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Xie J, Ma R, Li M, Li B, Xiong L. [Effect of intestinal nitrate on growth of Klebsiella pneumoniae and its regulatory mechanism]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2024; 44:757-764. [PMID: 38708510 DOI: 10.12122/j.issn.1673-4254.2024.04.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
OBJECTIVE To explore the effect of intestinal nitrates on the growth of Klebsiella pneumoniae and its regulatory mechanisms. METHODS K. pneumoniae strains with nitrate reductase narG and narZ single or double gene knockout or with NarXL gene knockout were constructed and observed for both aerobic and anaerobic growth in the presence of KNO3 using an automated bacterial growth analyzer and a spectrophotometer, respectively. The mRNA expressions of narG and narZ in K. pneumoniae in anaerobic cultures in the presence of KNO3 and the effect of the binary regulatory system NarXL on their expresisons were detected using qRT-PCR. Electrophoretic mobility shift assays (EMSA) and MST analysis were performed to explore the specific regulatory mechanisms of NarXL in sensing and utilizing nitrates. Competitive experiments were conducted to examine anaerobic growth advantages of narG and narZ gene knockout strains of K. pneumoniae in the presence of KNO3. RESULTS The presence of KNO3 in anaerobic conditions, but not in aerobic conditions, promoted bacterial growth more effectively in the wild-type K. pneumoniae strain than in the narXL gene knockout strain. In anaerobic conditions, the narXL gene knockout strain showed significantly lowered mRNA expressions of narG and narZ (P < 0.0001). EMSA and MST experiments demonstrated that the NarXL regulator could directly bind to narG and narZ promoter regions. The wild-type K. pneumoniae strain in anaerobic cultures showed significantly increased expressions of narG and narZ mRNAs in the presence of KNO3 (P < 0.01), and narG gene knockout resulted in significantly attenuated anaerobic growth and competitive growth abilities of K. pneumoniae in the presence of KNO3 (P < 0.01). CONCLUSION The binary regulatory system NarXL of K. pneumoniae can sense changes in intestinal nitrate concentration and directly regulate the expression of nitrate reductase genes narG and narZ to promote bacterial growth.
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Affiliation(s)
- J Xie
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China
| | - R Ma
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China
| | - M Li
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China
| | - B Li
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China
| | - L Xiong
- Department of Gastroenterology, Liyuan Hospital Affiliated to Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430077, China
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Pseudomonas aeruginosa and Staphylococcus aureus Display Differential Proteomic Responses to the Silver(I) Compound, SBC3. Antibiotics (Basel) 2023; 12:antibiotics12020348. [PMID: 36830259 PMCID: PMC9952281 DOI: 10.3390/antibiotics12020348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/27/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
The urgent need to combat antibiotic resistance and develop novel antimicrobial therapies has triggered studies on novel metal-based formulations. N-heterocyclic carbene (NHC) complexes coordinate transition metals to generate a broad range of anticancer and/or antimicrobial agents, with ongoing efforts being made to enhance the lipophilicity and drug stability. The lead silver(I) acetate complex, 1,3-dibenzyl-4,5-diphenylimidazol-2-ylidene (NHC*) (SBC3), has previously demonstrated promising growth and biofilm-inhibiting properties. In this work, the responses of two structurally different bacteria to SBC3 using label-free quantitative proteomics were characterised. Multidrug-resistant Pseudomonas aeruginosa (Gram-negative) and Staphylococcus aureus (Gram-positive) are associated with cystic fibrosis lung colonisation and chronic wound infections, respectively. SBC3 increased the abundance of alginate biosynthesis, the secretion system and drug detoxification proteins in P. aeruginosa, whilst a variety of pathways, including anaerobic respiration, twitching motility and ABC transport, were decreased in abundance. This contrasted the affected pathways in S. aureus, where increased DNA replication/repair and cell redox homeostasis and decreased protein synthesis, lipoylation and glucose metabolism were observed. Increased abundance of cell wall/membrane proteins was indicative of the structural damage induced by SBC3 in both bacteria. These findings show the potential broad applications of SBC3 in treating Gram-positive and Gram-negative bacteria.
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Martin LW, Gray AR, Brockway B, Lamont IL. Pseudomonas aeruginosa is oxygen-deprived during infection in cystic fibrosis lungs, reducing the effectiveness of antibiotics. FEMS Microbiol Lett 2023; 370:fnad076. [PMID: 37516450 PMCID: PMC10408701 DOI: 10.1093/femsle/fnad076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/04/2023] [Accepted: 07/20/2023] [Indexed: 07/31/2023] Open
Abstract
Pseudomonas aeruginosa infects the lungs of patients with cystic fibrosis. Sputum expectorated from the lungs of patients contains low levels of oxygen, indicating that P. aeruginosa may be oxygen-deprived during infection. During in vitro growth under oxygen-limiting conditions, a P. aeruginosa reference strain increases expression of a cytochrome oxidase with a high affinity for oxygen, and of nitrate and nitrite reductases that enable it to use nitrate instead of oxygen during respiration. Here, we quantified transcription of the genes encoding these three enzymes in sputum samples from 18 infected patients, and in bacteria isolated from the sputum samples and grown in aerobic and anaerobic culture. In culture, expression of all three genes was increased by averages of 20- to 500-fold in anaerobically grown bacteria compared with those grown aerobically, although expression levels varied greatly between isolates. Expression of the same genes in sputum was similar to that of the corresponding bacteria in anaerobic culture. The isolated bacteria were less susceptible to tobramycin and ciprofloxacin, two widely used anti-pseudomonal antibiotics, when grown anaerobically than when grown aerobically. Our findings show that P. aeruginosa experiences oxygen starvation during infection in cystic fibrosis, reducing the effectiveness of antibiotic treatment.
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Affiliation(s)
- Lois W Martin
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
| | - Andrew R Gray
- Biostatistics Centre, University of Otago, Dunedin 9016, New Zealand
| | - Ben Brockway
- Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Iain L Lamont
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
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The Contribution of Nitrate Dissimilation to Nitrate Consumption in narG- and napA-Containing Nitrate Reducers with Various Oxygen and Nitrate Supplies. Microbiol Spectr 2022; 10:e0069522. [PMID: 36453888 PMCID: PMC9769761 DOI: 10.1128/spectrum.00695-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Nitrate reducers containing narG or napA play an important role in the nitrogen cycle, but little is known about their functional differentiations in relation to environmental changes. In this study, three types of nitrate reducers in the genus Pseudomonas, including strains containing narG (G type), napA (A type) and both narG and napA (GA type), were selected to explore their functional performances under varied nitrate and oxygen concentrations. Their growth characteristics, nitrate consumption, and dissimilatory nitrate-reducing activity were investigated. Growth and nitrate consumption of all three types of strains were generally promoted with increasing oxygen and nitrate concentrations. However, their dissimilatory nitrate-reducing activities were restricted by oxygen supply. When supplied with 0.25 mM KNO3, A-type strains showed a higher growth rate but lower activity of dissimilatory nitrate reduction (DNR) than G-type strains, regardless of oxygen concentration. However, when nitrate concentration increased to 0.75 mM or 5 mM, G-type strains displayed stronger capability of nitrate consumption and DNR than A-type strains under anaerobic conditions, whereas under oxygenated conditions, A-type strains exhibited higher growth and nitrate consumption but weaker DNR than G-type strains. The GA-type strains appeared similar to G type under anaerobic conditions but performed more similarly to A type in aerobic environments. In summary, the nitrate consumption of narG-containing nitrate reducers is mainly caused by DNR in both anaerobic and aerobic environments, while the large proportion of nitrate consumption in A-type nitrate reducers under the aerobic condition is attributed to the assimilation by cell growth. IMPORTANCE Nitrate reducers containing narG or napA are ubiquitous, but little is known about their functional performance in various environments. Our study provides an important clue that the nitrate consumption of narG-containing strains is mainly caused by dissimilatory reduction in the environments, while that of napA-containing nitrate reducers under anaerobic conditions is ascribed to nitrate dissimilation but under the aerobic condition is attributed to the assimilation by cell growth. This finding broadens the understanding of aerobic nitrate reduction in the nitrogen cycle and highlights the important role of narG-containing bacteria in nitrate reduction under aerobic conditions.
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An Important Role of the Type VI Secretion System of Pseudomonas aeruginosa Regulated by Dnr in Response to Anaerobic Environments. Microbiol Spectr 2022; 10:e0153322. [PMID: 36301114 PMCID: PMC9769707 DOI: 10.1128/spectrum.01533-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The type VI secretion system (T6SS) is capable of secreting a variety of metal-binding proteins involved in metal ion uptake, and it mediates an active metal ion transport system that contributes to competition between bacteria. Pseudomonas aeruginosa H2-T6SS can increase molybdenum ion acquisition and enhance bacterial survival advantage by promoting the secretion of the molybdate-binding protein ModA, in which the expression of H2-T6SS core genes hcp2, hsiA2, and clpV2 is activated by anaerobic conditions and are all regulated by the global regulator Anr. Here, we report the regulation of T6SS by Dnr, a dedicated dissimilatory nitrate respiration regulator in P. aeruginosa. Of the three distinct T6SS loci carried by P. aeruginosa, only the anaerobic expression of H2-T6SS was activated by Dnr; H1-T6SS or H3-T6SS did not respond to anaerobically induced activation. We also demonstrated that Dnr promotes the anaerobic secretion of ModA, which acts as a potential substrate for H2-T6SS, providing an advantage not only for the anaerobic growth of bacteria but also for functional competition. Overall, this study elucidates the important role played by Dnr in mediating the anaerobic expression of T6SS in P. aeruginosa, indicating that the functional advantage of H2-T6SS in response to anaerobic induction may be a conditional environmental adaptation. It also extends our understanding of the function of Dnr as a specific regulator of dissimilatory nitrate respiration. IMPORTANCE The type VI secretion system (T6SS) plays an important role in bacterial competition by mediating the transport of active metal ions. Pseudomonas aeruginosa carries three distinct T6SS loci (H1-, H2-, and H3-T6SS). The H2-T6SS promotes the secretion of the molybdate-binding protein ModA for the acquisition of molybdenum ions to adapt to anaerobic survival. Here, we report that the specialized dissimilatory nitrate respiration regulator Dnr in P. aeruginosa controls the anaerobic expression of H2-T6SS and that this regulation is essential for ModA protein secretion, anaerobic growth, and bacterial competition. This study elucidates the regulatory mechanism of Dnr on H2-T6SS in P. aeruginosa, revealing an important role played by H2-T6SS in adapting to an anaerobic environment.
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Spero MA, Jones J, Lomenick B, Chou TF, Newman DK. Mechanisms of chlorate toxicity and resistance in Pseudomonas aeruginosa. Mol Microbiol 2022; 118:321-335. [PMID: 36271736 PMCID: PMC9589919 DOI: 10.1111/mmi.14972] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/31/2022] [Accepted: 08/04/2022] [Indexed: 11/28/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic bacterial pathogen that often encounters hypoxic/anoxic environments within the host, which increases its tolerance to many conventional antibiotics. Toward identifying novel treatments, we explored the therapeutic potential of chlorate, a pro-drug that kills hypoxic/anoxic, antibiotic-tolerant P. aeruginosa populations. While chlorate itself is relatively nontoxic, it is enzymatically reduced to the toxic oxidizing agent, chlorite, by hypoxically induced nitrate reductase. To better assess chlorate's therapeutic potential, we investigated mechanisms of chlorate toxicity and resistance in P. aeruginosa. We used transposon mutagenesis to identify genes that alter P. aeruginosa fitness during chlorate treatment, finding that methionine sulfoxide reductases (Msr), which repair oxidized methionine residues, support survival during chlorate stress. Chlorate treatment leads to proteome-wide methionine oxidation, which is exacerbated in a ∆msrA∆msrB strain. In response to chlorate, P. aeruginosa upregulates proteins involved in a wide range of functions, including metabolism, DNA replication/repair, protein repair, transcription, and translation, and these newly synthesized proteins are particularly vulnerable to methionine oxidation. The addition of exogenous methionine partially rescues P. aeruginosa survival during chlorate treatment, suggesting that widespread methionine oxidation contributes to death. Finally, we found that mutations that decrease nitrate reductase activity are a common mechanism of chlorate resistance.
