. Nature 2022; 604:371-376. [PMID: 35388216 PMCID: PMC9884178 DOI: 10.1038/s41586-022-04555-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 02/16/2022] [Indexed: 01/31/2023]
Abstract
The outer membrane of Gram-negative bacteria has an external leaflet that is largely composed of lipopolysaccharide, which provides a selective permeation barrier, particularly against antimicrobials1. The final and crucial step in the biosynthesis of lipopolysaccharide is the addition of a species-dependent O-antigen to the lipid A core oligosaccharide, which is catalysed by the O-antigen ligase WaaL2. Here we present structures of WaaL from Cupriavidus metallidurans, both in the apo state and in complex with its lipid carrier undecaprenyl pyrophosphate, determined by single-particle cryo-electron microscopy. The structures reveal that WaaL comprises 12 transmembrane helices and a predominantly α-helical periplasmic region, which we show contains many of the conserved residues that are required for catalysis. We observe a conserved fold within the GT-C family of glycosyltransferases and hypothesize that they have a common mechanism for shuttling the undecaprenyl-based carrier to and from the active site. The structures, combined with genetic, biochemical, bioinformatics and molecular dynamics simulation experiments, offer molecular details on how the ligands come in apposition, and allows us to propose a mechanistic model for catalysis. Together, our work provides a structural basis for lipopolysaccharide maturation in a member of the GT-C superfamily of glycosyltransferases.
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Affiliation(s)
- Khuram U Ashraf
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Rie Nygaard
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Owen N Vickery
- School of Life Sciences, University of Warwick, Coventry, UK
- Department of Chemistry, University of Warwick, Coventry, UK
| | - Satchal K Erramilli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Carmen M Herrera
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Thomas H McConville
- Department of Medicine, Division of Infectious Diseases, Columbia University Medical Center, New York, NY, USA
| | - Vasileios I Petrou
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ, USA
| | - Sabrina I Giacometti
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Meagan Belcher Dufrisne
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Kamil Nosol
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Allen P Zinkle
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Michael Loukeris
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY, USA
| | - Brian Kloss
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY, USA
| | | | - Ewa Swiezewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - David I Roper
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Anne-Catrin Uhlemann
- Department of Medicine, Division of Infectious Diseases, Columbia University Medical Center, New York, NY, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - M Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA.
| | - Phillip J Stansfeld
- School of Life Sciences, University of Warwick, Coventry, UK.
- Department of Chemistry, University of Warwick, Coventry, UK.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
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26
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Butler J, Kelly SD, Muddiman KJ, Besinis A, Upton M. Hospital sink traps as a potential source of the emerging multidrug-resistant pathogen Cupriavidus pauculus: characterization and draft genome sequence of strain MF1. J Med Microbiol 2022; 71. [PMID: 35113779 PMCID: PMC8941954 DOI: 10.1099/jmm.0.001501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Introduction.Cupriavidus pauculus is historically found in soil and water but has more recently been reported to cause human infection and death. Hospital sink traps can serve as a niche for bacterial persistence and a platform for horizontal gene transfer, with evidence of dissemination of pathogens in hospital plumbing systems driving nosocomial infection. Gap Statement. This paper presents the first C. pauculus strain isolated from a hospital sink trap. There are only six genome assemblies available on NCBI for C. pauculus; two of these are PacBio/Illumina hybrids. This paper presents the first ONT/Illumina hybrid assembly, with five contigs. The other assemblies available consist of 37, 38, 111 and 227 contigs. This paper also presents data on biofilm formation and lethal dose in Galleria mellonella; there is little published information describing these aspects of virulence. Aim. The aims were to identify the isolate found in a hospital sink trap, characterize its genome, and assess whether it could pose a risk to human health. Methodology. The genome was sequenced, and a hybrid assembly of short and long reads produced. Antimicrobial susceptibility was determined by the broth microdilution method. Virulence was assessed by measuring in vitro biofilm formation compared to Pseudomonas aeruginosa and in vivo lethality in Galleria mellonella larvae. Results. The isolate was confirmed to be a strain of C. pauculus, with a 6.8 Mb genome consisting of 6468 coding sequences and an overall G+C content of 63.9 mol%. The genome was found to contain 12 antibiotic resistance genes, 8 virulence factor genes and 33 metal resistance genes. The isolate can be categorized as resistant to meropenem, amoxicillin, amikacin, gentamicin and colistin, but susceptible to cefotaxime, cefepime, imipenem and ciprofloxacin. Clear biofilm formation was seen in all conditions over 72 h and exceeded that of P. aeruginosa when measured at 37 °C in R2A broth. Lethality in G. mellonella larvae over 48 h was relatively low. Conclusion. The appearance of a multidrug-resistant strain of C. pauculus in a known pathogen reservoir within a clinical setting should be considered concerning. Further work should be completed to compare biofilm formation and in vivo virulence between clinical and environmental strains, to determine how easily environmental strains may establish human infection. Infection control teams and clinicians should be aware of the emerging nature of this pathogen and further work is needed to minimize the impact of contaminated hospital plumbing systems on patient outcomes.
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Affiliation(s)
- James Butler
- School of Engineering, Computing and Mathematics, Faculty of Science and Engineering, University of Plymouth, Plymouth PL4 8AA, UK
| | - Sean D Kelly
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK
| | - Katie J Muddiman
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK
| | - Alexandros Besinis
- School of Engineering, Computing and Mathematics, Faculty of Science and Engineering, University of Plymouth, Plymouth PL4 8AA, UK.,Peninsula Dental School, Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK
| | - Mathew Upton
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK
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27
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Tan YZ, Mancia F. Structure and Function of Mycobacterial Arabinofuranosyltransferases. Subcell Biochem 2022; 99:379-391. [PMID: 36151383 DOI: 10.1007/978-3-031-00793-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The mycobacteria genus is responsible for numerous infectious diseases that have afflicted the human race since antiquity-tuberculosis and leprosy in particular. An important contributor to their evolutionary success is their unique cell envelope, which constitutes a quasi-impermeable barrier, protecting the microorganism from external threats, antibiotics included. The arabinofuranosyltransferases are a family of enzymes, unique to the Actinobacteria family that mycobacteria genus belongs to, that are critical to building of this cell envelope. In this chapter, we will analyze available structures of members of the mycobacterial arabinofuranosyltransferase, clarify their function, as well as explore the common themes present amongst this family of enzymes, as revealed by recent research.
