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Mousa WK, Abu-Izneid T, Salah-Tantawy A. High-throughput sequencing reveals the structure and metabolic resilience of desert microbiome confronting climate change. FRONTIERS IN PLANT SCIENCE 2024; 15:1294173. [PMID: 38510442 PMCID: PMC10953687 DOI: 10.3389/fpls.2024.1294173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/06/2024] [Indexed: 03/22/2024]
Abstract
Introduction Desert ecosystems harbor a unique microbial diversity that is crucial for ecological stability and biogeochemical cycles. An in-depth understanding of the biodiversity, compositions, and functions of these microbial communities is imperative to navigate global changes and confront potential threats and opportunities applicable to agricultural ecosystems amid climate change. Methods This study explores microbial communities in the rhizosphere and endosphere of desert plants native to the Arabian Peninsula using next-generation sequencing of the 16S rRNA gene (V3-V4 hypervariable region). Results Our results reveal that each microbial community has a diverse and unique microbial composition. Based on alpha and beta diversity indices, the rhizosphere microbiome is significantly diverse and richer in microbial taxa compared to the endosphere. The data reveals a shift towards fast-growing microbes with active metabolism, involvement in nutrient cycling, nitrogen fixation, and defense pathways. Our data reveals the presence of habitat-specific microbial communities in the desert, highlighting their remarkable resilience and adaptability to extreme environmental conditions. Notably, we observed the existence of radiation-resistant microbes such as Deinococcus radiotolerans, Kocuria sp., and Rubrobacter radiotolerans which can tolerate high levels of ionizing radiation. Additionally, examples of microbes exhibiting tolerance to challenging conditions include Nocardioides halotolerans, thriving in high-salinity environments, and hyperthermophilic microbes such as Quasibacillus thermotolerans. Moreover, functional analysis reveals enrichment in chaperon biosynthesis pathways associated with correct protein folding under heat stress conditions. Discussion Our research sheds light on the unique diversity of desert microbes and underscores their potential applications to increase the resilience of agriculture ecosystems, offering a promising strategy to fortify crops against the challenges posed by climate change, ultimately supporting sustainable food production for our ever-expanding global population.
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Affiliation(s)
- Walaa K. Mousa
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- Al Ain University (AAU) Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
- College of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Tareq Abu-Izneid
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- Al Ain University (AAU) Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Ahmed Salah-Tantawy
- Institute of Analytical and Environmental Sciences, College of Nuclear Science, National Tsing Hua University, Hsinchu, Taiwan
- Department of Zoology, Marine Science Division, College of Science, Al-Azhar University, Assiut, Egypt
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2
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Patrick J, Pettersson P, Mäler L. Lipid- and substrate-induced conformational and dynamic changes in a glycosyltransferase involved in E. coli LPS synthesis revealed by 19F and 31P NMR. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184209. [PMID: 37558175 DOI: 10.1016/j.bbamem.2023.184209] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/03/2023] [Accepted: 08/04/2023] [Indexed: 08/11/2023]
Abstract
WaaG is a glycosyltransferase (GT) involved in the synthesis of the bacterial cell wall, and in Escherichia coli it catalyzes the transfer of a glucose moiety from the donor substrate UDP-glucose onto the nascent lipopolysaccharide (LPS) molecule which when completed constitutes the major component of the bacterium's outermost defenses. Similar to other GTs of the GT-B fold, having two Rossman-like domains connected by a short linker, WaaG is believed to undergo complex inter-domain motions as part of its function to accommodate the nascent LPS and UDP-glucose in the catalytic site located in the cleft between the two domains. As the nascent LPS is bulky and membrane-bound, WaaG is a peripheral membrane protein, adding to the complexity of studying the enzyme in a biologically relevant environment. Using specific 5-fluoro-Trp labelling of native and inserted tryptophans and 19F NMR we herein studied the dynamic interactions of WaaG with lipids using bicelles, and with the donor substrate. Line-shape changes when bicelles are added to WaaG show that the dynamic behavior is altered when binding to the model membrane, while a chemical shift change indicates an altered environment around a tryptophan located in the C-terminal domain of WaaG upon interaction with UDP-glucose or UDP. A lipid-bound paramagnetic probe was used to confirm that the membrane interaction is mediated by a loop region located in the N-terminal domain. Furthermore, the hydrolysis of the donor substrate by WaaG was quantified by 31P NMR.
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Affiliation(s)
- Joan Patrick
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pontus Pettersson
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden; Department of Chemistry, Umeå University, Umeå, Sweden.
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3
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Xiao L, Qi Z, Song K, Lv R, Chen R, Zhao H, Wu H, Li C, Xin Y, Jin Y, Li X, Xu X, Tan Y, Du Z, Cui Y, Zhang X, Yang R, Zhao X, Song Y. Interplays of mutations in waaA, cmk, and ail contribute to phage resistance in Yersinia pestis. Front Cell Infect Microbiol 2023; 13:1174510. [PMID: 37305418 PMCID: PMC10254400 DOI: 10.3389/fcimb.2023.1174510] [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: 02/26/2023] [Accepted: 05/04/2023] [Indexed: 06/13/2023] Open
Abstract
Plague caused by Yersinia pestis remains a public health threat worldwide. Because multidrug-resistant Y. pestis strains have been found in both humans and animals, phage therapy has attracted increasing attention as an alternative strategy against plague. However, phage resistance is a potential drawback of phage therapies, and the mechanism of phage resistance in Y. pestis is yet to be investigated. In this study, we obtained a bacteriophage-resistant strain of Y. pestis (S56) by continuously challenging Y. pestis 614F with the bacteriophage Yep-phi. Genome analysis identified three mutations in strain S56: waaA* (9-bp in-frame deletion 249GTCATCGTG257), cmk* (10-bp frameshift deletion 15CCGGTGATAA24), and ail* (1-bp frameshift deletion A538). WaaA (3-deoxy-D-manno-octulosonic acid transferase) is a key enzyme in lipopolysaccharide biosynthesis. The waaA* mutation leads to decreased phage adsorption because of the failure to synthesize the lipopolysaccharide core. The mutation in cmk (encoding cytidine monophosphate kinase) increased phage resistance, independent of phage adsorption, and caused in vitro growth defects in Y. pestis. The mutation in ail inhibited phage adsorption while restoring the growth of the waaA null mutant and accelerating the growth of the cmk null mutant. Our results confirmed that mutations in the WaaA-Cmk-Ail cascade in Y. pestis contribute to resistance against bacteriophage. Our findings help in understanding the interactions between Y. pestis and its phages.
