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Díaz-Pérez AL, Díaz-Pérez C, Gaona-García RY, Hernández-Santoyo A, Lázaro-Mixteco PE, Reyes-De La Cruz H, Campos-García J. Study of peripheral domains in structure-function of isocitrate lyase (ICL) from Pseudomonas aeruginosa. World J Microbiol Biotechnol 2023; 39:339. [PMID: 37821748 DOI: 10.1007/s11274-023-03768-0] [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: 05/04/2023] [Accepted: 09/15/2023] [Indexed: 10/13/2023]
Abstract
The capacity of Pseudomonas aeruginosa to assimilate nutrients is essential for niche colonization and contributes to its pathogenicity. Isocitrate lyase (ICL), the first enzyme of the glyoxylate cycle, redirects isocitrate from the tricarboxylic acid cycle to render glyoxylate and succinate. P. aeruginosa ICL (PaICL) is regarded as a virulence factor due to its role in carbon assimilation during infection. The AceA/ICL protein family shares the catalytic domain I, triosephosphate isomerase barrel (TIM-barrel). The carboxyl terminus of domain I is essential for Escherichia coli ICL (EcICL) of subfamily 1. PaICL, which belongs to subfamily 3, has domain II inserted at the periphery of domain I, which is believed to participate in enzyme oligomerization. In addition, PaICL has the α13-loop-α14 (extended motif), which protrudes from the enzyme core, being of unknown function. This study investigates the role of domain II, the extended motif, and the carboxyl-terminus (C-ICL) and amino-terminus (N-ICL) regions in the function of the PaICL enzyme, also as their involvement in the virulence of P. aeruginosa PAO1. Deletion of domain II and the extended motif results in enzyme inactivation and structural instability of the enzyme. The His6-tag fusion at the C-ICL protein produced a less efficient enzyme than fusion at the N-ICL, but without affecting the acetate assimilation or virulence. The PaICL homotetrameric structure of the enzyme was more stable in the N-His6-ICL than in the C-His6-ICL, suggesting that the C-terminus is critical for the ICL quaternary conformation. The ICL-mutant A39 complemented with the recombinant proteins N-His6-ICL or C-His6-ICL were more virulent than the WT PAO1 strain. The findings indicate that the domain II and the extended motif are essential for the ICL structure/function, and the C-terminus is involved in its quaternary structure conformation, confirming that in P. aeruginosa, the ICL is essential for acetate assimilation and virulence.
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Affiliation(s)
- Alma Laura Díaz-Pérez
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. U-3, Ciudad Universitaria, 58030, Morelia, Mich., Mexico
| | - César Díaz-Pérez
- Facultad de Agrobiologia, Campus Celaya-Salvatierra, Universiad de Guanajuato, Guanajuato, Gto., Mexico
| | - Roxana Yughadi Gaona-García
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. U-3, Ciudad Universitaria, 58030, Morelia, Mich., Mexico
| | - Alejandra Hernández-Santoyo
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Pedro E Lázaro-Mixteco
- Facultad de Ingeniería Química, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich., Mexico
| | - Homero Reyes-De La Cruz
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. U-3, Ciudad Universitaria, 58030, Morelia, Mich., Mexico
| | - Jesús Campos-García
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. U-3, Ciudad Universitaria, 58030, Morelia, Mich., Mexico.
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2
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Olona A, Leishman S, Anand PK. The NLRP3 inflammasome: regulation by metabolic signals. Trends Immunol 2022; 43:978-989. [PMID: 36371361 DOI: 10.1016/j.it.2022.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/05/2022] [Accepted: 10/08/2022] [Indexed: 11/10/2022]
Abstract
Macrophages undergo profound metabolic reprogramming upon sensing infectious and sterile stimuli. This metabolic shift supports and regulates essential innate immune functions, including activation of the NLRP3 inflammasome. Within distinct metabolic networks, key enzymes play pivotal roles to control flux restraining detrimental inflammasome signaling. However, depending on the metabolic cues, specific enzymes and metabolites result in inflammasome activation outcomes which contrast other metabolic steps in the pathway. We posit that understanding which metabolic steps commit to discrete inflammasome fates will broaden our understanding of metabolic checkpoints to maintain homeostasis and offer better therapeutic options in human disease.
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Affiliation(s)
- Antoni Olona
- Department of Infectious Disease, Imperial College London, London, W12 0NN, UK; Program in Cardiovascular and Metabolic Disorders, and Centre for Computational Biology, Duke-NUS Medical School, Singapore
| | - Stuart Leishman
- Department of Infectious Disease, Imperial College London, London, W12 0NN, UK
| | - Paras K Anand
- Department of Infectious Disease, Imperial College London, London, W12 0NN, UK.
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3
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Sarkhel R, Apoorva S, Priyadarsini S, Sridhar HB, Bhure SK, Mahawar M. Malate synthase contributes to the survival of Salmonella Typhimurium against nutrient and oxidative stress conditions. Sci Rep 2022; 12:15979. [PMID: 36155623 PMCID: PMC9510125 DOI: 10.1038/s41598-022-20245-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 09/12/2022] [Indexed: 11/09/2022] Open
Abstract
To survive and replicate in the host, S. Typhimurium have evolved several metabolic pathways. The glyoxylate shunt is one such pathway that can utilize acetate for the synthesis of glucose and other biomolecules. This pathway is a bypass of the TCA cycle in which CO2 generating steps are omitted. Two enzymes involved in the glyoxylate cycle are isocitrate lyase (ICL) and malate synthase (MS). We determined the contribution of MS in the survival of S. Typhimurium under carbon limiting and oxidative stress conditions. The ms gene deletion strain (∆ms strain) grew normally in LB media but failed to grow in M9 minimal media supplemented with acetate as a sole carbon source. However, the ∆ms strain showed hypersensitivity (p < 0.05) to hypochlorite. Further, ∆ms strain has been significantly more susceptible to neutrophils. Interestingly, several folds induction of ms gene was observed following incubation of S. Typhimurium with neutrophils. Further, ∆ms strain showed defective colonization in poultry spleen and liver. In short, our data demonstrate that the MS contributes to the virulence of S. Typhimurium by aiding its survival under carbon starvation and oxidative stress conditions.
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4
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Xu X, Yan Y, Huang J, Zhang Z, Wang Z, Wu M, Liang H. Regulation of uric acid and glyoxylate metabolism by UgmR protein in Pseudomonas aeruginosa. Environ Microbiol 2022; 24:3242-3255. [PMID: 35702827 DOI: 10.1111/1462-2920.16088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa has evolved several systems to adapt to complex environments. The GntR family proteins play important roles in the regulation of metabolic processes and bacterial pathogenesis. In this study, we uncovered that the gene clusters of PA1513-PA1518 and PA1498-PA1502 in P. aeruginosa are required for uric acid and glyoxylate metabolism, respectively. We also identified a GntR family regulator UgmR that is involved in regulation of uric acid and glyoxylate metabolism. Promoter activity measurement and biochemical assays revealed that the UgmR directly represses the transcriptional activity of PA1513-PA1518 and PA1498-PA1502, and this inhibition was relieved by the addition of uric acid. Importantly, further experiments showed that UgmR also participates in the glyoxylate shunt. Collectively, these findings contribute to a better understanding of the UgmR factor involved in uric acid and glyoxylate metabolism, which provide insights into the complex metabolic pathways in P. aeruginosa. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Xuejie Xu
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Yunfang Yan
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Jiadai Huang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, SAR, China
| | - Zihao Zhang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Zhihan Wang
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND
| | - Min Wu
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND
| | - Haihua Liang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi, China.,College of Medicine, Southern University of Science and Technology, Shenzhen, China
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5
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Fatty Acid Homeostasis Tunes Flagellar Motility by Activating Phase 2 Flagellin Expression, Contributing to Salmonella Gut Colonization. Infect Immun 2022; 90:e0018422. [PMID: 35652649 DOI: 10.1128/iai.00184-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Long-chain-fatty-acid (LCFA) metabolism is a fundamental cellular process in bacteria that is involved in lipid homeostasis, energy production, and infection. However, the role of LCFA metabolism in Salmonella enterica serovar Typhimurium (S. Tm) gut infection remains unclear. Here, using a murine gastroenteritis infection model, we demonstrate involvement of LCFA metabolism in S. Tm gut colonization. The LCFA metabolism-associated transcriptional regulator FadR contributes to S. Tm gut colonization. fadR deletion alters the gene expression profile and leads to aberrant flagellar motility of S. Tm. Colonization defects in the fadR mutant are attributable to altered swimming behavior characterized by less frequently smooth swimming, resulting from reduced expression of the phase 2 flagellin FljB. Notably, changes in lipid LCFA composition by fadR deletion lead to reduced expression of fljB, which is restored by exogenous LCFA. Therefore, LCFA homeostasis may maintain proper flagellar motility by activating fljB expression, contributing to S. Tm gut colonization. Our findings improve the understanding of the effect of luminal LCFA on the virulence of enteric pathogens.
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Baty JJ, Huffines JT, Stoner SN, Scoffield JA. A Commensal Streptococcus Dysregulates the Pseudomonas aeruginosa Nitrosative Stress Response. Front Cell Infect Microbiol 2022; 12:817336. [PMID: 35619650 PMCID: PMC9127344 DOI: 10.3389/fcimb.2022.817336] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic infections in the cystic fibrosis (CF) airway are composed of both pathogenic and commensal bacteria. However, chronic Pseudomonas aeruginosa infections are the leading cause of lung deterioration in individuals with CF. Interestingly, oral commensals can translocate to the CF lung and their presence is associated with improved lung function, presumably due to their ability to antagonize P. aeruginosa. We have previously shown that one commensal, Streptococcus parasanguinis, produces hydrogen peroxide that reacts with nitrite to generate reactive nitrogen intermediates (RNI) which inhibit P. aeruginosa growth. In this study, we sought to understand the global impact of commensal-mediated RNI on the P. aeruginosa transcriptome. RNA sequencing analysis revealed that S. parasanguinis and nitrite-mediated RNI dysregulated expression of denitrification genes in a CF isolate of P. aeruginosa compared to when this isolate was only exposed to S. parasanguinis. Further, loss of a nitric oxide reductase subunit (norB) rendered an acute P. aeruginosa isolate more susceptible to S. parasanguinis-mediated RNI. Additionally, S. parasanguinis-mediated RNI inactivated P. aeruginosa aconitase activity. Lastly, we report that P. aeruginosa isolates recovered from CF individuals are uniquely hypersensitive to S. parasanguinis-mediated RNI compared to acute infection or environmental P. aeruginosa isolates. These findings illustrate that S. parasanguinis hinders the ability of P. aeruginosa to respond to RNI, which potentially prevents P. aeruginosa CF isolates from resisting commensal and host-induced RNI in the CF airway.
