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Manhas R, Rathore A, Havelikar U, Mahajan S, Gandhi SG, Mahapa A. Uncovering the potentiality of quinazoline derivatives against Pseudomonas aeruginosa with antimicrobial synergy and SAR analysis. J Antibiot (Tokyo) 2024; 77:365-381. [PMID: 38514856 DOI: 10.1038/s41429-024-00717-3] [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: 08/17/2023] [Revised: 02/10/2024] [Accepted: 02/27/2024] [Indexed: 03/23/2024]
Abstract
Antimicrobial resistance has emerged as a covert global health crisis, posing a significant threat to humanity. If left unaddressed, it is poised to become the foremost cause of mortality worldwide. Among the multitude of resistant bacterial pathogens, Pseudomonas aeruginosa, a Gram-negative, facultative bacterium, has been responsible for mild to deadly infections. It is now enlisted as a global critical priority pathogen by WHO. Urgent measures are required to combat this formidable pathogen, necessitating the development of novel anti-pseudomonal drugs. To confront this pressing issue, we conducted an extensive screening of 3561 compounds from the ChemDiv library, resulting in the discovery of potent anti-pseudomonal quinazoline derivatives. Among the identified compounds, IDD-8E has emerged as a lead molecule, exhibiting exceptional efficacy against P. aeruginosa while displaying no cytotoxicity. Moreover, IDD-8E demonstrated significant pseudomonal killing, disruption of pseudomonal biofilm and other anti-bacterial properties comparable to a well-known antibiotic rifampicin. Additionally, IDD-8E's synergy with different antibiotics further strengthens its potential as a powerful anti-pseudomonal agent. IDD-8E also exhibited significant antimicrobial efficacy against other ESKAPE pathogens. Moreover, we elucidated the Structure-Activity-Relationship (SAR) of IDD-8E targeting the essential WaaP protein in P. aeruginosa. Altogether, our findings emphasize the promise of IDD-8E as a clinical candidate for novel anti-pseudomonal drugs, offering hope in the battle against antibiotic resistance and its devastating impact on global health.
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Affiliation(s)
- Rakshit Manhas
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India
| | - Arti Rathore
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ujwal Havelikar
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India
| | - Shavi Mahajan
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India
| | - Sumit G Gandhi
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Avisek Mahapa
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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2
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Cummings RD. A periodic table of monosaccharides. Glycobiology 2024; 34:cwad088. [PMID: 37935401 DOI: 10.1093/glycob/cwad088] [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: 09/11/2023] [Revised: 10/23/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023] Open
Abstract
It is important to recognize the great diversity of monosaccharides commonly encountered in animals, plants, and microbes, as well as to organize them in a visually interesting style that also emphasizes their similarities and relatedness. This article discusses the nature of building blocks, monosaccharides, and monosaccharide derivatives-terms commonly used in discussing "glycomolecules" found in nature. To aid in awareness of monosaccharide diversity, here is presented a Periodic Table of Monosaccharides. The rationale is given for construction of the Table and the selection of 103 monosaccharides, which is largely based on those presented in the KEGG and SNFG websites of monosaccharides, and includes room to enlarge as new discoveries are made. The Table should have educational value and is intended to capture the attention and foster imagination of those not very familiar with glycosciences, and encourage researchers to delve deeper into this fascinating area.
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Affiliation(s)
- Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087-3 Blackfan Circle, Boston, MA 02115, United States
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3
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Ghenu AH, Amado A, Gordo I, Bank C. Epistasis decreases with increasing antibiotic pressure but not temperature. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220058. [PMID: 37004727 PMCID: PMC10067269 DOI: 10.1098/rstb.2022.0058] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
Predicting mutational effects is essential for the control of antibiotic resistance (ABR). Predictions are difficult when there are strong genotype-by-environment (G × E), gene-by-gene (G × G or epistatic) or gene-by-gene-by-environment (G × G × E) interactions. We quantified G × G × E effects in Escherichia coli across environmental gradients. We created intergenic fitness landscapes using gene knock-outs and single-nucleotide ABR mutations previously identified to vary in the extent of G × E effects in our environments of interest. Then, we measured competitive fitness across a complete combinatorial set of temperature and antibiotic dosage gradients. In this way, we assessed the predictability of 15 fitness landscapes across 12 different but related environments. We found G × G interactions and rugged fitness landscapes in the absence of antibiotic, but as antibiotic concentration increased, the fitness effects of ABR genotypes quickly overshadowed those of gene knock-outs, and the landscapes became smoother. Our work reiterates that some single mutants, like those conferring resistance or susceptibility to antibiotics, have consistent effects across genetic backgrounds in stressful environments. Thus, although epistasis may reduce the predictability of evolution in benign environments, evolution may be more predictable in adverse environments. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- Ana-Hermina Ghenu
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2780-156, Portugal
- Division of Theoretical Ecology and Evolution, Institut für Ökologie und Evolution, Universität Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - André Amado
- Division of Theoretical Ecology and Evolution, Institut für Ökologie und Evolution, Universität Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2780-156, Portugal
| | - Claudia Bank
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2780-156, Portugal
- Division of Theoretical Ecology and Evolution, Institut für Ökologie und Evolution, Universität Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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4
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Panteleev PV, Safronova VN, Kruglikov RN, Bolosov IA, Ovchinnikova TV. Genomic Insights into Bacterial Resistance to Proline-Rich Antimicrobial Peptide Bac7. MEMBRANES 2023; 13:438. [PMID: 37103865 PMCID: PMC10145973 DOI: 10.3390/membranes13040438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/10/2023] [Accepted: 04/16/2023] [Indexed: 06/19/2023]
Abstract
Proline-rich antimicrobial peptides (PrAMPs) having a potent antimicrobial activity and a modest toxicity toward mammalian cells attract much attention as new templates for the development of antibiotic drugs. However, a comprehensive understanding of mechanisms of bacterial resistance development to PrAMPs is necessary before their clinical application. In this study, development of the resistance to the proline-rich bovine cathelicidin Bac71-22 derivative was characterized in the multidrug-resistant Escherichia coli clinical isolate causing the urinary tract infection. Three Bac71-22-resistant strains with ≥16-fold increase in minimal inhibitory concentrations (MICs) were selected by serially passaging after four-week experimental evolution. It was shown that in salt-containing medium, the resistance was mediated by inactivation of the SbmA transporter. The absence of salt in the selection media affected both dynamics and main molecular targets under selective pressure: a point mutation leading to the amino acid substitution N159H in the WaaP kinase responsible for heptose I phosphorylation in the LPS structure was also found. This mutation led to a phenotype with a decreased susceptibility to both the Bac71-22 and polymyxin B. Screening of antimicrobial activities with the use of a wide panel of known AMPs, including the human cathelicidin LL-37 and conventional antibiotics, against selected strains indicated no significant cross-resistance effects.