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Affiliation(s)
- Lisheng Xiao
- Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
- School of Basic Medicine, Anhui Medical University, Hefei, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Zhizhen Qi
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Kai Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Ruichen Lv
- Hua Dong Research Institute for Medicine and Biotechniques, Nanjing, China
| | - Rong Chen
- Department of Laboratory Medicine, First Medical Center of Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China
| | - Haihong Zhao
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Hailian Wu
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Cunxiang Li
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Youquan Xin
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Yong Jin
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Xiang Li
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Xiaoqing Xu
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Zongmin Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Xuefei Zhang
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Xilin Zhao
- Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Yajun Song
- School of Basic Medicine, Anhui Medical University, Hefei, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
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4
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Meng JX, Wei XY, Guo H, Chen Y, Wang W, Geng HL, Yang X, Jiang J, Zhang XX. Metagenomic insights into the composition and function of the gut microbiota of mice infected with Toxoplasma gondii. Front Immunol 2023; 14:1156397. [PMID: 37090719 PMCID: PMC10118048 DOI: 10.3389/fimmu.2023.1156397] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/16/2023] [Indexed: 04/25/2023] Open
Abstract
Introduction Despite Toxoplasma gondii infection leading to dysbiosis and enteritis, the function of gut microbiota in toxoplasmosis has not been explored. Methods Here, shotgun metagenomics was employed to characterize the composition and function of mouse microbial community during acute and chronic T. gondii infection, respectively. Results The results revealed that the diversity of gut bacteria was decreased immediately after T. gondii infection, and was increased with the duration of infection. In addition, T. gondii infection led to gut microbiota dysbiosis both in acute and chronic infection periods. Therein, several signatures, including depression of Firmicutes to Bacteroidetes ratio and infection-enriched Proteobacteria, were observed in the chronic period, which may contribute to aggravated gut inflammation and disease severity. Functional analysis showed that a large amount of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and carbohydrate-active enzymes (CAZy) family displayed distinct variation in abundance between infected and healthy mice. The lipopolysaccharide biosynthesis related pathways were activated in the chronic infection period, which might lead to immune system imbalance and involve in intestinal inflammation. Moreover, microbial and functional spectrums were more disordered in chronic than acute infection periods, thus implying gut microbiota was more likely to participate in disease process in the chronically infected mice, even exacerbated immunologic derangement and disease progression. Discussion Our data indicate that the gut microbiota plays a potentially important role in protecting mice from T. gondii infection, and contributes to better understand the association between gut microbiota and toxoplasmosis.
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Affiliation(s)
- Jin-Xin Meng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Xin-Yu Wei
- College of Life Science, Changchun Sci-Tech University, Changchun, China
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Huanping Guo
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Yu Chen
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Wei Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Hong-Li Geng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Xing Yang
- Department of Medical Microbiology and Immunology, School of Basic Medicine, Dali University, Dali, Yunnan, China
| | - Jiang Jiang
- College of Life Science, Changchun Sci-Tech University, Changchun, China
| | - Xiao-Xuan Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
- *Correspondence: Xiao-Xuan Zhang,
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5
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Saïdi F, Gamboa Marin OJ, Veytia-Bucheli JI, Vinogradov E, Ravicoularamin G, Jolivet NY, Kezzo AA, Ramirez Esquivel E, Panda A, Sharma G, Vincent S, Gauthier C, Islam ST. Evaluation of Azido 3-Deoxy-d- manno-oct-2-ulosonic Acid (Kdo) Analogues for Click Chemistry-Mediated Metabolic Labeling of Myxococcus xanthus DZ2 Lipopolysaccharide. ACS OMEGA 2022; 7:34997-35013. [PMID: 36211050 PMCID: PMC9535733 DOI: 10.1021/acsomega.2c03711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Metabolic labeling paired with click chemistry is a powerful approach for selectively imaging the surfaces of diverse bacteria. Herein, we explored the feasibility of labeling the lipopolysaccharide (LPS) of Myxococcus xanthus-a Gram-negative predatory social bacterium known to display complex outer membrane (OM) dynamics-via growth in the presence of distinct azido (-N3) analogues of 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo). Determination of the LPS carbohydrate structure from strain DZ2 revealed the presence of one Kdo sugar in the core oligosaccharide, modified with phosphoethanolamine. The production of 8-azido-8-deoxy-Kdo (8-N3-Kdo) was then greatly improved over previous reports via optimization of the synthesis of its 5-azido-5-deoxy-d-arabinose precursor to yield gram amounts. The novel analogue 7-azido-7-deoxy-Kdo (7-N3-Kdo) was also synthesized, with both analogues capable of undergoing in vitro strain-promoted azide-alkyne cycloaddition (SPAAC) "click" chemistry reactions. Slower and faster growth of M. xanthus was displayed in the presence of 8-N3-Kdo and 7-N3-Kdo (respectively) compared to untreated cells, with differences also seen for single-cell gliding motility and type IV pilus-dependent swarm community expansion. While the surfaces of 8-N3-Kdo-grown cells were fluorescently labeled following treatment with dibenzocyclooctyne-linked fluorophores, the surfaces of 7-N3-Kdo-grown cells could not undergo fluorescent tagging. Activity analysis of the KdsB enzyme required to activate Kdo prior to its integration into nascent LPS molecules revealed that while 8-N3-Kdo is indeed a substrate of the enzyme, 7-N3-Kdo is not. Though a lack of M. xanthus cell aggregation was shown to expedite growth in liquid culture, 7-N3-Kdo-grown cells did not manifest differences in intrinsic clumping relative to untreated cells, suggesting that 7-N3-Kdo may instead be catabolized by the cells. Ultimately, these data provide important insights into the synthesis and cellular processing of valuable metabolic labels and establish a basis for the elucidation of fundamental principles of OM dynamism in live bacterial cells.