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7
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Duncan D, Auclair K. Itaconate: an antimicrobial metabolite of macrophages. CAN J CHEM 2022. [DOI: 10.1139/cjc-2021-0117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Itaconate is a conjugated 1,4-dicarboxylate produced by macrophages. This small molecule has recently received increasing attention due to its role in modulating the immune response of macrophages upon exposure to pathogens. Itaconate has also been proposed to play an antimicrobial function; however, this has not been explored as intensively. Consistent with the latter, itaconate is known to show antibacterial activity in vitro and was reported to inhibit isocitrate lyase, an enzyme required for survival of bacterial pathogens in mammalian systems. Recent studies have revealed bacterial growth inhibition under biologically relevant conditions. In addition, an antimicrobial role for itaconate is substantiated by the high concentration of itaconate found in bacteria-containing vacuoles, and by the production of itaconate-degrading enzymes in pathogens such as Salmonella enterica ser. Typhimurium, Pseudomonas aeruginosa, and Yersinia pestis. This review describes the current state of literature in understanding the role of itaconate as an antimicrobial agent in host–pathogen interactions.
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Affiliation(s)
- Dustin Duncan
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Karine Auclair
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
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8
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D'Arpa P, Karna SLR, Chen T, Leung KP. Pseudomonas aeruginosa transcriptome adaptations from colonization to biofilm infection of skin wounds. Sci Rep 2021; 11:20632. [PMID: 34667187 PMCID: PMC8526614 DOI: 10.1038/s41598-021-00073-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 09/07/2021] [Indexed: 11/09/2022] Open
Abstract
In burn patients Pseudomonas aeruginosa infection is a major cause of morbidity. Analysis of the pathogen's gene expression as it transitions from colonization to acute and then biofilm wound infection may provide strategies for infection control. Toward this goal, we seeded log-phase P. aeruginosa (PAO1) into 3-day-old, full-thickness excision wounds (rabbit ear) and harvested the bacteria during colonization (Hrs 2 and 6), acute infection (Hr 24), and biofilm infection (Days 5 and 9) for transcriptome analysis (RNA-Seq). After 2-6 h in the wound, genes for metabolism and cell replication were down-regulated while wound-adaptation genes were up-regulated (vs. expression in log-phase culture). As the infection progressed from acute to biofilm infection, more genes became up-regulated than down-regulated, but the down-regulated genes enriched in more pathways, likely because the genes and pathways that bacteria already colonizing wounds up-regulate to establish biofilm infection are less known. Across the stages of infection, carbon-utilization pathways shifted. During acute infection, itaconate produced by myeloid cells appears to have been a carbon source because myeloid cell infiltration and the expression of the host gene, ACOD1, for itaconate production peaked coincidently with the expression of the PAO1 genes for itaconate transport and catabolism. Additionally, branched-chain amino acids are suggested to be a carbon source in acute infection and in biofilm infection. In biofilm infection, fatty acid degradation was also up-regulated. These carbon sources feed into the glyoxylate cycle that was coincidently up-regulated, suggesting it provided the precursors for P. aeruginosa to synthesize macromolecules in establishing wound infection.
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Affiliation(s)
- Peter D'Arpa
- Combat Wound Repair Group and Tissue Regeneration Department, US Army Institute of Surgical Research, JBSA Fort Sam Houston, San Antonio, TX, USA.,The Geneva Foundation, Tacoma, USA
| | - S L Rajasekhar Karna
- Combat Wound Repair Group and Tissue Regeneration Department, US Army Institute of Surgical Research, JBSA Fort Sam Houston, San Antonio, TX, USA
| | - Tsute Chen
- The Forsyth Institute, Cambridge, MA, USA
| | - Kai P Leung
- Combat Wound Repair Group and Tissue Regeneration Department, US Army Institute of Surgical Research, JBSA Fort Sam Houston, San Antonio, TX, USA.
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Huyer LD, Mandla S, Wang Y, Campbell S, Yee B, Euler C, Lai BF, Bannerman D, Lin DSY, Montgomery M, Nemr K, Bender T, Epelman S, Mahadevan R, Radisic M. Macrophage immunomodulation through new polymers that recapitulate functional effects of itaconate as a power house of innate immunity. ADVANCED FUNCTIONAL MATERIALS 2021; 31:2003341. [PMID: 33708036 PMCID: PMC7942808 DOI: 10.1002/adfm.202003341] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 05/12/2023]
Abstract
Itaconate (ITA) is an emerging powerhouse of innate immunity with therapeutic potential that is limited in its ability to be administered in a soluble form. We developed a library of polyester materials that incorporate ITA into polymer backbones resulting in materials with inherent immunoregulatory behavior. Harnessing hydrolytic degradation release from polyester backbones, ITA polymers resulted in the mechanism specific immunoregulatory properties on macrophage polarization in vitro. In a functional assay, the polymer-released ITA inhibited bacterial growth on acetate. Translation to an in vivo model of biomaterial associated inflammation, intraperitoneal injection of ITA polymers demonstrated a rapid resolution of inflammation in comparison to a control polymer silicone, demonstrating the value of sustained biomimetic presentation of ITA.
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Affiliation(s)
- L. Davenport Huyer
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - S. Mandla
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Y. Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - S. Campbell
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - B. Yee
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - C. Euler
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - B. F. Lai
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - D. Bannerman
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - D. S. Y. Lin
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - M. Montgomery
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - K. Nemr
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - T. Bender
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - S. Epelman
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - R. Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - M. Radisic
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
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2-Aminopyridine Analogs Inhibit Both Enzymes of the Glyoxylate Shunt in Pseudomonas aeruginosa. Int J Mol Sci 2020; 21:ijms21072490. [PMID: 32260167 PMCID: PMC7177833 DOI: 10.3390/ijms21072490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 12/16/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen responsible for many hospital-acquired infections. P. aeruginosa can thrive in diverse infection scenarios by rewiring its central metabolism. An example of this is the production of biomass from C2 nutrient sources such as acetate via the glyoxylate shunt when glucose is not available. The glyoxylate shunt is comprised of two enzymes, isocitrate lyase (ICL) and malate synthase G (MS), and flux through the shunt is essential for the survival of the organism in mammalian systems. In this study, we characterized the mode of action and cytotoxicity of structural analogs of 2-aminopyridines, which have been identified by earlier work as being inhibitory to both shunt enzymes. Two of these analogs were able to inhibit ICL and MS in vitro and prevented growth of P. aeruginosa on acetate (indicating cell permeability). Moreover, the compounds exerted negligible cytotoxicity against three human cell lines and showed promising in vitro drug metabolism and safety profiles. Isothermal titration calorimetry was used to confirm binding of one of the analogs to ICL and MS, and the mode of enzyme inhibition was determined. Our data suggest that these 2-aminopyridine analogs have potential as anti-pseudomonal agents.
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Perinbam K, Chacko JV, Kannan A, Digman MA, Siryaporn A. A Shift in Central Metabolism Accompanies Virulence Activation in Pseudomonas aeruginosa. mBio 2020; 11:e02730-18. [PMID: 32156820 PMCID: PMC7064766 DOI: 10.1128/mbio.02730-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/28/2020] [Indexed: 01/24/2023] Open
Abstract
The availability of energy has significant impact on cell physiology. However, the role of cellular metabolism in bacterial pathogenesis is not understood. We investigated the dynamics of central metabolism during virulence induction by surface sensing and quorum sensing in early-stage biofilms of the multidrug-resistant bacterium Pseudomonas aeruginosa We established a metabolic profile for P. aeruginosa using fluorescence lifetime imaging microscopy (FLIM), which reports the activity of NADH in live cells. We identified a critical growth transition period during which virulence is activated. We performed FLIM measurements and direct measurements of NADH and NAD+ concentrations during this period. Here, planktonic (low-virulence) and surface-attached (virulence-activated) populations diverged into distinct metabolic states, with the surface-attached population exhibiting FLIM lifetimes that were associated with lower levels of enzyme-bound NADH and decreasing total NAD(H) production. We inhibited virulence by perturbing central metabolism using citrate and pyruvate, which further decreased the enzyme-bound NADH fraction and total NAD(H) production and suggested the involvement of the glyoxylate pathway in virulence activation in surface-attached populations. In addition, we induced virulence at an earlier time using the electron transport chain oxidase inhibitor antimycin A. Our results demonstrate the use of FLIM to noninvasively measure NADH dynamics in biofilms and suggest a model in which a metabolic rearrangement accompanies the virulence activation period.IMPORTANCE The rise of antibiotic resistance requires the development of new strategies to combat bacterial infection and pathogenesis. A major direction has been the development of drugs that broadly target virulence. However, few targets have been identified due to the species-specific nature of many virulence regulators. The lack of a virulence regulator that is conserved across species has presented a further challenge to the development of therapeutics. Here, we identify that NADH activity has an important role in the induction of virulence in the pathogen P. aeruginosa This finding, coupled with the ubiquity of NADH in bacterial pathogens, opens up the possibility of targeting enzymes that process NADH as a potential broad antivirulence approach.
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Affiliation(s)
- Kumar Perinbam
- Department of Physics and Astronomy, University of California, Irvine, Irvine, California, USA
| | - Jenu V Chacko
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, USA
| | - Anerudh Kannan
- Department of Physics and Astronomy, University of California, Irvine, Irvine, California, USA
| | - Michelle A Digman
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, USA
| | - Albert Siryaporn
- Department of Physics and Astronomy, University of California, Irvine, Irvine, California, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
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12
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Salmonella enterica Requires Lipid Metabolism Genes To Replicate in Proinflammatory Macrophages and Mice. Infect Immun 2019; 88:IAI.00776-19. [PMID: 31611277 DOI: 10.1128/iai.00776-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/06/2019] [Indexed: 12/28/2022] Open
Abstract
To survive and replicate during infection, pathogens utilize different carbon and energy sources depending on the nutritional landscape of their host microenvironment. Salmonella enterica serovar Typhimurium is an intracellular bacterial pathogen that occupies diverse cellular niches. While it is clear that Salmonella Typhimurium requires access to glucose during systemic infection, data on the need for lipid metabolism are mixed. We report that Salmonella Typhimurium strains lacking lipid metabolism genes were defective for systemic infection of mice. Bacterial lipid import, β-oxidation, and glyoxylate shunt genes were required for tissue colonization upon oral or intraperitoneal inoculation. In cultured macrophages, lipid import and β-oxidation genes were required for bacterial replication and/or survival only when the cell culture medium was supplemented with nonessential amino acids. Removal of glucose from tissue culture medium further enhanced these phenotypes and, in addition, conferred a requirement for glyoxylate shunt genes. We also observed that Salmonella Typhimurium needs lipid metabolism genes in proinflammatory but not anti-inflammatory macrophages. These results suggest that during systemic infection, the Salmonella Typhimurium that relies upon host lipids to replicate is within proinflammatory macrophages that have access to amino acids but not glucose. An improved understanding of the host microenvironments in which pathogens have specific metabolic requirements may facilitate the development of targeted approaches to treatment.
