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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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2
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Lipopolysaccharide of the Yersinia pseudotuberculosis Complex. Biomolecules 2021; 11:biom11101410. [PMID: 34680043 PMCID: PMC8533242 DOI: 10.3390/biom11101410] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/27/2021] [Accepted: 09/21/2021] [Indexed: 11/16/2022] Open
Abstract
Lipopolysaccharide (LPS), localized in the outer leaflet of the outer membrane, serves as the major surface component of the Gram-negative bacterial cell envelope responsible for the activation of the host's innate immune system. Variations of the LPS structure utilized by Gram-negative bacteria promote survival by providing resistance to components of the innate immune system and preventing recognition by TLR4. This review summarizes studies of the biosynthesis of Yersinia pseudotuberculosis complex LPSs, and the roles of their structural components in molecular mechanisms of yersiniae pathogenesis and immunogenesis.
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3
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Kawahara K. Variation, Modification and Engineering of Lipid A in Endotoxin of Gram-Negative Bacteria. Int J Mol Sci 2021; 22:2281. [PMID: 33668925 PMCID: PMC7956469 DOI: 10.3390/ijms22052281] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 12/12/2022] Open
Abstract
Lipid A of Gram-negative bacteria is known to represent a central role for the immunological activity of endotoxin. Chemical structure and biosynthetic pathways as well as specific receptors on phagocytic cells had been clarified by the beginning of the 21st century. Although the lipid A of enterobacteria including Escherichia coli share a common structure, other Gram-negative bacteria belonging to various classes of the phylum Proteobacteria and other taxonomical groups show wide variety of lipid A structure with relatively decreased endotoxic activity compared to that of E. coli. The structural diversity is produced from the difference of chain length of 3-hydroxy fatty acids and non-hydroxy fatty acids linked to their hydroxyl groups. In some bacteria, glucosamine in the backbone is substituted by another amino sugar, or phosphate groups bound to the backbone are modified. The variation of structure is also introduced by the enzymes that can modify electrostatic charges or acylation profiles of lipid A during or after its synthesis. Furthermore, lipid A structure can be artificially modified or engineered by the disruption and introduction of biosynthetic genes especially those of acyltransferases. These technologies may produce novel vaccine adjuvants or antagonistic drugs derived from endotoxin in the future.
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Affiliation(s)
- Kazuyoshi Kawahara
- Department of Biosciences, College of Science and Engineering, Kanto Gakuin University, Yokohama, Kanagawa 236-8501, Japan
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4
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Simpson BW, Trent MS. Pushing the envelope: LPS modifications and their consequences. Nat Rev Microbiol 2020; 17:403-416. [PMID: 31142822 DOI: 10.1038/s41579-019-0201-x] [Citation(s) in RCA: 255] [Impact Index Per Article: 63.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The defining feature of the Gram-negative cell envelope is the presence of two cellular membranes, with the specialized glycolipid lipopolysaccharide (LPS) exclusively found on the surface of the outer membrane. The surface layer of LPS contributes to the stringent permeability properties of the outer membrane, which is particularly resistant to permeation of many toxic compounds, including antibiotics. As a common surface antigen, LPS is recognized by host immune cells, which mount defences to clear pathogenic bacteria. To alter properties of the outer membrane or evade the host immune response, Gram-negative bacteria chemically modify LPS in a wide variety of ways. Here, we review key features and physiological consequences of LPS biogenesis and modifications.
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Affiliation(s)
- Brent W Simpson
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - M Stephen Trent
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA. .,Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA. .,Department of Microbiology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA.
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5
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Joo SH, Pemble CW, Yang EG, Raetz CRH, Chung HS. Biochemical and Structural Insights into an Fe(II)/α-Ketoglutarate/O 2-Dependent Dioxygenase, Kdo 3-Hydroxylase (KdoO). J Mol Biol 2018; 430:4036-4048. [PMID: 30092253 DOI: 10.1016/j.jmb.2018.07.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/27/2018] [Accepted: 07/27/2018] [Indexed: 11/18/2022]
Abstract
During lipopolysaccharide biosynthesis in several pathogens, including Burkholderia and Yersinia, 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) 3-hydroxylase, otherwise referred to as KdoO, converts Kdo to d-glycero-d-talo-oct-2-ulosonic acid (Ko) in an Fe(II)/α-ketoglutarate (α-KG)/O2-dependent manner. This conversion renders the bacterial outer membrane more stable and resistant to stresses such as an acidic environment. KdoO is a membrane-associated, deoxy-sugar hydroxylase that does not show significant sequence identity with any known enzymes, and its structural information has not been previously reported. Here, we report the biochemical and structural characterization of KdoO, Minf_1012 (KdoMI), from Methylacidiphilum infernorum V4. The de novo structure of KdoMI apoprotein indicates that KdoOMI consists of 13 α helices and 11 β strands, and has the jelly roll fold containing a metal binding motif, HXDX111H. Structures of KdoMI bound to Co(II), KdoMI bound to α-KG and Fe(III), and KdoMI bound to succinate and Fe(III), in addition to mutagenesis analysis, indicate that His146, His260, and Asp148 play critical roles in Fe(II) binding, while Arg127, Arg162, Arg174, and Trp176 stabilize α-KG. It was also observed that His225 is adjacent to the active site and plays an important role in the catalysis of KdoOMI without affecting substrate binding, possibly being involved in oxygen activation. The crystal structure of KdoOMI is the first completed structure of a deoxy-sugar hydroxylase, and the data presented here have provided mechanistic insights into deoxy-sugar hydroxylase, KdoO, and lipopolysaccharide biosynthesis.