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Affiliation(s)
- Fares Saïdi
- Institut
National de la Recherche Scientifique (INRS)−Centre Armand-Frappier
Santé Biotechnologie (AFSB), Université
du Québec, Institut Pasteur International Network, Laval, Quebec H7V 1B7, Canada
- PROTEO,
the Quebec Network for Research on Protein Function, Engineering,
and Applications, Université Laval, Quebec, Quebec G1V 0A6, Canada
| | - Oscar Javier Gamboa Marin
- Institut
National de la Recherche Scientifique (INRS)−Centre Armand-Frappier
Santé Biotechnologie (AFSB), Université
du Québec, Institut Pasteur International Network, Laval, Quebec H7V 1B7, Canada
- Unité
Mixte de Recherche INRS-UQAC, INRS−Centre AFSB, Université du Québec à Chicoutimi
(UQAC), Chicoutimi, Quebec G7H 2B1, Canada
| | - José Ignacio Veytia-Bucheli
- Department
of Chemistry, Laboratory of Bio-Organic Chemistry−Namur Research
Institute for Life Sciences (NARILIS), University
of Namur (UNamur), Namur 5000, Belgium
| | - Evgeny Vinogradov
- Vaccine
Program, Human Health Therapeutics Portfolio, National Research Council, Ottawa, Ontario K1A 0R6, Canada
| | - Gokulakrishnan Ravicoularamin
- Institut
National de la Recherche Scientifique (INRS)−Centre Armand-Frappier
Santé Biotechnologie (AFSB), Université
du Québec, Institut Pasteur International Network, Laval, Quebec H7V 1B7, Canada
- Unité
Mixte de Recherche INRS-UQAC, INRS−Centre AFSB, Université du Québec à Chicoutimi
(UQAC), Chicoutimi, Quebec G7H 2B1, Canada
| | - Nicolas Y. Jolivet
- Institut
National de la Recherche Scientifique (INRS)−Centre Armand-Frappier
Santé Biotechnologie (AFSB), Université
du Québec, Institut Pasteur International Network, Laval, Quebec H7V 1B7, Canada
- PROTEO,
the Quebec Network for Research on Protein Function, Engineering,
and Applications, Université Laval, Quebec, Quebec G1V 0A6, Canada
| | - Ahmad A. Kezzo
- Institut
National de la Recherche Scientifique (INRS)−Centre Armand-Frappier
Santé Biotechnologie (AFSB), Université
du Québec, Institut Pasteur International Network, Laval, Quebec H7V 1B7, Canada
- PROTEO,
the Quebec Network for Research on Protein Function, Engineering,
and Applications, Université Laval, Quebec, Quebec G1V 0A6, Canada
| | - Eric Ramirez Esquivel
- Institut
National de la Recherche Scientifique (INRS)−Centre Armand-Frappier
Santé Biotechnologie (AFSB), Université
du Québec, Institut Pasteur International Network, Laval, Quebec H7V 1B7, Canada
- PROTEO,
the Quebec Network for Research on Protein Function, Engineering,
and Applications, Université Laval, Quebec, Quebec G1V 0A6, Canada
| | - Adyasha Panda
- Institute
of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka 560100, India
| | - Gaurav Sharma
- Institute
of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka 560100, India
| | - Stéphane
P. Vincent
- Department
of Chemistry, Laboratory of Bio-Organic Chemistry−Namur Research
Institute for Life Sciences (NARILIS), University
of Namur (UNamur), Namur 5000, Belgium
| | - Charles Gauthier
- Institut
National de la Recherche Scientifique (INRS)−Centre Armand-Frappier
Santé Biotechnologie (AFSB), Université
du Québec, Institut Pasteur International Network, Laval, Quebec H7V 1B7, Canada
- Unité
Mixte de Recherche INRS-UQAC, INRS−Centre AFSB, Université du Québec à Chicoutimi
(UQAC), Chicoutimi, Quebec G7H 2B1, Canada
| | - Salim T. Islam
- Institut
National de la Recherche Scientifique (INRS)−Centre Armand-Frappier
Santé Biotechnologie (AFSB), Université
du Québec, Institut Pasteur International Network, Laval, Quebec H7V 1B7, Canada
- PROTEO,
the Quebec Network for Research on Protein Function, Engineering,
and Applications, Université Laval, Quebec, Quebec G1V 0A6, Canada
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6
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Molecular basis for polysaccharide recognition and modulated ATP hydrolysis by the O antigen ABC transporter. Nat Commun 2022; 13:5226. [PMID: 36064941 PMCID: PMC9445017 DOI: 10.1038/s41467-022-32597-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/08/2022] [Indexed: 11/08/2022] Open
Abstract
O antigens are ubiquitous protective extensions of lipopolysaccharides in the extracellular leaflet of the Gram-negative outer membrane. Following biosynthesis in the cytosol, the lipid-linked polysaccharide is transported to the periplasm by the WzmWzt ABC transporter. Often, O antigen secretion requires the chemical modification of its elongating terminus, which the transporter recognizes via a carbohydrate-binding domain (CBD). Here, using components from A. aeolicus, we identify the O antigen structure with methylated mannose or rhamnose as its cap. Crystal and cryo electron microscopy structures reveal how WzmWzt recognizes this cap between its carbohydrate and nucleotide-binding domains in a nucleotide-free state. ATP binding induces drastic conformational changes of its CBD, terminating interactions with the O antigen. ATPase assays and site directed mutagenesis reveal reduced hydrolytic activity upon O antigen binding, likely to facilitate polymer loading into the ABC transporter. Our results elucidate critical steps in the recognition and translocation of polysaccharides by ABC transporters.
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7
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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: 4] [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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8
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Schreiber T, Falk-Paulsen M, Kuiper J, Aden K, Noth R, Gisch N, Schreiber S, Rosenstiel P, Bewig B. IL23R on myeloid cells is involved in murine pulmonary granuloma formation. Exp Lung Res 2021; 47:344-353. [PMID: 34405744 DOI: 10.1080/01902148.2021.1962433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
PURPOSE OF THE STUDY The involvement of the IL-23/IL23R pathway is well known in the disease pathogenesis of sarcoidosis and other inflammatory diseases. To date, the pathogenic mechanism of IL-23 is most notably described on CD4+ Th17 lymphocytes. However, the function of the IL23R on myeloid cells in sarcoidosis is poorly understood. Thus, the aim of the study is to investigate the role of the IL23R on myeloid cell in pulmonary granuloma formation. Methods: We generated IL23RLysMCre mice lacking the IL23R gene in myeloid cells. The importance of IL23R in myeloid cells for the development of sarcoidosis was studied in a mouse model of inflammatory lung granuloma formation through embolization of PPD from Mycobacterium bovis-coated Sepharose beads into previously PPD-immunized mice. In addition the function of IL23R on myeloid cells was studied in LPS or IFNγ stimulated BMDMs and BMDCs. The mRNA and protein expression levels of relevant cytokines were analyzed by RT-PCR (TaqMan) and ELISA. The composition of immune cells in BALF was quantified by flow cytometry and alteration in granuloma sizes were observed by H&E stained lung sections. Results: Mycobacterium Ag-elicted pulmonary granulomas tend to be smaller in IL23RLysMCre mice and NF-κB dependent Th1 cytokines in the murine lungs are reduced compared to wildtype mice. In line, we observed that IL23R-deficient bone marrow-derived macrophages show a reduced production of Th1 cytokines after LPS stimulation. Conclusion: We here for the first time demonstrate a role for IL23R on myeloid cells in pulmonary inflammation and granuloma formation. Our findings provide essential insights in the pathogenesis of inflammatory lung diseases like sarcoidosis, which might be useful for the development of novel therapeutics targeting distinct immunological pathways like IL-23/IL23R.