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13
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Chew SY, Chee WJY, Than LTL. The glyoxylate cycle and alternative carbon metabolism as metabolic adaptation strategies of Candida glabrata: perspectives from Candida albicans and Saccharomyces cerevisiae. J Biomed Sci 2019; 26:52. [PMID: 31301737 PMCID: PMC6626413 DOI: 10.1186/s12929-019-0546-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/09/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Carbon utilization and metabolism are fundamental to every living organism for cellular growth. For intracellular human fungal pathogens such as Candida glabrata, an effective metabolic adaptation strategy is often required for survival and pathogenesis. As one of the host defence strategies to combat invading pathogens, phagocytes such as macrophages constantly impose restrictions on pathogens' access to their preferred carbon source, glucose. Surprisingly, it has been reported that engulfed C. glabrata are able to survive in this harsh microenvironment, further suggesting alternative carbon metabolism as a potential strategy for this opportunistic fungal pathogen to persist in the host. MAIN TEXT In this review, we discuss alternative carbon metabolism as a metabolic adaptation strategy for the pathogenesis of C. glabrata. As the glyoxylate cycle is an important pathway in the utilization of alternative carbon sources, we also highlight the key metabolic enzymes in the glyoxylate cycle and its necessity for the pathogenesis of C. glabrata. Finally, we explore the transcriptional regulatory network of the glyoxylate cycle. CONCLUSION Considering evidence from Candida albicans and Saccharomyces cerevisiae, this review summarizes the current knowledge of the glyoxylate cycle as an alternative carbon metabolic pathway of C. glabrata.
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Affiliation(s)
- Shu Yih Chew
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Wallace Jeng Yang Chee
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Leslie Thian Lung Than
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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14
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Kumar SS, Penesyan A, Elbourne LDH, Gillings MR, Paulsen IT. Catabolism of Nucleic Acids by a Cystic Fibrosis Pseudomonas aeruginosa Isolate: An Adaptive Pathway to Cystic Fibrosis Sputum Environment. Front Microbiol 2019; 10:1199. [PMID: 31214142 PMCID: PMC6555301 DOI: 10.3389/fmicb.2019.01199] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/13/2019] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa is a major cause of morbidity and mortality in patients with cystic fibrosis (CF). We undertook Biolog Phenotype Microarray testing of P. aeruginosa CF isolates to investigate their catabolic capabilities compared to P. aeruginosa laboratory strains PAO1 and PA14. One strain, PASS4, displayed an unusual phenotype, only showing strong respiration on adenosine and inosine. Further testing indicated that PASS4 could grow on DNA as a sole carbon source, with a higher biomass production than PAO1. This suggested that PASS4 was specifically adapted to metabolize extracellular DNA, a substrate present at high concentrations in the CF lung. Transcriptomic and proteomic profiling of PASS4 and PAO1 when grown with DNA as a sole carbon source identified a set of upregulated genes, including virulence and host-adaptation genes. PASS4 was unable to utilize N-Acetyl-D-glucosamine, and when we selected PASS4 mutants able to grow on this carbon source, they also displayed a gain in ability to catabolize a broad range of other carbon sources. Genome sequencing of the mutants revealed they all contained mutations within the purK gene, encoding a key protein in the de novo purine biosynthesis pathway. This suggested that PASS4 was a purine auxotroph. Growth assays in the presence of 2 mM adenosine and the complementation of PASS4 with an intact purK gene confirmed this conclusion. Purine auxotrophy may represent a viable microbial strategy for adaptation to DNA-rich environments such as the CF lung.
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Affiliation(s)
| | - Anahit Penesyan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | | | - Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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15
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Wu X, Siehnel RJ, Garudathri J, Staudinger BJ, Hisert KB, Ozer EA, Hauser AR, Eng JK, Manoil C, Singh PK, Bruce JE. In Vivo Proteome of Pseudomonas aeruginosa in Airways of Cystic Fibrosis Patients. J Proteome Res 2019; 18:2601-2612. [PMID: 31060355 DOI: 10.1021/acs.jproteome.9b00122] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Chronic airway infection with P. aeruginosa (PA) is a hallmark of cystic fibrosis (CF) disease. The mechanisms producing PA persistence in CF therapies remain poorly understood. To gain insight on PA physiology in patient airways and better understand how in vivo bacterial functioning differs from in vitro conditions, we investigated the in vivo proteomes of PA in 35 sputum samples from 11 CF patients. We developed a novel bacterial-enrichment method that relies on differential centrifugation and detergent treatment to enrich for bacteria to improve identification of PA proteome with CF sputum samples. Using two nonredundant peptides as a cutoff, a total of 1304 PA proteins were identified directly from CF sputum samples. The in vivo PA proteomes were compared with the proteomes of ex vivo-grown PA populations from the same patient sample. Label-free quantitation and proteome comparison revealed the in vivo up-regulation of siderophore TonB-dependent receptors, remodeling in central carbon metabolism including glyoxylate cycle and lactate utilization, and alginate overproduction. Knowledge of these in vivo proteome differences or others derived using the presented methodology could lead to future treatment strategies aimed at altering PA physiology in vivo to compromise infectivity or improve antibiotic efficacy.
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16
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Chew SY, Ho KL, Cheah YK, Ng TS, Sandai D, Brown AJP, Than LTL. Glyoxylate cycle gene ICL1 is essential for the metabolic flexibility and virulence of Candida glabrata. Sci Rep 2019; 9:2843. [PMID: 30808979 PMCID: PMC6391369 DOI: 10.1038/s41598-019-39117-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/17/2019] [Indexed: 11/08/2022] Open
Abstract
The human fungal pathogen Candida glabrata appears to utilise unique stealth, evasion and persistence strategies in subverting the onslaught of host immune response during systemic infection. However, macrophages actively deprive the intracellular fungal pathogen of glucose, and therefore alternative carbon sources probably support the growth and survival of engulfed C. glabrata. The present study aimed to investigate the role of the glyoxylate cycle gene ICL1 in alternative carbon utilisation and its importance for the virulence of C. glabrata. The data showed that disruption of ICL1 rendered C. glabrata unable to utilise acetate, ethanol or oleic acid. In addition, C. glabrata icl1∆ cells displayed significantly reduced biofilm growth in the presence of several alternative carbon sources. It was also found that ICL1 is crucial for the survival of C. glabrata in response to macrophage engulfment. Disruption of ICL1 also conferred a severe attenuation in the virulence of C. glabrata in the mouse model of invasive candidiasis. In conclusion, a functional glyoxylate cycle is essential for C. glabrata to utilise certain alternative carbon sources in vitro and to display full virulence in vivo. This reinforces the view that antifungal drugs that target fungal Icl1 have potential for future therapeutic intervention.
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Affiliation(s)
- Shu Yih Chew
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Yoke Kqueen Cheah
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Tzu Shan Ng
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Wilayah Persekutuan, Kuala Lumpur, Malaysia
| | - Doblin Sandai
- Infectomics Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Alistair J P Brown
- MRC Centre for Medical Mycology at the University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom
| | - Leslie Thian Lung Than
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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17
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Abstract
2017 marks the 60th anniversary of Krebs’ seminal paper on the glyoxylate shunt (and coincidentally, also the 80th anniversary of his discovery of the citric acid cycle). Sixty years on, we have witnessed substantial developments in our understanding of how flux is partitioned between the glyoxylate shunt and the oxidative decarboxylation steps of the citric acid cycle. The last decade has shown us that the beautifully elegant textbook mechanism that regulates carbon flux through the shunt in E. coli is an oversimplification of the situation in many other bacteria. The aim of this review is to assess how this new knowledge is impacting our understanding of flux control at the TCA cycle/glyoxylate shunt branch point in a wider range of genera, and to summarize recent findings implicating a role for the glyoxylate shunt in cellular functions other than metabolism.
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Affiliation(s)
- Stephen K. Dolan
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom;,
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom;,
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18
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Crousilles A, Dolan SK, Brear P, Chirgadze DY, Welch M. Gluconeogenic precursor availability regulates flux through the glyoxylate shunt in Pseudomonas aeruginosa. J Biol Chem 2018; 293:14260-14269. [PMID: 30030382 DOI: 10.1074/jbc.ra118.004514] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 07/18/2018] [Indexed: 11/06/2022] Open
Abstract
The glyoxylate shunt bypasses the oxidative decarboxylation steps of the tricarboxylic acid (TCA) cycle, thereby conserving carbon skeletons for gluconeogenesis and biomass production. In Escherichia coli, carbon flux is redirected through the first enzyme of the glyoxylate shunt, isocitrate lyase (ICL), following phosphorylation and inactivation of the TCA cycle enzyme, isocitrate dehydrogenase (ICD), by the kinase/phosphatase, AceK. In contrast, mycobacterial species lack AceK and employ a phosphorylation-insensitive isocitrate dehydrogenase (IDH), which is allosterically activated by the product of ICL activity, glyoxylate. However, Pseudomonas aeruginosa expresses IDH, ICD, ICL, and AceK, raising the question of how these enzymes are regulated to ensure proper flux distribution between the competing pathways. Here, we present the structure, kinetics, and regulation of ICL, IDH, and ICD from P. aeruginosa We found that flux partitioning is coordinated through reciprocal regulation of these enzymes, linking distribution of carbon flux to the availability of the key gluconeogenic precursors, oxaloacetate and pyruvate. Specifically, a greater abundance of these metabolites activated IDH and inhibited ICL, leading to increased TCA cycle flux. Regulation was also exerted through AceK-dependent phosphorylation of ICD; high levels of acetyl-CoA (which would be expected to accumulate when oxaloacetate is limiting) stimulated the kinase activity of AceK, whereas high levels of oxaloacetate stimulated its phosphatase activity. In summary, the TCA cycle-glyoxylate shunt branch point in P. aeruginosa has a complex enzymology that is profoundly different from those in other species characterized to date. Presumably, this reflects its predilection for consuming fatty acids, especially during infection scenarios.
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Affiliation(s)
- Audrey Crousilles
- From the Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom
| | - Stephen K Dolan
- From the Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom
| | - Paul Brear
- From the Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom
| | - Dimitri Y Chirgadze
- From the Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom
| | - Martin Welch
- From the Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom
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19
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Chevalier S, Bouffartigues E, Bodilis J, Maillot O, Lesouhaitier O, Feuilloley MGJ, Orange N, Dufour A, Cornelis P. Structure, function and regulation of Pseudomonas aeruginosa porins. FEMS Microbiol Rev 2017; 41:698-722. [PMID: 28981745 DOI: 10.1093/femsre/fux020] [Citation(s) in RCA: 218] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/24/2017] [Indexed: 12/11/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium belonging to the γ-proteobacteria. Like other members of the Pseudomonas genus, it is known for its metabolic versatility and its ability to colonize a wide range of ecological niches, such as rhizosphere, water environments and animal hosts, including humans where it can cause severe infections. Another particularity of P. aeruginosa is its high intrinsic resistance to antiseptics and antibiotics, which is partly due to its low outer membrane permeability. In contrast to Enterobacteria, pseudomonads do not possess general diffusion porins in their outer membrane, but rather express specific channel proteins for the uptake of different nutrients. The major outer membrane 'porin', OprF, has been extensively investigated, and displays structural, adhesion and signaling functions while its role in the diffusion of nutrients is still under discussion. Other porins include OprB and OprB2 for the diffusion of glucose, the two small outer membrane proteins OprG and OprH, and the two porins involved in phosphate/pyrophosphate uptake, OprP and OprO. The remaining nineteen porins belong to the so-called OprD (Occ) family, which is further split into two subfamilies termed OccD (8 members) and OccK (11 members). In the past years, a large amount of information concerning the structure, function and regulation of these porins has been published, justifying why an updated review is timely.