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Affiliation(s)
- Sang Hoon Joo
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA; Department of Pharmacy, Daegu Catholic University, Gyeongbuk 38430, South Korea
| | - Charles W Pemble
- Duke Macromolecular Crystallography Center, Duke University Medical Center, Durham, NC 27710, USA; Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Eun Gyeong Yang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Christian R H Raetz
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Hak Suk Chung
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA; Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea.
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6
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Gao SS, Naowarojna N, Cheng R, Liu X, Liu P. Recent examples of α-ketoglutarate-dependent mononuclear non-haem iron enzymes in natural product biosyntheses. Nat Prod Rep 2018; 35:792-837. [PMID: 29932179 PMCID: PMC6093783 DOI: 10.1039/c7np00067g] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: up to 2018 α-Ketoglutarate (αKG, also known as 2-oxoglutarate)-dependent mononuclear non-haem iron (αKG-NHFe) enzymes catalyze a wide range of biochemical reactions, including hydroxylation, ring fragmentation, C-C bond cleavage, epimerization, desaturation, endoperoxidation and heterocycle formation. These enzymes utilize iron(ii) as the metallo-cofactor and αKG as the co-substrate. Herein, we summarize several novel αKG-NHFe enzymes involved in natural product biosyntheses discovered in recent years, including halogenation reactions, amino acid modifications and tailoring reactions in the biosynthesis of terpenes, lipids, fatty acids and phosphonates. We also conducted a survey of the currently available structures of αKG-NHFe enzymes, in which αKG binds to the metallo-centre bidentately through either a proximal- or distal-type binding mode. Future structure-function and structure-reactivity relationship investigations will provide crucial information regarding how activities in this large class of enzymes have been fine-tuned in nature.
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Affiliation(s)
- Shu-Shan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Ronghai Cheng
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
| | - Xueting Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA. and State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
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Ushimaru R, Ruszczycky MW, Chang WC, Yan F, Liu YN, Liu HW. Substrate Conformation Correlates with the Outcome of Hyoscyamine 6β-Hydroxylase Catalyzed Oxidation Reactions. J Am Chem Soc 2018; 140:7433-7436. [PMID: 29870653 PMCID: PMC6488034 DOI: 10.1021/jacs.8b03729] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hyoscyamine 6β-hydroxylase (H6H) is an α-ketoglutarate dependent mononuclear nonheme iron enzyme that catalyzes C6-hydroxylation of hyoscyamine and oxidative cyclization of the resulting product to give the oxirane natural product scopolamine. Herein, the chemistry of H6H is investigated using hyoscyamine derivatives with modifications at the C6 or C7 position as well as substrate analogues possessing a 9-azabicyclo[3.3.1]nonane core. Results indicate that hydroxyl rebound is unlikely to take place during the cyclization reaction and that the hydroxylase versus oxidative cyclase activity of H6H is correlated with the presence of an exo-hydroxy group having syn-periplanar geometry with respect to the adjacent H atom to be abstracted.
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Affiliation(s)
- Richiro Ushimaru
- Department of Chemistry, and Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Mark W. Ruszczycky
- Department of Chemistry, and Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Wei-chen Chang
- Department of Chemistry, and Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Feng Yan
- Department of Chemistry, and Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yung-nan Liu
- Department of Chemistry, and Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hung-wen Liu
- Department of Chemistry, and Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
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8
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Wang T, Yu Y, Liang X, Luo S, He Z, Sun Z, Jiang Y, Omsland A, Zhou P, Song L. Lipid A Has Significance for Optimal Growth of Coxiella burnetii in Macrophage-Like THP-1 Cells and to a Lesser Extent in Axenic Media and Non-phagocytic Cells. Front Cell Infect Microbiol 2018; 8:192. [PMID: 29938202 PMCID: PMC6002510 DOI: 10.3389/fcimb.2018.00192] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 05/22/2018] [Indexed: 02/02/2023] Open
Abstract
Lipid A is an essential basal component of lipopolysaccharide of most Gram-negative bacteria. Inhibitors targeting LpxC, a conserved enzyme in lipid A biosynthesis, are antibiotic candidates against Gram-negative pathogens. Here we report the characterization of the role of lipid A in Coxiella burnetii growth in axenic media, monkey kidney cells (BGMK and Vero), and macrophage-like THP-1 cells by using a potent LpxC inhibitor -LPC-011. We first determined the susceptibility of C. burnetii LpxC to LPC-011 in a surrogate E. coli model. In E. coli, the minimum inhibitory concentration (MIC) of LPC-011 against C. burnetii LpxC is < 0.05 μg/mL, a value lower than the inhibitor's MIC against E. coli LpxC. Considering the inhibitor's problematic pharmacokinetic properties in vivo and Coxiella's culturing time up to 7 days, the stability of LPC-011 in cell cultures was assessed. We found that regularly changing inhibitor-containing media was required for sustained inhibition of C. burnetii LpxC in cells. Under inhibitor treatment, Coxiella has reduced growth yields in axenic media and during replication in non-phagocytic cells, and has a reduced number of productive vacuoles in such cells. Inhibiting lipid A biosynthesis in C. burnetii by the inhibitor was shown in a phase II strain transformed with chlamydial kdtA. This exogenous KdtA enzyme modifies Coxiella lipid A with an α-Kdo-(2 → 8)-α-Kdo epitope that can be detected by anti-chlamydia genus antibodies. In inhibitor-treated THP-1 cells, Coxiella shows severe growth defects characterized by poor vacuole formation and low growth yields. Coxiella progenies prepared from inhibitor-treated cells retain the capability of normally infecting all tested cells in the absence of the inhibitor, which suggests a dispensable role of lipid A for infection and early vacuole development. In conclusion, our data suggest that lipid A has significance for optimal development of Coxiella-containing vacuoles, and for robust multiplication of C. burnetii in macrophage-like THP-1 cells. Unlike many bacteria, C. burnetii replication in axenic media and non-phagocytic cells was less dependent on normal lipid A biosynthesis.