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Affiliation(s)
- Melanie A. Spero
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Present address: Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | - Jeff Jones
- Proteome Exploration Laboratory, Beckman Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tsui-Fen Chou
- Proteome Exploration Laboratory, Beckman Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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Supercharged MPNs? Automated Determination of High-Throughput Most Probable Number (htMPN) Using Chip-Based 3D Digital PCR. Appl Environ Microbiol 2022; 88:e0082222. [PMID: 35856687 PMCID: PMC9361819 DOI: 10.1128/aem.00822-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Surface plating on agar and most probable number (MPN) are the standard methods for determining bacterial viability but both have limitations. Here we present a novel cell count method, high-throughput MPN (htMPN), that uses a chip-based digital PCR instrument to accelerate and to improve the quantification of viable or sublethally injured cells. This method tracks growth of up to 20,000 individual bacterial cells on a single chip. Single cells were grown in the individual wells of the chip at their optimal temperature until the cell density was high enough to detect the fluorescent signal with cell-permeant or cell-impermeant DNA-intercalating fluorescent dyes. This method based on microfluidic devices implemented in digital PCR equipment was equivalent to surface plating in determining cell counts of Escherichia coli, Salmonella enterica serovar Typhimurium, Fructilactobacillus sanfranciscensis, Pseudomonas putida, and vegetative cells but not spores of Bacillus subtilis. Viable E. coli could be enumerated within 7 h. Culture of strict aerobes was restricted to strains that are capable of nitrate respiration; organisms requiring complex media that also contain double-stranded DNA were detected after treatment of growth media with DNase before inoculation. Our approach not only monitors the frequency distribution of bacterial growth and determines cell counts with high reliability but also detected heat-injured cells of S. Typhimurium that escaped detection by the surface plating. Overall, the method accelerates detection of viable bacterial cells, facilitates automation, and offers new possibilities for the analysis of individual bacterial cells. IMPORTANCE htMPN uses chip-based fluorescence acquisition and is a simple and compact tool for automatic viable cell enumeration with applications in microbiological research. This method applies to a wide range of anaerobic or facultative anaerobic species and improves accuracy by reducing the number of pipetting steps. In addition, the method offers an additional tool for single-cell microbiology. The single cell time-to-detection times have been used as an important criterion for the physiological state of bacterial cells after sublethal stress, and htMPNs support the acquisition of such data with an unprecedented number of cells. In particular, htMPN provides an anaerobic environment and enables a long incubation time to increase the recovery rate of sublethally injured cells. Given its reproducibility and reliability, our approach can potentially be applied to quantify viable cells in samples from environmental, clinical, or food samples to reduce the risk of underestimation of the number of viable bacterial cells.
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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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NorA, HmpX, and NorB Cooperate to Reduce NO Toxicity during Denitrification and Plant Pathogenesis in Ralstonia solanacearum. Microbiol Spectr 2022; 10:e0026422. [PMID: 35377234 PMCID: PMC9045102 DOI: 10.1128/spectrum.00264-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ralstonia solanacearum, which causes bacterial wilt disease of many crops, requires denitrifying respiration to survive in its plant host. In the hypoxic environment of plant xylem vessels, this pathogen confronts toxic oxidative radicals like nitric oxide (NO), which is generated by both bacterial denitrification and host defenses. R. solanacearum has multiple distinct mechanisms that could mitigate this stress, including putative NO-binding protein (NorA), nitric oxide reductase (NorB), and flavohaemoglobin (HmpX). During denitrification and tomato pathogenesis and in response to exogenous NO, R. solanacearum upregulated norA, norB, and hmpX. Single mutants lacking ΔnorB, ΔnorA, or ΔhmpX increased expression of many iron and sulfur metabolism genes, suggesting that the loss of even one NO detoxification system demands metabolic compensation. Single mutants suffered only moderate fitness reductions in host plants, possibly because they upregulated their remaining protective genes. However, ΔnorA/norB, ΔnorB/hmpX, and ΔnorA/hmpX double mutants grew poorly in denitrifying culture and in planta. It is likely that the loss of norA, norB, and hmpX is lethal, since the methods used to construct the double mutants could not generate a triple mutant. Functional aconitase activity assays showed that NorA, HmpX, and especially NorB are important for maintaining iron-sulfur cluster proteins. Additionally, plant defense genes were upregulated in tomatoes infected with the NO-overproducing ΔnorB mutant, suggesting that bacterial detoxification of NO reduces the ability of the plant host to perceive the presence of the pathogen. Thus, R. solanacearum's three NO detoxification systems each contribute to and are collectively essential for overcoming metabolic nitrosative stress during denitrification, for virulence and growth in the tomato, and for evading host plant defenses. IMPORTANCE The soilborne plant pathogen Ralstonia solanacearum (Rs) causes bacterial wilt, a serious and widespread threat to global food security. Rs is metabolically adapted to low-oxygen conditions, using denitrifying respiration to survive in the host and cause disease. However, bacterial denitrification and host defenses generate nitric oxide (NO), which is toxic and also alters signaling pathways in both the pathogen and its plant hosts. Rs mitigates NO with a trio of mechanistically distinct proteins: NO-reductase (NorB), predicted iron-binding (NorA), and oxidoreductase (HmpX). This redundancy, together with analysis of mutants and in-planta dual transcriptomes, indicates that maintaining low NO levels is integral to Rs fitness in tomatoes (because NO damages iron-cluster proteins) and to evading host recognition (because bacterially produced NO can trigger plant defenses).
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Lichtenberg M, Jakobsen TH, Kühl M, Kolpen M, Jensen PØ, Bjarnsholt T. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6574409. [PMID: 35472245 PMCID: PMC9438473 DOI: 10.1093/femsre/fuac018] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 04/04/2022] [Accepted: 04/24/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Mads Lichtenberg
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200, København, Denmark
| | - Tim Holm Jakobsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200, København, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark
| | - Mette Kolpen
- Department of Clinical Microbiology, Copenhagen University Hospital, Ole Maaløes vej 26, 2200, København, Denmark
| | - Peter Østrup Jensen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200, København, Denmark
- Department of Clinical Microbiology, Copenhagen University Hospital, Ole Maaløes vej 26, 2200, København, Denmark
| | - Thomas Bjarnsholt
- Corresponding author: Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200, København, Denmark. Tel: +45 20659888; E-mail:
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Lichtenberg M, Line L, Schrameyer V, Jakobsen TH, Rybtke ML, Toyofuku M, Nomura N, Kolpen M, Tolker-Nielsen T, Kühl M, Bjarnsholt T, Jensen PØ. Nitric-oxide-driven oxygen release in anoxic Pseudomonas aeruginosa. iScience 2021; 24:103404. [PMID: 34849468 PMCID: PMC8608891 DOI: 10.1016/j.isci.2021.103404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/29/2021] [Accepted: 11/03/2021] [Indexed: 11/19/2022] Open
Abstract
Denitrification supports anoxic growth of Pseudomonas aeruginosa in infections. Moreover, denitrification may provide oxygen (O2) resulting from dismutation of the denitrification intermediate nitric oxide (NO) as seen in Methylomirabilis oxyfera. To examine the prevalence of NO dismutation we studied O2 release by P. aeruginosa in airtight vials. P. aeruginosa rapidly depleted O2 but NO supplementation generated peaks of O2 at the onset of anoxia, and we demonstrate a direct role of NO in the O2 release. However, we were not able to detect genetic evidence for putative NO dismutases. The supply of endogenous O2 at the onset of anoxia could play an adaptive role when P. aeruginosa enters anaerobiosis. Furthermore, O2 generation by NO dismutation may be more widespread than indicated by the reports on the distribution of homologues genes. In general, NO dismutation may allow removal of nitrate by denitrification without release of the very potent greenhouse gas, nitrous oxide. Pseudomonas aeruginosa was found to release O2 at the onset of anoxia Peaks of O2 were amplified in a nitric oxide reductase (NOR) mutant The O2 release was mediated by nitric oxide (NO)
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Affiliation(s)
- Mads Lichtenberg
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Laura Line
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Verena Schrameyer
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark
| | - Tim Holm Jakobsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Morten Levin Rybtke
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Masanori Toyofuku
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, 305-8577 Tsukuba, Japan
| | - Nobuhiko Nomura
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, 305-8577 Tsukuba, Japan
| | - Mette Kolpen
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Peter Østrup Jensen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
- Center for Rheumatology and Spine Diseases, Institute for Inflammation Research, Rigshospitalet, 2100 Copenhagen, Denmark
- Corresponding author
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Ferrara S, Carrubba R, Santoro S, Bertoni G. The Small RNA ErsA Impacts the Anaerobic Metabolism of Pseudomonas aeruginosa Through Post-Transcriptional Modulation of the Master Regulator Anr. Front Microbiol 2021; 12:691608. [PMID: 34759894 PMCID: PMC8575079 DOI: 10.3389/fmicb.2021.691608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/27/2021] [Indexed: 01/05/2023] Open
Abstract
Pseudomonas aeruginosa is one of the most critical opportunistic pathogens in humans, able to cause both lethal acute and chronic lung infections. In previous work, we indicated that the small RNA ErsA plays a role in the regulatory network of P. aeruginosa pathogenicity in airways infection. To give further insight into the lifestyle functions that could be either directly or indirectly regulated by ErsA during infection, we reanalyzed the categories of genes whose transcription appeared dysregulated in an ersA knock-out mutant of the P. aeruginosa PAO1 reference strain. This preliminary analysis indicated ErsA as a candidate co-modulator of denitrification and in general, the anaerobiosis response, a characteristic physiologic state of P. aeruginosa during chronic infection of the lung of cystic fibrosis (CF) patients. To explain the pattern of dysregulation of the anaerobic-lifestyle genes in the lack of ErsA, we postulated that ErsA regulation could target the expression of Anr, a well-known transcription factor that modulates a broad regulon of anoxia-responsive genes, and also Dnr, required for the transcription activation of the denitrification machinery. Our results show that ErsA positively regulates Anr expression at the post-transcriptional level while no direct ErsA-mediated regulatory effect on Dnr was observed. However, Dnr is transcriptionally downregulated in the absence of ErsA and this is consistent with the well-characterized regulatory link between Anr and Dnr. Anr regulatory function is critical for P. aeruginosa anaerobic growth, both through denitrification and fermentation of arginine. Interestingly, we found that, differently from the laboratory strain PAO1, ErsA deletion strongly impairs the anaerobic growth by both denitrification and arginine fermentation of the RP73 clinical isolate, a multi-drug resistant P. aeruginosa CF-adapted strain. This suggests that P. aeruginosa adaptation to CF lung might result in a higher dependence on ErsA for the transduction of the multiple signals to the regulatory network of key functions for survivance in such a complex environment. Together, our results suggest that ErsA takes an upper place in the regulatory network of airways infection, transducing host inputs to biofilm-related factors, as underlined in our previous reports, and to functions that allow P. aeruginosa to thrive in low-oxygen conditions.