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Affiliation(s)
- Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
- Disease Intervention Technology Laboratory (DITL), Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, NY, USA
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28
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Tiwari V, Panta PR, Billiot CE, Douglass MV, Herrera CM, Trent MS, Doerrler WT. A Klebsiella pneumoniae DedA family membrane protein is required for colistin resistance and for virulence in wax moth larvae. Sci Rep 2021; 11:24365. [PMID: 34934166 PMCID: PMC8692421 DOI: 10.1038/s41598-021-03834-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/10/2021] [Indexed: 12/15/2022] Open
Abstract
Ineffectiveness of carbapenems against multidrug resistant pathogens led to the increased use of colistin (polymyxin E) as a last resort antibiotic. A gene belonging to the DedA family encoding conserved membrane proteins was previously identified by screening a transposon library of K. pneumoniae ST258 for sensitivity to colistin. We have renamed this gene dkcA (dedA of Klebsiella required for colistin resistance). DedA family proteins are likely membrane transporters required for viability of Escherichia coli and Burkholderia spp. at alkaline pH and for resistance to colistin in a number of bacterial species. Colistin resistance is often conferred via modification of the lipid A component of bacterial lipopolysaccharide with aminoarabinose (Ara4N) and/or phosphoethanolamine. Mass spectrometry analysis of lipid A of the ∆dkcA mutant shows a near absence of Ara4N in the lipid A, suggesting a requirement for DkcA for lipid A modification with Ara4N. Mutation of K. pneumoniae dkcA resulted in a reduction of the colistin minimal inhibitory concentration to approximately what is found with a ΔarnT strain. We also identify a requirement of DkcA for colistin resistance that is independent of lipid A modification, instead requiring maintenance of optimal membrane potential. K. pneumoniae ΔdkcA displays reduced virulence in Galleria mellonella suggesting colistin sensitivity can cause loss of virulence.
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Affiliation(s)
- Vijay Tiwari
- grid.64337.350000 0001 0662 7451Department of Biological Sciences, Louisiana State University, Baton Rouge, LA USA
| | - Pradip R. Panta
- grid.64337.350000 0001 0662 7451Department of Biological Sciences, Louisiana State University, Baton Rouge, LA USA
| | - Caitlin E. Billiot
- grid.64337.350000 0001 0662 7451Department of Biological Sciences, Louisiana State University, Baton Rouge, LA USA
| | - Martin V. Douglass
- grid.213876.90000 0004 1936 738XDepartment of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA USA
| | - Carmen M. Herrera
- grid.213876.90000 0004 1936 738XDepartment of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA USA
| | - M. Stephen Trent
- grid.213876.90000 0004 1936 738XDepartment of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA USA
| | - William T. Doerrler
- grid.64337.350000 0001 0662 7451Department of Biological Sciences, Louisiana State University, Baton Rouge, LA USA
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29
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Zhang S, Abbas M, Rehman MU, Wang M, Jia R, Chen S, Liu M, Zhu D, Zhao X, Gao Q, Tian B, Cheng A. Updates on the global dissemination of colistin-resistant Escherichia coli: An emerging threat to public health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 799:149280. [PMID: 34364270 DOI: 10.1016/j.scitotenv.2021.149280] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Colistin drug resistance is an emerging public health threat worldwide. The adaptability, existence and spread of colistin drug resistance in multiple reservoirs and ecological environmental settings is significantly increasing the rate of occurrence of multidrug resistant (MDR) bacteria such as Escherichia coli (E. coli). Here, we summarized the reports regarding molecular and biological characterization of mobile colistin resistance gene (mcr)-positive E. coli (MCRPEC), originating from diverse reservoirs, including but not limited to humans, environment, waste water treatment plants, wild, pets, and food producing animals. The MCRPEC revealed the abundance of clinically important resistance genes, which are responsible for MDR profile. A number of plasmid replicon types such as IncI2, IncX4, IncP, IncX, and IncFII with a predominance of IncI2 were facilitating the spread of colistin resistance. This study concludes the distribution of multiple sequence types of E. coli carrying mcr gene variants, which are possible threat to "One Health" perspective. In addition, we have briefly explained the newly known mechanisms of colistin resistance i.e. plasmid-encoded resistance determinant as well as presented the chromosomally-encoded resistance mechanisms. The transposition of ISApl1 into the chromosome and existence of intact Tn6330 are important for transmission and stability for mcr gene. Further, genetic environment of co-localized mcr gene with carbapenem-resistance or extended-spectrum β-lactamases genes has also been elaborated, which is limiting human beings to choose last resort antibiotics. Finally, environmental health and safety control measures along with spread mechanisms of mcr genes are discussed to avoid further propagation and environmental hazards of colistin resistance.
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Affiliation(s)
- Shaqiu Zhang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Muhammad Abbas
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Livestock and Dairy Development Department Lahore, Punjab 54000, Pakistan
| | - Mujeeb Ur Rehman
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Disease Investigation Laboratory, Livestock & Dairy Development Department, Zhob 85200, Balochistan, Pakistan
| | - Mingshu Wang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Renyong Jia
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Shun Chen
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Mafeng Liu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Dekang Zhu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Xinxin Zhao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Qun Gao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Bin Tian
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Anchun Cheng
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China.
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30
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Holman NDM, Wilkinson AJ, Smith MCM. Alanine-scanning mutagenesis of protein mannosyl-transferase from Streptomyces coelicolor reveals strong activity-stability correlation. MICROBIOLOGY (READING, ENGLAND) 2021; 167:001103. [PMID: 34676818 PMCID: PMC8698208 DOI: 10.1099/mic.0.001103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022]
Abstract
In Actinobacteria, protein O-mannosyl transferase (Pmt)-mediated protein O-glycosylation has an important role in cell envelope physiology. In S. coelicolor, defective Pmt leads to increased susceptibility to cell wall-targeting antibiotics, including vancomycin and β-lactams, and resistance to phage ϕC31. The aim of this study was to gain a deeper understanding of the structure and function of S. coelicolor Pmt. Sequence alignments and structural bioinformatics were used to identify target sites for an alanine-scanning mutagenesis study. Mutant alleles were introduced into pmt-deficient S. coelicolor strains using an integrative plasmid and scored for their ability to complement phage resistance and antibiotic hypersusceptibility phenotypes. Twenty-three highly conserved Pmt residues were each substituted for alanine. Six mutant alleles failed to complement the pmt▬ strains in either assay. Mapping the six corresponding residues onto a homology model of the three-dimensional structure of Pmt, indicated that five are positioned close to the predicted catalytic DE motif. Further mutagenesis to produce more conservative substitutions at these six residues produced Pmts that invariably failed to complement the DT1025 pmt▬ strain, indicating that strict residue conservation was necessary to preserve function. Cell fractionation and Western blotting of strains with the non-complementing pmt alleles revealed undetectable levels of the enzyme in either the membrane fractions or whole cell lysates. Meanwhile for all of the strains that complemented the antibiotic hypersusceptibility and phage resistance phenotypes, Pmt was readily detected in the membrane fraction. These data indicate a tight correlation between the activity of Pmt and its stability or ability to localize to the membrane.