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Affiliation(s)
- Sylvie Chevalier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Emeline Bouffartigues
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Josselin Bodilis
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Olivier Maillot
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Olivier Lesouhaitier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Marc G J Feuilloley
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Nicole Orange
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Alain Dufour
- IUEM, Laboratoire de Biotechnologie et Chimie Marines EA 3884, Université de Bretagne-Sud (UEB), 56321 Lorient, France
| | - Pierre Cornelis
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
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20
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McVey AC, Medarametla P, Chee X, Bartlett S, Poso A, Spring DR, Rahman T, Welch M. Structural and Functional Characterization of Malate Synthase G from Opportunistic Pathogen Pseudomonas aeruginosa. Biochemistry 2017; 56:5539-5549. [PMID: 28985053 DOI: 10.1021/acs.biochem.7b00852] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen recognized as a critical threat by the World Health Organization because of the dwindling number of effective therapies available to treat infections. Over the past decade, it has become apparent that the glyoxylate shunt plays a vital role in sustaining P. aeruginosa during infection scenarios. The glyoxylate shunt comprises two enzymes: isocitrate lyase and malate synthase isoform G. Inactivation of these enzymes has been reported to abolish the ability of P. aeruginosa to establish infection in a mammalian model system, yet we still lack the structural information to support drug design efforts. In this work, we describe the first X-ray crystal structure of P. aeruginosa malate synthase G in the apo form at 1.62 Å resolution. The enzyme is a monomer composed of four domains and is highly conserved with homologues found in other clinically relevant microorganisms. It is also dependent on Mg2+ for catalysis. Metal ion binding led to a change in the intrinsic fluorescence of the protein, allowing us to quantitate its affinity for Mg2+. We also identified putative drug binding sites in malate synthase G using computational analysis and, because of the high resolution of the experimental data, were further able to characterize its hydration properties. Our data reveal two promising binding pockets in malate synthase G that may be exploited for drug design.
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Affiliation(s)
- Alyssa C McVey
- Department of Biochemistry, University of Cambridge , Cambridge CB2 1QW, U.K
| | | | - Xavier Chee
- Department of Pharmacology, University of Cambridge , Cambridge CB2 1PD, U.K
| | - Sean Bartlett
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland , 70211 Kuopio, Finland.,Department of Internal Medicine VIII, University Hospital Tübingen , 72076 Tübingen, Germany
| | - David R Spring
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K
| | - Taufiq Rahman
- Department of Pharmacology, University of Cambridge , Cambridge CB2 1PD, U.K
| | - Martin Welch
- Department of Biochemistry, University of Cambridge , Cambridge CB2 1QW, U.K
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21
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Flynn JM, Phan C, Hunter RC. Genome-Wide Survey of Pseudomonas aeruginosa PA14 Reveals a Role for the Glyoxylate Pathway and Extracellular Proteases in the Utilization of Mucin. Infect Immun 2017; 85:e00182-17. [PMID: 28507068 PMCID: PMC5520445 DOI: 10.1128/iai.00182-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/08/2017] [Indexed: 01/06/2023] Open
Abstract
Chronic airway infections by the opportunistic pathogen Pseudomonas aeruginosa are a major cause of mortality in cystic fibrosis (CF) patients. Although this bacterium has been extensively studied for its virulence determinants, biofilm growth, and immune evasion mechanisms, comparatively little is known about the nutrient sources that sustain its growth in vivo Respiratory mucins represent a potentially abundant bioavailable nutrient source, although we have recently shown that canonical pathogens inefficiently use these host glycoproteins as a growth substrate. However, given that P. aeruginosa, particularly in its biofilm mode of growth, is thought to grow slowly in vivo, the inefficient use of mucin glycoproteins may be relevant to its persistence within the CF airways. To this end, we used whole-genome fitness analysis, combining transposon mutagenesis with high-throughput sequencing, to identify genetic determinants required for P. aeruginosa growth using intact purified mucins as a sole carbon source. Our analysis reveals a biphasic growth phenotype, during which the glyoxylate pathway and amino acid biosynthetic machinery are required for mucin utilization. Secondary analyses confirmed the simultaneous liberation and consumption of acetate during mucin degradation and revealed a central role for the extracellular proteases LasB and AprA. Together, these studies describe a molecular basis for mucin-based nutrient acquisition by P. aeruginosa and reveal a host-pathogen dynamic that may contribute to its persistence within the CF airways.
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Affiliation(s)
- Jeffrey M Flynn
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Chi Phan
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ryan C Hunter
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
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22
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Abdou E, Jiménez de Bagüés MP, Martínez-Abadía I, Ouahrani-Bettache S, Pantesco V, Occhialini A, Al Dahouk S, Köhler S, Jubier-Maurin V. RegA Plays a Key Role in Oxygen-Dependent Establishment of Persistence and in Isocitrate Lyase Activity, a Critical Determinant of In vivo Brucella suis Pathogenicity. Front Cell Infect Microbiol 2017; 7:186. [PMID: 28573107 PMCID: PMC5435760 DOI: 10.3389/fcimb.2017.00186] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 04/28/2017] [Indexed: 12/25/2022] Open
Abstract
For aerobic human pathogens, adaptation to hypoxia is a critical factor for the establishment of persistent infections, as oxygen availability is low inside the host. The two-component system RegB/A of Brucella suis plays a central role in the control of respiratory systems adapted to oxygen deficiency, and in persistence in vivo. Using an original "in vitro model of persistence" consisting in gradual oxygen depletion, we compared transcriptomes and proteomes of wild-type and ΔregA strains to identify the RegA-regulon potentially involved in the set-up of persistence. Consecutive to oxygen consumption resulting in growth arrest, 12% of the genes in B. suis were potentially controlled directly or indirectly by RegA, among which numerous transcriptional regulators were up-regulated. In contrast, genes or proteins involved in envelope biogenesis and in cellular division were repressed, suggesting a possible role for RegA in the set-up of a non-proliferative persistence state. Importantly, the greatest number of the RegA-repressed genes and proteins, including aceA encoding the functional IsoCitrate Lyase (ICL), were involved in energy production. A potential consequence of this RegA impact may be the slowing-down of the central metabolism as B. suis progressively enters into persistence. Moreover, ICL is an essential determinant of pathogenesis and long-term interactions with the host, as demonstrated by the strict dependence of B. suis on ICL activity for multiplication and persistence during in vivo infection. RegA regulates gene or protein expression of all functional groups, which is why RegA is a key regulator of B. suis in adaptation to oxygen depletion. This function may contribute to the constraint of bacterial growth, typical of chronic infection. Oxygen-dependent activation of two-component systems that control persistence regulons, shared by several aerobic human pathogens, has not been studied in Brucella sp. before. This work therefore contributes significantly to the unraveling of persistence mechanisms in this important zoonotic pathogen.
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Affiliation(s)
- Elias Abdou
- Institut de Recherche en Infectiologie de Montpellier UMR9004, Centre National de la Recherche Scientifique, Université de MontpellierMontpellier, France
| | - María P. Jiménez de Bagüés
- Unidad de Tecnología en Producción y Sanidad Animal, Centro de Investigación y Tecnología Agroalimentaria, Instituto Agroalimentario de Aragón (CITA-Universidad de Zaragoza)Zaragoza, Spain
| | - Ignacio Martínez-Abadía
- Institut de Recherche en Infectiologie de Montpellier UMR9004, Centre National de la Recherche Scientifique, Université de MontpellierMontpellier, France
| | - Safia Ouahrani-Bettache
- Institut de Recherche en Infectiologie de Montpellier UMR9004, Centre National de la Recherche Scientifique, Université de MontpellierMontpellier, France
| | - Véronique Pantesco
- Institut de Médecine Régénératrice et Biothérapie—U1183 Institut National de la Santé et de la Recherche MédicaleMontpellier, France
| | - Alessandra Occhialini
- Institut de Recherche en Infectiologie de Montpellier UMR9004, Centre National de la Recherche Scientifique, Université de MontpellierMontpellier, France
| | - Sascha Al Dahouk
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Stephan Köhler
- Institut de Recherche en Infectiologie de Montpellier UMR9004, Centre National de la Recherche Scientifique, Université de MontpellierMontpellier, France
| | - Véronique Jubier-Maurin
- Institut de Recherche en Infectiologie de Montpellier UMR9004, Centre National de la Recherche Scientifique, Université de MontpellierMontpellier, France
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23
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Metabolic flux analyses of Pseudomonas aeruginosa cystic fibrosis isolates. Metab Eng 2016; 38:251-263. [PMID: 27637318 DOI: 10.1016/j.ymben.2016.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/07/2016] [Accepted: 09/11/2016] [Indexed: 01/22/2023]
Abstract
Pseudomonas aeruginosa is a metabolically versatile wide-ranging opportunistic pathogen. In humans P. aeruginosa causes infections of the skin, urinary tract, blood, and the lungs of Cystic Fibrosis patients. In addition, P. aeruginosa's broad environmental distribution, relatedness to biotechnologically useful species, and ability to form biofilms have made it the focus of considerable interest. We used 13C metabolic flux analysis (MFA) and flux balance analysis to understand energy and redox production and consumption and to explore the metabolic phenotypes of one reference strain and five strains isolated from the lungs of cystic fibrosis patients. Our results highlight the importance of the oxidative pentose phosphate and Entner-Doudoroff pathways in P. aeruginosa growth. Among clinical strains we report two divergent metabolic strategies and identify changes between genetically related strains that have emerged during a chronic infection of the same patient. MFA revealed that the magnitude of fluxes through the glyoxylate cycle correlates with growth rates.