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Affiliation(s)
- Tao Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yonghui Yu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaofei Liang
- Department of Chemistry, Duke University, Durham, NC, United States
| | - Shengdong Luo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zemin He
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhihui Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Anders Omsland
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, United States
| | - Pei Zhou
- Department of Biochemistry, Duke University Medical Center, Durham, NC, United States
| | - Lihua Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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9
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Hassan AA, Maldonado RF, Dos Santos SC, Di Lorenzo F, Silipo A, Coutinho CP, Cooper VS, Molinaro A, Valvano MA, Sá-Correia I. Structure of O-Antigen and Hybrid Biosynthetic Locus in Burkholderia cenocepacia Clonal Variants Recovered from a Cystic Fibrosis Patient. Front Microbiol 2017. [PMID: 28642745 PMCID: PMC5462993 DOI: 10.3389/fmicb.2017.01027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Burkholderia cenocepacia is an opportunistic pathogen associated with chronic lung infections and increased risk of death in patients with cystic fibrosis (CF). In this work, we investigated the lipopolysaccharide (LPS) of clinical variants of B. cenocepacia that were collected from a CF patient over a period of 3.5 years, from the onset of infection until death by necrotizing pneumonia (cepacia syndrome). We report the chemical structure of the LPS molecule of various sequential isolates and the identification of a novel hybrid O-antigen (OAg) biosynthetic cluster. The OAg repeating unit of the LPS from IST439, the initial isolate, is a [→2)-β-D-Ribf-(1→4)-α-D-GalpNAc-(1→] disaccharide, which was not previously described in B. cenocepacia. The IST439 OAg biosynthetic gene cluster contains 7 of 23 genes that are closely homologous to genes found in B. multivorans, another member of the Burkholderia cepacia complex. None of the subsequent isolates expressed OAg. Genomic sequencing of these isolates enabled the identification of mutations within the OAg cluster, but none of these mutations could be associated with the loss of OAg. This study provides support to the notion that OAg LPS modifications are an important factor in the adaptation of B. cenocepacia to chronic infection and that the heterogeneity of OAgs relates to variation within the OAg gene cluster, indicating that the gene cluster might have been assembled through multiple horizontal transmission events.
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Affiliation(s)
- A A Hassan
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de LisboaLisboa, Portugal
| | - Rita F Maldonado
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de LisboaLisboa, Portugal
| | - Sandra C Dos Santos
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de LisboaLisboa, Portugal
| | - Flaviana Di Lorenzo
- Department of Chemical Sciences, University of Napoli Federico II Complesso Universitário Monte SantangeloNapoli, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Napoli Federico II Complesso Universitário Monte SantangeloNapoli, Italy
| | - Carla P Coutinho
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de LisboaLisboa, Portugal
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, PittsburghPA, United States
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli Federico II Complesso Universitário Monte SantangeloNapoli, Italy
| | - Miguel A Valvano
- The Wellcome-Wolfson Institute for Experimental Medicine, Queen's University BelfastBelfast, United Kingdom
| | - Isabel Sá-Correia
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de LisboaLisboa, Portugal
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10
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Fathy Mohamed Y, Hamad M, Ortega XP, Valvano MA. The LpxL acyltransferase is required for normal growth and penta-acylation of lipid A in Burkholderia cenocepacia. Mol Microbiol 2017; 104:144-162. [PMID: 28085228 DOI: 10.1111/mmi.13618] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2017] [Indexed: 12/27/2022]
Abstract
Lipid A anchors the lipopolysaccharide (LPS) to the outer membrane and is usually composed of a hexa-acylated diglucosamine backbone. Burkholderia cenocepacia, an opportunistic pathogen, produces a mixture of tetra- and penta-acylated lipid A. "Late" acyltransferases add secondary acyl chains to lipid A after the incorporation of four primary acyl chains to the diglucosamine backbone. Here, we report that B. cenocepacia has only one late acyltransferase, LpxL (BCAL0508), which adds a myristoyl chain to the 2' position of lipid A resulting in penta-acylated lipid A. We also identified PagL (BCAL0788), which acts as an outer membrane lipase by removing the primary β-hydroxymyristate (3-OH-C14:0) chain at the 3 position, leading to tetra-acylated lipid A. Unlike PagL, LpxL depletion caused reduced cell growth and defects in cell morphology, both of which were suppressed by overexpressing the LPS flippase MsbA (BCAL2408), suggesting that lipid A molecules lacking the fifth acyl chain contributed by LpxL are not good substrates for the flippase. We also show that intracellular B. cenocepacia within macrophages produced more penta-acylated lipid A, suggesting lipid A penta-acylation in B. cenocepacia is required not only for bacterial growth and morphology but also for adaptation to intracellular lifestyle.