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Affiliation(s)
| | - Anthony J. Wilkinson
- Structural Biology Laboratory, York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, UK
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31
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Taujale R, Zhou Z, Yeung W, Moremen KW, Li S, Kannan N. Mapping the glycosyltransferase fold landscape using interpretable deep learning. Nat Commun 2021; 12:5656. [PMID: 34580305 PMCID: PMC8476585 DOI: 10.1038/s41467-021-25975-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 08/31/2021] [Indexed: 12/28/2022] Open
Abstract
Glycosyltransferases (GTs) play fundamental roles in nearly all cellular processes through the biosynthesis of complex carbohydrates and glycosylation of diverse protein and small molecule substrates. The extensive structural and functional diversification of GTs presents a major challenge in mapping the relationships connecting sequence, structure, fold and function using traditional bioinformatics approaches. Here, we present a convolutional neural network with attention (CNN-attention) based deep learning model that leverages simple secondary structure representations generated from primary sequences to provide GT fold prediction with high accuracy. The model learns distinguishing secondary structure features free of primary sequence alignment constraints and is highly interpretable. It delineates sequence and structural features characteristic of individual fold types, while classifying them into distinct clusters that group evolutionarily divergent families based on shared secondary structural features. We further extend our model to classify GT families of unknown folds and variants of known folds. By identifying families that are likely to adopt novel folds such as GT91, GT96 and GT97, our studies expand the GT fold landscape and prioritize targets for future structural studies.
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Affiliation(s)
- Rahil Taujale
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Zhongliang Zhou
- Department of Computer Science, University of Georgia, Athens, GA, USA
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Sheng Li
- Department of Computer Science, University of Georgia, Athens, GA, USA
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
- Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
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32
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Structural Insights in Mammalian Sialyltransferases and Fucosyltransferases: We Have Come a Long Way, but It Is Still a Long Way Down. Molecules 2021; 26:molecules26175203. [PMID: 34500643 PMCID: PMC8433944 DOI: 10.3390/molecules26175203] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022] Open
Abstract
Mammalian cell surfaces are modified with complex arrays of glycans that play major roles in health and disease. Abnormal glycosylation is a hallmark of cancer; terminal sialic acid and fucose in particular have high levels in tumor cells, with positive implications for malignancy. Increased sialylation and fucosylation are due to the upregulation of a set of sialyltransferases (STs) and fucosyltransferases (FUTs), which are potential drug targets in cancer. In the past, several advances in glycostructural biology have been made with the determination of crystal structures of several important STs and FUTs in mammals. Additionally, how the independent evolution of STs and FUTs occurred with a limited set of global folds and the diverse modular ability of catalytic domains toward substrates has been elucidated. This review highlights advances in the understanding of the structural architecture, substrate binding interactions, and catalysis of STs and FUTs in mammals. While this general understanding is emerging, use of this information to design inhibitors of STs and FUTs will be helpful in providing further insights into their role in the manifestation of cancer and developing targeted therapeutics in cancer.
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33
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Augusto LA, Bourgeois-Nicolaos N, Breton A, Barreault S, Alonso EH, Gera S, Faraut-Derouin V, Semaan N, De Luca D, Chaby R, Doucet-Populaire F, Tissières P. Presence of 2-hydroxymyristate on endotoxins is associated with death in neonates with Enterobacter cloacae complex septic shock. iScience 2021; 24:102916. [PMID: 34409274 PMCID: PMC8361193 DOI: 10.1016/j.isci.2021.102916] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/11/2021] [Accepted: 07/27/2021] [Indexed: 11/29/2022] Open
Abstract
Enterobacter cloacae complex species are involved in infections among critically ill patients. After a recent E.cloacae outbreak of fulminant neonatal septic shock, we conducted a study to determine whether septic shock severity and its lethal consequence are related to structural features of the endotoxin (lipopolysaccharide [LPS]) of the strains isolated from hospitalized infants and more specifically its lipid A region. It appeared that the LPSs are very heterogeneous, carrying fifteen different molecular species of lipid A. The virulence was correlated with a structural feature identified by matrix-assisted laser desorption ionization–time of flight mass spectrometry and gas chromatography coupled with mass spectrometry: the presence of 2-hydroxymyristic acid as a secondary substituent in lipid A. This is the first published evidence linking LPS structural moiety to neonatal sepsis outcome and opens the possibility of using this fatty acid marker as a detection tool for high-risk patients, which could help reduce their mortality. Fifteen different molecular species of lipid A is found in E. cloacae complex 2-Hydroxymyristate moiety on Lipid A is a virulence marker of the E. cloacae complex Presence of 2-hydroxymyristate is associated with mortality in neonatal sepsis
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Affiliation(s)
- Luis A Augusto
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Nadège Bourgeois-Nicolaos
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.,Department of Bacteriology-Hygiene, AP-HP Paris-Saclay, Hôpital Antoine Béclère, Clamart Cedex, France
| | - Aude Breton
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Simon Barreault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.,Department of Pediatrics Intensive Care and Neonatal Medicine, AP-HP Université Paris -Saclay, Bicêtre Hospital, Paris, France
| | - Enrique Hernandez Alonso
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Stuti Gera
- Department of Bacteriology-Hygiene, AP-HP Paris-Saclay, Hôpital Antoine Béclère, Clamart Cedex, France
| | - Véronique Faraut-Derouin
- Department of Bacteriology-Hygiene, AP-HP Paris-Saclay, Hôpital Antoine Béclère, Clamart Cedex, France
| | - Nada Semaan
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.,Department of Pediatrics Intensive Care and Neonatal Medicine, AP-HP Université Paris -Saclay, Bicêtre Hospital, Paris, France
| | - Daniele De Luca
- Department of Neonatal Intensive Care, AP-HP Université Paris -Saclay, Hôpital Antoine Béclère, Clamart, France
| | - Richard Chaby
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Florence Doucet-Populaire
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.,Department of Bacteriology-Hygiene, AP-HP Paris-Saclay, Hôpital Antoine Béclère, Clamart Cedex, France
| | - Pierre Tissières
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.,Department of Pediatrics Intensive Care and Neonatal Medicine, AP-HP Université Paris -Saclay, Bicêtre Hospital, Paris, France.,FHU Sepsis, AP-HP/Université Paris-Saclay/Inserm, Le Kremlin-Bicêtre, France
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34
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The Xanthomonas RaxH-RaxR Two-Component Regulatory System Is Orthologous to the Zinc-Responsive Pseudomonas ColS-ColR System. Microorganisms 2021; 9:microorganisms9071458. [PMID: 34361895 PMCID: PMC8306577 DOI: 10.3390/microorganisms9071458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 01/08/2023] Open
Abstract
Genome sequence comparisons to infer likely gene functions require accurate ortholog assignments. In Pseudomonas spp., the sensor-regulator ColS-ColR two-component regulatory system responds to zinc and other metals to control certain membrane-related functions, including lipid A remodeling. In Xanthomonas spp., three different two-component regulatory systems, RaxH-RaxR, VgrS-VgrR, and DetS-DetR, have been denoted as ColS-ColR in several different genome annotations and publications. To clarify these assignments, we compared the sensor periplasmic domain sequences and found that those from Pseudomonas ColS and Xanthomonas RaxH share a similar size as well as the location of a Glu-X-X-Glu metal ion-binding motif. Furthermore, we determined that three genes adjacent to raxRH are predicted to encode enzymes that remodel the lipid A component of lipopolysaccharide. The modifications catalyzed by lipid A phosphoethanolamine transferase (EptA) and lipid A 1-phosphatase (LpxE) previously were detected in lipid A from multiple Xanthomonas spp. The third gene encodes a predicted lipid A glycosyl transferase (ArnT). Together, these results indicate that the Xanthomonas RaxH-RaxR system is orthologous to the Pseudomonas ColS-ColR system that regulates lipid A remodeling. To avoid future confusion, we recommend that the terms ColS and ColR no longer be applied to Xanthomonas spp., and that the Vgr, Rax, and Det designations be used instead.