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24
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Sethupathy S, Prasath KG, Ananthi S, Mahalingam S, Balan SY, Pandian SK. Proteomic analysis reveals modulation of iron homeostasis and oxidative stress response in Pseudomonas aeruginosa PAO1 by curcumin inhibiting quorum sensing regulated virulence factors and biofilm production. J Proteomics 2016; 145:112-126. [DOI: 10.1016/j.jprot.2016.04.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 04/15/2016] [Accepted: 04/17/2016] [Indexed: 01/01/2023]
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25
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Requirement of the isocitrate lyase gene ICL1 for VPS41-mediated starvation response in Cryptococcus neoformans. J Microbiol 2016; 54:487-91. [PMID: 27350614 DOI: 10.1007/s12275-016-6177-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 05/25/2016] [Accepted: 05/31/2016] [Indexed: 10/21/2022]
Abstract
Cryptococcus neoformans is a major cause of fungal meningitis in individuals with impaired immunity. Our previous studies have shown that the VPS41 gene plays a critical role in the survival of Cryptococcus neoformans under nitrogen starvation; however, the molecular mechanisms underlying VPS41-mediated starvation response remain to be elucidated. In the present study, we show that, under nitrogen starvation, VPS41 strongly enhanced ICL1 expression in C. neoformans and that overexpression of ICL1 in the vps41 mutant dramatically suppressed its defects in starvation response due to the loss of VPS41 function. Moreover, targeted deletion of ICL1 resulted in a dramatic decline in viability of C. neoformans cells under nitrogen deprivation. Taken together, our data suggest a model in which VPS41 up-regulates ICL1 expression, directly or indirectly, to promote survival of C. neoformans under nitrogen starvation.
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26
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Scoffield J, Silo-Suh L. Glycerol metabolism promotes biofilm formation by Pseudomonas aeruginosa. Can J Microbiol 2016; 62:704-10. [PMID: 27392247 DOI: 10.1139/cjm-2016-0119] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pseudomonas aeruginosa causes persistent infections in the airways of cystic fibrosis (CF) patients. Airway sputum contains various host-derived nutrients that can be utilized by P. aeruginosa, including phosphotidylcholine, a major component of host cell membranes. Phosphotidylcholine can be degraded by P. aeruginosa to glycerol and fatty acids to increase the availability of glycerol in the CF lung. In this study, we explored the role that glycerol metabolism plays in biofilm formation by P. aeruginosa. We report that glycerol metabolism promotes biofilm formation by both a chronic CF isolate (FRD1) and a wound isolate (PAO1) of P. aeruginosa. Moreover, loss of the GlpR regulator, which represses the expression of genes involved in glycerol metabolism, enhances biofilm formation in FRD1 through the upregulation of Pel polysaccharide. Taken together, our results suggest that glycerol metabolism may be a key factor that contributes to P. aeruginosa persistence by promoting biofilm formation.
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Affiliation(s)
- Jessica Scoffield
- a Department of Pediatric Dentistry, 1919 7th Avenue South, Room SDB 801, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Laura Silo-Suh
- b Department of Basic Medical Sciences, Mercer University, School of Medicine, Macon, GA 31207, USA
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27
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Suh SJ, Shuman J, Carroll LP, Silo-Suh L. BEEP: An assay to detect bio-energetic and envelope permeability alterations in Pseudomonas aeruginosa. J Microbiol Methods 2016; 125:81-6. [PMID: 27089860 DOI: 10.1016/j.mimet.2016.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/13/2016] [Accepted: 04/13/2016] [Indexed: 12/21/2022]
Abstract
We developed an effective and rapid assay to detect both bio-energetic and envelope permeability (BEEP) alterations of Pseudomonas aeruginosa. The assay is based on quantification of extracellular ATP in bacterial cultures using luciferase as a reporter. To demonstrate the validity of our assay we conducted a biased screen of a transposon insertion library in P. aeruginosa strain PAO1 in order to expedite the isolation of mutants with defects in bioenergetic pathways. We successfully isolated insertion mutants that were reduced for extracellular ATP accumulation and identified the corresponding mutations that caused the phenotype. Most of the genes identified from this analysis were associated with energy metabolism and several appeared to be potentially novel bioenergetic targets. In addition, we show that treatment of P. aeruginosa strain PAO1 with antibiotics that disrupt the bacterial cell envelope leads to greater extracellular ATP accumulation. In summary, increases in extracellular ATP accumulation above wild type levels indicated a perturbation of membrane permeability while decreases in extracellular ATP accumulation indicated defects in bioenergetics.
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Affiliation(s)
- Sang-Jin Suh
- Department of Biological Sciences, Auburn University, AL 36849, United States.
| | - Jon Shuman
- Division of Basic Medical Sciences, Mercer University School of Medicine, Macon, GA 31207, United States.
| | - Leslie P Carroll
- Division of Basic Medical Sciences, Mercer University School of Medicine, Macon, GA 31207, United States.
| | - Laura Silo-Suh
- Division of Basic Medical Sciences, Mercer University School of Medicine, Macon, GA 31207, United States.
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Lassek C, Berger A, Zühlke D, Wittmann C, Riedel K. Proteome and carbon flux analysis of Pseudomonas aeruginosa clinical isolates from different infection sites. Proteomics 2016; 16:1381-5. [PMID: 26959854 DOI: 10.1002/pmic.201500228] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 01/31/2016] [Accepted: 03/03/2016] [Indexed: 11/11/2022]
Abstract
Pseudomonas aeruginosa is known as opportunistic pathogen frequently isolated from different infection sites. To investigate the expression rates of P. aeruginosa proteins commonly expressed by different clinical isolates, absolute protein quantities were determined employing a gel-free and data-independent LC-IMS(E) approach. Moreover, the metabolic diversity of these isolates was investigated by (13) C-metabolic flux analyses. 812 proteins were reproducibly identified and absolutely quantified for the reference strain P. aeruginosa PAO1, 363 of which were also identified and relatively quantified in all isolates. Whilst the majority of these proteins were expressed in constant amounts, expression rates of 42 proteins were highly variable between the isolates. Notably, the outer membrane protein OprH and the response regulator PhoP were strongly expressed in burned wounds isolates compared to lung/urinary tract isolates. Moreover, proteins involved in iron/amino acids uptake were found to be highly abundant in urinary tract isolates. The fluxome data revealed a conserved glycolysis, and a niche-specific divergence in fluxes through the glyoxylate shunt and the TCA cycle among the isolates. The integrated proteome/fluxome analysis did not indicate straightforward correlation between the protein amount and flux, but rather points to additional layers of regulation that mediate metabolic adaption of P. aeruginosa to different host environments. All MS data have been deposited in the ProteomeXchange with identifier PXD002373 (http://proteomecentral.proteomexchange.org/dataset/PXD002373).
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Affiliation(s)
- Christian Lassek
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Antje Berger
- Institute of Biochemical Engineering, TU Braunschweig, Braunschweig, Germany
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany.,Helmholtz Centre for Infection Research, Braunschweig, Germany
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29
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Ahn S, Jung J, Jang IA, Madsen EL, Park W. Role of Glyoxylate Shunt in Oxidative Stress Response. J Biol Chem 2016; 291:11928-38. [PMID: 27036942 DOI: 10.1074/jbc.m115.708149] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Indexed: 12/16/2022] Open
Abstract
The glyoxylate shunt (GS) is a two-step metabolic pathway (isocitrate lyase, aceA; and malate synthase, glcB) that serves as an alternative to the tricarboxylic acid cycle. The GS bypasses the carbon dioxide-producing steps of the tricarboxylic acid cycle and is essential for acetate and fatty acid metabolism in bacteria. GS can be up-regulated under conditions of oxidative stress, antibiotic stress, and host infection, which implies that it plays important but poorly explored roles in stress defense and pathogenesis. In many bacterial species, including Pseudomonas aeruginosa, aceA and glcB are not in an operon, unlike in Escherichia coli In P. aeruginosa, we explored relationships between GS genes and growth, transcription profiles, and biofilm formation. Contrary to our expectations, deletion of aceA in P. aeruginosa improved cell growth under conditions of oxidative and antibiotic stress. Transcriptome data suggested that aceA mutants underwent a metabolic shift toward aerobic denitrification; this was supported by additional evidence, including up-regulation of denitrification-related genes, decreased oxygen consumption without lowering ATP yield, increased production of denitrification intermediates (NO and N2O), and increased cyanide resistance. The aceA mutants also produced a thicker exopolysaccharide layer; that is, a phenotype consistent with aerobic denitrification. A bioinformatic survey across known bacterial genomes showed that only microorganisms capable of aerobic metabolism possess the glyoxylate shunt. This trend is consistent with the hypothesis that the GS plays a previously unrecognized role in allowing bacteria to tolerate oxidative stress.
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Affiliation(s)
- Sungeun Ahn
- From the Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea and
| | - Jaejoon Jung
- From the Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea and
| | - In-Ae Jang
- From the Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea and
| | - Eugene L Madsen
- the Department of Microbiology, Cornell University, Ithaca, New York 14853
| | - Woojun Park
- From the Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea and
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30
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Crousilles A, Maunders E, Bartlett S, Fan C, Ukor EF, Abdelhamid Y, Baker Y, Floto A, Spring DR, Welch M. Which microbial factors really are important in Pseudomonas aeruginosa infections? Future Microbiol 2015; 10:1825-36. [DOI: 10.2217/fmb.15.100] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Over the last two decades, tens of millions of dollars have been invested in understanding virulence in the human pathogen, Pseudomonas aeruginosa. However, the top ‘hits’ obtained in a recent TnSeq analysis aimed at identifying those genes that are conditionally essential for infection did not include most of the known virulence factors identified in these earlier studies. Instead, it seems that P. aeruginosa faces metabolic challenges in vivo, and unless it can overcome these, it fails to thrive and is cleared from the host. In this review, we look at the kinds of metabolic pathways that the pathogen seems to find essential, and comment on how this knowledge might be therapeutically exploited.
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Affiliation(s)
- Audrey Crousilles
- Department of Biochemistry (Hopkins Building), Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Eve Maunders
- Department of Biochemistry (Hopkins Building), Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Sean Bartlett
- Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Catherine Fan
- Department of Biochemistry (Hopkins Building), Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Emem-Fong Ukor
- Department of Respiratory Medicine, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Yassmin Abdelhamid
- Department of Biochemistry (Hopkins Building), Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Ysobel Baker
- Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Andres Floto
- Department of Respiratory Medicine, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - David R Spring
- Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Martin Welch
- Department of Biochemistry (Hopkins Building), Tennis Court Road, Cambridge, CB2 1QW, UK
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31
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Couto N, Schooling SR, Dutcher JR, Barber J. Proteome Profiles of Outer Membrane Vesicles and Extracellular Matrix of Pseudomonas aeruginosa Biofilms. J Proteome Res 2015; 14:4207-22. [PMID: 26303878 DOI: 10.1021/acs.jproteome.5b00312] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the present work, two different proteomic platforms, gel-based and gel-free, were used to map the matrix and outer membrane vesicle exoproteomes of Pseudomonas aeruginosa PAO1 biofilms. These two proteomic strategies allowed us a confident identification of 207 and 327 proteins from enriched outer membrane vesicles and whole matrix isolated from biofilms. Because of the physicochemical characteristics of these subproteomes, the two strategies showed complementarity, and thus, the most comprehensive analysis of P. aeruginosa exoproteome to date was achieved. Under our conditions, outer membrane vesicles contribute approximately 20% of the whole matrix proteome, demonstrating that membrane vesicles are an important component of the matrix. The proteomic profiles were analyzed in terms of their biological context, namely, a biofilm. Accordingly relevant metabolic processes involved in cellular adaptation to the biofilm lifestyle as well as those related to P. aeruginosa virulence capabilities were a key feature of the analyses. The diversity of the matrix proteome corroborates the idea of high heterogeneity within the biofilm; cells can display different levels of metabolism and can adapt to local microenvironments making this proteomic analysis challenging. In addition to analyzing our own primary data, we extend the analysis to published data by other groups in order to deepen our understanding of the complexity inherent within biofilm populations.