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Affiliation(s)
- Tina Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany.,First Medical Department, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany.,Hospital Bethanien Solingen, Clinic of Pneumology and Allergology, Center for Sleep Medicine and Respiratory Care, Solingen, Germany
| | - Maren Falk-Paulsen
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Jan Kuiper
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany.,First Medical Department, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Rainer Noth
- First Medical Department, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Area Infections, Leibniz Lung Center, Borstel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany.,First Medical Department, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Burkhard Bewig
- First Medical Department, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
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9
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Kim S, Jo S, Kim MS, Shin DH. A study of Rose Bengal against a 2-keto-3-deoxy-d- manno-octulosonate cytidylyltransferase as an antibiotic candidate. J Enzyme Inhib Med Chem 2021; 35:1414-1421. [PMID: 32588669 PMCID: PMC7717453 DOI: 10.1080/14756366.2020.1751150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Frequent occurrences of multi-drug resistance of pathogenic Gram-negative bacteria threaten human beings. The CMP-2-keto-3-deoxy-d-manno-octulosonic acid biosynthesis pathway is one of the new targets for antibiotic design. 2-Keto-3-deoxy-d-manno-octulosonate cytidylyltransferase (KdsB) is the key enzyme in this pathway. KdsB proteins from Burkholderia pseudomallei (Bp), B. thailandensis (Bt), Pseudomonas aeruginosa (Pa), and Chlamydia psittaci (Cp) have been assayed to find inhibitors. Interestingly, Rose Bengal (4,5,6,7-tetrachloro-2′,4′,5′,7′-tetraiodofluorescein) was turned out to be an inhibitor of three KdsBs (BpKdsB, BtKdsB, and PaKdsB) with promising IC50 values and increased thermostability. The inhibitory enzyme kinetics of Rose Bengal revealed that it is competitive with 2-keto-3-deoxy-manno-octulosonic acid (KDO) but non-competitive against cytidine 5′-triphosphate (CTP). Induced-fit docking analysis of PaKdsB revealed that Arg160 and Arg185 together with other interactions in the substrate binding site seemed to play an important role in binding with Rose Bengal. We suggest that Rose Bengal can be used as the scaffold to develop potential antibiotics.
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Affiliation(s)
- Suwon Kim
- Graduate School of Pharmaceutical Sciences, Ewha Woman's University, Seoul, Republic of Korea
| | - Seri Jo
- Graduate School of Pharmaceutical Sciences, Ewha Woman's University, Seoul, Republic of Korea
| | - Mi-Sun Kim
- Graduate School of Pharmaceutical Sciences, Ewha Woman's University, Seoul, Republic of Korea
| | - Dong Hae Shin
- Graduate School of Pharmaceutical Sciences, Ewha Woman's University, Seoul, Republic of Korea
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10
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Bi Y, Zimmer J. Structure and Ligand-Binding Properties of the O Antigen ABC Transporter Carbohydrate-Binding Domain. Structure 2019; 28:252-258.e2. [PMID: 31879128 DOI: 10.1016/j.str.2019.11.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 11/13/2019] [Accepted: 11/27/2019] [Indexed: 10/25/2022]
Abstract
A hallmark of Gram-negative bacteria is an asymmetric outer membrane containing lipopolysaccharides (LPSs) in the extracellular leaflet. LPS molecules consist of lipid A, which is connected to the inner and outer core oligosaccharides. This LPS core structure is extended in the periplasm by the O antigen, a variable and serotype-defining polysaccharide. In the ABC transporter-dependent LPS biosynthesis pathway, the WzmWzt transporter secretes the complete O antigen across the inner membrane for ligation to the LPS core. In some O antigen transporters, the nucleotide-binding domain of Wzt is fused C-terminally to a carbohydrate-binding domain (CBD) that interacts with the O antigen chain. Here, we present the crystal structure of the Aquifex aeolicus CBD that reveals a conserved flat and a variable twisted jelly-roll surface. The CBD dimer is stabilized by mutual β strand exchange. Microbial glycan array binding studies with the isolated CBD provide insights into its interaction with complex carbohydrates.
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Affiliation(s)
- Yunchen Bi
- School of Medicine, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Jochen Zimmer
- School of Medicine, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA.
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11
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Lipinski S, Pfeuffer S, Arnold P, Treitz C, Aden K, Ebsen H, Falk-Paulsen M, Gisch N, Fazio A, Kuiper J, Luzius A, Billmann-Born S, Schreiber S, Nuñez G, Beer HD, Strowig T, Lamkanfi M, Tholey A, Rosenstiel P. Prdx4 limits caspase-1 activation and restricts inflammasome-mediated signaling by extracellular vesicles. EMBO J 2019; 38:e101266. [PMID: 31544965 PMCID: PMC6792017 DOI: 10.15252/embj.2018101266] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 08/05/2019] [Accepted: 08/21/2019] [Indexed: 12/15/2022] Open
Abstract
Inflammasomes are cytosolic protein complexes, which orchestrate the maturation of active IL‐1β by proteolytic cleavage via caspase‐1. Although many principles of inflammasome activation have been described, mechanisms that limit inflammasome‐dependent immune responses remain poorly defined. Here, we show that the thiol‐specific peroxidase peroxiredoxin‐4 (Prdx4) directly regulates IL‐1β generation by interfering with caspase‐1 activity. We demonstrate that caspase‐1 and Prdx4 form a redox‐sensitive regulatory complex via caspase‐1 cysteine 397 that leads to caspase‐1 sequestration and inactivation. Mice lacking Prdx4 show an increased susceptibility to LPS‐induced septic shock. This effect was phenocopied in mice carrying a conditional deletion of Prdx4 in the myeloid lineage (Prdx4‐ΔLysMCre). Strikingly, we demonstrate that Prdx4 co‐localizes with inflammasome components in extracellular vesicles (EVs) from inflammasome‐activated macrophages. Purified EVs are able to transmit a robust IL‐1β‐dependent inflammatory response in vitro and also in recipient mice in vivo. Loss of Prdx4 boosts the pro‐inflammatory potential of EVs. These findings identify Prdx4 as a critical regulator of inflammasome activity and provide new insights into remote cell‐to‐cell communication function of inflammasomes via macrophage‐derived EVs.