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Affiliation(s)
- Silvia Ferrara
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Riccardo Carrubba
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Silvia Santoro
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Giovanni Bertoni
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
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13
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Zhang IH, Mullen S, Ciccarese D, Dumit D, Martocello DE, Toyofuku M, Nomura N, Smriga S, Babbin AR. Ratio of Electron Donor to Acceptor Influences Metabolic Specialization and Denitrification Dynamics in Pseudomonas aeruginosa in a Mixed Carbon Medium. Front Microbiol 2021; 12:711073. [PMID: 34566916 PMCID: PMC8461185 DOI: 10.3389/fmicb.2021.711073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/09/2021] [Indexed: 11/29/2022] Open
Abstract
Denitrifying microbes sequentially reduce nitrate (NO3 -) to nitrite (NO2 -), NO, N2O, and N2 through enzymes encoded by nar, nir, nor, and nos. Some denitrifiers maintain the whole four-gene pathway, but others possess partial pathways. Partial denitrifiers may evolve through metabolic specialization whereas complete denitrifiers may adapt toward greater metabolic flexibility in nitrogen oxide (NOx -) utilization. Both exist within natural environments, but we lack an understanding of selective pressures driving the evolution toward each lifestyle. Here we investigate differences in growth rate, growth yield, denitrification dynamics, and the extent of intermediate metabolite accumulation under varying nutrient conditions between the model complete denitrifier Pseudomonas aeruginosa and a community of engineered specialists with deletions in the denitrification genes nar or nir. Our results in a mixed carbon medium indicate a growth rate vs. yield tradeoff between complete and partial denitrifiers, which varies with total nutrient availability and ratios of organic carbon to NOx -. We found that the cultures of both complete and partial denitrifiers accumulated nitrite and that the metabolic lifestyle coupled with nutrient conditions are responsible for the extent of nitrite accumulation.
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Affiliation(s)
- Irene H. Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
- Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Susan Mullen
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Davide Ciccarese
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Diana Dumit
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Donald E. Martocello
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Masanori Toyofuku
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Steven Smriga
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
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14
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Specific and Global RNA Regulators in Pseudomonas aeruginosa. Int J Mol Sci 2021; 22:ijms22168632. [PMID: 34445336 PMCID: PMC8395346 DOI: 10.3390/ijms22168632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/05/2021] [Accepted: 08/08/2021] [Indexed: 01/20/2023] Open
Abstract
Pseudomonas aeruginosa (Pae) is an opportunistic pathogen showing a high intrinsic resistance to a wide variety of antibiotics. It causes nosocomial infections that are particularly detrimental to immunocompromised individuals and to patients suffering from cystic fibrosis. We provide a snapshot on regulatory RNAs of Pae that impact on metabolism, pathogenicity and antibiotic susceptibility. Different experimental approaches such as in silico predictions, co-purification with the RNA chaperone Hfq as well as high-throughput RNA sequencing identified several hundreds of regulatory RNA candidates in Pae. Notwithstanding, using in vitro and in vivo assays, the function of only a few has been revealed. Here, we focus on well-characterized small base-pairing RNAs, regulating specific target genes as well as on larger protein-binding RNAs that sequester and thereby modulate the activity of translational repressors. As the latter impact large gene networks governing metabolism, acute or chronic infections, these protein-binding RNAs in conjunction with their cognate proteins are regarded as global post-transcriptional regulators.
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15
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Pang J, Liu L, Liu X, Wang Y, Chen B, Wu S, Yao J, Xu X. A novel identified Pseudomonas aeruginosa, which exhibited nitrate- and nitrite-dependent methane oxidation abilities, could alleviate the disadvantages caused by nitrate supplementation in rumen fluid fermentation. Microb Biotechnol 2021; 14:1397-1408. [PMID: 33305892 PMCID: PMC8313268 DOI: 10.1111/1751-7915.13726] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 11/28/2022] Open
Abstract
After the occurrence of nitrate-dependent anaerobic methane oxidation (AMO) in rumen fluid culture was proved, the organisms that perform the denitrifying anaerobic methane oxidizing (DAMO) process in the rumen of dairy goat were investigated by establishing two enrichment culture systems, which were supplied with methane as the sole carbon source and NaNO3 or NaNO2 as the electron acceptor. Several Operational Taxonomic Units (OTU) belonging to Proteobacteria became dominant in the two enrichment systems. The identified Pseudomonas aeruginosa, which was isolated from the NaNO2 enrichment system, could individually perform a whole denitrifying anaerobic methane oxidizing process. Further in vitro rumen fermentation showed that supplementation with the isolated P. aeruginosa could reduce methane emissions, alleviate the nitrite accumulation and prevent the decrease in propionic acid product caused by nitrate supplementation.
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Affiliation(s)
- Jie Pang
- College of Animal Science and TechnologyNorthwest A&F UniversityShaanxi712100China
| | - Lihui Liu
- College of Animal Science and TechnologyNorthwest A&F UniversityShaanxi712100China
| | - Xiaopeng Liu
- College of Animal Science and TechnologyNorthwest A&F UniversityShaanxi712100China
| | - Yi Wang
- College of Animal Science and TechnologyNorthwest A&F UniversityShaanxi712100China
| | - Bin Chen
- College of Animal Science and TechnologyNorthwest A&F UniversityShaanxi712100China
| | - Shengru Wu
- College of Animal Science and TechnologyNorthwest A&F UniversityShaanxi712100China
| | - Junhu Yao
- College of Animal Science and TechnologyNorthwest A&F UniversityShaanxi712100China
| | - Xiurong Xu
- College of Animal Science and TechnologyNorthwest A&F UniversityShaanxi712100China
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16
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Jéglot A, Sørensen SR, Schnorr KM, Plauborg F, Elsgaard L. Temperature Sensitivity and Composition of Nitrate-Reducing Microbiomes from a Full-Scale Woodchip Bioreactor Treating Agricultural Drainage Water. Microorganisms 2021; 9:1331. [PMID: 34207422 PMCID: PMC8235139 DOI: 10.3390/microorganisms9061331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 02/06/2023] Open
Abstract
Denitrifying woodchip bioreactors (WBR), which aim to reduce nitrate (NO3-) pollution from agricultural drainage water, are less efficient when cold temperatures slow down the microbial transformation processes. Conducting bioaugmentation could potentially increase the NO3- removal efficiency during these specific periods. First, it is necessary to investigate denitrifying microbial populations in these facilities and understand their temperature responses. We hypothesized that seasonal changes and subsequent adaptations of microbial populations would allow for enrichment of cold-adapted denitrifying bacterial populations with potential use for bioaugmentation. Woodchip material was sampled from an operating WBR during spring, fall, and winter and used for enrichments of denitrifiers that were characterized by studies of metagenomics and temperature dependence of NO3- depletion. The successful enrichment of psychrotolerant denitrifiers was supported by the differences in temperature response, with the apparent domination of the phylum Proteobacteria and the genus Pseudomonas. The enrichments were found to have different microbiomes' composition and they mainly differed with native woodchip microbiomes by a lower abundance of the genus Flavobacterium. Overall, the performance and composition of the enriched denitrifying population from the WBR microbiome indicated a potential for efficient NO3- removal at cold temperatures that could be stimulated by the addition of selected cold-adapted denitrifying bacteria.
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Affiliation(s)
- Arnaud Jéglot
- Department of Agroecology, Aarhus University, Blichers Allé 20, 8830 Tjele, Denmark; (F.P.); (L.E.)
- WATEC Centre for Water Technology, Department of Agroecology, Aarhus University, Blichers Allé 20, 8830 Tjele, Denmark
| | | | - Kirk M. Schnorr
- Novozymes A/S, Biologiens Vej 2, 2800 Kongens Lyngby, Denmark; (S.R.S.); (K.M.S.)
| | - Finn Plauborg
- Department of Agroecology, Aarhus University, Blichers Allé 20, 8830 Tjele, Denmark; (F.P.); (L.E.)
- WATEC Centre for Water Technology, Department of Agroecology, Aarhus University, Blichers Allé 20, 8830 Tjele, Denmark
| | - Lars Elsgaard
- Department of Agroecology, Aarhus University, Blichers Allé 20, 8830 Tjele, Denmark; (F.P.); (L.E.)
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17
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Hassett DJ, Kovall RA, Schurr MJ, Kotagiri N, Kumari H, Satish L. The Bactericidal Tandem Drug, AB569: How to Eradicate Antibiotic-Resistant Biofilm Pseudomonas aeruginosa in Multiple Disease Settings Including Cystic Fibrosis, Burns/Wounds and Urinary Tract Infections. Front Microbiol 2021; 12:639362. [PMID: 34220733 PMCID: PMC8245851 DOI: 10.3389/fmicb.2021.639362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/07/2021] [Indexed: 11/13/2022] Open
Abstract
The life-threatening pandemic concerning multi-drug resistant (MDR) bacteria is an evolving problem involving increased hospitalizations, billions of dollars in medical costs and a remarkably high number of deaths. Bacterial pathogens have demonstrated the capacity for spontaneous or acquired antibiotic resistance and there is virtually no pool of organisms that have not evolved such potentially clinically catastrophic properties. Although many diseases are linked to such organisms, three include cystic fibrosis (CF), burn/blast wounds and urinary tract infections (UTIs), respectively. Thus, there is a critical need to develop novel, effective antimicrobials for the prevention and treatment of such problematic infections. One of the most formidable, naturally MDR bacterial pathogens is Pseudomonas aeruginosa (PA) that is particularly susceptible to nitric oxide (NO), a component of our innate immune response. This susceptibility sets the translational stage for the use of NO-based therapeutics during the aforementioned human infections. First, we discuss how such NO therapeutics may be able to target problematic infections in each of the aforementioned infectious scenarios. Second, we describe a recent discovery based on years of foundational information, a novel drug known as AB569. AB569 is capable of forming a "time release" of NO from S-nitrosothiols (RSNO). AB569, a bactericidal tandem consisting of acidified NaNO2 (A-NO2 -) and Na2-EDTA, is capable of killing all pathogens that are associated with the aforementioned disorders. Third, we described each disease state in brief, the known or predicted effects of AB569 on the viability of PA, its potential toxicity and highly remote possibility for resistance to develop. Finally, we conclude that AB569 can be a viable alternative or addition to conventional antibiotic regimens to treat such highly problematic MDR bacterial infections for civilian and military populations, as well as the economical burden that such organisms pose.
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Affiliation(s)
- Daniel J Hassett
- Department of Molecular Genetics, Biochemistry and Microbiology, Cincinnati, OH, United States
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, Cincinnati, OH, United States
| | - Michael J Schurr
- Department of Immunology and Microbiology, University of Colorado Health Sciences, Denver, CO, United States
| | - Nalinikanth Kotagiri
- Division of Pharmacy, University of Colorado Health Sciences, Denver, CO, United States
| | - Harshita Kumari
- Division of Pharmacy, University of Colorado Health Sciences, Denver, CO, United States
| | - Latha Satish
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Shriners Hospitals for Children-Cincinnati, Cincinnati, OH, United States
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18
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Gushchin I, Aleksenko VA, Orekhov P, Goncharov IM, Nazarenko VV, Semenov O, Remeeva A, Gordeliy V. Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity. Int J Mol Sci 2021; 22:5933. [PMID: 34072989 PMCID: PMC8199190 DOI: 10.3390/ijms22115933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/18/2022] Open
Abstract
Under anaerobic conditions, bacteria may utilize nitrates and nitrites as electron acceptors. Sensitivity to nitrous compounds is achieved via several mechanisms, some of which rely on sensor histidine kinases (HKs). The best studied nitrate- and nitrite-sensing HKs (NSHKs) are NarQ and NarX from Escherichia coli. Here, we review the function of NSHKs, analyze their natural diversity, and describe the available structural information. In particular, we show that around 6000 different NSHK sequences forming several distinct clusters may now be found in genomic databases, comprising mostly the genes from Beta- and Gammaproteobacteria as well as from Bacteroidetes and Chloroflexi, including those from anaerobic ammonia oxidation (annamox) communities. We show that the architecture of NSHKs is mostly conserved, although proteins from Bacteroidetes lack the HAMP and GAF-like domains yet sometimes have PAS. We reconcile the variation of NSHK sequences with atomistic models and pinpoint the structural elements important for signal transduction from the sensor domain to the catalytic module over the transmembrane and cytoplasmic regions spanning more than 200 Å.