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Affiliation(s)
- Narciso Couto
- Michael Barber Centre for Mass Spectrometry, Manchester Institute for Biotechnology, University of Manchester , Princess Road, Manchester, M1 7DN, U.K
| | - Sarah R Schooling
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph , Guelph, ON N1G 2W1, Canada.,Department of Physics, University of Guelph , Guelph, ON N1G 2W1, Canada
| | - John R Dutcher
- Department of Physics, University of Guelph , Guelph, ON N1G 2W1, Canada
| | - Jill Barber
- Michael Barber Centre for Mass Spectrometry, Manchester Institute for Biotechnology, University of Manchester , Princess Road, Manchester, M1 7DN, U.K.,Manchester Pharmacy School, University of Manchester , Stopford Building, Oxford Road, Manchester, M13 9PT, U.K
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32
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Daniels JB, Scoffield J, Woolnough JL, Silo-Suh L. Impact of glycerol-3-phosphate dehydrogenase on virulence factor production by Pseudomonas aeruginosa. Can J Microbiol 2015; 60:857-63. [PMID: 25409940 DOI: 10.1139/cjm-2014-0485] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pseudomonas aeruginosa establishes life-long chronic infections in the cystic fibrosis (CF) lung by utilizing various adaptation strategies. Some of these strategies include altering metabolic pathways to utilize readily available nutrients present in the host environment. The airway sputum contains various host-derived nutrients that can be utilized by P. aeruginosa, including phosphatidylcholine, a major component of lung surfactant. Pseudomonas aeruginosa can degrade phosphatidylcholine to glycerol and fatty acids to increase the availability of usable carbon sources in the CF lung. In this study, we show that some CF-adapted P. aeruginosa isolates utilize glycerol more efficiently as a carbon source than nonadapted isolates. Furthermore, a mutation in a gene required for glycerol utilization impacts the production of several virulence factors in both acute and chronic isolates of P. aeruginosa. Taken together, the results suggest that interference with this metabolic pathway may have potential therapeutic benefits.
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Affiliation(s)
- Jonathan B Daniels
- a Department of Basic Medical Sciences, Mercer University, School of Medicine, 1550 College Street, Macon, GA 31207, USA
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The fatty acid signaling molecule cis-2-decenoic acid increases metabolic activity and reverts persister cells to an antimicrobial-susceptible state. Appl Environ Microbiol 2014; 80:6976-91. [PMID: 25192989 DOI: 10.1128/aem.01576-14] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Persister cells, which are tolerant to antimicrobials, contribute to biofilm recalcitrance to therapeutic agents. In turn, the ability to kill persister cells is believed to significantly improve efforts in eradicating biofilm-related, chronic infections. While much research has focused on elucidating the mechanism(s) by which persister cells form, little is known about the mechanism or factors that enable persister cells to revert to an active and susceptible state. Here, we demonstrate that cis-2-decenoic acid (cis-DA), a fatty acid signaling molecule, is able to change the status of Pseudomonas aeruginosa and Escherichia coli persister cells from a dormant to a metabolically active state without an increase in cell number. This cell awakening is supported by an increase of the persister cells' respiratory activity together with changes in protein abundance and increases of the transcript expression levels of several metabolic markers, including acpP, 16S rRNA, atpH, and ppx. Given that most antimicrobials target actively growing cells, we also explored the effect of cis-DA on enhancing antibiotic efficacy in killing persister cells due to their inability to keep a persister cell state. Compared to antimicrobial treatment alone, combinational treatments of persister cell subpopulations with antimicrobials and cis-DA resulted in a significantly greater decrease in cell viability. In addition, the presence of cis-DA led to a decrease in the number of persister cells isolated. We thus demonstrate the ability of a fatty acid signaling molecule to revert bacterial cells from a tolerant phenotype to a metabolically active, antimicrobial-sensitive state.
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Abstract
The evolutionary success of bacteria depends greatly on their capacity to continually generate phenotypic diversity. Structured environments are particularly favorable for diversification because of attenuated clonal interference, which renders selective sweeps nearly impossible and enhances opportunities for adaptive radiation. We examined at the microscale level the emergence and the spatial and temporal dynamics of phenotypic diversity and their underlying causes in Escherichia coli colonies. An important dynamic heterogeneity in the growth, metabolic activity, morphology, gene expression patterns, stress response induction, and death patterns among cells within colonies was observed. Genetic analysis indicated that the phenotypic variation resulted mostly from mutations and that indole production, oxidative stress, and the RpoS-regulated general stress response played an important role in the generation of diversity. We observed the emergence and persistence of phenotypic variants within single colonies that exhibited variable fitness compared to the parental strain. Some variants showed improved capacity to produce biofilms, whereas others were able to use different nutrients or to tolerate antibiotics or oxidative stress. Taken together, our data show that bacterial colonies provide an ecological opportunity for the generation and maintenance of vast phenotypic diversity, which may increase the probability of population survival in unpredictable environments.
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35
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Berger A, Dohnt K, Tielen P, Jahn D, Becker J, Wittmann C. Robustness and plasticity of metabolic pathway flux among uropathogenic isolates of Pseudomonas aeruginosa. PLoS One 2014; 9:e88368. [PMID: 24709961 PMCID: PMC3977821 DOI: 10.1371/journal.pone.0088368] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 01/06/2014] [Indexed: 01/09/2023] Open
Abstract
Pseudomonas aeruginosa is a human pathogen that frequently causes urinary tract and catheter-associated urinary tract infections. Here, using 13C-metabolic flux analysis, we conducted quantitative analysis of metabolic fluxes in the model strain P. aeruginosa PAO1 and 17 clinical isolates. All P. aeruginosa strains catabolized glucose through the Entner-Doudoroff pathway with fully respiratory metabolism and no overflow. Together with other NADPH supplying reactions, this high-flux pathway provided by far more NADPH than needed for anabolism: a benefit for the pathogen to counteract oxidative stress imposed by the host. P. aeruginosa recruited the pentose phosphate pathway exclusively for biosynthesis. In contrast to glycolytic metabolism, which was conserved among all isolates, the flux through pyruvate metabolism, the tricarboxylic acid cycle, and the glyoxylate shunt was highly variable, likely caused by adaptive processes in individual strains during infection. This aspect of metabolism was niche-specific with respect to the corresponding flux because strains isolated from the urinary tract clustered separately from those originating from catheter-associated infections. Interestingly, most glucose-grown strains exhibited significant flux through the glyoxylate shunt. Projection into the theoretical flux space, which was computed using elementary flux-mode analysis, indicated that P. aeruginosa metabolism is optimized for efficient growth and exhibits significant potential for increasing NADPH supply to drive oxidative stress response.
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Affiliation(s)
- Antje Berger
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Katrin Dohnt
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Petra Tielen
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Dieter Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Judith Becker
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
- * E-mail:
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36
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Bacterial itaconate degradation promotes pathogenicity. Nat Chem Biol 2014; 10:371-7. [PMID: 24657929 DOI: 10.1038/nchembio.1482] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 02/14/2014] [Indexed: 12/30/2022]
Abstract
Itaconate (methylenesuccinate) was recently identified as a mammalian metabolite whose production is substantially induced during macrophage activation. This compound is a potent inhibitor of isocitrate lyase, a key enzyme of the glyoxylate cycle, which is a pathway required for the survival of many pathogens inside the eukaryotic host. Here we show that numerous bacteria, notably many pathogens such as Yersinia pestis and Pseudomonas aeruginosa, have three genes for itaconate degradation. They encode itaconate coenzyme A (CoA) transferase, itaconyl-CoA hydratase and (S)-citramalyl-CoA lyase, formerly referred to as CitE-like protein. These genes are known to be crucial for survival of some pathogens in macrophages. The corresponding enzymes convert itaconate into the cellular building blocks pyruvate and acetyl-CoA, thus enabling the bacteria to metabolize itaconate and survive in macrophages. The itaconate degradation and detoxification pathways of Yersinia and Pseudomonas are the result of convergent evolution. This work revealed a common persistence factor operating in many pathogenic bacteria.
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37
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Wynosky-Dolfi MA, Snyder AG, Philip NH, Doonan PJ, Poffenberger MC, Avizonis D, Zwack EE, Riblett AM, Hu B, Strowig T, Flavell RA, Jones RG, Freedman BD, Brodsky IE. Oxidative metabolism enables Salmonella evasion of the NLRP3 inflammasome. ACTA ACUST UNITED AC 2014; 211:653-68. [PMID: 24638169 PMCID: PMC3978275 DOI: 10.1084/jem.20130627] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Salmonella lacking the TCA enzyme aconitase trigger NLRP3 inflammasome activation in infected macrophages, leading to elevated inflammatory responses and reduced virulence. Microbial infection triggers assembly of inflammasome complexes that promote caspase-1–dependent antimicrobial responses. Inflammasome assembly is mediated by members of the nucleotide binding domain leucine-rich repeat (NLR) protein family that respond to cytosolic bacterial products or disruption of cellular processes. Flagellin injected into host cells by invading Salmonella induces inflammasome activation through NLRC4, whereas NLRP3 is required for inflammasome activation in response to multiple stimuli, including microbial infection, tissue damage, and metabolic dysregulation, through mechanisms that remain poorly understood. During systemic infection, Salmonella avoids NLRC4 inflammasome activation by down-regulating flagellin expression. Macrophages exhibit delayed NLRP3 inflammasome activation after Salmonella infection, suggesting that Salmonella may evade or prevent the rapid activation of the NLRP3 inflammasome. We therefore screened a Salmonella Typhimurium transposon library to identify bacterial factors that limit NLRP3 inflammasome activation. Surprisingly, absence of the Salmonella TCA enzyme aconitase induced rapid NLRP3 inflammasome activation. This inflammasome activation correlated with elevated levels of bacterial citrate, and required mitochondrial reactive oxygen species and bacterial citrate synthase. Importantly, Salmonella lacking aconitase displayed NLRP3- and caspase-1/11–dependent attenuation of virulence, and induced elevated serum IL-18 in wild-type mice. Together, our data link Salmonella genes controlling oxidative metabolism to inflammasome activation and suggest that NLRP3 inflammasome evasion promotes systemic Salmonella virulence.