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5
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Laffargue T, Moulis C, Remaud-Simeon M. Phosphorylated polysaccharides: Applications, natural abundance, and new-to-nature structures generated by chemical and enzymatic functionalization. Biotechnol Adv 2023; 65:108140. [PMID: 36958536 DOI: 10.1016/j.biotechadv.2023.108140] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/14/2023] [Accepted: 03/18/2023] [Indexed: 03/25/2023]
Abstract
Polysaccharides are foreseen as serious candidates for the future generation of polymers, as they are biosourced and biodegradable materials. Their functionalisation is an attractive way to modify their properties, thereby increasing their range of applications. Introduction of phosphate groups in polysaccharide chains for the stimulation of the immune system was first described in the nineteen seventies. Since then, the use of phosphorylated polysaccharides has been proposed in various domains, such as healthcare, water treatment, cosmetic, biomaterials, etc. These alternative usages capitalize on newly acquired physico-chemical or biological properties, leading to materials as diverse as flame-resistant agents or drug delivery systems. Phosphorylated polysaccharides are found in Nature and need to be extracted to assess their biological potential. However, they are not abundant, often present complex backbones hard to characterize, and most of them have a low phosphate content. These drawbacks have pushed forward the development of chemical phosphorylation employing a wide variety of phosphorylating agents to obtain polysaccharides with a large range of phosphate content. Chemical phosphorylation requires the use of harsh conditions and toxic, petroleum-based solvents, which hinders their exploitation in the food and health industry. Over the last 20 years, although enzymes are regiospecific catalysts that work in aqueous and mild conditions, enzymatic phosphorylation has been little investigated. To date, only three families of enzymes have been used for the in vitro phosphorylation of polysaccharides. Considering the number of unresolved metabolic pathways leading to phosphorylated polysaccharides, the huge diversity of kinase sequences, and the recent progress in protein engineering one can envision native and engineered kinases as promising tools for polysaccharide phosphorylation.
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Affiliation(s)
- Thibaud Laffargue
- Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 135, Avenue de Rangueil, CEDEX 04, F-31077 Toulouse, France
| | - Claire Moulis
- Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 135, Avenue de Rangueil, CEDEX 04, F-31077 Toulouse, France
| | - Magali Remaud-Simeon
- Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 135, Avenue de Rangueil, CEDEX 04, F-31077 Toulouse, France.
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6
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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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7
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Palmieri E, Arato V, Oldrini D, Ricchetti B, Aruta MG, Pansegrau W, Marchi S, Giusti F, Ferlenghi I, Rossi O, Alfini R, Giannelli C, Gasperini G, Necchi F, Micoli F. Stability of Outer Membrane Vesicles-Based Vaccines, Identifying the Most Appropriate Methods to Detect Changes in Vaccine Potency. Vaccines (Basel) 2021; 9:229. [PMID: 33800727 PMCID: PMC7998687 DOI: 10.3390/vaccines9030229] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 01/15/2023] Open
Abstract
Ensuring the stability of vaccines is crucial to successfully performing global immunization programs. Outer Membrane Vesicles (OMV) are receiving great attention as vaccine platforms. OMV are complex molecules and few data have been collected so far on their stability. OMV produced by bacteria, genetically modified to increase their spontaneous release, simplifying their production, are also known as Generalized Modules for Membrane Antigens (GMMA). We have performed accelerated stability studies on GMMA from different pathogens and verified the ability of physico-chemical and immunological methods to detect possible changes. High-temperature conditions (100 °C for 40 min) did not affect GMMA stability and immunogenicity in mice, in contrast to the effect of milder temperatures for a longer period of time (37 °C or 50 °C for 4 weeks). We identified critical quality attributes to monitor during stability assessment that could impact vaccine efficacy. In particular, specific recognition of antigens by monoclonal antibodies through competitive ELISA assays may replace in vivo tests for the potency assessment of GMMA-based vaccines.
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Affiliation(s)
- Elena Palmieri
- GSK Vaccines Institute for Global Health (GVGH) S.r.l., Via Fiorentina 1, 53100 Siena, Italy; (E.P.); (V.A.); (D.O.); (B.R.); (M.G.A.); (O.R.); (R.A.); (C.G.); (G.G.); (F.N.)
| | - Vanessa Arato
- GSK Vaccines Institute for Global Health (GVGH) S.r.l., Via Fiorentina 1, 53100 Siena, Italy; (E.P.); (V.A.); (D.O.); (B.R.); (M.G.A.); (O.R.); (R.A.); (C.G.); (G.G.); (F.N.)
| | - Davide Oldrini
- GSK Vaccines Institute for Global Health (GVGH) S.r.l., Via Fiorentina 1, 53100 Siena, Italy; (E.P.); (V.A.); (D.O.); (B.R.); (M.G.A.); (O.R.); (R.A.); (C.G.); (G.G.); (F.N.)
| | - Beatrice Ricchetti
- GSK Vaccines Institute for Global Health (GVGH) S.r.l., Via Fiorentina 1, 53100 Siena, Italy; (E.P.); (V.A.); (D.O.); (B.R.); (M.G.A.); (O.R.); (R.A.); (C.G.); (G.G.); (F.N.)
| | - Maria Grazia Aruta
- GSK Vaccines Institute for Global Health (GVGH) S.r.l., Via Fiorentina 1, 53100 Siena, Italy; (E.P.); (V.A.); (D.O.); (B.R.); (M.G.A.); (O.R.); (R.A.); (C.G.); (G.G.); (F.N.)
| | - Werner Pansegrau
- GSK, Via Fiorentina 1, 53100 Siena, Italy; (W.P.); (S.M.); (F.G.); (I.F.)
| | - Sara Marchi
- GSK, Via Fiorentina 1, 53100 Siena, Italy; (W.P.); (S.M.); (F.G.); (I.F.)
| | - Fabiola Giusti
- GSK, Via Fiorentina 1, 53100 Siena, Italy; (W.P.); (S.M.); (F.G.); (I.F.)
| | - Ilaria Ferlenghi
- GSK, Via Fiorentina 1, 53100 Siena, Italy; (W.P.); (S.M.); (F.G.); (I.F.)
| | - Omar Rossi
- GSK Vaccines Institute for Global Health (GVGH) S.r.l., Via Fiorentina 1, 53100 Siena, Italy; (E.P.); (V.A.); (D.O.); (B.R.); (M.G.A.); (O.R.); (R.A.); (C.G.); (G.G.); (F.N.)
| | - Renzo Alfini
- GSK Vaccines Institute for Global Health (GVGH) S.r.l., Via Fiorentina 1, 53100 Siena, Italy; (E.P.); (V.A.); (D.O.); (B.R.); (M.G.A.); (O.R.); (R.A.); (C.G.); (G.G.); (F.N.)
| | - Carlo Giannelli
- GSK Vaccines Institute for Global Health (GVGH) S.r.l., Via Fiorentina 1, 53100 Siena, Italy; (E.P.); (V.A.); (D.O.); (B.R.); (M.G.A.); (O.R.); (R.A.); (C.G.); (G.G.); (F.N.)
| | - Gianmarco Gasperini
- GSK Vaccines Institute for Global Health (GVGH) S.r.l., Via Fiorentina 1, 53100 Siena, Italy; (E.P.); (V.A.); (D.O.); (B.R.); (M.G.A.); (O.R.); (R.A.); (C.G.); (G.G.); (F.N.)
| | - Francesca Necchi
- GSK Vaccines Institute for Global Health (GVGH) S.r.l., Via Fiorentina 1, 53100 Siena, Italy; (E.P.); (V.A.); (D.O.); (B.R.); (M.G.A.); (O.R.); (R.A.); (C.G.); (G.G.); (F.N.)
| | - Francesca Micoli
- GSK Vaccines Institute for Global Health (GVGH) S.r.l., Via Fiorentina 1, 53100 Siena, Italy; (E.P.); (V.A.); (D.O.); (B.R.); (M.G.A.); (O.R.); (R.A.); (C.G.); (G.G.); (F.N.)