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Affiliation(s)
- Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vladimir A. Aleksenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan M. Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vera V. Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
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19
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Cianciulli Sesso A, Lilić B, Amman F, Wolfinger MT, Sonnleitner E, Bläsi U. Gene Expression Profiling of Pseudomonas aeruginosa Upon Exposure to Colistin and Tobramycin. Front Microbiol 2021; 12:626715. [PMID: 33995291 PMCID: PMC8120321 DOI: 10.3389/fmicb.2021.626715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/31/2021] [Indexed: 11/22/2022] Open
Abstract
Pseudomonas aeruginosa (Pae) is notorious for its high-level resistance toward clinically used antibiotics. In fact, Pae has rendered most antimicrobials ineffective, leaving polymyxins and aminoglycosides as last resort antibiotics. Although several resistance mechanisms of Pae are known toward these drugs, a profounder knowledge of hitherto unidentified factors and pathways appears crucial to develop novel strategies to increase their efficacy. Here, we have performed for the first time transcriptome analyses and ribosome profiling in parallel with strain PA14 grown in synthetic cystic fibrosis medium upon exposure to polymyxin E (colistin) and tobramycin. This approach did not only confirm known mechanisms involved in colistin and tobramycin susceptibility but revealed also as yet unknown functions/pathways. Colistin treatment resulted primarily in an anti-oxidative stress response and in the de-regulation of the MexT and AlgU regulons, whereas exposure to tobramycin led predominantly to a rewiring of the expression of multiple amino acid catabolic genes, lower tricarboxylic acid (TCA) cycle genes, type II and VI secretion system genes and genes involved in bacterial motility and attachment, which could potentially lead to a decrease in drug uptake. Moreover, we report that the adverse effects of tobramycin on translation are countered with enhanced expression of genes involved in stalled ribosome rescue, tRNA methylation and type II toxin-antitoxin (TA) systems.
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Affiliation(s)
- Anastasia Cianciulli Sesso
- Max Perutz Labs, Vienna Biocenter (VBC), Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Branislav Lilić
- Max Perutz Labs, Vienna Biocenter (VBC), Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Fabian Amman
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Michael T Wolfinger
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Elisabeth Sonnleitner
- Max Perutz Labs, Vienna Biocenter (VBC), Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Udo Bläsi
- Max Perutz Labs, Vienna Biocenter (VBC), Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
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20
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Shen L, Gao L, Yang M, Zhang J, Wang Y, Feng Y, Wang L, Wang S. Deletion of the PA4427-PA4431 Operon of Pseudomonas aeruginosa PAO1 Increased Antibiotics Resistance and Reduced Virulence and Pathogenicity by Affecting Quorum Sensing and Iron Uptake. Microorganisms 2021; 9:microorganisms9051065. [PMID: 34069209 PMCID: PMC8156433 DOI: 10.3390/microorganisms9051065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/06/2021] [Accepted: 05/10/2021] [Indexed: 12/06/2022] Open
Abstract
The respiratory chain is very important for bacterial survival and pathogenicity, yet the roles of the respiratory chain in P. aeruginosa remain to be fully elucidated. Here, we not only proved experimentally that the operon PA4427-PA4431 of Pseudomonas aeruginosa PAO1 encodes respiratory chain complex III (cytobc1), but also found that it played important roles in virulence and pathogenicity. PA4429–31 deletion reduced the production of the virulence factors, including pyocyanin, rhamnolipids, elastase, and extracellular polysaccharides, and it resulted in a remarkable decrease in pathogenicity, as demonstrated in the cabbage and Drosophila melanogaster infection models. Furthermore, RNA-seq analysis showed that PA4429–31 deletion affected the expression levels of the genes related to quorum-sensing systems and the transport of iron ions, and the iron content was also reduced in the mutant strain. Taken together, we comprehensively illustrated the function of the operon PA4427–31 and its application potential as a treatment target in P. aeruginosa infection.
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21
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Durand S, Guillier M. Transcriptional and Post-transcriptional Control of the Nitrate Respiration in Bacteria. Front Mol Biosci 2021; 8:667758. [PMID: 34026838 PMCID: PMC8139620 DOI: 10.3389/fmolb.2021.667758] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 03/29/2021] [Indexed: 12/02/2022] Open
Abstract
In oxygen (O2) limiting environments, numerous aerobic bacteria have the ability to shift from aerobic to anaerobic respiration to release energy. This process requires alternative electron acceptor to replace O2 such as nitrate (NO3 -), which has the next best reduction potential after O2. Depending on the organism, nitrate respiration involves different enzymes to convert NO3 - to ammonium (NH4 +) or dinitrogen (N2). The expression of these enzymes is tightly controlled by transcription factors (TFs). More recently, bacterial small regulatory RNAs (sRNAs), which are important regulators of the rapid adaptation of microorganisms to extremely diverse environments, have also been shown to control the expression of genes encoding enzymes or TFs related to nitrate respiration. In turn, these TFs control the synthesis of multiple sRNAs. These results suggest that sRNAs play a central role in the control of these metabolic pathways. Here we review the complex interplay between the transcriptional and the post-transcriptional regulators to efficiently control the respiration on nitrate.
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Affiliation(s)
- Sylvain Durand
- CNRS, UMR 8261, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Maude Guillier
- CNRS, UMR 8261, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
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22
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de Pina LC, da Silva FSH, Galvão TC, Pauer H, Ferreira RBR, Antunes LCM. The role of two-component regulatory systems in environmental sensing and virulence in Salmonella. Crit Rev Microbiol 2021; 47:397-434. [PMID: 33751923 DOI: 10.1080/1040841x.2021.1895067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Adaptation to environments with constant fluctuations imposes challenges that are only overcome with sophisticated strategies that allow bacteria to perceive environmental conditions and develop an appropriate response. The gastrointestinal environment is a complex ecosystem that is home to trillions of microorganisms. Termed microbiota, this microbial ensemble plays important roles in host health and provides colonization resistance against pathogens, although pathogens have evolved strategies to circumvent this barrier. Among the strategies used by bacteria to monitor their environment, one of the most important are the sensing and signalling machineries of two-component systems (TCSs), which play relevant roles in the behaviour of all bacteria. Salmonella enterica is no exception, and here we present our current understanding of how this important human pathogen uses TCSs as an integral part of its lifestyle. We describe important aspects of these systems, such as the stimuli and responses involved, the processes regulated, and their roles in virulence. We also dissect the genomic organization of histidine kinases and response regulators, as well as the input and output domains for each TCS. Lastly, we explore how these systems may be promising targets for the development of antivirulence therapeutics to combat antibiotic-resistant infections.
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Affiliation(s)
- Lucindo Cardoso de Pina
- Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Biociências, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Programa de Pós-Graduação Ciência para o Desenvolvimento, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Teca Calcagno Galvão
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Heidi Pauer
- Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Rio de Janeiro, Brazil
| | | | - L Caetano M Antunes
- Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Rio de Janeiro, Brazil.,Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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23
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McGill SL, Yung Y, Hunt KA, Henson MA, Hanley L, Carlson RP. Pseudomonas aeruginosa reverse diauxie is a multidimensional, optimized, resource utilization strategy. Sci Rep 2021; 11:1457. [PMID: 33446818 PMCID: PMC7809481 DOI: 10.1038/s41598-020-80522-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/17/2020] [Indexed: 12/19/2022] Open
Abstract
Pseudomonas aeruginosa is a globally-distributed bacterium often found in medical infections. The opportunistic pathogen uses a different, carbon catabolite repression (CCR) strategy than many, model microorganisms. It does not utilize a classic diauxie phenotype, nor does it follow common systems biology assumptions including preferential consumption of glucose with an 'overflow' metabolism. Despite these contradictions, P. aeruginosa is competitive in many, disparate environments underscoring knowledge gaps in microbial ecology and systems biology. Physiological, omics, and in silico analyses were used to quantify the P. aeruginosa CCR strategy known as 'reverse diauxie'. An ecological basis of reverse diauxie was identified using a genome-scale, metabolic model interrogated with in vitro omics data. Reverse diauxie preference for lower energy, nonfermentable carbon sources, such as acetate or succinate over glucose, was predicted using a multidimensional strategy which minimized resource investment into central metabolism while completely oxidizing substrates. Application of a common, in silico optimization criterion, which maximizes growth rate, did not predict the reverse diauxie phenotypes. This study quantifies P. aeruginosa metabolic strategies foundational to its wide distribution and virulence including its potentially, mutualistic interactions with microorganisms found commonly in the environment and in medical infections.
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Affiliation(s)
- S Lee McGill
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Yeni Yung
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Kristopher A Hunt
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.,Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, 98115, USA
| | - Michael A Henson
- Department of Chemical Engineering, Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, 01003, USA
| | - Luke Hanley
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Ross P Carlson
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA. .,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA.
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Mobilization of Iron Stored in Bacterioferritin Is Required for Metabolic Homeostasis in Pseudomonas aeruginosa. Pathogens 2020; 9:pathogens9120980. [PMID: 33255203 PMCID: PMC7760384 DOI: 10.3390/pathogens9120980] [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: 10/16/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Iron homeostasis offers a significant bacterial vulnerability because pathogens obtain essential iron from their mammalian hosts, but host-defenses maintain vanishingly low levels of free iron. Although pathogens have evolved mechanisms to procure host-iron, these depend on well-regulated iron homeostasis. To disrupt iron homeostasis, our work has targeted iron mobilization from the iron storage protein bacterioferritin (BfrB) by blocking a required interaction with its cognate ferredoxin partner (Bfd). The blockade of the BfrB–Bfd complex by deletion of the bfd gene (Δbfd) causes iron to irreversibly accumulate in BfrB. In this study we used mass spectrometry and NMR spectroscopy to compare the proteomic response and the levels of key intracellular metabolites between wild type (wt) and isogenic ΔbfdP. aeruginosa strains. We find that the irreversible accumulation of unusable iron in BfrB leads to acute intracellular iron limitation, even if the culture media is iron-sufficient. Importantly, the iron limitation and concomitant iron metabolism dysregulation trigger a cascade of events that lead to broader metabolic homeostasis disruption, which includes sulfur limitation, phenazine-mediated oxidative stress, suboptimal amino acid synthesis and altered carbon metabolism.