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35
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Ghirga F, Stefanelli R, Cavinato L, Lo Sciuto A, Corradi S, Quaglio D, Calcaterra A, Casciaro B, Loffredo MR, Cappiello F, Morelli P, Antonelli A, Rossolini GM, Mangoni M, Mancone C, Botta B, Mori M, Ascenzioni F, Imperi F. A novel colistin adjuvant identified by virtual screening for ArnT inhibitors. J Antimicrob Chemother 2021; 75:2564-2572. [PMID: 32514531 PMCID: PMC7443731 DOI: 10.1093/jac/dkaa200] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/31/2020] [Accepted: 04/21/2020] [Indexed: 12/20/2022] Open
Abstract
Background Colistin is a last-resort treatment option for many MDR Gram-negative bacteria. The covalent addition of l-aminoarabinose to the lipid A moiety of LPS is the main colistin resistance mechanism in the human pathogen Pseudomonas aeruginosa. Objectives Identification (by in silico screening of a chemical library) of potential inhibitors of ArnT, which catalyses the last committed step of lipid A aminoarabinosylation, and their validation in vitro as colistin adjuvants. Methods The available ArnT crystal structure was used for a docking-based virtual screening of an in-house library of natural products. The resulting putative ArnT inhibitors were tested in growth inhibition assays using a reference colistin-resistant P. aeruginosa strain. The most promising compound was further characterized for its range of activity, specificity and cytotoxicity. Additionally, the effect of the compound on lipid A aminoarabinosylation was verified by MS analyses of lipid A. Results A putative ArnT inhibitor (BBN149) was discovered by molecular docking and demonstrated to specifically potentiate colistin activity in colistin-resistant P. aeruginosa isolates, without relevant effect on colistin-susceptible strains. BBN149 also showed adjuvant activity against colistin-resistant Klebsiella pneumoniae and low toxicity to bronchial epithelial cells. Lipid A aminoarabinosylation was reduced in BBN149-treated cells, although only partially. Conclusions This study demonstrates that in silico screening targeting ArnT can successfully identify inhibitors of colistin resistance and provides a promising lead compound for the development of colistin adjuvants for the treatment of MDR bacterial infections.
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Affiliation(s)
- Francesca Ghirga
- Center for Life Nano Science@Sapienza, Italian Institute of Technology, Rome, Italy
| | - Roberta Stefanelli
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy.,Department of Sciences, 'Department of Excellence 2018 - 2022', Roma Tre University, Rome, Italy
| | - Luca Cavinato
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Alessandra Lo Sciuto
- Department of Sciences, 'Department of Excellence 2018 - 2022', Roma Tre University, Rome, Italy
| | - Silvia Corradi
- Center for Life Nano Science@Sapienza, Italian Institute of Technology, Rome, Italy.,Department of Chemistry and Technology of Drugs, 'Department of Excellence 2018 - 2022', Sapienza University of Rome, Rome, Italy
| | - Deborah Quaglio
- Department of Chemistry and Technology of Drugs, 'Department of Excellence 2018 - 2022', Sapienza University of Rome, Rome, Italy
| | - Andrea Calcaterra
- Department of Chemistry and Technology of Drugs, 'Department of Excellence 2018 - 2022', Sapienza University of Rome, Rome, Italy
| | - Bruno Casciaro
- Center for Life Nano Science@Sapienza, Italian Institute of Technology, Rome, Italy
| | - Maria Rosa Loffredo
- Department of Biochemical Sciences, Sapienza University of Rome, Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Floriana Cappiello
- Department of Biochemical Sciences, Sapienza University of Rome, Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Patrizia Morelli
- Microbiology Laboratory, Giannina Gaslini Institute, Genoa, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Marialuisa Mangoni
- Department of Biochemical Sciences, Sapienza University of Rome, Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Carmine Mancone
- Department of Molecular Medicine, 'Department of Excellence 2018 - 2022', Sapienza University of Rome, Rome, Italy
| | - Bruno Botta
- Department of Chemistry and Technology of Drugs, 'Department of Excellence 2018 - 2022', Sapienza University of Rome, Rome, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, 'Department of Excellence 2018 - 2022', University of Siena, Siena, Italy
| | - Fiorentina Ascenzioni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Francesco Imperi
- Department of Sciences, 'Department of Excellence 2018 - 2022', Roma Tre University, Rome, Italy
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36
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Bai L, Li H. Protein N-glycosylation and O-mannosylation are catalyzed by two evolutionarily related GT-C glycosyltransferases. Curr Opin Struct Biol 2021; 68:66-73. [PMID: 33445129 PMCID: PMC8222153 DOI: 10.1016/j.sbi.2020.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/14/2020] [Accepted: 12/23/2020] [Indexed: 11/30/2022]
Abstract
The structural folds of glycosyltransferases are categorized into three superfamilies: GT-A, GT-B, and GT-C. Few structures of GT-C fold existed in the Protein Data Bank prior to the recent advent of high-resolution cryo-EM, because the glycosyltransferases are large membrane proteins that are difficult to crystallize. The use of cryo-EM has resulted in the structures of several key GT-C glycosyltransferases. Here we summarize the latest structural features of and mechanistic insights into these membrane enzyme complexes.
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Affiliation(s)
- Lin Bai
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing 100083, PR China.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503, United States.