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8
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Rcs Phosphorelay Responses to Truncated Lipopolysaccharide-Induced Cell Envelope Stress in Yersinia enterocolitica. Molecules 2020; 25:molecules25235718. [PMID: 33287412 PMCID: PMC7730088 DOI: 10.3390/molecules25235718] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 01/22/2023] Open
Abstract
Lipopolysaccharide (LPS) is the major component of the outer membrane of Gram-negative bacteria, and its integrity is monitored by various stress response systems. Although the Rcs system is involved in the envelope stress response and regulates genes controlling numerous bacterial cell functions of Yersinia enterocolitica, whether it can sense the truncated LPS in Y. enterocolitica remains unclear. In this study, the deletion of the Y. enterocolitica waaF gene truncated the structure of LPS and produced a deep rough LPS. The truncated LPS increased the cell surface hydrophobicity and outer membrane permeability, generating cell envelope stress. The truncated LPS also directly exposed the smooth outer membrane to the external environment and attenuated the resistance to adverse conditions, such as impaired survival under polymyxin B and sodium dodecyl sulfate (SDS) exposure. Further phenotypic experiment and gene expression analysis indicated that the truncated LPS was correlated with the activation of the Rcs phosphorelay, thereby repressing cell motility and biofilm formation. Our findings highlight the importance of LPS integrity in maintaining membrane function and broaden the understanding of Rcs phosphorelay signaling in response to cell envelope stress, thus opening new avenues to develop effective antimicrobial agents for combating Y. enterocolitica infections.
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Wu IW, Gao SS, Chou HC, Yang HY, Chang LC, Kuo YL, Dinh MCV, Chung WH, Yang CW, Lai HC, Hsieh WP, Su SC. Integrative metagenomic and metabolomic analyses reveal severity-specific signatures of gut microbiota in chronic kidney disease. Am J Cancer Res 2020; 10:5398-5411. [PMID: 32373220 PMCID: PMC7196299 DOI: 10.7150/thno.41725] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 03/24/2020] [Indexed: 01/09/2023] Open
Abstract
Chronic kidney disease (CKD) is a serious healthcare dilemma, associated with specific changes in gut microbiota and circulating metabolome. Yet, the functional capacity of CKD microbiome and its intricate relationship with the host metabolism at different stages of disease are less understood. Methods: Here, shotgun sequencing of fecal samples and targeted metabolomics profiling of serum bile acids, short- and medium-chain fatty acids, and uremic solutes were performed in a cohort of CKD patients with different severities and non-CKD controls. Results: We identified that levels of 13 microbial species and 6 circulating metabolites were significantly altered across early to advanced stages or only in particular stage(s). Among these, Prevotella sp. 885 (decreased) was associated with urea excretion, while caproic acid (decreased) and p-cresyl sulfate (elevated) were positively and negatively correlated with the glomerular filtration rate, respectively. In addition, we identified gut microbial species linked to changes in circulating metabolites. Microbial genes related to secondary bile acid biosynthesis were differentially abundant at the early stage, while pathway modules related to lipid metabolism and lipopolysaccharide biosynthesis were enriched in the CKD microbiome at the advanced stage, suggesting that changes in microbial metabolism and host inflammation may contribute to renal health. Further, we identified metagenomic and metabolomic markers to discriminate cases of different severities from the controls, among which Bacteroides eggerthii individually was of particular value in early diagnosis. Conclusions: Our dual-omics data reveal the connections between intestinal microbes and circulating metabolites perturbed in CKD, which may be of etiological and diagnostic importance.
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Abstract
The cell envelope is the first line of defense between a bacterium and the world-at-large. Often, the initial steps that determine the outcome of chemical warfare, bacteriophage infections, and battles with other bacteria or the immune system greatly depend on the structure and composition of the bacterial cell surface. One of the most studied bacterial surface molecules is the glycolipid known as lipopolysaccharide (LPS), which is produced by most Gram-negative bacteria. Much of the initial attention LPS received in the early 1900s was owed to its ability to stimulate the immune system, for which the glycolipid was commonly known as endotoxin. It was later discovered that LPS also creates a permeability barrier at the cell surface and is a main contributor to the innate resistance that Gram-negative bacteria display against many antimicrobials. Not surprisingly, these important properties of LPS have driven a vast and still prolific body of literature for more than a hundred years. LPS research has also led to pioneering studies in bacterial envelope biogenesis and physiology, mostly using Escherichia coli and Salmonella as model systems. In this review, we will focus on the fundamental knowledge we have gained from studies of the complex structure of the LPS molecule and the biochemical pathways for its synthesis, as well as the transport of LPS across the bacterial envelope and its assembly at the cell surface.
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11
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Kreamer NNK, Chopra R, Caughlan RE, Fabbro D, Fang E, Gee P, Hunt I, Li M, Leon BC, Muller L, Vash B, Woods AL, Stams T, Dean CR, Uehara T. Acylated-acyl carrier protein stabilizes the Pseudomonas aeruginosa WaaP lipopolysaccharide heptose kinase. Sci Rep 2018; 8:14124. [PMID: 30237436 PMCID: PMC6147952 DOI: 10.1038/s41598-018-32379-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 09/06/2018] [Indexed: 12/13/2022] Open
Abstract
Phosphorylation of Pseudomonas aeruginosa lipopolysaccharide (LPS) is important for maintaining outer membrane integrity and intrinsic antibiotic resistance. We solved the crystal structure of the LPS heptose kinase WaaP, which is essential for growth of P. aeruginosa. WaaP was structurally similar to eukaryotic protein kinases and, intriguingly, was complexed with acylated-acyl carrier protein (acyl-ACP). WaaP produced by in vitro transcription-translation was insoluble unless acyl-ACP was present. WaaP variants designed to perturb the acyl-ACP interaction were less stable in cells and exhibited reduced kinase function. Mass spectrometry identified myristyl-ACP as the likely physiological binding partner for WaaP in P. aeruginosa. Together, these results demonstrate that acyl-ACP is required for WaaP protein solubility and kinase function. To the best of our knowledge, this is the first report describing acyl-ACP in the role of a cofactor necessary for the production and stability of a protein partner.
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Affiliation(s)
- Naomi N K Kreamer
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | - Rajiv Chopra
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA.
| | - Ruth E Caughlan
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | - Doriano Fabbro
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Eric Fang
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | - Patricia Gee
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Ian Hunt
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Min Li
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | - Barbara C Leon
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | - Lionel Muller
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Brian Vash
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Angela L Woods
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | - Travis Stams
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Charles R Dean
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | - Tsuyoshi Uehara
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, CA, USA.
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12
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Mulla RS, Beecroft MS, Pal R, Aguilar JA, Pitarch-Jarque J, García-España E, Lurie-Luke E, Sharples GJ, Gareth Williams JA. On the Antibacterial Activity of Azacarboxylate Ligands: Lowered Metal Ion Affinities for Bis-amide Derivatives of EDTA do not mean Reduced Activity. Chemistry 2018; 24:7137-7148. [PMID: 29570870 DOI: 10.1002/chem.201800026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Indexed: 12/23/2022]
Abstract
EDTA is widely used as an inhibitor of bacterial growth, affecting the uptake and control of metal ions by microorganisms. We describe the synthesis and characterisation of two symmetrical bis-amide derivatives of EDTA, featuring glycyl or pyridyl substituents: AmGly2 and AmPy2 . Metal ion affinities (logK) have been evaluated for a range of metals (Mg2+ , Ca2+ , Fe3+ , Mn2+ , Zn2+ ), revealing less avid binding compared to EDTA. The solid-state structures of AmGly2 and of its Mg2+ complex have been determined crystallographically. The latter shows an unusual 7-coordinate, capped octahedral Mg2+ centre. The antibacterial activities of the two ligands and of EDTA have been evaluated against a range of health-relevant bacterial species, three Gram negative (Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumoniae) and a Gram positive (Staphylococcus aureus). The AmPy2 ligand is the only one that displays a significant inhibitory effect against K. pneumoniae, but is less effective against the other organisms. AmGly2 exhibits a more powerful inhibitory effect against E. coli at lower concentrations than EDTA (<3 mm) or AmPy2 , but loses its efficacy at higher concentrations. The growth inhibition of EDTA and AmGly2 on mutant E. coli strains with defects in outer-membrane lipopolysaccharide (LPS) structures has been assessed to provide insight into the unexpected behaviour. Taken together, the results contradict the assumption of a simple link between metal ion affinity and antimicrobial efficacy.