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Affiliation(s)
- Yasmine Fathy Mohamed
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, BT9 7BL, UK.,Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Mohamad Hamad
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Ximena P Ortega
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Miguel A Valvano
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, BT9 7BL, UK.,Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada, N6A 5C1
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11
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Hashimoto M, Ozono M, Furuyashiki M, Baba R, Hashiguchi S, Suda Y, Fukase K, Fujimoto Y. Characterization of a Novel d-Glycero-d-talo-oct-2-ulosonic acid-substituted Lipid A Moiety in the Lipopolysaccharide Produced by the Acetic Acid Bacterium Acetobacter pasteurianus NBRC 3283. J Biol Chem 2016; 291:21184-21194. [PMID: 27539854 DOI: 10.1074/jbc.m116.751271] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Indexed: 01/17/2023] Open
Abstract
Acetobacter pasteurianus is an aerobic Gram-negative rod that is used in the fermentation process used to produce the traditional Japanese black rice vinegar kurozu. Previously, we found that a hydrophobic fraction derived from kurozu stimulates Toll-like receptors to produce cytokines. LPSs, particularly LPS from A. pasteurianus, are strong candidates for the immunostimulatory component of kurozu. The LPS of A. pasteurianus remains stable in acidic conditions during the 2 years of the abovementioned fermentation process. Thus, we hypothesized that its stability results from its structure. In this study, we isolated the LPS produced by A. pasteurianus NBRC 3283 bacterial cells and characterized the structure of its lipid A component. The lipid A moiety was obtained by standard weak acid hydrolysis of the LPS. However, the hydrolysis was incomplete because a certain proportion of the LPS contained acid-stable d-glycero-d-talo-oct-2-ulosonic acid (Ko) residues instead of the acid-labile 3-deoxy-d-manno-oct-2-ulosonic acid residues that are normally found in typical LPS. Even so, we obtained a Ko-substituted lipid A with a novel sugar backbone, α-Man(1-4)[α-Ko(2-6)]β-GlcN3N(1-6)α-GlcN(1-1)α-GlcA. Its reducing end GlcN(1-1)GlcA bond was also found to be quite acid-stable. Six fatty acids were attached to the backbone. Both the whole LPS and the lipid A moiety induced TNF-α production in murine cells via Toll-like receptor 4, although their activity was weaker than those of Escherichia coli LPS and lipid A. These results suggest that the structurally atypical A. pasteurianus lipid A found in this study remains stable and, hence, retains its immunostimulatory activity during acetic acid fermentation.
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Affiliation(s)
- Masahito Hashimoto
- From the Department of Chemistry, Biotechnology, and Chemical Engineering, Kagoshima University, Kagoshima 890-0065, Japan,
| | - Mami Ozono
- From the Department of Chemistry, Biotechnology, and Chemical Engineering, Kagoshima University, Kagoshima 890-0065, Japan
| | - Maiko Furuyashiki
- From the Department of Chemistry, Biotechnology, and Chemical Engineering, Kagoshima University, Kagoshima 890-0065, Japan
| | - Risako Baba
- From the Department of Chemistry, Biotechnology, and Chemical Engineering, Kagoshima University, Kagoshima 890-0065, Japan
| | - Shuhei Hashiguchi
- From the Department of Chemistry, Biotechnology, and Chemical Engineering, Kagoshima University, Kagoshima 890-0065, Japan
| | - Yasuo Suda
- From the Department of Chemistry, Biotechnology, and Chemical Engineering, Kagoshima University, Kagoshima 890-0065, Japan
| | - Koichi Fukase
- the Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560-0043, Japan, and
| | - Yukari Fujimoto
- the Faculty of Science and Technology, Keio University, Kanagawa 223-8522, Japan
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12
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Maldonado RF, Sá-Correia I, Valvano MA. Lipopolysaccharide modification in Gram-negative bacteria during chronic infection. FEMS Microbiol Rev 2016; 40:480-93. [PMID: 27075488 PMCID: PMC4931227 DOI: 10.1093/femsre/fuw007] [Citation(s) in RCA: 372] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/23/2015] [Accepted: 03/10/2016] [Indexed: 12/16/2022] Open
Abstract
The Gram-negative bacterial lipopolysaccharide (LPS) is a major component of the outer membrane that plays a key role in host-pathogen interactions with the innate immune system. During infection, bacteria are exposed to a host environment that is typically dominated by inflammatory cells and soluble factors, including antibiotics, which provide cues about regulation of gene expression. Bacterial adaptive changes including modulation of LPS synthesis and structure are a conserved theme in infections, irrespective of the type or bacteria or the site of infection. In general, these changes result in immune system evasion, persisting inflammation and increased antimicrobial resistance. Here, we review the modifications of LPS structure and biosynthetic pathways that occur upon adaptation of model opportunistic pathogens (Pseudomonas aeruginosa, Burkholderia cepacia complex bacteria, Helicobacter pylori and Salmonella enterica) to chronic infection in respiratory and gastrointestinal sites. We also discuss the molecular mechanisms of these variations and their role in the host-pathogen interaction.