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37
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The MCR-3 inside linker appears as a facilitator of colistin resistance. Cell Rep 2021; 35:109135. [PMID: 34010644 DOI: 10.1016/j.celrep.2021.109135] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/23/2020] [Accepted: 04/23/2021] [Indexed: 01/08/2023] Open
Abstract
An evolving family of mobile colistin resistance (MCR) enzymes is threatening public health. However, the molecular mechanism by which the MCR enzyme as a rare member of lipid A-phosphoethanolamine (PEA) transferases gains the ability to confer phenotypic colistin resistance remains enigmatic. Here, we report an unusual example that genetic duplication and amplification produce a functional variant (Ah762) of MCR-3 in certain Aeromonas species. The lipid A-binding cavity of Ah762 is functionally defined. Intriguingly, we locate a hinge linker of Ah762 (termed Linker 59) that determines the MCR. Genetic and biochemical characterization reveals that Linker 59 behaves as a facilitator to render inactive MCR variants to regain the ability of colistin resistance. Along with molecular dynamics (MD) simulation, isothermal titration calorimetry (ITC) suggests that this facilitator guarantees the formation of substrate phosphatidylethanolamine (PE)-accessible pocket within MCR-3-like enzymes. Therefore, our finding defines an MCR-3 inside facilitator for colistin resistance.
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38
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Eade CR, Wallen TW, Gates CE, Oliverio CL, Scarbrough BA, Reid AJ, Jorgenson MA, Young KD, Troutman JM. Making the Enterobacterial Common Antigen Glycan and Measuring Its Substrate Sequestration. ACS Chem Biol 2021; 16:691-700. [PMID: 33740380 DOI: 10.1021/acschembio.0c00983] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The enterobacterial common antigen (ECA), a three-sugar repeat unit polysaccharide produced by Enterobacteriaceae family members, impacts bacterial outer membrane permeability, and its biosynthesis affects the glycan landscape of the organism. ECA synthesis impacts the production of other polysaccharides by reducing the availability of shared substrates, the most notable of which is the 55-carbon polyisoprenoid bactoprenyl phosphate (BP), which serves as a carrier for the production of numerous bacterial glycans including ECA, peptidoglycan, O-antigen, and more. Here, using a combination of in vitro enzymatic synthesis and liquid chromatography-mass spectrometry (LC-MS) analysis of bacterial lysates, we provide biochemical evidence for the effect on endogenous polyisoprenoid pools from cell culture that arises from glycan pathway disruption. In this work, we have cloned and expressed each gene involved in ECA repeat unit biosynthesis and reconstituted the pathway in vitro, providing LC-MS characterized standards for the investigation of cellular glycan-linked intermediates and BP. We then generated ECA deficient mutants in genes associated with production of the polysaccharide, which we suspected would accumulate materials identical to our standards. We found that indeed accumulated products from these cells were indistinguishable from our enzymatically prepared standards, and moreover we observed a concomitant decrease in cellular BP levels with each mutant. This work provides the first direct biochemical evidence for the sequestration of BP upon the genetic disruption of glycan biosynthesis pathways in bacteria. This work also provides methods for the direct assessment of both the ECA glycan, and a new understanding of the dynamic interdependence of the bacterial polysaccharide repertoire.
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Affiliation(s)
- Colleen R. Eade
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Timothy W. Wallen
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Claire E. Gates
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Biological and Biomedical Sciences Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Cassidy L. Oliverio
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Beth A. Scarbrough
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Amanda J. Reid
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Matthew A. Jorgenson
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Kevin D. Young
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Jerry M. Troutman
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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39
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Modifications of cell wall polymers in Gram-positive bacteria by multi-component transmembrane glycosylation systems. Curr Opin Microbiol 2021; 60:24-33. [PMID: 33578058 PMCID: PMC8035078 DOI: 10.1016/j.mib.2021.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/12/2021] [Accepted: 01/22/2021] [Indexed: 11/22/2022]
Abstract
Secondary cell wall polymers fulfil diverse and important functions within the cell wall of Gram-positive bacteria. Here, we will provide a brief overview of the principles of teichoic acid and complex secondary cell wall polysaccharide biosynthesis pathways in Firmicutes and summarize the recently revised mechanism for the decoration of teichoic acids with d-alanines. Many cell wall polymers are decorated with glycosyl groups, either intracellularly or extracellularly. The main focus of this review will be on the extracellular glycosylation mechanism and recent advances that have been made in the identification of enzymes involved in this process. Based on the proteins involved, we propose to rename the system to multi-component transmembrane glycosylation system in place of three-component glycosylation system.
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40
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Eisenhaber B, Sinha S, Jadalanki CK, Shitov VA, Tan QW, Sirota FL, Eisenhaber F. Conserved sequence motifs in human TMTC1, TMTC2, TMTC3, and TMTC4, new O-mannosyltransferases from the GT-C/PMT clan, are rationalized as ligand binding sites. Biol Direct 2021; 16:4. [PMID: 33436046 PMCID: PMC7801869 DOI: 10.1186/s13062-021-00291-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/04/2021] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The human proteins TMTC1, TMTC2, TMTC3 and TMTC4 have been experimentally shown to be components of a new O-mannosylation pathway. Their own mannosyl-transferase activity has been suspected but their actual enzymatic potential has not been demonstrated yet. So far, sequence analysis of TMTCs has been compromised by evolutionary sequence divergence within their membrane-embedded N-terminal region, sequence inaccuracies in the protein databases and the difficulty to interpret the large functional variety of known homologous proteins (mostly sugar transferases and some with known 3D structure). RESULTS Evolutionary conserved molecular function among TMTCs is only possible with conserved membrane topology within their membrane-embedded N-terminal regions leading to the placement of homologous long intermittent loops at the same membrane side. Using this criterion, we demonstrate that all TMTCs have 11 transmembrane regions. The sequence segment homologous to Pfam model DUF1736 is actually just a loop between TM7 and TM8 that is located in the ER lumen and that contains a small hydrophobic, but not membrane-embedded helix. Not only do the membrane-embedded N-terminal regions of TMTCs share a common fold and 3D structural similarity with subgroups of GT-C sugar transferases. The conservation of residues critical for catalysis, for binding of a divalent metal ion and of the phosphate group of a lipid-linked sugar moiety throughout enzymatically and structurally well-studied GT-Cs and sequences of TMTCs indicates that TMTCs are actually sugar-transferring enzymes. We present credible 3D structural models of all four TMTCs (derived from their closest known homologues 5ezm/5f15) and find observed conserved sequence motifs rationalized as binding sites for a metal ion and for a dolichyl-phosphate-mannose moiety. CONCLUSIONS With the results from both careful sequence analysis and structural modelling, we can conclusively say that the TMTCs are enzymatically active sugar transferases belonging to the GT-C/PMT superfamily. The DUF1736 segment, the loop between TM7 and TM8, is critical for catalysis and lipid-linked sugar moiety binding. Together with the available indirect experimental data, we conclude that the TMTCs are not only part of an O-mannosylation pathway in the endoplasmic reticulum of upper eukaryotes but, actually, they are the sought mannosyl-transferases.