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Affiliation(s)
- Simone Lipinski
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Steffen Pfeuffer
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Philipp Arnold
- Anatomical Institute, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Christian Treitz
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-University, Kiel, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.,1st Department of Internal Medicine, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Henriette Ebsen
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Maren Falk-Paulsen
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Antonella Fazio
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Jan Kuiper
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Anne Luzius
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Susanne Billmann-Born
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Stefan Schreiber
- 1st Department of Internal Medicine, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Gabriel Nuñez
- Department of Pathology, School of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Hans-Dietmar Beer
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland.,Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mohamed Lamkanfi
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium
| | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-University, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
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12
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Kutschera A, Dawid C, Gisch N, Schmid C, Raasch L, Gerster T, Schäffer M, Smakowska-Luzan E, Belkhadir Y, Vlot AC, Chandler CE, Schellenberger R, Schwudke D, Ernst RK, Dorey S, Hückelhoven R, Hofmann T, Ranf S. Bacterial medium-chain 3-hydroxy fatty acid metabolites trigger immunity in
Arabidopsis
plants. Science 2019; 364:178-181. [DOI: 10.1126/science.aau1279] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 01/02/2019] [Accepted: 03/12/2019] [Indexed: 04/09/2023]
Abstract
A fatty acid triggers immune responses
Plants and animals respond to the microbial communities around them, whether in antagonistic or mutualistic ways. Some of these interactions are mediated by lipopolysaccharide—a large, complex, and irregular molecule on the surface of most Gram-negative bacteria. Studying the small mustard plant
Arabidopsis
, Kutschera
et al.
identified a 3-hydroxydecanoyl chain as the structural element sensed by the plant's lectin receptor kinase. Indeed, synthetic 3-hydroxydecanoic acid alone was sufficient to produce a response. A small microbial metabolite may thus suffice to trigger immune responses.
Science
, this issue p.
178
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Affiliation(s)
- Alexander Kutschera
- Chair of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
| | - Corinna Dawid
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Parkallee 1-40, 23845 Borstel, Germany
| | - Christian Schmid
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
| | - Lars Raasch
- Chair of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
| | - Tim Gerster
- Chair of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
| | - Milena Schäffer
- Chair of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
| | - Elwira Smakowska-Luzan
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Youssef Belkhadir
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - A. Corina Vlot
- Helmholtz Zentrum Muenchen, Department of Environmental Science, Institute of Biochemical Plant Pathology, 85764 Neuherberg, Germany
| | - Courtney E. Chandler
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201, USA
| | - Romain Schellenberger
- RIBP-EA 4707, SFR Condorcet-FR CNRS 3417, University of Reims Champagne-Ardenne, 51100 Reims, France
| | - Dominik Schwudke
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Parkallee 1-40, 23845 Borstel, Germany
| | - Robert K. Ernst
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201, USA
| | - Stéphan Dorey
- RIBP-EA 4707, SFR Condorcet-FR CNRS 3417, University of Reims Champagne-Ardenne, 51100 Reims, France
| | - Ralph Hückelhoven
- Chair of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
| | - Thomas Hofmann
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
| | - Stefanie Ranf
- Chair of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
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13
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Current Progress in the Structural and Biochemical Characterization of Proteins Involved in the Assembly of Lipopolysaccharide. Int J Microbiol 2018; 2018:5319146. [PMID: 30595696 PMCID: PMC6286764 DOI: 10.1155/2018/5319146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/29/2018] [Indexed: 12/25/2022] Open
Abstract
The lipid component of the outer leaflet of the outer membrane of Gram-negative bacteria is primarily composed of the glycolipid lipopolysaccharide (LPS), which serves to form a protective barrier against hydrophobic toxins and many antibiotics. LPS is comprised of three regions: the lipid A membrane anchor, the nonrepeating core oligosaccharide, and the repeating O-antigen polysaccharide. The lipid A portion is also referred to as endotoxin as its overstimulation of the toll-like receptor 4 during systemic infection precipitates potentially fatal septic shock. Because of the importance of LPS for the viability and virulence of human pathogens, understanding how LPS is synthesized and transported to the outer leaflet of the outer membrane is important for developing novel antibiotics to combat resistant Gram-negative strains. The following review describes the current state of our understanding of the proteins responsible for the synthesis and transport of LPS with an emphasis on the contribution of protein structures to our understanding of their functions. Because the lipid A portion of LPS is relatively well conserved, a detailed description of the biosynthetic enzymes in the Raetz pathway of lipid A synthesis is provided. Conversely, less well-conserved biosynthetic enzymes later in LPS synthesis are described primarily to demonstrate conserved principles of LPS synthesis. Finally, the conserved LPS transport systems are described in detail.
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14
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Di Lorenzo F, Billod JM, Martín-Santamaría S, Silipo A, Molinaro A. Gram-Negative Extremophile Lipopolysaccharides: Promising Source of Inspiration for a New Generation of Endotoxin Antagonists. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700113] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Flaviana Di Lorenzo
- Department of Chemical Sciences; University of Naples Federico II; via Cinthia 480126 80126 Naples Italy
| | - Jean-Marc Billod
- Department of Chemical and Physical Biology; CIB Centro de Investigaciones Biológicas; Ramiro de Maeztu 9 28040 Madrid Spain
| | - Sonsoles Martín-Santamaría
- Department of Chemical and Physical Biology; CIB Centro de Investigaciones Biológicas; Ramiro de Maeztu 9 28040 Madrid Spain
| | - Alba Silipo
- Department of Chemical Sciences; University of Naples Federico II; via Cinthia 480126 80126 Naples Italy
| | - Antonio Molinaro
- Department of Chemical Sciences; University of Naples Federico II; via Cinthia 480126 80126 Naples Italy
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15
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Ranf S, Gisch N, Schäffer M, Illig T, Westphal L, Knirel YA, Sánchez-Carballo PM, Zähringer U, Hückelhoven R, Lee J, Scheel D. A lectin S-domain receptor kinase mediates lipopolysaccharide sensing in Arabidopsis thaliana. Nat Immunol 2015; 16:426-33. [PMID: 25729922 DOI: 10.1038/ni.3124] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 02/11/2014] [Indexed: 12/25/2022]
Abstract
The sensing of microbe-associated molecular patterns (MAMPs) triggers innate immunity in animals and plants. Lipopolysaccharide (LPS) from Gram-negative bacteria is a potent MAMP for mammals, with the lipid A moiety activating proinflammatory responses via Toll-like receptor 4 (TLR4). Here we found that the plant Arabidopsis thaliana specifically sensed LPS of Pseudomonas and Xanthomonas. We isolated LPS-insensitive mutants defective in the bulb-type lectin S-domain-1 receptor-like kinase LORE (SD1-29), which were hypersusceptible to infection with Pseudomonas syringae. Targeted chemical degradation of LPS from Pseudomonas species suggested that LORE detected mainly the lipid A moiety of LPS. LORE conferred sensitivity to LPS onto tobacco after transient expression, which demonstrated a key function in LPS sensing and indicated the possibility of engineering resistance to bacteria in crop species.