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Affiliation(s)
- Rita F. Maldonado
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon 1049-001, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon 1049-001, Portugal
| | - Miguel A. Valvano
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5C1, Canada
- Centre for Infection and Immunity, Queen's University Belfast, Belfast BT9 7BL, UK
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13
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Henderson JC, Zimmerman SM, Crofts AA, Boll JM, Kuhns LG, Herrera CM, Trent MS. The Power of Asymmetry: Architecture and Assembly of the Gram-Negative Outer Membrane Lipid Bilayer. Annu Rev Microbiol 2016; 70:255-78. [PMID: 27359214 DOI: 10.1146/annurev-micro-102215-095308] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Determining the chemical composition of biological materials is paramount to the study of natural phenomena. Here, we describe the composition of model gram-negative outer membranes, focusing on the predominant assembly, an asymmetrical bilayer of lipid molecules. We also give an overview of lipid biosynthetic pathways and molecular mechanisms that organize this material into the outer membrane bilayer. An emphasis is placed on the potential of these pathways as targets for antibiotic development. We discuss deviations in composition, through bacterial cell surface remodeling, and alternative modalities to the asymmetric lipid bilayer. Outer membrane lipid alterations of current microbiological interest, such as lipid structures found in commensal bacteria, are emphasized. Additionally, outer membrane components could potentially be engineered to develop vaccine platforms. Observations related to composition and assembly of gram-negative outer membranes will continue to generate novel discoveries, broaden biotechnologies, and reveal profound mysteries to compel future research.
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Affiliation(s)
- Jeremy C Henderson
- Department of Molecular Biosciences, The University of Texas at Austin, Texas 78712
| | - Shawn M Zimmerman
- Department of Infectious Diseases, The University of Georgia, Athens, Georgia 30602;
| | - Alexander A Crofts
- Department of Molecular Biosciences, The University of Texas at Austin, Texas 78712
| | - Joseph M Boll
- Department of Molecular Biosciences, The University of Texas at Austin, Texas 78712
| | - Lisa G Kuhns
- Department of Infectious Diseases, The University of Georgia, Athens, Georgia 30602;
| | - Carmen M Herrera
- Department of Infectious Diseases, The University of Georgia, Athens, Georgia 30602;
| | - M Stephen Trent
- Department of Infectious Diseases, The University of Georgia, Athens, Georgia 30602;
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14
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Noszczyńska M, Kasperkiewicz K, Duda KA, Podhorodecka J, Rabsztyn K, Gwizdała K, Świerzko AS, Radziejewska-Lebrecht J, Holst O, Skurnik M. Serological characterization of the enterobacterial common antigen substitution of the lipopolysaccharide of Yersinia enterocolitica O : 3. Microbiology (Reading) 2015; 161:219-227. [DOI: 10.1099/mic.0.083493-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Magdalena Noszczyńska
- Department of Microbiology, University of Silesia, Jagiellońska 28, PL- 40-032 Katowice, Poland
| | - Katarzyna Kasperkiewicz
- Department of Microbiology, University of Silesia, Jagiellońska 28, PL- 40-032 Katowice, Poland
| | - Katarzyna Anna Duda
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Joanna Podhorodecka
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
- Department of Microbiology, University of Silesia, Jagiellońska 28, PL- 40-032 Katowice, Poland
| | - Kamila Rabsztyn
- Department of Microbiology, University of Silesia, Jagiellońska 28, PL- 40-032 Katowice, Poland
| | - Karolina Gwizdała
- Department of Microbiology, University of Silesia, Jagiellońska 28, PL- 40-032 Katowice, Poland
| | - Anna Stanisława Świerzko
- Department of Immunobiology of Infections, Institute of Medical Biology, PAS, Lodowa 106, PL- 93-232 Łódź, Poland
| | | | - Otto Holst
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Mikael Skurnik
- Helsinki University Central Hospital Laboratory Diagnostics, FIN-00270 Helsinki, Finland
- Department of Bacteriology and Immunology, Haartman Institute, and Research Programs Unit, Immunobiology, University of Helsinki, FIN-00014, Helsinki, Finland
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15
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Chung HS, Yang EG, Hwang D, Lee JE, Guan Z, Raetz CRH. Kdo hydroxylase is an inner core assembly enzyme in the Ko-containing lipopolysaccharide biosynthesis. Biochem Biophys Res Commun 2014; 452:789-94. [PMID: 25204504 DOI: 10.1016/j.bbrc.2014.08.153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 08/31/2014] [Indexed: 11/16/2022]
Abstract
The lipopolysaccharide (LPS) isolated from certain important Gram-negative pathogens including a human pathogen Yersinia pestis and opportunistic pathogens Burkholderia mallei and Burkholderia pseudomallei contains d-glycero-d-talo-oct-2-ulosonic acid (Ko), an isosteric analog of 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo). Kdo 3-hydroxylase (KdoO), a Fe(2+)/α-KG/O2 dependent dioxygenase from Burkholderia ambifaria and Yersinia pestis is responsible for Ko formation with Kdo2-lipid A as a substrate, but in which stage KdoO functions during the LPS biosynthesis has not been established. Here we purify KdoO from B. ambifaria (BaKdoO) to homogeneity for the first time and characterize its substrates. BaKdoO utilizes Kdo2-lipid IVA or Kdo2-lipid A as a substrate, but not Kdo-lipid IVAin vivo as well as in vitro and Kdo-(Hep)kdo-lipid A in vitro. These data suggest that KdoO is an inner core assembly enzyme that functions after the Kdo-transferase KdtA but before the heptosyl-transferase WaaC enzyme during the Ko-containing LPS biosynthesis.