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Affiliation(s)
- Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.
- Genome Institute of Singapore (BII), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
| | - Swati Sinha
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Chaitanya K Jadalanki
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Vladimir A Shitov
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
- Siberian State Medical University, Moskovskiy Trakt, 2, Tomsk, Tomsk Oblast, 634050, Russia
| | - Qiao Wen Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
- School of Biological Science (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Fernanda L Sirota
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.
- Genome Institute of Singapore (BII), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
- School of Biological Science (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
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41
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Bohl H, Bai L, Li H. Recent Progress in Structural Studies on the GT-C Superfamily of Protein Glycosyltransferases. Subcell Biochem 2021; 96:259-271. [PMID: 33252732 DOI: 10.1007/978-3-030-58971-4_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Protein glycosylation is an essential covalent modification involved in protein secretion, stability, binding, folding, and activity. One or more sugars may be O-, N-, S-, or C-linked to specific amino acids by glycosyltransferases, which catalyze the transfer of these sugars from a phosphate-containing carrier molecule. Most glycosyltransferases are members of the GT-A, GT-B, or GT-C structural superfamilies. GT-C enzymes are integral membrane proteins that utilize a phospho-isoprenoid carrier for sugar transfer. To-date, two families of GT-Cs involved in protein glycosylation have been structurally characterized: the family represented by PglB, AglB, and Stt3, which catalyzes oligosaccharide transfer to Asn, and the family represented by Pmt1 and Pmt2, which catalyzes mannose transfer to Thr or Ser. This chapter reviews progress made over recent years on the structure and function of these two GT-C families.
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Affiliation(s)
- Heather Bohl
- Structural Biology Program, Van Andel Institute, Grand Rapids, Michigan, 49503, USA
| | - Lin Bai
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, 100083, Beijing, P. R. China
| | - Huilin Li
- Structural Biology Program, Van Andel Institute, Grand Rapids, Michigan, 49503, USA.
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42
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McConville TH, Annavajhala MK, Giddins MJ, Macesic N, Herrera CM, Rozenberg FD, Bhushan GL, Ahn D, Mancia F, Trent MS, Uhlemann AC. CrrB Positively Regulates High-Level Polymyxin Resistance and Virulence in Klebsiella pneumoniae. Cell Rep 2020; 33:108313. [PMID: 33113377 PMCID: PMC7656232 DOI: 10.1016/j.celrep.2020.108313] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/16/2020] [Accepted: 10/05/2020] [Indexed: 12/20/2022] Open
Abstract
Polymyxin resistance (PR) threatens the treatment of carbapenem-resistant Klebsiella pneumoniae (CRKP) infections. PR frequently arises through chemical modification of the lipid A portion of lipopolysaccharide. Various mutations are implicated in PR, including in three two-component systems—CrrA/B, PmrA/B, and PhoP/Q—and the negative regulator MgrB. Few have been functionally validated. Therefore, here we adapt a CRISPR-Cas9 system to CRKP to elucidate how mutations in clinical CRKP isolates induce PR. We demonstrate that CrrB is a positive regulator of PR, and common clinical mutations lead to the addition of both 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosophethanolamine (pEtN) to lipid A, inducing notably higher polymyxin minimum inhibitory concentrations than mgrB disruption. Additionally, crrB mutations cause a significant virulence increase at a fitness cost, partially from activation of the pentose phosphate pathway. Our data demonstrate the importance of CrrB in high-level PR and establish important differences across crrB alleles in balancing resistance with fitness and virulence. McConville et al. leverage CRISPR-Cas to demonstrate that mutations in crrB induce high-level polymyxin resistance in Klebsiella pneumoniae via the addition of L-Ara4N and pEtN to lipid A. CrrB mutations also increase virulence while conferring a fitness cost and alter carbon metabolism through activation of the pentose phosphate pathway.
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Affiliation(s)
- Thomas H McConville
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Medini K Annavajhala
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Marla J Giddins
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nenad Macesic
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, 3004 VIC, Australia
| | - Carmen M Herrera
- Departments of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Felix D Rozenberg
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Gitanjali L Bhushan
- Division of Pediatric Critical Care, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Danielle Ahn
- Division of Pediatric Critical Care, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Filippo Mancia
- Department of Physiology, Columbia University, New York, NY 10032, USA
| | - M Stephen Trent
- Departments of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA.
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43
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Quaglio D, Mangoni ML, Stefanelli R, Corradi S, Casciaro B, Vergine V, Lucantoni F, Cavinato L, Cammarone S, Loffredo MR, Cappiello F, Calcaterra A, Erazo S, Ghirga F, Mori M, Imperi F, Ascenzioni F, Botta B. ent-Beyerane Diterpenes as a Key Platform for the Development of ArnT-Mediated Colistin Resistance Inhibitors. J Org Chem 2020; 85:10891-10901. [PMID: 32806095 PMCID: PMC8009527 DOI: 10.1021/acs.joc.0c01459] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Colistin is a last-resort antibiotic for the treatment of multidrug resistant Gram-negative bacterial infections. Recently, a natural ent-beyerene diterpene was identified as a promising inhibitor of the enzyme responsible for colistin resistance mediated by lipid A aminoarabinosylation in Gram-negative bacteria, namely, ArnT (undecaprenyl phosphate-alpha-4-amino-4-deoxy-l-arabinose arabinosyl transferase). Here, semisynthetic analogues of hit were designed, synthetized, and tested against colistin-resistant Pseudomonas aeruginosa strains including clinical isolates to exploit the versatility of the diterpene scaffold. Microbiological assays coupled with molecular modeling indicated that for a more efficient colistin adjuvant activity, likely resulting from inhibition of the ArnT activity by the selected compounds and therefore from their interaction with the catalytic site of ArnT, an ent-beyerane scaffold is required along with an oxalate-like group at C-18/C-19 or a sugar residue at C-19 to resemble L-Ara4N. The ent-beyerane skeleton is identified for the first time as a privileged scaffold for further cost-effective development of valuable colistin resistance inhibitors.