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Affiliation(s)
| | | | - Robert Pal
- Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Juan A Aguilar
- Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Javier Pitarch-Jarque
- Instituto de Ciencia Molecular, Universidad de Valencia, C/ Catedrático José Beltrán 2, 46980, Paterna, Valencia, Spain
| | - Enrique García-España
- Instituto de Ciencia Molecular, Universidad de Valencia, C/ Catedrático José Beltrán 2, 46980, Paterna, Valencia, Spain
| | - Elena Lurie-Luke
- Procter and Gamble Technical Centres Limited, Rusham Park, Whitehall Lane, Egham, Surrey, TW20 9NW, UK
| | - Gary J Sharples
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
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Jahn LJ, Munck C, Ellabaan MMH, Sommer MOA. Adaptive Laboratory Evolution of Antibiotic Resistance Using Different Selection Regimes Lead to Similar Phenotypes and Genotypes. Front Microbiol 2017; 8:816. [PMID: 28553265 PMCID: PMC5425606 DOI: 10.3389/fmicb.2017.00816] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/21/2017] [Indexed: 12/01/2022] Open
Abstract
Antibiotic resistance is a global threat to human health, wherefore it is crucial to study the mechanisms of antibiotic resistance as well as its emergence and dissemination. One way to analyze the acquisition of de novo mutations conferring antibiotic resistance is adaptive laboratory evolution. However, various evolution methods exist that utilize different population sizes, selection strengths, and bottlenecks. While evolution in increasing drug gradients guarantees high-level antibiotic resistance promising to identify the most potent resistance conferring mutations, other selection regimes are simpler to implement and therefore allow higher throughput. The specific regimen of adaptive evolution may have a profound impact on the adapted cell state. Indeed, substantial effects of the selection regime on the resulting geno- and phenotypes have been reported in the literature. In this study we compare the geno- and phenotypes of Escherichia coli after evolution to Amikacin, Piperacillin, and Tetracycline under four different selection regimes. Interestingly, key mutations that confer antibiotic resistance as well as phenotypic changes like collateral sensitivity and cross-resistance emerge independently of the selection regime. Yet, lineages that underwent evolution under mild selection displayed a growth advantage independently of the acquired level of antibiotic resistance compared to lineages adapted under maximal selection in a drug gradient. Our data suggests that even though different selection regimens result in subtle genotypic and phenotypic differences key adaptations appear independently of the selection regime.
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Affiliation(s)
- Leonie J Jahn
- Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkHørsholm, Denmark
| | - Christian Munck
- Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkHørsholm, Denmark
| | - Mostafa M H Ellabaan
- Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkHørsholm, Denmark
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkHørsholm, Denmark
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May KL, Silhavy TJ. Making a membrane on the other side of the wall. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1386-1393. [PMID: 27742351 DOI: 10.1016/j.bbalip.2016.10.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/20/2016] [Accepted: 10/04/2016] [Indexed: 12/11/2022]
Abstract
The outer membrane (OM) of Gram-negative bacteria is positioned at the frontline of the cell's interaction with its environment and provides a barrier against influx of external toxins while still allowing import of nutrients and excretion of wastes. It is a remarkable asymmetric bilayer with a glycolipid surface-exposed leaflet and a glycerophospholipid inner leaflet. Lipid asymmetry is key to OM barrier function and several different systems actively maintain this lipid asymmetry. All OM components are synthesized in the cytosol before being secreted and assembled into a contiguous membrane on the other side of the cell wall. Work in recent years has uncovered the pathways that transport and assemble most of the OM components. However, our understanding of how phospholipids are delivered to the OM remains notably limited. Here we will review seminal works in phospholipid transfer performed some 40years ago and place more recent insights in their context. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
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Affiliation(s)
- Kerrie L May
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA.
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15
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Frirdich E, Whitfield C. Review: Lipopolysaccharide inner core oligosaccharide structure and outer membrane stability in human pathogens belonging to the Enterobacteriaceae. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/09680519050110030201] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In the Enterobacteriaceae, the outer membrane is primarily comprised of lipopolysaccharides. The lipopolysaccharide molecule is important in mediating interactions between the bacterium and its environment and those regions of the molecule extending further away from the cell surface show a higher amount of structural diversity. The hydrophobic lipid A is highly conserved, due to its important role in the structural integrity of the outer membrane. Attached to the lipid A region is the core oligosaccharide. The inner core oligosaccharide (lipid A proximal) backbone is also well conserved. However, non-stoichiometric substitutions of the basic inner core structure lead to structural variation and microheterogeneity. These include the addition of negatively charged groups (phosphate or galacturonic acid), ethanolamine derivatives, and glycose residues (Kdo, rhamnose, galactose, glucosamine, N-acetylglucosamine, heptose, Ko). The genetics and biosynthesis of these substitutions is beginning to be elucidated. Modification of heptose residues with negatively charged molecules (such as phosphate in Escherichia coli and Salmonella and galacturonic acid in Klebsiella pneumoniae ) has been shown to be involved in maintaining membrane stability. However, the biological role(s) of the remaining substitutions is unknown.