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Affiliation(s)
- Hak Suk Chung
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea; Department of Biological Chemistry, KIST Campus, Korea University of Science and Technology (UST), Seoul 136-791, Republic of Korea.
| | - Eun Gyeong Yang
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea; Department of Biological Chemistry, KIST Campus, Korea University of Science and Technology (UST), Seoul 136-791, Republic of Korea
| | - Dohyeon Hwang
- Department of Biological Chemistry, KIST Campus, Korea University of Science and Technology (UST), Seoul 136-791, Republic of Korea
| | - Ji Eun Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Christian R H Raetz
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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16
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Lodowska J, Wolny D, Węglarz L. The sugar 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) as a characteristic component of bacterial endotoxin — a review of its biosynthesis, function, and placement in the lipopolysaccharide core. Can J Microbiol 2013; 59:645-55. [DOI: 10.1139/cjm-2013-0490] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The sugar 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) is a characteristic component of bacterial lipopolysaccharide (LPS, endotoxin). It connects the carbohydrate part of LPS with C6 of glucosamine or 2,3-diaminoglucose of lipid A by acid-labile α-ketosidic linkage. The number of Kdo units present in LPS, the way they are connected, and the occurrence of other substituents (P, PEtn, PPEtn, Gal, or β-l-Ara4N) account for structural diversity of the inner core region of endotoxin. In a majority of cases, Kdo is crucial to the viability and growth of bacterial cells. In this paper, the biosynthesis of Kdo and the mechanism of its incorporation into the LPS structure, as well as the location of this unique component in the endotoxin core structures, have been described.
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Affiliation(s)
- Jolanta Lodowska
- Department of Biochemistry, Faculty of Pharmacy, Medical University of Silesia, Narcyzow 1 Street, 41-200 Sosnowiec, Poland
| | - Daniel Wolny
- Department of Biopharmacy, Faculty of Pharmacy, Medical University of Silesia, Narcyzow 1 St., 41-200 Sosnowiec, Poland
| | - Ludmiła Węglarz
- Department of Biochemistry, Faculty of Pharmacy, Medical University of Silesia, Narcyzow 1 Street, 41-200 Sosnowiec, Poland
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17
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Henderson JC, O'Brien JP, Brodbelt JS, Trent MS. Isolation and chemical characterization of lipid A from gram-negative bacteria. J Vis Exp 2013:e50623. [PMID: 24084191 DOI: 10.3791/50623] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Lipopolysaccharide (LPS) is the major cell surface molecule of gram-negative bacteria, deposited on the outer leaflet of the outer membrane bilayer. LPS can be subdivided into three domains: the distal O-polysaccharide, a core oligosaccharide, and the lipid A domain consisting of a lipid A molecular species and 3-deoxy-D-manno-oct-2-ulosonic acid residues (Kdo). The lipid A domain is the only component essential for bacterial cell survival. Following its synthesis, lipid A is chemically modified in response to environmental stresses such as pH or temperature, to promote resistance to antibiotic compounds, and to evade recognition by mediators of the host innate immune response. The following protocol details the small- and large-scale isolation of lipid A from gram-negative bacteria. Isolated material is then chemically characterized by thin layer chromatography (TLC) or mass-spectrometry (MS). In addition to matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) MS, we also describe tandem MS protocols for analyzing lipid A molecular species using electrospray ionization (ESI) coupled to collision induced dissociation (CID) and newly employed ultraviolet photodissociation (UVPD) methods. Our MS protocols allow for unequivocal determination of chemical structure, paramount to characterization of lipid A molecules that contain unique or novel chemical modifications. We also describe the radioisotopic labeling, and subsequent isolation, of lipid A from bacterial cells for analysis by TLC. Relative to MS-based protocols, TLC provides a more economical and rapid characterization method, but cannot be used to unambiguously assign lipid A chemical structures without the use of standards of known chemical structure. Over the last two decades isolation and characterization of lipid A has led to numerous exciting discoveries that have improved our understanding of the physiology of gram-negative bacteria, mechanisms of antibiotic resistance, the human innate immune response, and have provided many new targets in the development of antibacterial compounds.
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Affiliation(s)
- Jeremy C Henderson
- Section of Molecular Genetics and Microbiology, The University of Texas at Austin
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18
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Needham BD, Trent MS. Fortifying the barrier: the impact of lipid A remodelling on bacterial pathogenesis. Nat Rev Microbiol 2013; 11:467-81. [PMID: 23748343 PMCID: PMC6913092 DOI: 10.1038/nrmicro3047] [Citation(s) in RCA: 396] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Gram-negative bacteria decorate their outermost surface structure, lipopolysaccharide, with elaborate chemical moieties, which effectively disguises them from immune surveillance and protects them from the onslaught of host defences. Many of these changes occur on the lipid A moiety of lipopolysaccharide, a component that is crucial for host recognition of Gram-negative infection. In this Review, we describe the regulatory mechanisms controlling lipid A modification and discuss the impact of modifications on pathogenesis, bacterial physiology and bacterial interactions with the host immune system.