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Nitrate Respiration in Thermus thermophilus NAR1: from Horizontal Gene Transfer to Internal Evolution. Genes (Basel) 2020; 11:genes11111308. [PMID: 33158244 PMCID: PMC7694296 DOI: 10.3390/genes11111308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
Genes coding for enzymes of the denitrification pathway appear randomly distributed among isolates of the ancestral genus Thermus, but only in few strains of the species Thermus thermophilus has the pathway been studied to a certain detail. Here, we review the enzymes involved in this pathway present in T. thermophilus NAR1, a strain extensively employed as a model for nitrate respiration, in the light of its full sequence recently assembled through a combination of PacBio and Illumina technologies in order to counteract the systematic errors introduced by the former technique. The genome of this strain is divided in four replicons, a chromosome of 2,021,843 bp, two megaplasmids of 370,865 and 77,135 bp and a small plasmid of 9799 pb. Nitrate respiration is encoded in the largest megaplasmid, pTTHNP4, within a region that includes operons for O2 and nitrate sensory systems, a nitrate reductase, nitrate and nitrite transporters and a nitrate specific NADH dehydrogenase, in addition to multiple insertion sequences (IS), suggesting its mobility-prone nature. Despite nitrite is the final product of nitrate respiration in this strain, the megaplasmid encodes two putative nitrite reductases of the cd1 and Cu-containing types, apparently inactivated by IS. No nitric oxide reductase genes have been found within this region, although the NorR sensory gene, needed for its expression, is found near the inactive nitrite respiration system. These data clearly support that partial denitrification in this strain is the consequence of recent deletions and IS insertions in genes involved in nitrite respiration. Based on these data, the capability of this strain to transfer or acquire denitrification clusters by horizontal gene transfer is discussed.
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Mapping of the Denitrification Pathway in Burkholderia thailandensis by Genome-Wide Mutant Profiling. J Bacteriol 2020; 202:JB.00304-20. [PMID: 32900830 DOI: 10.1128/jb.00304-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
Burkholderia thailandensis is a soil saprophyte that is closely related to the pathogen Burkholderia pseudomallei, the etiological agent of melioidosis in humans. The environmental niches and infection sites occupied by these bacteria are thought to contain only limited concentrations of oxygen, where they can generate energy via denitrification. However, knowledge of the underlying molecular basis of the denitrification pathway in these bacteria is scarce. In this study, we employed a transposon sequencing (Tn-Seq) approach to identify genes conferring a fitness benefit for anaerobic growth of B. thailandensis Of the 180 determinants identified, several genes were shown to be required for growth under denitrifying conditions: the nitrate reductase operon narIJHGK2K1, the aniA gene encoding a previously unknown nitrite reductase, and the petABC genes encoding a cytochrome bc 1, as well as three novel regulators that control denitrification. Our Tn-Seq data allowed us to reconstruct the entire denitrification pathway of B. thailandensis and shed light on its regulation. Analyses of growth behaviors combined with measurements of denitrification metabolites of various mutants revealed that nitrate reduction provides sufficient energy for anaerobic growth, an important finding in light of the fact that some pathogenic Burkholderia species can use nitrate as a terminal electron acceptor but are unable to complete denitrification. Finally, we demonstrated that a nitrous oxide reductase mutant is not affected for anaerobic growth but is defective in biofilm formation and accumulates N2O, which may play a role in the dispersal of B. thailandensis biofilms.IMPORTANCE Burkholderia thailandensis is a soil-dwelling saprophyte that is often used as surrogate of the closely related pathogen Burkholderia pseudomallei, the causative agent of melioidosis and a classified biowarfare agent. Both organisms are adapted to grow under oxygen-limited conditions in rice fields by generating energy through denitrification. Microoxic growth of B. pseudomallei is also considered essential for human infections. Here, we have used a Tn-Seq approach to identify the genes encoding the enzymes and regulators required for growth under denitrifying conditions. We show that a mutant that is defective in the conversion of N2O to N2, the last step in the denitrification process, is unaffected in microoxic growth but is severely impaired in biofilm formation, suggesting that N2O may play a role in biofilm dispersal. Our study identified novel targets for the development of therapeutic agents to treat meliodiosis.
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Liu RR, Tian Y, Zhou EM, Xiong MJ, Xiao M, Li WJ. Distinct Expression of the Two NO-Forming Nitrite Reductases in Thermus antranikianii DSM 12462 T Improved Environmental Adaptability. MICROBIAL ECOLOGY 2020; 80:614-626. [PMID: 32474659 DOI: 10.1007/s00248-020-01528-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 05/14/2020] [Indexed: 05/21/2023]
Abstract
Hot spring ecosystems are analogous to some thermal environments on the early Earth and represent ideal models to understand life forms and element cycling on the early Earth. Denitrification, an important component of biogeochemical nitrogen cycle, is highly active in hot springs. Nitrite (NO2-) reduction to nitric oxide (NO) is the significant and rate-limiting pathway in denitrification and is catalyzed by two types of nitrite reductases, encoded by nirS and nirK genes. NirS and NirK were originally considered incompatible in most denitrifying organisms, although a few strains have been reported to possess both genes. Herein, we report the functional division of nirS and nirK in Thermus, a thermophilic genus widespread in thermal ecosystems. Transcriptional levels of nirS and nirK coexisting in Thermus antranikianii DSM 12462T were measured to assess the effects of nitrite, oxygen, and stimulation time. Thirty-nine Thermus strains were used to analyze the phylogeny and distribution of nirS and nirK; six representative strains were used to assess the denitrification phenotype. The results showed that both genes were actively transcribed and expressed independently in T. antranikianii DSM 12462T. Strains with both nirS and nirK had a wider range of nitrite adaptation and revealed nir-related physiological adaptations in Thermus: nirK facilitated adaptation to rapid changes and extended the adaptation range of nitrite under oxygen-limited conditions, while nirS expression was higher under oxic and relatively stable conditions.
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Affiliation(s)
- Rui-Rui Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ye Tian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - En-Min Zhou
- School of Resource Environment and Earth Science, Yunnan Institute of Geography, Yunnan University, Kunming, 650091, People's Republic of China
| | - Meng-Jie Xiong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Min Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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28
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Abdelhamed H, Nho SW, Karsi A, Lawrence ML. The role of denitrification genes in anaerobic growth and virulence of Flavobacterium columnare. J Appl Microbiol 2020; 130:1062-1074. [PMID: 32955778 DOI: 10.1111/jam.14855] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 11/28/2022]
Abstract
AIMS Comparative genomics analyses indicated that the Flavobacterium columnare genome has unique denitrification genes relative to Flavobacterium psychrophilum and Flavobacterium johnsoniae, including nasA (nitrate reductase), nirS (nitrite reductase), norB (nitric oxide reductase) and nosZ (nitrous oxide reductase). The current study determines the roles of nasA, nirS, norB and nosZ in anaerobic growth, nitrate reduction, biofilm formation and virulence. METHODS AND RESULTS Four in-frame deletion mutants in virulent F. columnare strain 94-081 were constructed by allelic exchange using pCP29 plasmid. Compared with parent strain 94-081, FcΔnasA,FcΔnirS and FcΔnosZ mutants did not grow as well anaerobically, whereas the growth of FcΔnorB strain was similar to the parent strain (FcWT). Exogenous nitrate was not significantly consumed under anaerobic conditions in FcΔnasA, FcΔnirS and FcΔnosZ compared to parent strain 94-081. Under anaerobic conditions, Fc∆nasA, Fc∆norB and Fc∆nosZ formed significantly less biofilm than the wild type strain at 24 and 96 h, but FcΔnirS was not significantly affected. The nitrite reductase mutant FcΔnirS was highly attenuated in catfish, whereas FcΔnasA, FcΔnorB and FcΔnosZ had similar virulence to FcWT. CONCLUSIONS These results show, for the first time, that denitrification genes enable F. columnare to grow anaerobically using nitrate as an electron acceptor, and nitrite reductase contributes to F. columnare virulence. SIGNIFICANCE AND IMPACT OF THE STUDY These findings indicate potential for F. columnare to grow in nitrate-rich anaerobic zones in catfish production ponds, and they suggest that a Fc∆nirS strain could be useful as a safe live vaccine if it protects catfish against columnaris disease.
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Affiliation(s)
- H Abdelhamed
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - S W Nho
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - A Karsi
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - M L Lawrence
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
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29
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The Nitrite Transporter Facilitates Biofilm Formation via Suppression of Nitrite Reductase and Is a New Antibiofilm Target in Pseudomonas aeruginosa. mBio 2020; 11:mBio.00878-20. [PMID: 32636243 PMCID: PMC7343986 DOI: 10.1128/mbio.00878-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial biofilms play roles in infections and avoidance of host defense mechanisms of medically important pathogens and increase the antibiotic resistance of the bacteria. Nitric oxide (NO) is reported to be involved in both biofilm formation and dispersal, which are conflicting processes. The mechanism by which NO regulates biofilm dispersal is relatively understood, but there are no reports about how NO is involved in biofilm formation. Here, by investigating the mechanism by which complestatin inhibits biofilm formation, we describe a novel mechanism for governing biofilm formation in Escherichia coli and Pseudomonas aeruginosa. Nitrite transporter is required for biofilm formation via regulation of NO levels and subsequent c-di-GMP production. Additionally, the nitrite transporter contributes more to P. aeruginosa virulence than quorum sensing. Thus, this study identifies nitrite transporters as new antibiofilm targets for future practical and therapeutic agent development. Biofilm-forming bacteria, including the Gram-negative Pseudomonas aeruginosa, cause multiple types of chronic infections and are responsible for serious health burdens in humans, animals, and plants. Nitric oxide (NO) has been shown to induce biofilm dispersal via triggering a reduction in cyclic-di-GMP levels in a variety of bacteria. However, how NO, at homeostatic levels, also facilitates biofilm formation is unknown. Here, we found that complestatin, a structural analog of vancomycin isolated from Streptomyces, inhibits P. aeruginosa biofilm formation by upregulating NO production via nitrite reductase (NIR) induction and c-di-GMP degradation via phosphodiesterase (PDE) stimulation. The complestatin protein target was identified as a nitrite transporter from a genome-wide screen using the Keio Escherichia coli knockout library and confirmed using nitrite transporter knockout and overexpression strains. We demonstrated that the nitrite transporter stimulated biofilm formation by controlled NO production via appropriate NIR suppression and subsequent diguanylate cyclase (DGC) activation, not PDE activity, and c-di-GMP production in E. coli and P. aeruginosa. Thus, this study provides a mechanism for NO-mediated biofilm formation, which was previously not understood.
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30
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Zhao X, Liu B, Wang X, Chen C, Ren N, Xing D. Single molecule sequencing reveals response of manganese-oxidizing microbiome to different biofilter media in drinking water systems. WATER RESEARCH 2020; 171:115424. [PMID: 31887545 DOI: 10.1016/j.watres.2019.115424] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
Rapid sand biofiltration (RSBF) is widely used for the removal of contaminants from drinking water treatment systems. Biofilm microbiomes in the biofilter media play essential roles in biotransformation of contaminants, but is not comprehensively understood. This study reports on Mn(II) oxidation and the core microbiomes in magnetite sand RSBF (MagS-RSBF) and manganese sand RSBF (MnS-RSBF). MnS-RSBF showed a relatively higher Mn(II) removal rate (40-91.2%) than MagS-RSBF during the start-up. MagS-RSBF and MnS-RSBF had similar Mn(II) removal rates (94.13% and 99.16%) over stable operation for 80 days. Mn(II) removal rates at different depths in the MnS-RSBF reactor significantly changed with operation time, and the filter in the upper layer of MnS-RSBF made the largest contribution to Mn(II) oxidation once operation had stabilized. PacBio single molecule sequencing of full-length 16S rRNA gene indicated that biofilter medium had a significant impact on the core microbiomes of the biofilms from the two biofilters. The magnetite sand biofilter facilitated the enrichment of Mn(II)-oxidizing biofilms. The dominant populations consisted of Pedomicrobium, Pseudomonas, and Hyphomicrobium in the RSBF, which have been affiliated with putative manganese-oxidizing bacteria (MnOB). The relative abundance of Pedomicrobium manganicum increased with operation time in both RSBF reactors. In addition, Nordella oligomobilis and Derxia gummosa were statistically correlated with Mn(II) oxidation. Species-species co-occurrence networks indicated that the microbiome of MnS-RSBF had more complex correlations than that of MagS-RSBF, implying that biofilter medium substantially shaped the microbial community in the RSBF. Hyphomicrobium and nitrite-oxidizing Nitrospira moscoviensis were positively correlated. The core microbiomes' composition of both RSBF reactors converged over operation time. A hybrid biofilter medium with magnetite sand and manganese sand may therefore be best in rapid sand filtration for Mn(II) oxidation.