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Affiliation(s)
- Emilisa Frirdich
- Department of Microbiology, University of Guelph, Guelph, Ontario, Canada
| | - Chris Whitfield
- Department of Microbiology, University of Guelph, Guelph, Ontario, Canada,
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16
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Konovalova A, Mitchell AM, Silhavy TJ. A lipoprotein/β-barrel complex monitors lipopolysaccharide integrity transducing information across the outer membrane. eLife 2016; 5. [PMID: 27282389 PMCID: PMC4942254 DOI: 10.7554/elife.15276] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/07/2016] [Indexed: 11/13/2022] Open
Abstract
Lipoprotein RcsF is the OM component of the Rcs envelope stress response. RcsF exists in complexes with β-barrel proteins (OMPs) allowing it to adopt a transmembrane orientation with a lipidated N-terminal domain on the cell surface and a periplasmic C-terminal domain. Here we report that mutations that remove BamE or alter a residue in the RcsF trans-lumen domain specifically prevent assembly of the interlocked complexes without inactivating either RcsF or the OMP. Using these mutations we demonstrate that these RcsF/OMP complexes are required for sensing OM outer leaflet stress. Using mutations that alter the positively charged surface-exposed domain, we show that RcsF monitors lateral interactions between lipopolysaccharide (LPS) molecules. When these interactions are disrupted by cationic antimicrobial peptides, or by the loss of negatively charged phosphate groups on the LPS molecule, this information is transduced to the RcsF C-terminal signaling domain located in the periplasm to activate the stress response. DOI:http://dx.doi.org/10.7554/eLife.15276.001 Many disease-causing bacteria have an outer membrane that surrounds and protects the cell, while many hosts of these bacteria produce molecules called antimicrobial peptides that disrupt this outer membrane. In response to this attack, bacteria have evolved a defense system to reinforce their membrane when antimicrobial peptides are present. However, it was not clear how the bacteria sensed these peptides. One clue came from a recent discovery that the bacterial protein required for sensing the peptides is threaded through a barrel-shaped protein to expose a section of it on the bacterial cell’s surface. Now, Konovalova et al. have tested if this surface-exposed domain directly detects damage to the outer membrane caused by the antimicrobial peptides. The investigation revealed several mutants of Escherichia coli that still make the sensor protein but are unable to thread it through the barrel-shaped protein and place a portion on the cell surface. Konovalova et al. showed that these mutants are essentially “blind” to the presence of antimicrobial peptides, and thus prove that it is the surface-exposed domain that works as the sensor. Antimicrobial peptides bind to a major component of the outer membrane and disrupt its normal interactions. Further experiments showed that positively charged sites in surface-exposed domain of the sensor are required to detect these changes and transmit this information inside the cell. Future studies are now needed to understand how the sensor is assembled inside the barrel-shaped protein, and how the danger signal is sent across the membranes that envelope bacterial cells to activate the defense system inside the cell. DOI:http://dx.doi.org/10.7554/eLife.15276.002
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Affiliation(s)
- Anna Konovalova
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Princeton, United States
| | - Angela M Mitchell
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Princeton, United States
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Princeton, United States
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17
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Effects of Lipopolysaccharide Core Sugar Deficiency on Colanic Acid Biosynthesis in Escherichia coli. J Bacteriol 2016; 198:1576-1584. [PMID: 27002133 DOI: 10.1128/jb.00094-16] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/12/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED When 10 Escherichia coli mutant strains with defects in lipopolysaccharide (LPS) core biosynthesis were grown on agar medium at 30°C, four of them, the ΔwaaF, ΔwaaG, ΔwaaP, and ΔwaaB strains, formed mucoid colonies, while the other six, the ΔwaaU, ΔwaaR, ΔwaaO, ΔwaaC, ΔwaaQ, and ΔwaaY strains, did not. Using light microscopy with tannin mordant staining, the presence of exopolysaccharide around the cells of the mutants that formed mucoid colonies could be discerned. The ΔwaaF mutant produced the largest amounts of exopolysaccharide, regardless of whether it was grown on agar or in liquid medium. The exopolysaccharide was isolated from the liquid growth medium of ΔwaaF cells, hydrolyzed, and analyzed by high-performance liquid chromatography with an ion-exchange column, and the results indicated that the exopolysaccharide was consistent with colanic acid. When the key genes related to the biosynthesis of colanic acid, i.e., wza, wzb, wzc, and wcaA, were deleted in the ΔwaaF background, the exopolysaccharide could not be produced any more, further confirming that it was colanic acid. Colanic acid could not be produced in strains in which rcsA, rcsB, rcsD, or rcsF was deleted in the ΔwaaF background, but a reduced level of colanic acid production was detected when the rcsC gene was deleted, suggesting that a change of lipopolysaccharide structure in ΔwaaF cells might be sensed by the RcsCDB phosphorelay system, leading to the production of colanic acid. The results demonstrate that E. coli cells can activate colanic acid production through the RcsCDB phosphorelay system in response to a structural deficiency of lipopolysaccharide. IMPORTANCE Lipopolysaccharide and colanic acid are important forms of exopolysaccharide for Escherichia coli cells. Their metabolism and biological significance have been investigated, but their interrelation with the cell stress response process is not understood. This study demonstrates, for the first time, that E. coli cells can activate colanic acid production through the RcsCDB phosphorelay system in response to a structural change of lipopolysaccharide, suggesting that bacterial cells can monitor the outer membrane integrity, which is essential for cell survival and damage repair.
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Piek S, Kahler CM. A comparison of the endotoxin biosynthesis and protein oxidation pathways in the biogenesis of the outer membrane of Escherichia coli and Neisseria meningitidis. Front Cell Infect Microbiol 2012; 2:162. [PMID: 23267440 PMCID: PMC3526765 DOI: 10.3389/fcimb.2012.00162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 12/01/2012] [Indexed: 01/13/2023] Open
Abstract
The Gram-negative bacterial cell envelope consists of an inner membrane (IM) that surrounds the cytoplasm and an asymmetrical outer-membrane (OM) that forms a protective barrier to the external environment. The OM consists of lipopolysaccahride (LPS), phospholipids, outer membrane proteins (OMPs), and lipoproteins. Oxidative protein folding mediated by periplasmic oxidoreductases is required for the biogenesis of the protein components, mainly constituents of virulence determinants such as pili, flagella, and toxins, of the Gram-negative OM. Recently, periplasmic oxidoreductases have been implicated in LPS biogenesis of Escherichia coli and Neisseria meningitidis. Differences in OM biogenesis, in particular the transport pathways for endotoxin to the OM, the composition and role of the protein oxidation, and isomerization pathways and the regulatory networks that control them have been found in these two Gram-negative species suggesting that although form and function of the OM is conserved, the pathways required for the biosynthesis of the OM and the regulatory circuits that control them have evolved to suit the lifestyle of each organism.
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Affiliation(s)
- Susannah Piek
- Department of Pathology and Laboratory Medicine, The University of Western Australia Perth, WA, Australia
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19
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Lipopolysaccharide (LPS) inner-core phosphates are required for complete LPS synthesis and transport to the outer membrane in Pseudomonas aeruginosa PAO1. mBio 2011; 2:mBio.00142-11. [PMID: 21810964 PMCID: PMC3147165 DOI: 10.1128/mbio.00142-11] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Gram-negative outer membrane (OM) integrity is maintained in part by Mg2+ cross-links between phosphates on lipid A and on core sugars of adjacent lipopolysaccharide (LPS) molecules. In contrast to other Gram-negative bacteria, waaP, encoding an inner-core kinase, could not be inactivated in Pseudomonas aeruginosa. To examine this further, expression of the kinases WaaP or WapP/WapQ/PA5006 was placed under the control of the arabinose-regulated pBAD promoter. Growth of these strains was arabinose dependent, confirming that core phosphorylation is essential in P. aeruginosa. Transmission electron micrographs of kinase-depleted cells revealed marked invaginations of the inner membrane. SDS-PAGE of total LPS from WaaP-depleted cells showed accumulation of a fast-migrating band. Mass spectrometry (MS) analysis revealed that LPS from these cells exhibits a unique truncated core consisting of two 3-deoxy-d-manno-octulosonic acids (Kdo), two l-glycero-d-manno-heptoses (Hep), and one hexose but completely devoid of phosphates, indicating that phosphorylation by WaaP is necessary for subsequent core phosphorylations. MS analysis of lipid A from WaaP-depleted cells revealed extensive 4-amino-4-deoxy-l-arabinose modification. OM prepared from these cells by Sarkosyl extraction of total membranes or by sucrose density gradient centrifugation lacked truncated LPS. Instead, truncated LPS was detected in the inner membrane fractions, consistent with impaired transport/assembly of this species into the OM. Gram-negative bacteria have an outer membrane (OM) comprised of a phospholipid inner leaflet and a lipopolysaccharide (LPS) outer leaflet. The OM protects cells from toxic molecules and is important for survival during infection. The LPS core kinase gene waaP can be deleted in several Gram-negative bacteria but not in Pseudomonas aeruginosa. We used a controlled-expression system to deplete WaaP directly in P. aeruginosa cells, which halted growth. WaaP depletion also caused gross changes in cell morphology and led to the accumulation of an aberrant LPS lacking several core sugars and all core phosphates. The aberrant LPS failed to reach the OM, suggesting that WaaP is essential in P. aeruginosa because it is required to produce the full-length LPS that is recognized by the OM transport/assembly machinery in this organism. Therefore, WaaP may constitute a good target for the development of novel antipseudomonal agents.