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Affiliation(s)
- Brittany D Needham
- The Institute of Cellular and Molecular Biology, The University of Texas at Austin, 78712, USA
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19
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Zähringer U, Kawahara K, Kosma P. Isolation and structural characterization of a (Kdo-isosteric) D-glycero-α-D-talo-oct-2-ulopyranosidonic acid (Ko) interlinking lipid A and core oligosaccharide in the lipopolysaccharide of Acinetobacter calcoaceticus NCTC 10305. Carbohydr Res 2013; 378:63-70. [PMID: 23743267 DOI: 10.1016/j.carres.2013.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 04/30/2013] [Accepted: 05/02/2013] [Indexed: 11/25/2022]
Abstract
In Acinetobacter calcoaceticus NCTC 10305 and A. haemolyticus NCTC 10305 lipopolysaccharide (LPS) a Kdo (3-deoxy-D-manno-oct-2-ulosonic acid)-related octulosonic acid (Ko) interlinks the lipid A with the core-oligosaccharide. This Ko replaces the first Kdo (Kdo(I)) attached to the lipid A backbone in the LPS. The only structural difference between Kdo and Ko is the 3-hydroxylation. After the discovery of the final step in Ko-biosynthesis it is now generally accepted that Ko is structurally related to Kdo, although a final proof so far is lacking. In the present paper we describe the stereochemical determination of the natural Ko isolated from the LPS of A. calcoaceticus NCTC 10305 by chemical, mass spectrometry (MS), and (1)H and (13)C NMR spectroscopy. Our results show that in A. calcoaceticusd-glycero-α-D-talo-oct-2-ulopyranosonic acid (DgαDt-Kop) represents the Kdo-related sugar interlinking the core-oligosaccharide and the lipid A backbone.
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Affiliation(s)
- Ulrich Zähringer
- Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, D-23845 Borstel, Germany.
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20
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Knirel Y, Anisimov A. Lipopolysaccharide of Yersinia pestis, the Cause of Plague: Structure, Genetics, Biological Properties. Acta Naturae 2012; 4:46-58. [PMID: 23150803 PMCID: PMC3492934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The present review summarizes data pertaining to the composition and structure of the carbohydrate moiety (core oligosaccharide) and lipid component (lipid A) of the various forms of lipopolysaccharide (LPS), one of the major pathogenicity factors ofYersinia pestis, the cause of plague. The review addresses the functions and the biological significance of genes for the biosynthesis of LPS, as well as the biological properties of LPS in strains from various intraspecies groups ofY. pestis and their mutants, including the contribution of LPS to the resistance of bacteria to factors of the innate immunity of both insect-vectors and mammal-hosts. Special attention is paid to temperature-dependent variations in the LPS structure, their genetic control and roles in the pathogenesis of plague. The evolutionary aspect is considered based on a comparison of the structure and genetics of the LPS ofY. pestis and other enteric bacteria, including otherYersinia species. The prospects of development of live plague vaccines created on the basis ofY. pestis strains with the genetically modified LPS are discussed.
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Affiliation(s)
- Y.A. Knirel
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky
prospect, 47, Moscow, Russia, 119991
| | - A.P. Anisimov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk,
Moscow Region, Russia, 142279
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21
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Han W, Wu B, Li L, Zhao G, Woodward R, Pettit N, Cai L, Thon V, Wang PG. Defining function of lipopolysaccharide O-antigen ligase WaaL using chemoenzymatically synthesized substrates. J Biol Chem 2011; 287:5357-65. [PMID: 22158874 DOI: 10.1074/jbc.m111.308486] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The WaaL-mediated ligation of O-antigen onto the core region of the lipid A-core block is an important step in the lipopolysaccharide (LPS) biosynthetic pathway. Although the LPS biosynthesis has been largely characterized, only a limited amount of in vitro biochemical evidence has been established for the ligation reaction. Such limitations have primarily resulted from the barriers in purifying WaaL homologues and obtaining chemically defined substrates. Accordingly, we describe herein a chemical biology approach that enabled the reconstitution of this ligation reaction. The O-antigen repeating unit (O-unit) of Escherichia coli O86 was first enzymatically assembled via sequential enzymatic glycosylation of a chemically synthesized GalNAc-pyrophosphate-undecaprenyl precursor. Subsequent expression of WaaL through use of a chaperone co-expression system then enabled the demonstration of the in vitro ligation between the synthesized donor (O-unit-pyrophosphate-undecaprenyl) and the isolated lipid A-core acceptor. The previously reported ATP and divalent metal cation dependence were not observed using this system. Further analyses of other donor substrates revealed that WaaL possesses a highly relaxed specificity toward both the lipid moiety and the glycan moiety of the donor. Lastly, three conserved amino acid residues identified by sequence alignment were found essential for the WaaL activity. Taken together, the present work represents an in vitro systematic investigation of the WaaL function using a chemical biology approach, providing a system that could facilitate the elucidation of the mechanism of WaaL-catalyzed ligation reaction.