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Affiliation(s)
- Xin Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Bingfeng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Xiuheng Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China.
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Blakeway LV, Tan A, Jurcisek JA, Bakaletz LO, Atack JM, Peak IR, Seib KL. The Moraxella catarrhalis phase-variable DNA methyltransferase ModM3 is an epigenetic regulator that affects bacterial survival in an in vivo model of otitis media. BMC Microbiol 2019; 19:276. [PMID: 31818247 PMCID: PMC6902483 DOI: 10.1186/s12866-019-1660-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 11/22/2019] [Indexed: 12/23/2022] Open
Abstract
Background Moraxella catarrhalis is a leading cause of otitis media (OM) and chronic obstructive pulmonary disease (COPD). M. catarrhalis contains a Type III DNA adenine methyltransferase (ModM) that is phase-variably expressed (i.e., its expression is subject to random, reversible ON/OFF switching). ModM has six target recognition domain alleles (modM1–6), and we have previously shown that modM2 is the predominant allele, while modM3 is associated with OM. Phase-variable DNA methyltransferases mediate epigenetic regulation and modulate pathogenesis in several bacteria. ModM2 of M. catarrhalis regulates the expression of a phasevarion containing genes important for colonization and infection. Here we describe the phase-variable expression of modM3, the ModM3 methylation site and the suite of genes regulated within the ModM3 phasevarion. Results Phase-variable expression of modM3, mediated by variation in length of a 5′-(CAAC)n-3′ tetranucleotide repeat tract in the open reading frame was demonstrated in M. catarrhalis strain CCRI-195ME with GeneScan fragment length analysis and western immunoblot. We determined that ModM3 is an active N6-adenine methyltransferase that methylates the sequence 5′-ACm6ATC-3′. Methylation was detected at all 4446 5′-ACATC-3′ sites in the genome when ModM3 is expressed. RNASeq analysis identified 31 genes that are differentially expressed between modM3 ON and OFF variants, including five genes that are involved in the response to oxidative and nitrosative stress, with potential roles in biofilm formation and survival in anaerobic environments. An in vivo chinchilla (Chinchilla lanigera) model of otitis media demonstrated that transbullar challenge with the modM3 OFF variant resulted in an increased middle ear bacterial load compared to a modM3 ON variant. In addition, co-infection experiments with NTHi and M. catarrhalis modM3 ON or modM3 OFF variants revealed that phase variation of modM3 altered survival of NTHi in the middle ear during early and late stage infection. Conclusions Phase variation of ModM3 epigenetically regulates the expression of a phasevarion containing multiple genes that are potentially important in the progression of otitis media.
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Affiliation(s)
- Luke V Blakeway
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Aimee Tan
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Joseph A Jurcisek
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH, 43215, USA
| | - Lauren O Bakaletz
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH, 43215, USA
| | - John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Ian R Peak
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia.,School of Medical Science, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia.
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Enkai S, Inaoka DK, Kouguchi H, Irie T, Yagi K, Kita K. Mitochondrial complex III in larval stage of Echinococcus multilocularis as a potential chemotherapeutic target and in vivo efficacy of atovaquone against primary hydatid cysts. Parasitol Int 2019; 75:102004. [PMID: 31678356 DOI: 10.1016/j.parint.2019.102004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 12/20/2022]
Abstract
Echinococcus multilocularis employs aerobic and anaerobic respiration pathways for its survival in the specialized environment of the host. Under anaerobic conditions, fumarate respiration has been identified as a promising target for drug development against E. multilocularis larvae, although the relevance of oxidative phosphorylation in its survival remains unclear. Here, we focused on the inhibition of mitochondrial cytochrome bc1 complex (complex III) and evaluated aerobic respiratory activity using mitochondrial fractions from E. multilocularis protoscoleces. An enzymatic assay revealed that the mitochondrial fractions possessed NADH-cytochrome c reductase (mitochondrial complexes I and III) and succinate-cytochrome c reductase (mitochondrial complexes II and III) activities in the aerobic pathway. Enzymatic analysis showed that atovaquone, a commercially available anti-malarial drug, inhibited mitochondrial complex III at 1.5 nM (IC50). In addition, culture experiments revealed the ability of atovaquone to kill protoscoleces under aerobic conditions, but not under anaerobic conditions, indicating that protoscoleces altered their respiration system to oxidative phosphorylation or fumarate respiration depending on the oxygen supply. Furthermore, combined administration of atovaquone with atpenin A5, a quinone binding site inhibitor of complex II, completely killed protoscoleces in the culture. Thus, inhibition of both complex II and complex III was essential for strong antiparasitic effect on E. multilocularis. Additionally, we demonstrated that oral administration of atovaquone significantly reduced primary alveolar hydatid cyst development in the mouse liver, compared with the untreated control, indicating that complex III is a promising target for development of anti-echinococcal drug.
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Affiliation(s)
- Shigehiro Enkai
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.
| | - Daniel Ken Inaoka
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; Department of Host-Defense Biochemistry, Institute of tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Hirokazu Kouguchi
- Department of Infectious Diseases, Hokkaido Institute of Public Health, N19 W12, Kita-Ku, Sapporo, Hokkaido 060-0819, Japan
| | - Takao Irie
- Department of Infectious Diseases, Hokkaido Institute of Public Health, N19 W12, Kita-Ku, Sapporo, Hokkaido 060-0819, Japan
| | - Kinpei Yagi
- Department of Infectious Diseases, Hokkaido Institute of Public Health, N19 W12, Kita-Ku, Sapporo, Hokkaido 060-0819, Japan
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; Department of Host-Defense Biochemistry, Institute of tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
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Gaimster H, Alston M, Richardson DJ, Gates AJ, Rowley G. Transcriptional and environmental control of bacterial denitrification and N2O emissions. FEMS Microbiol Lett 2019; 365:4768087. [PMID: 29272423 DOI: 10.1093/femsle/fnx277] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/18/2017] [Indexed: 12/18/2022] Open
Abstract
In oxygen-limited environments, denitrifying bacteria can switch from oxygen-dependent respiration to nitrate (NO3-) respiration in which the NO3- is sequentially reduced via nitrite (NO2-), nitric oxide (NO) and nitrous oxide (N2O) to dinitrogen (N2). However, atmospheric N2O continues to rise, a significant proportion of which is microbial in origin. This implies that the enzyme responsible for N2O reduction, nitrous oxide reductase (NosZ), does not always carry out the final step of denitrification either efficiently or in synchrony with the rest of the pathway. Despite a solid understanding of the biochemistry underpinning denitrification, there is a relatively poor understanding of how environmental signals and respective transcriptional regulators control expression of the denitrification apparatus. This minireview describes the current picture for transcriptional regulation of denitrification in the model bacterium, Paracoccus denitrificans, highlighting differences in other denitrifying bacteria where appropriate, as well as gaps in our understanding. Alongside this, the emerging role of small regulatory RNAs in regulation of denitrification is discussed. We conclude by speculating how this information, aside from providing a better understanding of the denitrification process, can be translated into development of novel greenhouse gas mitigation strategies.
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Affiliation(s)
- Hannah Gaimster
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Mark Alston
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Andrew J Gates
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Gary Rowley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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34
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Influence of graphene oxide and biochar on anaerobic degradation of petroleum hydrocarbons. J Biosci Bioeng 2019; 128:72-79. [DOI: 10.1016/j.jbiosc.2019.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 12/17/2018] [Accepted: 01/13/2019] [Indexed: 11/18/2022]
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35
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Ütkür FÖ, Schmid A, Bühler B. Anaerobic C-H Oxyfunctionalization: Coupling of Nitrate Reduction and Quinoline Hydroxylation in Recombinant Pseudomonas putida. Biotechnol J 2019; 14:e1800615. [PMID: 31144783 DOI: 10.1002/biot.201800615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 05/20/2019] [Indexed: 11/09/2022]
Abstract
Whole-cell biocatalysis for C-H oxyfunctionalization depends on and is often limited by O2 mass transfer. In contrast to oxygenases, molybdenum hydroxylases use water instead of O2 as an oxygen donor and thus have the potential to relieve O2 mass transfer limitations. Molybdenum hydroxylases may even allow anaerobic oxyfunctionalization when coupled to anaerobic respiration. To evaluate this option, the coupling of quinoline hydroxylation to denitrification is tested under anaerobic conditions employing Pseudomonas putida (P. putida) 86, capable of aerobic growth on quinoline. P. putida 86 reduces both nitrate and nitrite, but at low rates, which does not enable significant growth and quinoline hydroxylation. Introduction of the nitrate reductase from Pseudomonas aeruginosa enables considerable specific quinoline hydroxylation activity (6.9 U gCDW -1 ) under anaerobic conditions with nitrate as an electron acceptor and 2-hydroxyquinoline as the sole product (further metabolization depends on O2 ). Hydroxylation-derived electrons are efficiently directed to nitrate, accounting for 38% of the respiratory activity. This study shows that molybdenum hydroxylase-based whole-cell biocatalysts enable completely anaerobic carbon oxyfunctionalization when coupled to alternative respiration schemes such as nitrate respiration.
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Affiliation(s)
- Fatma Özde Ütkür
- Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Strasse 66, Dortmund, 44227, Germany
| | - Andreas Schmid
- Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Strasse 66, Dortmund, 44227, Germany.,Department of Solar Materials, Helmholtz-Centre for Environmental Research GmbH-UFZ, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Bruno Bühler
- Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Strasse 66, Dortmund, 44227, Germany.,Department of Solar Materials, Helmholtz-Centre for Environmental Research GmbH-UFZ, Permoserstrasse 15, 04318, Leipzig, Germany
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36
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Anaerobiosis influences virulence properties of Pseudomonas aeruginosa cystic fibrosis isolates and the interaction with Staphylococcus aureus. Sci Rep 2019; 9:6748. [PMID: 31043640 PMCID: PMC6494883 DOI: 10.1038/s41598-019-42952-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/03/2019] [Indexed: 01/08/2023] Open
Abstract
The airways of individuals with cystic fibrosis (CF) are abundantly colonised by Staphylococcus aureus and Pseudomonas aeruginosa. Co-infecting hypoxic regions of static mucus within CF airways, together with decreases in pulmonary function, mucus plugging and oxygen consumption by host neutrophils gives rise to regions of anoxia. This study determined the impact of anaerobiosis upon S. aureus-P. aeruginosa interactions in planktonic co-culture and mixed species biofilms in vitro. Whilst anoxia reduced the ability for P. aeruginosa CF isolates to dominate over S. aureus, this occurred in an isolate dependent manner. Investigations into the underlying mechanisms suggest that the anti-staphylococcal compound facilitating P. aeruginosa dominance under normoxia and anoxia is greater than 3 kDa in size and is heat-stable. Not all interspecies interactions studied were antagonistic, as S. aureus exoproducts were shown to restore and enhance P. aeruginosa motility under normoxia and anoxia in an isolate dependent manner. Collectively, this study suggests changes in oxygen availability within regions of the CF lung is likely to influence interspecies interactions and in turn, potentially influence disease progression.