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Affiliation(s)
- Stefanie Ranf
- 1] Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany. [2] Phytopathology, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Nicolas Gisch
- Division of Immunochemistry/Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Milena Schäffer
- Phytopathology, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Tina Illig
- Phytopathology, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Lore Westphal
- Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Yuriy A Knirel
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Patricia M Sánchez-Carballo
- Division of Immunochemistry/Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Ulrich Zähringer
- Division of Immunochemistry/Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Ralph Hückelhoven
- Phytopathology, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Justin Lee
- Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Dierk Scheel
- Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
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16
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Emptage RP, Tonthat NK, York JD, Schumacher MA, Zhou P. Structural basis of lipid binding for the membrane-embedded tetraacyldisaccharide-1-phosphate 4'-kinase LpxK. J Biol Chem 2014; 289:24059-68. [PMID: 25023290 DOI: 10.1074/jbc.m114.589986] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The membrane-bound tetraacyldisaccharide-1-phosphate 4'-kinase, LpxK, catalyzes the sixth step of the lipid A (Raetz) biosynthetic pathway and is a viable antibiotic target against emerging Gram-negative pathogens. We report the crystal structure of lipid IVA, the LpxK product, bound to the enzyme, providing a rare glimpse into interfacial catalysis and the surface scanning strategy by which many poorly understood lipid modification enzymes operate. Unlike the few previously structurally characterized proteins that bind lipid A or its precursors, LpxK binds almost exclusively to the glucosamine/phosphate moieties of the lipid molecule. Steady-state kinetic analysis of multiple point mutants of the lipid-binding pocket pinpoints critical residues involved in substrate binding, and characterization of N-terminal helix truncation mutants uncovers the role of this substructure as a hydrophobic membrane anchor. These studies make critical contributions to the limited knowledge surrounding membrane-bound enzymes that act upon lipid substrates and provide a structural template for designing small molecule inhibitors targeting this essential kinase.
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Affiliation(s)
- Ryan P Emptage
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710 and
| | - Nam K Tonthat
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710 and
| | - John D York
- the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205
| | - Maria A Schumacher
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710 and
| | - Pei Zhou
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710 and
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17
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Klein G, Kobylak N, Lindner B, Stupak A, Raina S. Assembly of lipopolysaccharide in Escherichia coli requires the essential LapB heat shock protein. J Biol Chem 2014; 289:14829-53. [PMID: 24722986 DOI: 10.1074/jbc.m113.539494] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Here, we describe two new heat shock proteins involved in the assembly of LPS in Escherichia coli, LapA and LapB (lipopolysaccharide assembly protein A and B). lapB mutants were identified based on an increased envelope stress response. Envelope stress-responsive pathways control key steps in LPS biogenesis and respond to defects in the LPS assembly. Accordingly, the LPS content in ΔlapB or Δ(lapA lapB) mutants was elevated, with an enrichment of LPS derivatives with truncations in the core region, some of which were pentaacylated and exhibited carbon chain polymorphism. Further, the levels of LpxC, the enzyme that catalyzes the first committed step of lipid A synthesis, were highly elevated in the Δ(lapA lapB) mutant. Δ(lapA lapB) mutant accumulated extragenic suppressors that mapped either to lpxC, waaC, and gmhA, or to the waaQ operon (LPS biosynthesis) and lpp (Braun's lipoprotein). Increased synthesis of either FabZ (3-R-hydroxymyristoyl acyl carrier protein dehydratase), slrA (novel RpoE-regulated non-coding sRNA), lipoprotein YceK, toxin HicA, or MurA (UDP-N-acetylglucosamine 1-carboxyvinyltransferase) suppressed some of the Δ(lapA lapB) defects. LapB contains six tetratricopeptide repeats and, at the C-terminal end, a rubredoxin-like domain that was found to be essential for its activity. In pull-down experiments, LapA and LapB co-purified with LPS, Lpt proteins, FtsH (protease), DnaK, and DnaJ (chaperones). A specific interaction was also observed between WaaC and LapB. Our data suggest that LapB coordinates assembly of proteins involved in LPS synthesis at the plasma membrane and regulates turnover of LpxC, thereby ensuring balanced biosynthesis of LPS and phospholipids consistent with its essentiality.
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Affiliation(s)
- Gracjana Klein
- From the Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland and the Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, 23845 Borstel, Germany
| | - Natalia Kobylak
- From the Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland and
| | - Buko Lindner
- the Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, 23845 Borstel, Germany
| | - Anna Stupak
- From the Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland and
| | - Satish Raina
- From the Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland and the Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, 23845 Borstel, Germany
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18
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Abstract
Lipopolysaccharide molecules represent a unique family of glycolipids based on a highly conserved lipid moiety known as lipid A. These molecules are produced by most gram-negative bacteria, in which they play important roles in the integrity of the outer-membrane permeability barrier and participate extensively in host-pathogen interplay. Few bacteria contain lipopolysaccharide molecules composed only of lipid A. In most forms, lipid A is glycosylated by addition of the core oligosaccharide that, in some bacteria, provides an attachment site for a long-chain O-antigenic polysaccharide. The complexity of lipopolysaccharide structures is reflected in the processes used for their biosynthesis and export. Rapid growth and cell division depend on the bacterial cell's capacity to synthesize and export lipopolysaccharide efficiently and in large amounts. We review recent advances in those processes, emphasizing the reactions that are essential for viability.
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Affiliation(s)
- Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada;
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19
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Emptage RP, Pemble CW, York JD, Raetz CRH, Zhou P. Mechanistic characterization of the tetraacyldisaccharide-1-phosphate 4'-kinase LpxK involved in lipid A biosynthesis. Biochemistry 2013; 52:2280-90. [PMID: 23464738 DOI: 10.1021/bi400097z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The sixth step in the lipid A biosynthetic pathway involves phosphorylation of the tetraacyldisaccharide-1-phosphate (DSMP) intermediate by the cytosol-facing inner membrane kinase LpxK, a member of the P-loop-containing nucleoside triphosphate (NTP) hydrolase superfamily. We report the kinetic characterization of LpxK from Aquifex aeolicus and the crystal structures of LpxK in complex with ATP in a precatalytic binding state, the ATP analogue AMP-PCP in the closed catalytically competent conformation, and a chloride anion revealing an inhibitory conformation of the nucleotide-binding P-loop. We demonstrate that LpxK activity in vitro requires the presence of a detergent micelle and formation of a ternary LpxK-ATP/Mg(2+)-DSMP complex. Using steady-state kinetics, we have identified crucial active site residues, leading to the proposal that the interaction of D99 with H261 acts to increase the pKa of the imidazole moiety, which in turn serves as the catalytic base to deprotonate the 4'-hydroxyl of the DSMP substrate. The fact that an analogous mechanism has not yet been observed for other P-loop kinases highlights LpxK as a distinct member of the P-loop kinase family, a notion that is also reflected through its localization at the membrane, lipid substrate, and overall structure.
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Affiliation(s)
- Ryan P Emptage
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.