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Affiliation(s)
- Weiqing Han
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, USA
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22
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Charusanti P, Chauhan S, McAteer K, Lerman JA, Hyduke DR, Motin VL, Ansong C, Adkins JN, Palsson BO. An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. BMC SYSTEMS BIOLOGY 2011; 5:163. [PMID: 21995956 PMCID: PMC3220653 DOI: 10.1186/1752-0509-5-163] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 10/13/2011] [Indexed: 11/20/2022]
Abstract
Background Yersinia pestis is a gram-negative bacterium that causes plague, a disease linked historically to the Black Death in Europe during the Middle Ages and to several outbreaks during the modern era. Metabolism in Y. pestis displays remarkable flexibility and robustness, allowing the bacterium to proliferate in both warm-blooded mammalian hosts and cold-blooded insect vectors such as fleas. Results Here we report a genome-scale reconstruction and mathematical model of metabolism for Y. pestis CO92 and supporting experimental growth and metabolite measurements. The model contains 815 genes, 678 proteins, 963 unique metabolites and 1678 reactions, accurately simulates growth on a range of carbon sources both qualitatively and quantitatively, and identifies gaps in several key biosynthetic pathways and suggests how those gaps might be filled. Furthermore, our model presents hypotheses to explain certain known nutritional requirements characteristic of this strain. Conclusions Y. pestis continues to be a dangerous threat to human health during modern times. The Y. pestis genome-scale metabolic reconstruction presented here, which has been benchmarked against experimental data and correctly reproduces known phenotypes, provides an in silico platform with which to investigate the metabolism of this important human pathogen.
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Affiliation(s)
- Pep Charusanti
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.
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23
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Identification of the lipopolysaccharide core of Yersinia pestis and Yersinia pseudotuberculosis as the receptor for bacteriophage φA1122. J Bacteriol 2011; 193:4963-72. [PMID: 21764935 DOI: 10.1128/jb.00339-11] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
φA1122 is a T7-related bacteriophage infecting most isolates of Yersinia pestis, the etiologic agent of plague, and used by the CDC in the identification of Y. pestis. φA1122 infects Y. pestis grown both at 20 °C and at 37 °C. Wild-type Yersinia pseudotuberculosis strains are also infected but only when grown at 37 °C. Since Y. pestis expresses rough lipopolysaccharide (LPS) missing the O-polysaccharide (O-PS) and expression of Y. pseudotuberculosis O-PS is largely suppressed at temperatures above 30 °C, it has been assumed that the phage receptor is rough LPS. We present here several lines of evidence to support this. First, a rough derivative of Y. pseudotuberculosis was also φA1122 sensitive when grown at 22 °C. Second, periodate treatment of bacteria, but not proteinase K treatment, inhibited the phage binding. Third, spontaneous φA1122 receptor mutants of Y. pestis and rough Y. pseudotuberculosis could not be isolated, indicating that the receptor was essential for bacterial growth under the applied experimental conditions. Fourth, heterologous expression of the Yersinia enterocolitica O:3 LPS outer core hexasaccharide in both Y. pestis and rough Y. pseudotuberculosis effectively blocked the phage adsorption. Fifth, a gradual truncation of the core oligosaccharide into the Hep/Glc (L-glycero-D-manno-heptose/D-glucopyranose)-Kdo/Ko (3-deoxy-D-manno-oct-2-ulopyranosonic acid/D-glycero-D-talo-oct-2-ulopyranosonic acid) region in a series of LPS mutants was accompanied by a decrease in phage adsorption, and finally, a waaA mutant expressing only lipid A, i.e., also missing the Kdo/Ko region, was fully φA1122 resistant. Our data thus conclusively demonstrated that the φA1122 receptor is the Hep/Glc-Kdo/Ko region of the LPS core, a common structure in Y. pestis and Y. pseudotuberculosis.
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González-Silva N, López-Lara IM, Reyes-Lamothe R, Taylor AM, Sumpton D, Thomas-Oates J, Geiger O. The dioxygenase-encoding olsD gene from Burkholderia cenocepacia causes the hydroxylation of the amide-linked fatty acyl moiety of ornithine-containing membrane lipids. Biochemistry 2011; 50:6396-408. [PMID: 21707055 DOI: 10.1021/bi200706v] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Burkholderia cenocepacia is an important opportunistic pathogen, and one of the most striking features of the Burkholderia genus is the collection of polar lipids present in its membrane, including phosphatidylethanolamine (PE) and ornithine-containing lipids (OLs), as well as the 2-hydroxylated derivatives of PE and OLs (2-OH-PE and 2-OH-OLs, respectively), which differ from the standard versions by virtue of the presence of a hydroxyl group at C2 (2-OH) of an esterified fatty acyl residue. Similarly, a lipid A-esterified myristoyl group from Salmonella typhimurium can have a 2-hydroxy modification that is due to the LpxO enzyme. We thus postulated that 2-hydroxylation of 2-OH-OLs might be catalyzed by a novel dioxygenase homologue of LpxO. In B. cenocepacia, we have now identified two open reading frames (BCAM1214 and BCAM2401) homologous to LpxO from S. typhimurium. The introduction of bcam2401 (designated olsD) into Sinorhizobium meliloti leads to the formation of one new lipid and in B. cenocepacia of two new lipids. Surprisingly, the lipid modifications on OLs due to OlsD occur on the amide-linked fatty acyl chain. This is the first report of a hydroxyl modification of OLs on the amide-linked fatty acyl moiety. Formation of hydroxylated OLs occurs only when the biosynthesis pathway for nonmodified standard OLs is intact. The hydroxyl modification of OLs on the amide-linked fatty acyl moiety occurs only under acid stress conditions. An assay has been developed for the OlsD dioxygenase, and an initial characterization of the enzyme is presented.
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Affiliation(s)
- Napoleón González-Silva
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos CP62251, Mexico
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25
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Knirel YA, Shevelev SD, Perepelov AV. Higher aldulosonic acids: components of bacterial glycans. MENDELEEV COMMUNICATIONS 2011. [DOI: 10.1016/j.mencom.2011.07.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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