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Zhou Y, Qin Y, Liu X, Feng Z, Zhu H, Yao Q. Soil Bacterial Function Associated With Stylo (Legume) and Bahiagrass (Grass) Is Affected More Strongly by Soil Chemical Property Than by Bacterial Community Composition. Front Microbiol 2019; 10:798. [PMID: 31031740 PMCID: PMC6473644 DOI: 10.3389/fmicb.2019.00798] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 03/28/2019] [Indexed: 01/06/2023] Open
Abstract
Soil microbes are driver of nutrient cycling, with microbial function affected by community composition and soil chemical property. Legume and grass are ubiquitous in many ecosystems, however, their differential effects on microbial function are less understood. Here we constructed compartmented rhizobox planted with stylo (Stylosanthes guianensis, legume) or bahiagrass (Paspalum natatum, grass) to compare their influences on bacterial function and to investigate the determinant of bacterial function. Soils in root compartment and in near (0–5 mm from root compartment) or far (10–15 mm from root compartment) rhizosphere were sampled. Soil chemical properties, bacterial community composition and function were characterized. Results indicate that plant species and distance significantly affected bacterial function. The activities of beta-xylosidase, nitrate reductase and phosphomonoesterase were higher in stylo soil than in bahiagrass soil, while leucine-aminopeptidase activity and nosZ abundance were vice versa. Rhizosphere effect was obvious for the activities of beta-glucosidase, beta-xylosidase, chitinase, and the abundances of AOB-amoA, nirS, nosZ. Statistical analysis revealed that soil chemical property was significantly associated with bacterial function, with a higher coefficient than bacterial community composition. These data suggest that stylo and bahiagrass differentially affect bacterial function, which is affected more strongly by soil chemical property than by community composition.
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Affiliation(s)
- Yang Zhou
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, Guangdong Engineering Research Center for Grass Science, Guangzhou, China.,Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, China
| | - Yongqiang Qin
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, Guangdong Engineering Research Center for Grass Science, Guangzhou, China
| | - Xiaodi Liu
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, Guangdong Engineering Research Center for Grass Science, Guangzhou, China
| | - Zengwei Feng
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, Guangdong Engineering Research Center for Grass Science, Guangzhou, China
| | - Honghui Zhu
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, China
| | - Qing Yao
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, Guangdong Engineering Research Center for Grass Science, Guangzhou, China
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38
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Joshi C, Patel P, Palep H, Kothari V. Validation of the anti-infective potential of a polyherbal 'Panchvalkal' preparation, and elucidation of the molecular basis underlining its efficacy against Pseudomonas aeruginosa. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2019; 19:19. [PMID: 30654785 PMCID: PMC6335721 DOI: 10.1186/s12906-019-2428-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 01/02/2019] [Indexed: 02/02/2023]
Abstract
BACKGROUND A Panchvalkal formulation (Pentaphyte P-5®) mentioned in ancient texts of Indian traditional medicine was investigated for its anti-infective potential against Pseudomonas aeruginosa. METHODS Effect of the test formulation on bacterial growth and pigment production was evaluated by broth dilution assay. In vivo efficacy was evaluated using Caenorhabditis elegans as the model host. Whole transcriptome approach was taken to study the effect of test formulation on bacterial gene expression. RESULTS This formulation in vitro was found to be capable of affecting quorum sensing (QS)-regulated traits (pyocyanin, pyoverdine, biofilm) of Pseudomonas aeruginosa. In combination with antibiotics, it enhanced susceptibility of the test bacterium to antibiotics like cephalexin and tetracycline. Effect of Panchvalkal formulation (PF) on QS-regulated traits of P. aeruginosa was not reversed even after repeated exposure of the bacterium to PF. In vivo efficacy of PF was demonstrated employing Caenorhabditis elegans as the model host, wherein PF-treated bacteria were able to kill lesser worms than their extract-unexposed counterparts. Whole transcriptome study revealed that approximately 14% of the P. aeruginosa genome was expressed differently under the influence of PF. CONCLUSIONS Major mechanisms through which Panchvalkal seems to exert its anti-virulence effect are generation of nitrosative and oxidative stress, and disturbing iron and molybdenum homeostasis, besides interfering with QS machinery. This study is a good demonstration of the therapeutic utility of the 'polyherbalism' concept, so common in ayurved. It also demonstrates utility of the modern 'omics' tools for validating the traditional medicine i.e. ayuromics.
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Affiliation(s)
- Chinmayi Joshi
- Institute of Science, Nirma University, Ahmedabad, 382481 India
| | - Pooja Patel
- Institute of Science, Nirma University, Ahmedabad, 382481 India
| | | | - Vijay Kothari
- Institute of Science, Nirma University, Ahmedabad, 382481 India
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Abstract
SIGNIFICANCE The molecule nitric oxide (NO) has been shown to regulate behaviors in bacteria, including biofilm formation. NO detection and signaling in bacteria is typically mediated by hemoproteins such as the bis-(3',5')-cyclic dimeric adenosine monophosphate-specific phosphodiesterase YybT, the transcriptional regulator dissimilative nitrate respiration regulator, or heme-NO/oxygen binding (H-NOX) domains. H-NOX domains are well-characterized primary NO sensors that are capable of detecting nanomolar NO and influencing downstream signal transduction in many bacterial species. However, many bacteria, including the human pathogen Pseudomonas aeruginosa, respond to nanomolar concentrations of NO but do not contain an annotated H-NOX domain, indicating the existence of an additional nanomolar NO-sensing protein (NosP). Recent Advances: A newly discovered bacterial hemoprotein called NosP may also act as a primary NO sensor in bacteria, in addition to, or in place of, H-NOX. NosP was first described as a regulator of a histidine kinase signal transduction pathway that is involved in biofilm formation in P. aeruginosa. CRITICAL ISSUES The molecular details of NO signaling in bacteria are still poorly understood. There are still many bacteria that are NO responsive but do encode either H-NOX or NosP domains in their genomes. Even among bacteria that encode H-NOX or NosP, many questions remain. FUTURE DIRECTIONS The molecular mechanisms of NO regulation in many bacteria remain to be established. Future studies are required to gain knowledge about the mechanism of NosP signaling. Advancements on structural and molecular understanding of heme-based sensors in bacteria could lead to strategies to alleviate or control bacterial biofilm formation or persistent biofilm-related infections.
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Affiliation(s)
| | - Lisa-Marie Nisbett
- 2 Graduate Program in Biochemistry and Structural Biology, Stony Brook University , Stony Brook, New York
| | - Bezalel Bacon
- 2 Graduate Program in Biochemistry and Structural Biology, Stony Brook University , Stony Brook, New York
| | - Elizabeth Boon
- 1 Department of Chemistry, Stony Brook University , Stony Brook, New York.,2 Graduate Program in Biochemistry and Structural Biology, Stony Brook University , Stony Brook, New York.,3 Institute of Chemical Biology and Drug Design, Stony Brook University , Stony Brook, New York
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40
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Fléchard M, Duchesne R, Tahrioui A, Bouffartigues E, Depayras S, Hardouin J, Lagy C, Maillot O, Tortuel D, Azuama CO, Clamens T, Duclairoir-Poc C, Catel-Ferreira M, Gicquel G, Feuilloley MGJ, Lesouhaitier O, Heipieper HJ, Groleau MC, Déziel É, Cornelis P, Chevalier S. The absence of SigX results in impaired carbon metabolism and membrane fluidity in Pseudomonas aeruginosa. Sci Rep 2018; 8:17212. [PMID: 30464317 PMCID: PMC6249292 DOI: 10.1038/s41598-018-35503-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/23/2018] [Indexed: 12/21/2022] Open
Abstract
In Pseudomonas aeruginosa, SigX is an extra-cytoplasmic function σ factor that belongs to the cell wall stress response network. In previous studies, we made the puzzling observation that sigX mutant growth was severely affected in rich lysogeny broth (LB) but not in minimal medium. Here, through comparative transcriptomic and proteomic analysis, we show that the absence of SigX results in dysregulation of genes, whose products are mainly involved in transport, carbon and energy metabolisms. Production of most of these genes is controlled by carbon catabolite repression (CCR), a key regulatory system than ensures preferential carbon source uptake and utilization, substrate prioritization and metabolism. The strong CCR response elicited in LB was lowered in a sigX mutant, suggesting altered nutrient uptake. Since the absence of SigX affects membrane composition and fluidity, we suspected membrane changes to cause such phenotype. The detergent polysorbate 80 (PS80) can moderately destabilize the envelope resulting in non-specific increased nutrient intake. Remarkably, growth, membrane fluidity and expression of dysregulated genes in the sigX mutant strain were restored in LB supplemented with PS80. Altogether, these data suggest that SigX is indirectly involved in CCR regulation, possibly via its effects on membrane integrity and fluidity.
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Affiliation(s)
- Maud Fléchard
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Rachel Duchesne
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Ali Tahrioui
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Emeline Bouffartigues
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Ségolène Depayras
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Julie Hardouin
- Normandie Université, Université de Rouen Normandie, Laboratoire Polymères Biopolymères Surfaces, PBS, UMR, 6270 CNRS, Mont-Saint-Aignan, France
| | - Coralie Lagy
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Olivier Maillot
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Damien Tortuel
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Cecil Onyedikachi Azuama
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Thomas Clamens
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Cécile Duclairoir-Poc
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Manuella Catel-Ferreira
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Gwendoline Gicquel
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Marc G J Feuilloley
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Olivier Lesouhaitier
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Hermann J Heipieper
- Department of Environmental Biotechnology, UFZ Helmholtz Centre for Environmental Research, Leipzig, Germany
| | | | - Éric Déziel
- INRS-Institut Armand-Frappier, Laval, Québec, Canada
| | - Pierre Cornelis
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Sylvie Chevalier
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France.
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41
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Carreira C, Mestre O, Nunes RF, Moura I, Pauleta SR. Genomic organization, gene expression and activity profile of Marinobacter hydrocarbonoclasticus denitrification enzymes. PeerJ 2018; 6:e5603. [PMID: 30258713 PMCID: PMC6152468 DOI: 10.7717/peerj.5603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 08/18/2018] [Indexed: 12/19/2022] Open
Abstract
Background Denitrification is one of the main pathways of the N-cycle, during which nitrate is converted to dinitrogen gas, in four consecutive reactions that are each catalyzed by a different metalloenzyme. One of the intermediate metabolites is nitrous oxide, which has a global warming impact greater then carbon dioxide and which atmospheric concentration has been increasing in the last years. The four denitrification enzymes have been isolated and biochemically characterized from Marinobacter hydrocarbonoclasticus in our lab. Methods Bioinformatic analysis of the M. hydrocarbonoclasticus genome to identify the genes involved in the denitrification pathway. The relative gene expression of the gene encoding the catalytic subunits of those enzymes was analyzed during the growth under microoxic conditions. The consumption of nitrate and nitrite, and the reduction of nitric oxide and nitrous oxide by whole-cells was monitored during anoxic and microoxic growth in the presence of 10 mM sodium nitrate at pH 7.5. Results The bioinformatic analysis shows that genes encoding the enzymes and accessory factors required for each step of the denitrification pathway are clustered together. An unusual feature is the co-existence of genes encoding a q- and a c-type nitric oxide reductase, with only the latter being transcribed at similar levels as the ones encoding the catalytic subunits of the other denitrifying enzymes, when cells are grown in the presence of nitrate under microoxic conditions. Using either a batch- or a closed system, nitrate is completely consumed in the beginning of the growth, with transient formation of nitrite, and whole-cells can reduce nitric oxide and nitrous oxide from mid-exponential phase until being collected (time-point 50 h). Discussion M. hydrocarbonoclasticus cells can reduce nitric and nitrous oxide in vivo, indicating that the four denitrification steps are active. Gene expression profile together with promoter regions analysis indicates the involvement of a cascade regulatory mechanism triggered by FNR-type in response to low oxygen tension, with nitric oxide and nitrate as secondary effectors, through DNR and NarXL, respectively. This global characterization of the denitrification pathway of a strict marine bacterium, contributes to the understanding of the N-cycle and nitrous oxide release in marine environments.