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20
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SoxRS-mediated lipopolysaccharide modification enhances resistance against multiple drugs in Escherichia coli. J Bacteriol 2009; 191:4441-50. [PMID: 19376854 DOI: 10.1128/jb.01474-08] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Lipopolysaccharide (LPS) is a major constituent of the outer membrane of gram-negative bacteria that serves as a barrier against harmful molecules, including antibiotics. The waaYZ locus that encodes the LPS core biosynthetic function in Escherichia coli was found to be induced strongly by superoxide generators but not by H(2)O(2), ethanol, or heat shock. This induction was dependent on SoxRS, a superoxide and nitric oxide sensing system, through a soxbox in the waaY promoter that binds SoxS. A DeltawaaYZ mutant became more sensitive to some superoxide generators, and the activation of SoxR by these drugs became more sensitized in the mutant. Through phenotypic microarray analysis, we found that the mutant became sensitive to a wide variety of chemicals not restricted to oxidizing agents. We found that the mutant is under envelope stress and is altered in LPS composition, as monitored by the level of sigma(E) activation and changes in the electrophoretic mobility of LPS, respectively. waaY expression was also regulated by MarA (multiple-antibiotic resistance regulator), which shares a binding site (soxbox) with SoxS, and was induced by salicylate, a nonoxidative compound. These results demonstrate a novel way of protecting gram-negative bacteria against various compounds by modifying LPS, possibly through phosphorylation. Since either oxidant or nonoxidant compounds elicit resistance toward themselves and other toxic drugs, this mechanism could serve as an efficient way for pathogenic bacteria to enhance survival during antibiotic treatment within an oxidant-rich host immune environment.
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21
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Modulation of hexa-acyl pyrophosphate lipid A population under Escherichia coli phosphate (Pho) regulon activation. J Bacteriol 2008; 190:5256-64. [PMID: 18515419 DOI: 10.1128/jb.01536-07] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Environmental phosphate is an important signal for microorganism gene regulation, and it has recently been shown to trigger some key bacterial virulence mechanisms. In many bacteria, the Pho regulon is the major circuit involved in adaptation to phosphate limitation. The Pho regulon is controlled jointly by the two-component regulatory system PhoR/PhoB and by the phosphate-specific transport (Pst) system, which both belong to the Pho regulon. We showed that a pst mutation results in virulence attenuation in extraintestinal pathogenic Escherichia coli (ExPEC) strains. Our results indicate that the bacterial cell surface of the pst mutants is altered. In this study, we show that pst mutants of ExPEC strains display an increased sensitivity to different cationic antimicrobial peptides and vancomycin. Remarkably, the hexa-acylated 1-pyrophosphate form of lipid A is significantly less abundant in pst mutants. Among differentially expressed genes in the pst mutant, lpxT coding for an enzyme that transfers a phosphoryl group to lipid A, forming the 1-diphosphate species, was found to be downregulated. Our results strongly suggest that the Pho regulon is involved in lipid A modifications, which could contribute to bacterial surface perturbations. Since the Pho regulon and the Pst system are conserved in many bacteria, such a lipid A modification mechanism could be widely distributed among gram-negative bacterial species.
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22
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Krupa A, Srinivasan N. Diversity in domain architectures of Ser/Thr kinases and their homologues in prokaryotes. BMC Genomics 2005; 6:129. [PMID: 16171520 PMCID: PMC1262709 DOI: 10.1186/1471-2164-6-129] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2004] [Accepted: 09/19/2005] [Indexed: 11/17/2022] Open
Abstract
Background Ser/Thr/Tyr kinases (STYKs) commonly found in eukaryotes have been recently reported in many bacterial species. Recent studies elucidating their cellular functions have established their roles in bacterial growth and development. However functions of a large number of bacterial STYKs still remain elusive. The organisation of domains in a large dataset of bacterial STYKs has been investigated here in order to recognise variety in domain combinations which determine functions of bacterial STYKs. Results Using sensitive sequence and profile search methods, domain organisation of over 600 STYKs from 125 prokaryotic genomes have been examined. Kinase catalytic domains of STYKs tethered to a wide range of enzymatic domains such as phosphatases, HSP70, peptidyl prolyl isomerases, pectin esterases and glycoproteases have been identified. Such distinct preferences for domain combinations are not known to be present in either the Histidine kinase or the eukaryotic STYK families. Domain organisation of STYKs specific to certain groups of bacteria has also been noted in the current anlaysis. For example, Hydrophobin like domains in Mycobacterial STYK and penicillin binding domains in few STYKs of Gram-positive organisms and FHA domains in cyanobacterial STYKs. Homologues of characterised substrates of prokaryotic STYKs have also been identified. Conclusion The domains and domain architectures of most of the bacterial STYKs identified are very different from the known domain organisation in STYKs of eukaryotes. This observation highlights distinct biological roles of bacterial STYKs compared to eukaryotic STYKs. Bacterial STYKs reveal high diversity in domain organisation. Some of the modular organisations conserved across diverse bacterial species suggests their central role in bacterial physiology. Unique domain architectures of few other groups of STYKs reveal recruitment of functions specific to the species.
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Affiliation(s)
- A Krupa
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
- Cell Cycle Control Laboratory, London Research Institute, Cancer Research – UK, South Mimms, Hertfordshire, EN6 3LD UK
| | - N Srinivasan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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23
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McArthur F, Andersson CE, Loutet S, Mowbray SL, Valvano MA. Functional analysis of the glycero-manno-heptose 7-phosphate kinase domain from the bifunctional HldE protein, which is involved in ADP-L-glycero-D-manno-heptose biosynthesis. J Bacteriol 2005; 187:5292-300. [PMID: 16030223 PMCID: PMC1196024 DOI: 10.1128/jb.187.15.5292-5300.2005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The core oligosaccharide component of the lipopolysaccharide can be subdivided into inner and outer core regions. In Escherichia coli, the inner core consists of two 3-deoxy-d-manno-octulosonic acid and three glycero-manno-heptose residues. The HldE protein participates in the biosynthesis of ADP-glycero-manno-heptose precursors used in the assembly of the inner core. HldE comprises two functional domains: an N-terminal region with homology to the ribokinase superfamily (HldE1 domain) and a C-terminal region with homology to the cytidylyltransferase superfamily (HldE2 domain). We have employed the structure of the E. coli ribokinase as a template to model the HldE1 domain and predict critical amino acids required for enzyme activity. Mutation of these residues renders the protein inactive as determined in vivo by functional complementation analysis. However, these mutations did not affect the secondary or tertiary structure of purified HldE1, as judged by fluorescence spectroscopy and circular dichroism. Furthermore, in vivo coexpression of wild-type, chromosomally encoded HldE and mutant HldE1 proteins with amino acid substitutions in the predicted ATP binding site caused a dominant negative phenotype as revealed by increased bacterial sensitivity to novobiocin. Copurification experiments demonstrated that HldE and HldE1 form a complex in vivo. Gel filtration chromatography resulted in the detection of a dimer as the predominant form of the native HldE1 protein. Altogether, our data support the notions that the HldE functional unit is a dimer and that structural components present in each HldE1 monomer are required for enzymatic activity.