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Affiliation(s)
- Meghan A Wynosky-Dolfi
- Department of Pathobiology, School of Veterinary Medicine; and 2 Immunology Graduate Group and 3 Cell and Molecular Biology Graduate Group, University of Pennsylvania, Kennett Square, PA 19104
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38
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Oliver KE, Silo-Suh L. Impact of D-amino acid dehydrogenase on virulence factor production by a Pseudomonas aeruginosa. Can J Microbiol 2013; 59:598-603. [PMID: 24011342 DOI: 10.1139/cjm-2013-0289] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Chronic Pseudomonas aeruginosa infections remain the leading cause of lung dysfunction and mortality for cystic fibrosis (CF) patients. Many other bacteria inhabit the CF lung, but P. aeruginosa utilizes novel strategies that allow it to colonize this environment as the predominant bacterial pathogen. D-Amino acid dehydrogenase encoded by dadA is highly expressed by P. aeruginosa within the CF lung, and it is required for optimal production of hydrogen cyanide by some CF-adapted isolates. To better understand the increased significance of D-amino acid dehydrogenase in P. aeruginosa physiology, we characterized the contribution of the dad operon to virulence factor production. In this study, we determined that DadA is required for optimal production of pyocyanin, pyoverdine, and rhamnolipid by CF-adapted and non-CF-adapted isolates of P. aeruginosa. In addition, DadA is required for optimal production of alginate, biofilm formation, and virulence of a CF-adapted isolated of P. aeruginosa in an alfalfa seedling model of infection. Taken together, the results indicate that DadA plays a pleiotropic role in the production of important virulence factors by P. aeruginosa.
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Affiliation(s)
- Kathryn E Oliver
- a Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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39
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Szabo AM, Endresz V, Somogyvari F, Miczak A, Faludi I. Isocitrate lyase encoding plasmids in BCG cause increased survival in ApoB100-only LDLR-/- mice. Mol Biol Rep 2013; 40:4721-5. [PMID: 23653002 DOI: 10.1007/s11033-013-2568-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 04/29/2013] [Indexed: 10/26/2022]
Abstract
We studied the role of isocitrate lyase in the interaction between Mycobacterium bovis BCG and mice. ApoB100-only LDLR-/- (B6;129S-ApoBtm2SgyLdlrtm1Her/J) mice were inoculated with M. bovis BCG harbouring plasmids carrying the gene for isocitrate lyase. The presence of ~29 times more copies of this gene resulted in a higher bacterial yield in the spleens and lungs of the infected mice. The spleen was 3-4 times heavier, and in the spleen the bacteria survived over 10 days longer than did the bacteria with the control plasmid. Propionate was less toxic for bacteria carrying icl plasmids in vitro. This recombinant BCG can be a possible vaccine candidate.
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Affiliation(s)
- Agnes Mira Szabo
- Department of Medical Microbiology and Immunobiology, University of Szeged, Dóm tér 10, Szeged, 6720, Hungary.
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40
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LaRock CN, Yu J, Horswill AR, Parsek MR, Minion FC. Transcriptome analysis of acyl-homoserine lactone-based quorum sensing regulation in Yersinia pestis [corrected]. PLoS One 2013; 8:e62337. [PMID: 23620823 PMCID: PMC3631167 DOI: 10.1371/journal.pone.0062337] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 03/20/2013] [Indexed: 11/19/2022] Open
Abstract
The etiologic agent of bubonic plague, Yersinia pestis, senses self-produced, secreted chemical signals in a process named quorum sensing. Though the closely related enteric pathogen Y. pseudotuberculosis uses quorum sensing system to regulate motility, the role of quorum sensing in Y. pestis has been unclear. In this study we performed transcriptional profiling experiments to identify Y. pestis quorum sensing regulated functions. Our analysis revealed that acyl-homoserine lactone-based quorum sensing controls the expression of several metabolic functions. Maltose fermentation and the glyoxylate bypass are induced by acyl-homoserine lactone signaling. This effect was observed at 30°C, indicating a potential role for quorum sensing regulation of metabolism at temperatures below the normal mammalian temperature. It is proposed that utilization of alternative carbon sources may enhance growth and/or survival during prolonged periods in natural habitats with limited nutrient sources, contributing to maintenance of plague in nature.
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Affiliation(s)
- Christopher N. LaRock
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Jing Yu
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Alexander R. Horswill
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Matthew R. Parsek
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - F. Chris Minion
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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41
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Behrends V, Bell TJ, Liebeke M, Cordes-Blauert A, Ashraf SN, Nair C, Zlosnik JEA, Williams HD, Bundy JG. Metabolite profiling to characterize disease-related bacteria: gluconate excretion by Pseudomonas aeruginosa mutants and clinical isolates from cystic fibrosis patients. J Biol Chem 2013; 288:15098-109. [PMID: 23572517 PMCID: PMC3663530 DOI: 10.1074/jbc.m112.442814] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Metabolic footprinting of supernatants has been proposed as a tool for assigning gene function. We used NMR spectroscopy to measure the exometabolome of 86 single-gene transposon insertion mutant strains (mutants from central carbon metabolism and regulatory mutants) of the opportunistic pathogen Pseudomonas aeruginosa, grown on a medium designed to represent the nutritional content of cystic fibrosis sputum. Functionally related genes had similar metabolic profiles. E.g. for two-component system mutants, the cognate response regulator and sensor kinase genes clustered tightly together. Some strains had metabolic phenotypes (metabotypes) that could be related to the known gene function. E.g. pyruvate dehydrogenase mutants accumulated large amounts of pyruvate in the medium. In other cases, the metabolic phenotypes were not easily interpretable. The rpoN mutant, which lacks the alternative σ factor RpoN (σ54), accumulated high levels of gluconate in the medium. In addition, endometabolome profiling of intracellular metabolites identified a number of systemic metabolic changes. We linked this to indirect regulation of the catabolite repression protein Crc via the non-coding RNA crcZ and found that a crcZ (but not crc) mutant also shared the high-gluconate phenotype. We profiled an additional set of relevant metabolic enzymes and transporters, including Crc targets, and showed that the Crc-regulated edd mutant (gluconate-6-phosphate dehydratase) had similar gluconate levels as the rpoN mutant. Finally, a set of clinical isolates showed patient- and random amplification of polymorphic DNA (RAPD) type-specific differences in gluconate production, which were associated significantly with resistance across four antibiotics (tobramycin, ciprofloxacin, aztreonam, and imipenem), indicating that this has potential clinical relevance.
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Affiliation(s)
- Volker Behrends
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
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The unexpected discovery of a novel low-oxygen-activated locus for the anoxic persistence of Burkholderia cenocepacia. ISME JOURNAL 2013; 7:1568-81. [PMID: 23486248 PMCID: PMC3721108 DOI: 10.1038/ismej.2013.36] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 01/25/2013] [Accepted: 01/28/2013] [Indexed: 12/11/2022]
Abstract
Burkholderia cenocepacia is a Gram-negative aerobic bacterium that belongs to a group of opportunistic pathogens displaying diverse environmental and pathogenic lifestyles. B. cenocepacia is known for its ability to cause lung infections in people with cystic fibrosis and it possesses a large 8 Mb multireplicon genome encoding a wide array of pathogenicity and fitness genes. Transcriptomic profiling across nine growth conditions was performed to identify the global gene expression changes made when B. cenocepacia changes niches from an environmental lifestyle to infection. In comparison to exponential growth, the results demonstrated that B. cenocepacia changes expression of over one-quarter of its genome during conditions of growth arrest, stationary phase and surprisingly, under reduced oxygen concentrations (6% instead of 20.9% normal atmospheric conditions). Multiple virulence factors are upregulated during these growth arrest conditions. A unique discovery from the comparative expression analysis was the identification of a distinct, co-regulated 50-gene cluster that was significantly upregulated during growth under low oxygen conditions. This gene cluster was designated the low-oxygen-activated (lxa) locus and encodes six universal stress proteins and proteins predicted to be involved in metabolism, transport, electron transfer and regulation. Deletion of the lxa locus resulted in B. cenocepacia mutants with aerobic growth deficiencies in minimal medium and compromised viability after prolonged incubation in the absence of oxygen. In summary, transcriptomic profiling of B. cenocepacia revealed an unexpected ability of aerobic Burkholderia to persist in the absence of oxygen and identified the novel lxa locus as key determinant of this important ecophysiological trait.
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Filiatrault MJ, Tombline G, Wagner VE, Van Alst N, Rumbaugh K, Sokol P, Schwingel J, Iglewski BH. Pseudomonas aeruginosa PA1006, which plays a role in molybdenum homeostasis, is required for nitrate utilization, biofilm formation, and virulence. PLoS One 2013; 8:e55594. [PMID: 23409004 PMCID: PMC3568122 DOI: 10.1371/journal.pone.0055594] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 12/27/2012] [Indexed: 12/31/2022] Open
Abstract
Pseudomonas aeruginosa (Pae) is a clinically important opportunistic pathogen. Herein, we demonstrate that the PA1006 protein is critical for all nitrate reductase activities, growth as a biofilm in a continuous flow system, as well as virulence in mouse burn and rat lung model systems. Microarray analysis revealed that ΔPA1006 cells displayed extensive alterations in gene expression including nitrate-responsive, quorum sensing (including PQS production), and iron-regulated genes, as well as molybdenum cofactor and Fe-S cluster biosynthesis factors, members of the TCA cycle, and Type VI Secretion System components. Phenotype Microarray™ profiles of ΔPA1006 aerobic cultures using Biolog plates also revealed a reduced ability to utilize a number of TCA cycle intermediates as well as a failure to utilize xanthine as a sole source of nitrogen. As a whole, these data indicate that the loss of PA1006 confers extensive changes in Pae metabolism. Based upon homology of PA1006 to the E. coli YhhP protein and data from the accompanying study, loss of PA1006 persulfuration and/or molybdenum homeostasis are likely the cause of extensive metabolic alterations that impact biofilm development and virulence in the ΔPA1006 mutant.
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Affiliation(s)
- Melanie J. Filiatrault
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Gregory Tombline
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Victoria E. Wagner
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Nadine Van Alst
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Kendra Rumbaugh
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Pam Sokol
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Johanna Schwingel
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Barbara H. Iglewski
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- * E-mail:
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Chung JCS, Rzhepishevska O, Ramstedt M, Welch M. Type III secretion system expression in oxygen-limited Pseudomonas aeruginosa cultures is stimulated by isocitrate lyase activity. Open Biol 2013; 3:120131. [PMID: 23363478 PMCID: PMC3603453 DOI: 10.1098/rsob.120131] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen and a common cause of chronic infections in individuals with cystic fibrosis (CF). Oxygen limitation was recently reported to regulate the expression of a major virulence determinant in P. aeruginosa, the type III secretion system (T3SS). Here, we show that expression of the T3SS in oxygen-limited growth conditions is strongly dependent on the glyoxylate shunt enzyme, isocitrate lyase (ICL; encoded by aceA), which was previously shown to be highly expressed in CF isolates. ICL-dependent regulation of the T3SS did not alter the expression level of the master transcriptional regulator, ExsA, but did affect expression of the T3 structural proteins, effectors and regulators (ExsC, ExsD and ExsE). An aceA mutant displayed enhanced biofilm formation during anaerobic growth, which suggested that AceA-dependent modulation of type III secretion might impinge upon the RetS/LadS signalling pathways. Indeed, our data suggest that RetS is able to mediate some of its effects through AceA, as expression of aceA in trans partially restored T3SS expression in a retS mutant. Our findings indicate that AceA is a key player in the metabolic regulation of T3SS expression during oxygen-limited growth of P. aeruginosa. To the best of our knowledge, this is the first demonstration that the T3SS can be regulated by factors that do not affect ExsA expression levels.