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Affiliation(s)
- Deborah Quaglio
- Department of Chemistry and Technology of Drugs, "Department of Excellence 2018-2022", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Maria Luisa Mangoni
- Laboratory Affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Roberta Stefanelli
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Laboratory Affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Via dei Sardi 70, 00185 Rome, Italy.,Department of Science, Roma Tre University, Viale Guglielmo Marconi 446, 00146 Rome, Italy
| | - Silvia Corradi
- Department of Chemistry and Technology of Drugs, "Department of Excellence 2018-2022", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy.,Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, 00161 Rome, Italy
| | - Bruno Casciaro
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, 00161 Rome, Italy
| | - Valeria Vergine
- Department of Chemistry and Technology of Drugs, "Department of Excellence 2018-2022", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Federica Lucantoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Laboratory Affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Via dei Sardi 70, 00185 Rome, Italy
| | - Luca Cavinato
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Laboratory Affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Via dei Sardi 70, 00185 Rome, Italy
| | - Silvia Cammarone
- Department of Chemistry and Technology of Drugs, "Department of Excellence 2018-2022", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Maria Rosa Loffredo
- Laboratory Affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Floriana Cappiello
- Laboratory Affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Andrea Calcaterra
- Department of Chemistry and Technology of Drugs, "Department of Excellence 2018-2022", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Silvia Erazo
- Department of Pharmacological and Toxicological Chemistry, Faculty of Chemical and Pharmaceutical Sciences, University of Chile, 1058 Santiago, Chile
| | - Francesca Ghirga
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, 00161 Rome, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, "Department of Excellence 2018-2022", University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Francesco Imperi
- Department of Science, Roma Tre University, Viale Guglielmo Marconi 446, 00146 Rome, Italy
| | - Fiorentina Ascenzioni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Laboratory Affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Via dei Sardi 70, 00185 Rome, Italy
| | - Bruno Botta
- Department of Chemistry and Technology of Drugs, "Department of Excellence 2018-2022", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
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44
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Tan YZ, Rodrigues J, Keener JE, Zheng RB, Brunton R, Kloss B, Giacometti SI, Rosário AL, Zhang L, Niederweis M, Clarke OB, Lowary TL, Marty MT, Archer M, Potter CS, Carragher B, Mancia F. Cryo-EM structure of arabinosyltransferase EmbB from Mycobacterium smegmatis. Nat Commun 2020; 11:3396. [PMID: 32636380 PMCID: PMC7341804 DOI: 10.1038/s41467-020-17202-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/18/2020] [Indexed: 01/21/2023] Open
Abstract
Arabinosyltransferase B (EmbB) belongs to a family of membrane-bound glycosyltransferases that build the lipidated polysaccharides of the mycobacterial cell envelope, and are targets of anti-tuberculosis drug ethambutol. We present the 3.3 Å resolution single-particle cryo-electron microscopy structure of Mycobacterium smegmatis EmbB, providing insights on substrate binding and reaction mechanism. Mutations that confer ethambutol resistance map mostly around the putative active site, suggesting this to be the location of drug binding.
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Affiliation(s)
- Yong Zi Tan
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA
| | - José Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal
| | - James E Keener
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Ruixiang Blake Zheng
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Richard Brunton
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Brian Kloss
- Center on Membrane Protein Production and Analysis, New York Structural Biology Center, New York, NY, 10027, USA
| | - Sabrina I Giacometti
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Ana L Rosário
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal
| | - Lei Zhang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
- Department of Anesthesiology, Columbia University, New York, NY, 10032, USA
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
- Institute of Biological Chemistry, Academia Sinica, Academia Road, Section 2, #128, Nangang, Taipei, 11529, Taiwan
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
- Bio5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal
| | - Clinton S Potter
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA.
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA.
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45
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Plasmid gene for putative integral membrane protein affects formation of lipopolysaccharide and motility in Azospirillum brasilense Sp245. Folia Microbiol (Praha) 2020; 65:963-972. [PMID: 32607666 DOI: 10.1007/s12223-020-00805-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/17/2020] [Indexed: 10/24/2022]
Abstract
The bacterium Azospirillum brasilense can swim and swarm owing to the work of polar and lateral flagella. Its major surface glycopolymers consist of lipopolysaccharides (LPS) and Calcofluor-binding polysaccharides (Cal+ phenotype). Motility and surface glycopolymers are important for the interactions of plant-associated bacteria with plants. The facultative plant endophyte A. brasilense Sp245 produces two antigenically different LPS, LpsI, and LpsII, containing identical O-polysaccharides. Previously, using vector pJFF350 for random Omegon-Km mutagenesis, we constructed a mutant of Sp245 named KM018 that still possessed flagella, although paralyzed. The mutant was no longer able to produce Calcofluor-binding polysaccharides and LpsII. Because of the limited experimental data on the genetic aspects of surface glycopolymer production and flagellar motility in azospirilla, the aim of this study was to identify and examine in more detail the coding sequence of strain Sp245, inactivated in the mutant. We found that pJFF350 was integrated into a coding sequence for a putative integral membrane protein of unknown function (AZOBR_p60025) located in the sixth plasmid of Sp245. To clarify the role of the putative protein, we cloned AZOBR_p60025 in the expression vector pRK415 and used it for the genetic complementation of mutant KM018. The SDS-PAGE, immunodiffusion, and linear immunoelectrophoresis analyses showed that in strain KM018 (pRK415-p60025), the wild-type LpsI+ LpsII+ profile was restored. The complemented mutant had a Cal+ phenotype and it was capable of swimming and swarming motility. Thus, the AZOBR_p60025-encoded protein significantly affects the composition of the major cell-surface glycopolymers and the single-cell and social motility of azospirilla.
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46
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Adak T, Morales DL, Cook AJ, Grigg JC, Murphy MEP, Tanner ME. ArnD is a deformylase involved in polymyxin resistance. Chem Commun (Camb) 2020; 56:6830-6833. [PMID: 32432293 DOI: 10.1039/d0cc02241a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The modification of lipid A with cationic 4-amino-4-deoxy-l-arabinose residues serves to confer resistance against cationic peptide antibiotics in Gram-negative bacteria. In this work, the enzyme ArnD is shown to act as a metal-dependent deformylase in the biosynthesis of this carbohydrate.
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Affiliation(s)
- Taniya Adak
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
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47
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Caffalette CA, Kuklewicz J, Spellmon N, Zimmer J. Biosynthesis and Export of Bacterial Glycolipids. Annu Rev Biochem 2020; 89:741-768. [DOI: 10.1146/annurev-biochem-011520-104707] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Complex carbohydrates are essential for many biological processes, from protein quality control to cell recognition, energy storage, and cell wall formation. Many of these processes are performed in topologically extracellular compartments or on the cell surface; hence, diverse secretion systems evolved to transport the hydrophilic molecules to their sites of action. Polyprenyl lipids serve as ubiquitous anchors and facilitators of these transport processes. Here, we summarize and compare bacterial biosynthesis pathways relying on the recognition and transport of lipid-linked complex carbohydrates. In particular, we compare transporters implicated in O antigen and capsular polysaccharide biosyntheses with those facilitating teichoic acid and N-linked glycan transport. Further, we discuss recent insights into the generation, recognition, and recycling of polyprenyl lipids.