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Affiliation(s)
- Fiona McArthur
- Department of Microbiology and Immunology, Siebens Drake Research Institute, Schulich School of Medicine, University of Western Ontario, London, Ontario N6A 5C1, Canada
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24
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Kaniuk NA, Vinogradov E, Li J, Monteiro MA, Whitfield C. Chromosomal and plasmid-encoded enzymes are required for assembly of the R3-type core oligosaccharide in the lipopolysaccharide of Escherichia coli O157:H7. J Biol Chem 2004; 279:31237-50. [PMID: 15155763 DOI: 10.1074/jbc.m401879200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The type R3 core oligosaccharide predominates in the lipopolysaccharides from enterohemorrhagic Escherichia coli isolates including O157:H7. The R3 core biosynthesis (waa) genetic locus contains two genes, waaD and waaJ, that are predicted to encode glycosyltransferases involved in completion of the outer core. Through determination of the structures of the lipopolysaccharide core in precise mutants and biochemical analyses of enzyme activities, WaaJ was shown to be a UDP-glucose:(galactosyl) lipopolysaccharide alpha-1,2-glucosyltransferase, and WaaD was shown to be a UDP-glucose:(glucosyl)lipopolysaccharide alpha-1,2-glucosyltransferase. The residue added by WaaJ was identified as the ligation site for O polysaccharide, and this was confirmed by determination of the structure of the linkage region in serotype O157 lipopolysaccharide. The initial O157 repeat unit begins with an N-acetylgalactosamine residue in a beta-anomeric configuration, whereas the biological repeat unit for O157 contains alpha-linked N-acetylgalactosamine residues. With the characterization of WaaJ and WaaD, the activities of all of the enzymes encoded by the R3 waa locus are either known or predicted from homology data with a high level of confidence. However, when core oligosaccharide structure is considered, the origin of an additional alpha-1,3-linked N-acetylglucosamine residue in the outer core is unknown. The gene responsible for a nonstoichiometric alpha-1,7-linked N-acetylglucosamine substituent in the heptose (inner core) region was identified on the large virulence plasmids of E. coli O157 and Shigella flexneri serotype 2a. This is the first plasmid-encoded core oligosaccharide biosynthesis enzyme reported in E. coli.
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Affiliation(s)
- Natalia A Kaniuk
- Department of Microbiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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25
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Alakomi HL, Saarela M, Helander IM. Effect of EDTA on Salmonella enterica serovar Typhimurium involves a component not assignable to lipopolysaccharide release. MICROBIOLOGY (READING, ENGLAND) 2003; 149:2015-2021. [PMID: 12904541 DOI: 10.1099/mic.0.26312-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The effect of EDTA on Salmonella enterica serovar Typhimurium was studied in different growth phases with cells grown with or without Ca(2+) and Mg(2+) supplementation. EDTA affected the outer membrane much more strongly in the early exponential phase than in the mid- or late exponential phase, as indicated by uptake of 1-N-phenylnaphthylamine (a nonpolar hydrophobic probe, M(r) 219), and detergent (SDS) susceptibility. This effect was, however, not paralleled by LPS release (determined by measuring LPS-specific fatty acids or 14C-labelled LPS in cell-free supernatants, per a standardized cell density), which remained unchanged as a function of the growth curve. The conclusion from these results is that in the early exponential phase the effect of EDTA in S. enterica involves a component that is independent of LPS release.
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Affiliation(s)
- H-L Alakomi
- VTT Biotechnology, PO Box 1500, FIN-02044 VTT, Espoo, Finland
| | - M Saarela
- VTT Biotechnology, PO Box 1500, FIN-02044 VTT, Espoo, Finland
| | - I M Helander
- Department of Applied Chemistry and Microbiology, Division of Microbiology, University of Helsinki, PO Box 56, FIN-00014 University of Helsinki, Finland
- VTT Biotechnology, PO Box 1500, FIN-02044 VTT, Espoo, Finland
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26
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Møller AK, Leatham MP, Conway T, Nuijten PJM, de Haan LAM, Krogfelt KA, Cohen PS. An Escherichia coli MG1655 lipopolysaccharide deep-rough core mutant grows and survives in mouse cecal mucus but fails to colonize the mouse large intestine. Infect Immun 2003; 71:2142-52. [PMID: 12654836 PMCID: PMC152069 DOI: 10.1128/iai.71.4.2142-2152.2003] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability of E. coli strains to colonize the mouse large intestine has been correlated with their ability to grow in cecal and colonic mucus. In the present study, an E. coli MG1655 strain was mutagenized with a mini-Tn5 Km (kanamycin) transposon, and mutants were tested for the ability to grow on agar plates with mouse cecal mucus as the sole source of carbon and nitrogen. One mutant, designated MD42 (for mucus defective), grew poorly on cecal-mucus agar plates but grew well on Luria agar plates and on glucose minimal-agar plates. Sequencing revealed that the insertion in MD42 was in the waaQ gene, which is involved in lipopolysaccharide (LPS) core biosynthesis. Like "deep-rough" E. coli mutants, MD42 was hypersensitive to sodium dodecyl sulfate (SDS), bile salts, and the hydrophobic antibiotic novobiocin. Furthermore, its LPS core oligosaccharide was truncated, like that of a deep-rough mutant. MD42 initially grew in the large intestines of streptomycin-treated mice but then failed to colonize (<10(2) CFU per g of feces), whereas its parent colonized at levels between 10(7) and 10(8) CFU per g of feces. When mouse cecal mucosal sections were hybridized with an E. coli-specific rRNA probe, MD42 was observed in cecal mucus as clumps 24 h postfeeding, whereas its parent was present almost exclusively as single cells, suggesting that clumping may play a role in preventing MD42 colonization. Surprisingly, MD42 grew nearly as well as its parent during growth in undiluted, highly viscous cecal mucus isolated directly from the mouse cecum and, like its parent, survived well after reaching stationary phase, suggesting that there are no antimicrobials in mucus that prevent MD42 colonization. After mini-mariner transposon mutagenesis, an SDS-resistant suppressor mutant of MD42 was isolated. The mini-mariner insertion was shown to be in the bipA gene, a known regulator of E. coli surface components. When grown in Luria broth, the LPS core of the suppressor mutant remained truncated; however, the LPS core was not truncated when the suppressor mutant was grown in the presence of SDS. Moreover, when the suppressor mutant was grown in the presence of SDS and fed to mice, it colonized the mouse large intestine. Collectively, the data presented here suggest that BipA may play a role in E. coli MG1655 LPS core biosynthesis and that because MD42 forms clumps in intestinal mucus, it is unable to colonize the mouse large intestine.