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Affiliation(s)
- Jade C S Chung
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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Fahnoe KC, Flanagan ME, Gibson G, Shanmugasundaram V, Che Y, Tomaras AP. Non-traditional antibacterial screening approaches for the identification of novel inhibitors of the glyoxylate shunt in gram-negative pathogens. PLoS One 2012; 7:e51732. [PMID: 23240059 PMCID: PMC3519852 DOI: 10.1371/journal.pone.0051732] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 11/08/2012] [Indexed: 01/06/2023] Open
Abstract
Antibacterial compounds that affect bacterial viability have traditionally been identified, confirmed, and characterized in standard laboratory media. The historical success of identifying new antibiotics via this route has justifiably established a traditional means of screening for new antimicrobials. The emergence of multi-drug-resistant (MDR) bacterial pathogens has expedited the need for new antibiotics, though many in the industry have questioned the source(s) of these new compounds. As many pharmaceutical companies' chemical libraries have been exhaustively screened via the traditional route, we have concluded that all compounds with any antibacterial potential have been identified. While new compound libraries and platforms are being pursued, it also seems prudent to screen the libraries we currently have in hand using alternative screening approaches. One strategy involves screening under conditions that better reflect the environment pathogens experience during an infection, and identifying in vivo essential targets and pathways that are dispensable for growth in standard laboratory media in vitro. Here we describe a novel screening strategy for identifying compounds that inhibit the glyoxylate shunt in Pseudomonas aeruginosa, a pathway that is required for bacterial survival in the pulmonary environment. We demonstrate that these compounds, which were not previously identified using traditional screening approaches, have broad-spectrum antibacterial activity when they are tested under in vivo-relevant conditions. We also show that these compounds have potent activity on both enzymes that comprise the glyoxylate shunt, a feature that was supported by computational homology modeling. By dual-targeting both enzymes in this pathway, we would expect to see a reduced propensity for resistance development to these compounds. Taken together, these data suggest that understanding the in vivo environment that bacterial pathogens must tolerate, and adjusting the antibacterial screening paradigm to reflect those conditions, could identify novel antibiotics for the treatment of serious MDR pathogens.
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Affiliation(s)
- Kelly C. Fahnoe
- Antibacterials Research Unit, Pfizer Worldwide Research & Development, Groton, Connecticut, United States of America
| | - Mark E. Flanagan
- Antibacterials Research Unit, Pfizer Worldwide Research & Development, Groton, Connecticut, United States of America
| | - Glenn Gibson
- Antibacterials Research Unit, Pfizer Worldwide Research & Development, Groton, Connecticut, United States of America
| | - Veerabahu Shanmugasundaram
- Antibacterials Research Unit, Pfizer Worldwide Research & Development, Groton, Connecticut, United States of America
| | - Ye Che
- Antibacterials Research Unit, Pfizer Worldwide Research & Development, Groton, Connecticut, United States of America
| | - Andrew P. Tomaras
- Antibacterials Research Unit, Pfizer Worldwide Research & Development, Groton, Connecticut, United States of America
- * E-mail:
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Behrends V, Ryall B, Zlosnik JEA, Speert DP, Bundy JG, Williams HD. Metabolic adaptations ofPseudomonas aeruginosaduring cystic fibrosis chronic lung infections. Environ Microbiol 2012; 15:398-408. [DOI: 10.1111/j.1462-2920.2012.02840.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Reen FJ, Clarke SL, Legendre C, McSweeney CM, Eccles KS, Lawrence SE, O'Gara F, McGlacken GP. Structure–function analysis of the C-3 position in analogues of microbial behavioural modulators HHQ and PQS. Org Biomol Chem 2012; 10:8903-10. [DOI: 10.1039/c2ob26823j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Genomic expression analysis reveals strategies of Burkholderia cenocepacia to adapt to cystic fibrosis patients' airways and antimicrobial therapy. PLoS One 2011; 6:e28831. [PMID: 22216120 PMCID: PMC3244429 DOI: 10.1371/journal.pone.0028831] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 11/15/2011] [Indexed: 12/20/2022] Open
Abstract
Pulmonary colonization of cystic fibrosis (CF) patients with Burkholderia cenocepacia or other bacteria of the Burkholderia cepacia complex (Bcc) is associated with worse prognosis and increased risk of death. During colonization, the bacteria may evolve under the stressing selection pressures exerted in the CF lung, in particular, those resulting from challenges of the host immune defenses, antimicrobial therapy, nutrient availability and oxygen limitation. Understanding the adaptive mechanisms that promote successful colonization and long-term survival of B. cenocepacia in the CF lung is essential for an improved therapeutic outcome of chronic infections. To get mechanistic insights into these adaptive strategies a transcriptomic analysis, based on DNA microarrays, was explored in this study. The genomic expression levels in two clonal variants isolated during long-term colonization of a CF patient who died from the cepacia syndrome were compared. One of the isolates examined, IST439, is the first B. cenocepacia isolate retrieved from the patient and the other isolate, IST4113, was obtained three years later and is more resistant to different classes of antimicrobials. Approximately 1000 genes were found to be differently expressed in the two clonal variants reflecting a marked reprogramming of genomic expression. The up-regulated genes in IST4113 include those involved in translation, iron uptake (in particular, in ornibactin biosynthesis), efflux of drugs and in adhesion to epithelial lung tissue and to mucin. Alterations related with adaptation to the nutritional environment of the CF lung and to an oxygen-limited environment are also suggested to be a key feature of transcriptional reprogramming occurring during long-term colonization, antibiotic therapy and the progression of the disease.
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Naughton S, Parker D, Seemann T, Thomas T, Turnbull L, Rose B, Bye P, Cordwell S, Whitchurch C, Manos J. Pseudomonas aeruginosa AES-1 exhibits increased virulence gene expression during chronic infection of cystic fibrosis lung. PLoS One 2011; 6:e24526. [PMID: 21935417 PMCID: PMC3174184 DOI: 10.1371/journal.pone.0024526] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 08/12/2011] [Indexed: 01/26/2023] Open
Abstract
Pseudomonas aeruginosa, the leading cause of morbidity and mortality in people with cystic fibrosis (CF), adapts for survival in the CF lung through both mutation and gene expression changes. Frequent clonal strains such as the Australian Epidemic Strain-1 (AES-1), have increased ability to establish infection in the CF lung and to superimpose and replace infrequent clonal strains. Little is known about the factors underpinning these properties. Analysis has been hampered by lack of expression array templates containing CF-strain specific genes. We sequenced the genome of an acute infection AES-1 isolate from a CF infant (AES-1R) and constructed a non-redundant micro-array (PANarray) comprising AES-1R and seven other sequenced P. aeruginosa genomes. The unclosed AES-1R genome comprised 6.254Mbp and contained 6957 putative genes, including 338 not found in the other seven genomes. The PANarray contained 12,543 gene probe spots; comprising 12,147 P. aeruginosa gene probes, 326 quality-control probes and 70 probes for non-P. aeruginosa genes, including phage and plant genes. We grew AES-1R and its isogenic pair AES-1M, taken from the same patient 10.5 years later and not eradicated in the intervening period, in our validated artificial sputum medium (ASMDM) and used the PANarray to compare gene expression of both in duplicate. 675 genes were differentially expressed between the isogenic pairs, including upregulation of alginate, biofilm, persistence genes and virulence-related genes such as dihydroorotase, uridylate kinase and cardiolipin synthase, in AES-1M. Non-PAO1 genes upregulated in AES-1M included pathogenesis-related (PAGI-5) genes present in strains PACS2 and PA7, and numerous phage genes. Elucidation of these genes' roles could lead to targeted treatment strategies for chronically infected CF patients.
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Affiliation(s)
- Sharna Naughton
- Department of Infectious Diseases and Immunology, University of Sydney, Sydney, Australia
| | - Dane Parker
- Department of Microbiology, Monash University, Melbourne, Australia
| | - Torsten Seemann
- Victorian Bioinformatics Consortium, Monash University, Melbourne, Australia
| | - Torsten Thomas
- School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio-Innovation, University of New South Wales, Sydney, Australia
| | - Lynne Turnbull
- Department of Microbiology, Monash University, Melbourne, Australia
- The ithree institute, University of Technology, Sydney, Australia
| | - Barbara Rose
- Department of Infectious Diseases and Immunology, University of Sydney, Sydney, Australia
| | - Peter Bye
- Department of Respiratory Medicine, Royal Prince Alfred Hospital, Sydney, Australia
- Sydney Medical School, University of Sydney, Sydney, Australia
| | - Stuart Cordwell
- School of Molecular Biosciences, University of Sydney, Sydney, Australia
| | - Cynthia Whitchurch
- Department of Microbiology, Monash University, Melbourne, Australia
- The ithree institute, University of Technology, Sydney, Australia
| | - Jim Manos
- Department of Infectious Diseases and Immunology, University of Sydney, Sydney, Australia
- * E-mail:
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50
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Reen FJ, Mooij MJ, Holcombe LJ, McSweeney CM, McGlacken GP, Morrissey JP, O'Gara F. The Pseudomonas quinolone signal (PQS), and its precursor HHQ, modulate interspecies and interkingdom behaviour. FEMS Microbiol Ecol 2011; 77:413-28. [PMID: 21539583 DOI: 10.1111/j.1574-6941.2011.01121.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The Pseudomonas quinolone signal (PQS), and its precursor 2-heptyl-4-quinolone (HHQ), play a key role in coordinating virulence in the important cystic fibrosis pathogen Pseudomonas aeruginosa. The discovery of HHQ analogues in Burkholderia and other microorganisms led us to investigate the possibility that these compounds can influence interspecies behaviour. We found that surface-associated phenotypes were repressed in Gram-positive and Gram-negative bacteria as well as in pathogenic yeast in response to PQS and HHQ. Motility was repressed in a broad range of bacteria, while biofilm formation in Bacillus subtilis and Candida albicans was repressed in the presence of HHQ, though initial adhesion was unaffected. Furthermore, HHQ exhibited potent bacteriostatic activity against several Gram-negative bacteria, including pathogenic Vibrio vulnificus. Structure-function analysis using synthetic analogues provided an insight into the molecular properties that underpin the ability of these compounds to influence microbial behaviour, revealing the alkyl chain to be fundamental. Defining the influence of these molecules on microbial-eukaryotic-host interactions will facilitate future therapeutic strategies which seek to combat microorganisms that are recalcitrant to conventional antimicrobial agents.
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Affiliation(s)
- F Jerry Reen
- BIOMERIT Research Centre, Department of Microbiology, University College Cork, Ireland
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