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20
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Guiral M, Prunetti L, Aussignargues C, Ciaccafava A, Infossi P, Ilbert M, Lojou E, Giudici-Orticoni MT. The hyperthermophilic bacterium Aquifex aeolicus: from respiratory pathways to extremely resistant enzymes and biotechnological applications. Adv Microb Physiol 2013; 61:125-94. [PMID: 23046953 DOI: 10.1016/b978-0-12-394423-8.00004-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aquifex aeolicus isolated from a shallow submarine hydrothermal system belongs to the order Aquificales which constitute an important component of the microbial communities at elevated temperatures. This hyperthermophilic chemolithoautotrophic bacterium, which utilizes molecular hydrogen, molecular oxygen, and inorganic sulfur compounds to flourish, uses the reductive TCA cycle for CO(2) fixation. In this review, the intricate energy metabolism of A. aeolicus is described. As the chemistry of sulfur is complex and multiple sulfur species can be generated, A. aeolicus possesses a multitude of different enzymes related to the energy sulfur metabolism. It contains also membrane-embedded [NiFe] hydrogenases as well as oxidases enzymes involved in hydrogen and oxygen utilization. We have focused on some of these proteins that have been extensively studied and characterized as super-resistant enzymes with outstanding properties. We discuss the potential use of hydrogenases in an attractive H(2)/O(2) biofuel cell in replacement of chemical catalysts. Using complete genomic sequence and biochemical data, we present here a global view of the energy-generating mechanisms of A. aeolicus including sulfur compounds reduction and oxidation pathways as well as hydrogen and oxygen utilization.
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Affiliation(s)
- Marianne Guiral
- Unité de Bioénergétique et Ingénierie des Protéines, UMR7281-FR3479, CNRS, Aix-Marseille Université, Marseille, France.
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Eveleigh RJ, Meehan CJ, Archibald JM, Beiko RG. Being Aquifex aeolicus: Untangling a hyperthermophile's checkered past. Genome Biol Evol 2013; 5:2478-97. [PMID: 24281050 PMCID: PMC3879981 DOI: 10.1093/gbe/evt195] [Citation(s) in RCA: 20] [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] [Accepted: 11/22/2013] [Indexed: 12/20/2022] Open
Abstract
Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyperthermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Previous phylogenomic analyses focused on Aquifex aeolicus identified Thermotogae and Aquificae either as successive early branches or sisters in a rooted bacterial phylogeny, but many phylogenies and cellular traits have suggested a stronger affiliation with the Epsilonproteobacteria. Different scenarios for the evolution of the Aquificae yield different phylogenetic predictions. Here, we outline these scenarios and consider the fit of the available data, including three sequenced Aquificae genomes, to different sets of predictions. Evidence from phylogenetic profiles and trees suggests that the Epsilonproteobacteria have the strongest affinities with the three Aquificae analyzed. However, this pattern is shown by only a minority of encoded proteins, and the Archaea, many lineages of thermophilic bacteria, and members of genus Clostridium and class Deltaproteobacteria also show strong connections to the Aquificae. The phylogenetic affiliations of different functional subsystems showed strong biases: Most but not all genes implicated in the core translational apparatus tended to group Aquificae with Thermotogae, whereas a wide range of metabolic and cellular processes strongly supported the link between Aquificae and Epsilonproteobacteria. Depending on which sets of genes are privileged, either Thermotogae or Epsilonproteobacteria is the most plausible adjacent lineage to the Aquificae. Both scenarios require massive sharing of genes to explain the history of this enigmatic group, whose history is further complicated by specific affinities of different members of Aquificae to different partner lineages.
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Affiliation(s)
- Robert J.M. Eveleigh
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Conor J. Meehan
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - John M. Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Robert G. Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
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Platelet factor 4 binding to lipid A of Gram-negative bacteria exposes PF4/heparin-like epitopes. Blood 2012; 120:3345-52. [DOI: 10.1182/blood-2012-06-434985] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
AbstractThe positively charged chemokine platelet factor 4 (PF4) forms immunogenic complexes with heparin and other polyanions. Resulting antibodies can induce the adverse drug effect heparin-induced thrombocytopenia. PF4 also binds to bacteria, thereby exposing the same neoantigen(s) as with heparin. In this study, we identified the negatively charged lipopolysaccharide (LPS) as the PF4 binding structure on Gram-negative bacteria. We demonstrate by flow cytometry that mutant bacteria with progressively truncated LPS structures show increasingly enhanced PF4 binding activity. PF4 bound strongest to mutants lacking the O-antigen and core structure of LPS, but still exposing lipid A on their surfaces. Strikingly, PF4 bound more efficiently to bisphosphorylated lipid A than to monophosphorylated lipid A, suggesting that phosphate residues of lipid A mediate PF4 binding. Interactions of PF4 with Gram-negative bacteria, where only the lipid A part of LPS is exposed, induce epitopes on PF4 resembling those on PF4/heparin complexes as shown by binding of human anti-PF4/heparin antibodies. As both the lipid A on the surface of Gram-negative bacteria and the amino acids of PF4 contributing to polyanion binding are highly conserved, our results further support the hypothesis that neoepitope formation on PF4 after binding to bacteria is an ancient host defense mechanism.
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Crystal structure of LpxK, the 4'-kinase of lipid A biosynthesis and atypical P-loop kinase functioning at the membrane interface. Proc Natl Acad Sci U S A 2012; 109:12956-61. [PMID: 22826246 DOI: 10.1073/pnas.1206072109] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
In Gram-negative bacteria, the hydrophobic anchor of the outer membrane lipopolysaccharide is lipid A, a saccharolipid that plays key roles in both viability and pathogenicity of these organisms. The tetraacyldisaccharide 4'-kinase (LpxK) of the diverse P-loop-containing nucleoside triphosphate hydrolase superfamily catalyzes the sixth step in the biosynthetic pathway of lipid A, and is the only known P-loop kinase to act upon a lipid substrate at the membrane. Here, we report the crystal structures of apo- and ADP/Mg(2+)-bound forms of Aquifex aeolicus LpxK to a resolution of 1.9 Å and 2.2 Å, respectively. LpxK consists of two α/β/α sandwich domains connected by a two-stranded β-sheet linker. The N-terminal domain, which has most structural homology to other family members, is responsible for catalysis at the P-loop and positioning of the disaccharide-1-phosphate substrate for phosphoryl transfer on the inner membrane. The smaller C-terminal domain, a substructure unique to LpxK, helps bind the nucleotide substrate and Mg(2+) cation using a 25° hinge motion about its base. Activity was severely reduced in alanine point mutants of conserved residues D138 and D139, which are not directly involved in ADP or Mg(2+) binding in our structures, indicating possible roles in phosphoryl acceptor positioning or catalysis. Combined structural and kinetic studies have led to an increased understanding of the enzymatic mechanism of LpxK and provided the framework for structure-based antimicrobial design.