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Affiliation(s)
- Annette K Møller
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
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Kaniuk NA, Monteiro MA, Parker CT, Whitfield C. Molecular diversity of the genetic loci responsible for lipopolysaccharide core oligosaccharide assembly within the genus Salmonella. Mol Microbiol 2002; 46:1305-18. [PMID: 12453217 DOI: 10.1046/j.1365-2958.2002.03243.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The waa locus on the chromosome of Salmonella enterica encodes enzymes involved in the assembly of the core oligosaccharide region of the lipopolysaccharide (LPS) molecule. To date, there are two known core structures in Salmonella, represented by serovars Typhimurium (subspecies I) and Arizonae (subspecies IIIA). The waa locus for serovar Typhimurium has been characterized. Here, the corresponding locus from serovar Arizonae is described, and the molecular basis for the distinctive structures is established. Eleven of the 13 open reading frames (ORFs) are shared by the two loci and encode conserved proteins of known function. Two polymorphic regions distinguish the waa loci. One involves the waaK gene, the product of which adds a terminal alpha-1,2-linked N-acetylglucosamine residue that characterizes the serovar Typhimurium core oligosaccharide. There is an extensive internal deletion within waaK of serovar Arizonae. The serovar Arizonae locus contains a novel ORF (waaH) between the waaB and waaP genes. Structural analyses and in vitro glycosyltransferase assays identified WaaH as the UDP-glucose:(glucosyl) LPS alpha-1,2-glucosyltransferase responsible for the addition of the characteristic terminal glucose residue found in serovar Arizonae. Isolates comprising the Salmonella Reference Collections, SARC (representing the eight subspecies of S. enterica) and SARB (representing subspecies I), were examined to assess the distribution of the waa locus polymorphic regions in natural populations. These comparative studies identified additional waa locus polymorphisms, shedding light on the genetic basis for diversity in the LPS core oligosaccharides of Salmonella isolates and identifying potential sources of further novel LPS structures.
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Affiliation(s)
- Natalia A Kaniuk
- Department of Microbiology, University of Guelph, Guelph, ON, Canada, N1G 2W1
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Valvano MA, Messner P, Kosma P. Novel pathways for biosynthesis of nucleotide-activated glycero-manno-heptose precursors of bacterial glycoproteins and cell surface polysaccharides. MICROBIOLOGY (READING, ENGLAND) 2002; 148:1979-1989. [PMID: 12101286 DOI: 10.1099/00221287-148-7-1979] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Miguel A Valvano
- Department of Microbiology and Immunology and Medicine, University of Western Ontario, London, Ontario, N6A 5C1, Canada1
| | - Paul Messner
- Zentrum für Ultrastrukturforschung und Ludwig Boltzmann-Institut für Molekulare Nanotechnologie, Universität für Bodenkultur Wien, A-1180 Wien, Austria2
| | - Paul Kosma
- Institut für Chemie, Universität für Bodenkultur Wien, A-1190 Wien, Austria3
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29
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Zhao X, Wenzel CQ, Lam JS. Nonradiolabeling assay for WaaP, an essential sugar kinase involved in biosynthesis of core lipopolysaccharide of Pseudomonas aeruginosa. Antimicrob Agents Chemother 2002; 46:2035-7. [PMID: 12019135 PMCID: PMC127274 DOI: 10.1128/aac.46.6.2035-2037.2002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
waaP is present in the lipopolysaccharide (LPS) core gene clusters of a wide range of gram-negative bacteria, and is an essential gene in Pseudomonas aeruginosa. The WaaP protein is a sugar kinase that adds phosphate to heptose I in the core oligosaccharide. This study describes the standardization and utility of a chemiluminescence-based enzyme-linked immunosorbent assay for the detection of WaaP kinase activity. Important features of the assay include high sensitivity, the preparation of dephosphorylated LPS as a substrate, and the use of monoclonal antibody 7-4 that specifically recognizes phosphate substituents in the LPS core.
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Affiliation(s)
- Xin Zhao
- Canadian Bacterial Diseases Network, Department of Microbiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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30
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Krupa A, Srinivasan N. Lipopolysaccharide phosphorylating enzymes encoded in the genomes of Gram-negative bacteria are related to the eukaryotic protein kinases. Protein Sci 2002; 11:1580-4. [PMID: 12021457 PMCID: PMC2373617 DOI: 10.1110/ps.3560102] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
By means of profile-matching procedures, conservation of functionally important residues, and fold-recognition techniques, we show that two distinct families of lipopolysaccharide kinases encoded in the genomes of Gram-negative bacteria are related to each other and to two distinct classes of proteins, namely eukaryotic protein kinases and right open reading frame (RIO1). Members of one of the lipopolysaccharide kinase families are identified only in pathogenic bacteria. Phosphorylation by these enzymes is relevant in the construction of outer membrane, immune response, and pathogenic virulence. The class of proteins called RIO1, also related to eukaryotic protein kinases and previously known to occur only in archaea and eukaryotes, are now identified in eubacteria as well. It has been suggested here that RIO1 proteins are intermediately related to lipopolysaccharide kinases and eukaryotic protein kinases implying an evolutionary relationship between the three classes of proteins.
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Affiliation(s)
- A Krupa
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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Zhao X, Lam JS. WaaP of Pseudomonas aeruginosa is a novel eukaryotic type protein-tyrosine kinase as well as a sugar kinase essential for the biosynthesis of core lipopolysaccharide. J Biol Chem 2002; 277:4722-30. [PMID: 11741974 DOI: 10.1074/jbc.m107803200] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
WaaP of P. aeruginosa is a crucial sugar kinase that phosphorylates HepI in the inner core region of lipopolysaccharide (LPS). WaaP shares homology with eukaryotic protein kinases in the conserved functional motifs (I-IX), indicating that it is also a protein kinase. This interpretation is substantiated by several lines of evidence including the following: (i) site-directed mutagenesis on catalytic domain residues abrogated the protein kinase activity; (ii) positive reaction in immunoblotting with anti-phosphotyrosine monoclonal antibody PY20; (iii) matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry and proteolytic peptide mapping showing excess mass equivalent to eight phosphate substituents on the tyrosine residues in WaaP; and (iv) WaaP is capable of catalyzing tyrosine self-phosphorylation as well as phosphorylating an exogenous synthetic co-polymer poly(Glu, Tyr). Thus, WaaP possesses dual kinase functions, and it utilizes a catalytic mechanism similar to that of the eukaryotic protein kinases. WaaP was localized to the cytoplasm, suggesting that phosphorylation of the LPS core occurred prior to translocation to the periplasm and attachment of O-antigen. A chemiluminescence-based enzyme-linked immunosorbent assay (ELISA) was developed to measure the kinetics of the WaaP sugar kinase activity, and the results showed that the K(m) was 0.22 mm for ATP and 14.4 microm for hydrofluoric acid-treated LPS, V(max) was 408.24 pmol min(-1), and k(cat) was 27.23 min(-1).
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Affiliation(s)
- Xin Zhao
- Canadian Bacterial Diseases Network, Department of Microbiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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32
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Abstract
Bacterial lipopolysaccharides (LPS) typically consist of a hydrophobic domain known as lipid A (or endotoxin), a nonrepeating "core" oligosaccharide, and a distal polysaccharide (or O-antigen). Recent genomic data have facilitated study of LPS assembly in diverse Gram-negative bacteria, many of which are human or plant pathogens, and have established the importance of lateral gene transfer in generating structural diversity of O-antigens. Many enzymes of lipid A biosynthesis like LpxC have been validated as targets for development of new antibiotics. Key genes for lipid A biosynthesis have unexpectedly also been found in higher plants, indicating that eukaryotic lipid A-like molecules may exist. Most significant has been the identification of the plasma membrane protein TLR4 as the lipid A signaling receptor of animal cells. TLR4 belongs to a family of innate immunity receptors that possess a large extracellular domain of leucine-rich repeats, a single trans-membrane segment, and a smaller cytoplasmic signaling region that engages the adaptor protein MyD88. The expanding knowledge of TLR4 specificity and its downstream signaling pathways should provide new opportunities for blocking inflammation associated with infection.
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Affiliation(s)
- Christian R H Raetz
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.
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