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Affiliation(s)
- Christopher A. Caffalette
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Jeremi Kuklewicz
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Nicholas Spellmon
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Jochen Zimmer
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
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48
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Massip C, Coullaud-Gamel M, Gaudru C, Amoureux L, Doleans-Jordheim A, Hery-Arnaud G, Marchandin H, Oswald E, Segonds C, Guet-Revillet H. In vitro activity of 20 antibiotics against Cupriavidus clinical strains. J Antimicrob Chemother 2020; 75:1654-1658. [PMID: 32163570 PMCID: PMC7225898 DOI: 10.1093/jac/dkaa066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Clémence Massip
- Service de Bactériologie-Hygiène, CHU de Toulouse, Toulouse, France.,IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Mathieu Coullaud-Gamel
- Service de Bactériologie-Hygiène, CHU de Toulouse, Toulouse, France.,Lycée Stéphane Hessel, Toulouse, France
| | - Cécile Gaudru
- Service de Bactériologie-Hygiène, CHU de Toulouse, Toulouse, France.,IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Lucie Amoureux
- Laboratoire de Bactériologie, CHU Dijon, Dijon, France.,UMR 6249 CNRS Chrono-environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Anne Doleans-Jordheim
- Laboratoire de Bactériologie, Instituts des Agents Infectieux, Centre de Biologie et Pathologie Nord, Hospices Civils de Lyon, Lyon, France.,Equipe de Recherche Bactéries Pathogènes Opportunistes et Environnement, UMR CNRS 5557 Ecologie Microbienne, Université Lyon 1 et VetAgro Sup, Villeurbanne, France
| | - Geneviève Hery-Arnaud
- Département de Bactériologie-Virologie, Hygiène et Parasitologie-Mycologie, Centre Hospitalier Régional Universitaire (CHRU) de Brest, Brest, France.,INSERM, EFS, UMR 1078 'Génétique, Génomique Fonctionnelle et Biotechnologies', Univ Brest, F-29200 Brest, France
| | - Hélène Marchandin
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Département de Microbiologie, CHU Nîmes, Nîmes, France
| | - Eric Oswald
- Service de Bactériologie-Hygiène, CHU de Toulouse, Toulouse, France.,IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Christine Segonds
- Observatoire Burkholderia cepacia, CHU de Toulouse, Toulouse/Vaincre la Mucoviscidose, Paris, France
| | - Hélène Guet-Revillet
- Service de Bactériologie-Hygiène, CHU de Toulouse, Toulouse, France.,IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France.,Observatoire Burkholderia cepacia, CHU de Toulouse, Toulouse/Vaincre la Mucoviscidose, Paris, France
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49
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Tan YZ, Zhang L, Rodrigues J, Zheng RB, Giacometti SI, Rosário AL, Kloss B, Dandey VP, Wei H, Brunton R, Raczkowski AM, Athayde D, Catalão MJ, Pimentel M, Clarke OB, Lowary TL, Archer M, Niederweis M, Potter CS, Carragher B, Mancia F. Cryo-EM Structures and Regulation of Arabinofuranosyltransferase AftD from Mycobacteria. Mol Cell 2020; 78:683-699.e11. [PMID: 32386575 PMCID: PMC7263364 DOI: 10.1016/j.molcel.2020.04.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/21/2020] [Accepted: 04/13/2020] [Indexed: 01/21/2023]
Abstract
Mycobacterium tuberculosis causes tuberculosis, a disease that kills over 1 million people each year. Its cell envelope is a common antibiotic target and has a unique structure due, in part, to two lipidated polysaccharides-arabinogalactan and lipoarabinomannan. Arabinofuranosyltransferase D (AftD) is an essential enzyme involved in assembling these glycolipids. We present the 2.9-Å resolution structure of M. abscessus AftD, determined by single-particle cryo-electron microscopy. AftD has a conserved GT-C glycosyltransferase fold and three carbohydrate-binding modules. Glycan array analysis shows that AftD binds complex arabinose glycans. Additionally, AftD is non-covalently complexed with an acyl carrier protein (ACP). 3.4- and 3.5-Å structures of a mutant with impaired ACP binding reveal a conformational change, suggesting that ACP may regulate AftD function. Mutagenesis experiments using a conditional knockout constructed in M. smegmatis confirm the essentiality of the putative active site and the ACP binding for AftD function.
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Affiliation(s)
- Yong Zi Tan
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA; National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Lei Zhang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - José Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | | | - Sabrina I Giacometti
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Ana L Rosário
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Brian Kloss
- Center on Membrane Protein Production and Analysis, New York Structural Biology Center, New York, NY 10027, USA
| | - Venkata P Dandey
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Hui Wei
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Richard Brunton
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Ashleigh M Raczkowski
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Diogo Athayde
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Maria João Catalão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Madalena Pimentel
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA; Department of Anesthesiology, Columbia University, New York, NY 10032, USA
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; Institute of Biological Chemistry, Academia Sinica, Academia Road, Section 2, #128 Nangang, Taipei 11529, Taiwan
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Clinton S Potter
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.
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50
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Cryo-EM snapshots of mycobacterial arabinosyltransferase complex EmbB 2-AcpM 2. Protein Cell 2020; 11:505-517. [PMID: 32363534 PMCID: PMC7305291 DOI: 10.1007/s13238-020-00726-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 11/27/2019] [Indexed: 01/26/2023] Open
Abstract
Inhibition of Mycobacterium tuberculosis (Mtb) cell wall assembly is an established strategy for anti-TB chemotherapy. Arabinosyltransferase EmbB, which catalyzes the transfer of arabinose from the donor decaprenyl-phosphate-arabinose (DPA) to its arabinosyl acceptor is an essential enzyme for Mtb cell wall synthesis. Analysis of drug resistance mutations suggests that EmbB is the main target of the front-line anti-TB drug, ethambutol. Herein, we report the cryo-EM structures of Mycobacterium smegmatis EmbB in its “resting state” and DPA-bound “active state”. EmbB is a fifteen-transmembrane-spanning protein, assembled as a dimer. Each protomer has an associated acyl-carrier-protein (AcpM) on their cytoplasmic surface. Conformational changes upon DPA binding indicate an asymmetric movement within the EmbB dimer during catalysis. Functional studies have identified critical residues in substrate recognition and catalysis, and demonstrated that ethambutol inhibits transferase activity of EmbB by competing with DPA. The structures represent the first step directed towards a rational approach for anti-TB drug discovery.
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