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Structural and mechanistic analysis of the membrane-embedded glycosyltransferase WaaA required for lipopolysaccharide synthesis. Proc Natl Acad Sci U S A 2012; 109:6253-8. [PMID: 22474366 DOI: 10.1073/pnas.1119894109] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
WaaA is a key enzyme in the biosynthesis of LPS, a critical component of the outer envelope of Gram-negative bacteria. Embedded in the cytoplasmic face of the inner membrane, WaaA catalyzes the transfer of 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) to the lipid A precursor of LPS. Here we present crystal structures of the free and CMP-bound forms of WaaA from Aquifex aeolicus, an ancient Gram-negative hyperthermophile. These structures reveal details of the CMP-binding site and implicate a unique sequence motif (GGS/TX(5)GXNXLE) in Kdo binding. In addition, a cluster of highly conserved amino acid residues was identified which represents the potential membrane-attachment and acceptor-substrate binding site of WaaA. A series of site-directed mutagenesis experiments revealed critical roles for glycine 30 and glutamate 31 in Kdo transfer. Our results provide the structural basis of a critical reaction in LPS biosynthesis and allowed the development of a detailed model of the catalytic mechanism of WaaA.
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25
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Schmidt H, Mesters JR, Wu J, Woodard RW, Hilgenfeld R, Mamat U. Evidence for a two-metal-ion mechanism in the cytidyltransferase KdsB, an enzyme involved in lipopolysaccharide biosynthesis. PLoS One 2011; 6:e23231. [PMID: 21826242 PMCID: PMC3149649 DOI: 10.1371/journal.pone.0023231] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 07/13/2011] [Indexed: 01/22/2023] Open
Abstract
Lipopolysaccharide (LPS) is located on the surface of Gram-negative bacteria and is responsible for maintaining outer membrane stability, which is a prerequisite for cell survival. Furthermore, it represents an important barrier against hostile environmental factors such as antimicrobial peptides and the complement cascade during Gram-negative infections. The sugar 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) is an integral part of LPS and plays a key role in LPS functionality. Prior to its incorporation into the LPS molecule, Kdo has to be activated by the CMP-Kdo synthetase (CKS). Based on the presence of a single Mg2+ ion in the active site, detailed models of the reaction mechanism of CKS have been developed previously. Recently, a two-metal-ion hypothesis suggested the involvement of two Mg2+ ions in Kdo activation. To further investigate the mechanistic aspects of Kdo activation, we kinetically characterized the CKS from the hyperthermophilic organism Aquifex aeolicus. In addition, we determined the crystal structure of this enzyme at a resolution of 2.10 Å and provide evidence that two Mg2+ ions are part of the active site of the enzyme.
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Affiliation(s)
- Helgo Schmidt
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany
| | - Jeroen R. Mesters
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany
| | - Jing Wu
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ronald W. Woodard
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany
- Laboratory for Structural Biology of Infection and Inflammation, DESY, Hamburg, Germany
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (RH); (UM)
| | - Uwe Mamat
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
- * E-mail: (RH); (UM)
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26
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Sutcliffe IC. A phylum level perspective on bacterial cell envelope architecture. Trends Microbiol 2010; 18:464-70. [DOI: 10.1016/j.tim.2010.06.005] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 05/04/2010] [Accepted: 06/18/2010] [Indexed: 01/03/2023]
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Chung HS, Raetz CRH. Interchangeable domains in the Kdo transferases of Escherichia coli and Haemophilus influenzae. Biochemistry 2010; 49:4126-37. [PMID: 20394418 DOI: 10.1021/bi100343e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Kdo(2)-lipid A, a conserved substructure of lipopolysaccharide, plays critical roles in Gram-negative bacterial survival and interaction with host organisms. Inhibition of Kdo biosynthesis in Escherichia coli results in cell death and accumulation of the tetra-acylated precursor lipid IV(A). E. coli KdtA (EcKdtA) is a bifunctional enzyme that transfers two Kdo units from two CMP-Kdo molecules to lipid IV(A). In contrast, Haemophilus influenzae KdtA (HiKdtA) transfers only one Kdo unit. E. coli CMR300, which lacks Kdo transferase because of a deletion in kdtA, can be rescued to grow in broth at 37 degrees C if multiple copies of msbA are provided in trans. MsbA, the inner membrane transporter for nascent lipopolysaccharide, prefers hexa-acylated to tetra-acylated lipid A, but with the excess MsbA present in CMR300, lipid IV(A) is efficiently exported to the outer membrane. CMR300 is hypersensitive to hydrophobic antibiotics and bile salts and does not grow at 42 degrees C. Expressing HiKdtA in CMR300 results in the accumulation of Kdo-lipid IV(A) in place of lipid IV(A) without suppression of its growth phenotypes at 30 degrees C. EcKdtA restores intact lipopolysaccharide, together with normal antibiotic resistance, detergent resistance, and growth at 42 degrees C. To determine which residues are important for the mono- or bifunctional character of KdtA, protein chimeras were constructed using EcKdtA and HiKdtA. These chimeras, which are catalytically active, were characterized by in vitro assays and in vivo complementation. The N-terminal half of KdtA, especially the first 30 amino acid residues, specifies whether one or two Kdo units are transferred to lipid IV(A).
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Affiliation(s)
- Hak Suk Chung
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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28
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Wirth R, Sikorski J, Brambilla E, Misra M, Lapidus A, Copeland A, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Han C, Detter JC, Tapia R, Bruce D, Goodwin L, Pitluck S, Pati A, Anderson I, Ivanova N, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Bilek Y, Hader T, Land M, Hauser L, Chang YJ, Jeffries CD, Tindall BJ, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Thermocrinis albus type strain (HI 11/12). Stand Genomic Sci 2010; 2:194-202. [PMID: 21304702 PMCID: PMC3035279 DOI: 10.4056/sigs.761490] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Thermocrinis albus Eder and Huber 2002 is one of three species in the genus Thermocrinis in the family Aquificaceae. Members of this family have become of significant interest because of their involvement in global biogeochemical cycles in high-temperature ecosystems. This interest had already spurred several genome sequencing projects for members of the family. We here report the first completed genome sequence a member of the genus Thermocrinis and the first type strain genome from a member of the family Aquificaceae. The 1,500,577 bp long genome with its 1,603 protein-coding and 47 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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29
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Cipolla L, Gabrielli L, Bini D, Russo L, Shaikh N. Kdo: a critical monosaccharide for bacteria viability. Nat Prod Rep 2010; 27:1618-29. [DOI: 10.1039/c004750n] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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