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Affiliation(s)
- Cíntia Carreira
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.,Biological Chemistry Lab, LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Olga Mestre
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Rute F Nunes
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Isabel Moura
- Biological Chemistry Lab, LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Sofia R Pauleta
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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42
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Hirakawa H, Kurabayashi K, Tanimoto K, Tomita H. Oxygen Limitation Enhances the Antimicrobial Activity of Fosfomycin in Pseudomonas aeruginosa Following Overexpression of glpT Which Encodes Glycerol-3-Phosphate/Fosfomycin Symporter. Front Microbiol 2018; 9:1950. [PMID: 30186264 PMCID: PMC6110920 DOI: 10.3389/fmicb.2018.01950] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/02/2018] [Indexed: 12/25/2022] Open
Abstract
Fosfomycin is resurfacing as a "last resort drug" to treat infections caused by multidrug resistant pathogens. This drug has a remarkable benefit in that its activity increases under oxygen-limited conditions unlike other commonly used antimicrobials such as β-lactams, fluoroquinolones and aminoglycosides. Especially, utility of fosfomycin has being evaluated with particular interest to treat chronic biofilm infections caused by Pseudomonas aeruginosa because it often encounters anaerobic situations. Here, we showed that P. aeruginosa PAO1, commonly used in many laboratories, becomes more susceptible to fosfomycin when grown anaerobically, and studied on how fosfomycin increases its activity under anaerobic conditions. Results of transport assay and gene expression study indicated that PAO1 cells grown anaerobically exhibit a higher expression of glpT encoding a glycerol-3-phosphate transporter which is responsible for fosfomycin uptake, then lead to increased intracellular accumulation of the drug. Elevated expression of glpT in anaerobic cultures depended on ANR, a transcriptional regulator that is activated under anaerobic conditions. Purified ANR protein bound to the DNA fragment from glpT region upstream, suggesting it is an activator of glpT gene expression. We found that increased susceptibility to fosfomycin was also observed in a clinical isolate which has a promoted biofilm phenotype and its glpT and anr genes are highly conserved with those of PAO1. We conclude that increased antibacterial activity of fosfomycin to P. aeruginosa under anaerobic conditions is attributed to elevated expression of GlpT following activation of ANR, then leads to increased uptake of the drug.
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Affiliation(s)
- Hidetada Hirakawa
- Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi, Japan
| | - Kumiko Kurabayashi
- Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi, Japan
| | - Koichi Tanimoto
- Laboratory of Bacterial Drug Resistance, Graduate School of Medicine, Gunma University, Maebashi, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi, Japan.,Laboratory of Bacterial Drug Resistance, Graduate School of Medicine, Gunma University, Maebashi, Japan
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43
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Significant enhancement of nitrous oxide energy yields from wastewater achieved by bioaugmentation with a recombinant strain of Pseudomonas aeruginosa. Sci Rep 2018; 8:11916. [PMID: 30093706 PMCID: PMC6085377 DOI: 10.1038/s41598-018-30326-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/27/2018] [Indexed: 12/17/2022] Open
Abstract
Nitrous oxide (N2O) is formed during wastewater nitrogen removal processes. It is a strong greenhouse gas, however, if properly captured it can also be used as a renewable energy source. In this study, a nosZ-deficient strain of Pseudomonas aeruginosa was constructed. During growth under denitrifying conditions, the nosZ-deficient strain was more highly transcribing other genes from the denitrification pathway (narG, nirS, and norB) than the wild-type strain. This strain could also convert 85% of NO2--N to N2O when it was grown with acetate compared to <0.6% by the wild-type strain. When a bioreactor treating synthetic wastewater with high NO2--N concentrations (700 mg/L) was inoculated with this strain, the N2O conversion efficiencies were >73% and N2O comprised 73~81% of the biogas being generated. The energy yield from wastewater in bioaugmented reactors also reached levels as high as 1260 kJ/m3. These results are significant and show that bioaugmentation of reactors during denitrification treatment processes with nosZ-deficient strains of Pseudomonas or other core denitrifying bacteria might be an effective way to enhance N2O recovery.
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44
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Fan Z, Xu C, Pan X, Dong Y, Ren H, Jin Y, Bai F, Cheng Z, Jin S, Wu W. Mechanisms of RsaL mediated tolerance to ciprofloxacin and carbenicillin in Pseudomonas aeruginosa. Curr Genet 2018; 65:213-222. [DOI: 10.1007/s00294-018-0863-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/05/2018] [Accepted: 06/22/2018] [Indexed: 02/07/2023]
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45
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D'Amico K, Filiatrault MJ. The conserved hypothetical protein PSPTO_3957 is essential for virulence in the plant pathogen Pseudomonas syringae pv. tomato DC3000. FEMS Microbiol Lett 2018; 364:fnx004. [PMID: 28073812 DOI: 10.1093/femsle/fnx004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/09/2017] [Indexed: 11/13/2022] Open
Abstract
The plant pathogen Pseudomonas syringae accounts for substantial crop losses and is considered an important agricultural issue. To better manage disease in the field, it is important to have an understanding of the underlying genetic mechanisms that mediate virulence. There are a substantial number of genes in sequenced bacterial genomes, including P. syringae, that encode for conserved hypothetical proteins; some of these have been functionally characterized in other Pseudomonads and have been demonstrated to play important roles in disease. PSPTO_3957 encodes a conserved hypothetical protein of unknown function. To evaluate the role of PSPTO_3957 in P. syringae pv. tomato DC3000, a PSPTO_3957 deletion mutant was constructed. Here, we show that PSPTO_3957 does not influence growth on rich media, motility or biofilm formation but is necessary for nitrate assimilation and full virulence in P. syringae. Our results have revealed an important role for PSPTO_3957 in the biology of P. syringae. Given the conservation of this protein among many bacteria, this protein might serve as an attractive target for disease management of this and other bacterial plant pathogens.
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Affiliation(s)
- Katherine D'Amico
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.,Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, US Department of Agriculture, Ithaca, NY 14853, USA
| | - Melanie J Filiatrault
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.,Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, US Department of Agriculture, Ithaca, NY 14853, USA
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46
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Chevalier S, Bouffartigues E, Bazire A, Tahrioui A, Duchesne R, Tortuel D, Maillot O, Clamens T, Orange N, Feuilloley MGJ, Lesouhaitier O, Dufour A, Cornelis P. Extracytoplasmic function sigma factors in Pseudomonas aeruginosa. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:706-721. [PMID: 29729420 DOI: 10.1016/j.bbagrm.2018.04.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/06/2018] [Accepted: 04/30/2018] [Indexed: 01/26/2023]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa, like all members of the genus Pseudomonas, has the capacity to thrive in very different environments, ranging from water, plant roots, to animals, including humans to whom it can cause severe infections. This remarkable adaptability is reflected in the number of transcriptional regulators, including sigma factors in this bacterium. Among those, the 19 to 21 extracytoplasmic sigma factors (ECFσ) are endowed with different regulons and functions, including the iron starvation σ (PvdS, FpvI, HasI, FecI, FecI2 and others), the cell wall stress ECFσ AlgU, SigX and SbrI, and the unorthodox σVreI involved in the expression of virulence. Recently published data show that these ECFσ have separate regulons although presenting some cross-talk. We will present evidence that these different ECFσ are involved in the expression of different phenotypes, ranging from cell-wall stress response, production of extracellular polysaccharides, formation of biofilms, to iron acquisition.
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Affiliation(s)
- Sylvie Chevalier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France.
| | - Emeline Bouffartigues
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Alexis Bazire
- IUEM, Université de Bretagne-Sud (UBL), Laboratoire de Biotechnologie et Chimie Marines EA 3884, Lorient, France
| | - Ali Tahrioui
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Rachel Duchesne
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Damien Tortuel
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Olivier Maillot
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Thomas Clamens
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Nicole Orange
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Marc G J Feuilloley
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Olivier Lesouhaitier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Alain Dufour
- IUEM, Université de Bretagne-Sud (UBL), Laboratoire de Biotechnologie et Chimie Marines EA 3884, Lorient, France
| | - Pierre Cornelis
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
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Phenazines Regulate Nap-Dependent Denitrification in Pseudomonas aeruginosa Biofilms. J Bacteriol 2018; 200:JB.00031-18. [PMID: 29463605 DOI: 10.1128/jb.00031-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 02/14/2018] [Indexed: 12/29/2022] Open
Abstract
Microbes in biofilms face the challenge of substrate limitation. In particular, oxygen often becomes limited for cells in Pseudomonas aeruginosa biofilms growing in the laboratory or during host colonization. Previously we found that phenazines, antibiotics produced by P. aeruginosa, balance the intracellular redox state of cells in biofilms. Here, we show that genes involved in denitrification are induced in phenazine-null (Δphz) mutant biofilms grown under an aerobic atmosphere, even in the absence of nitrate. This finding suggests that resident cells employ a bet-hedging strategy to anticipate the potential availability of nitrate and counterbalance their highly reduced redox state. Consistent with our previous characterization of aerobically grown colonies supplemented with nitrate, we found that the pathway that is induced in Δphz mutant colonies combines the nitrate reductase activity of the periplasmic enzyme Nap with the downstream reduction of nitrite to nitrogen gas catalyzed by the enzymes Nir, Nor, and Nos. This regulatory relationship differs from the denitrification pathway that functions under anaerobic growth, with nitrate as the terminal electron acceptor, which depends on the membrane-associated nitrate reductase Nar. We identified the sequences in the promoter regions of the nap and nir operons that are required for the effects of phenazines on expression. We also show that specific phenazines have differential effects on nap gene expression. Finally, we provide evidence that individual steps of the denitrification pathway are catalyzed at different depths within aerobically grown biofilms, suggesting metabolic cross-feeding between community subpopulations.IMPORTANCE An understanding of the unique physiology of cells in biofilms is critical to our ability to treat fungal and bacterial infections. Colony biofilms of the opportunistic pathogen Pseudomonas aeruginosa grown under an aerobic atmosphere but without nitrate express a denitrification pathway that differs from that used for anaerobic growth. We report that the components of this pathway are induced by electron acceptor limitation and that they are differentially expressed over the biofilm depth. These observations suggest that (i) P. aeruginosa exhibits "bet hedging," in that it expends energy and resources to prepare for nitrate availability when other electron acceptors are absent, and (ii) cells in distinct biofilm microniches may be able to exchange substrates to catalyze full denitrification.
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Abstract
Pseudomonas aeruginosa, a Gram-negative bacterium, is characterized by its versatility that enables persistent survival under adverse conditions. It can grow on diverse energy sources and readily acquire resistance to antimicrobial agents. As an opportunistic human pathogen, it also causes chronic infections inside the anaerobic mucus airways of cystic fibrosis patients. As a strict respirer, P. aeruginosa can grow by anaerobic nitrate ( [Formula: see text] ) respiration. Nitric oxide (NO) produced as an intermediate during anaerobic respiration exerts many important effects on the biological characteristics of P. aeruginosa. This review provides information regarding (i) how P. aeruginosa grows by anaerobic respiration, (ii) mechanisms by which NO is produced under such growth, and (iii) bacterial adaptation to NO. We also review the clinical relevance of NO in the fitness of P. aeruginosa and the use of NO as a potential therapeutic for treating P. aeruginosa infection.
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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: 200] [Impact Index Per Article: 28.6] [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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50
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Tata M, Amman F, Pawar V, Wolfinger MT, Weiss S, Häussler S, Bläsi U. The Anaerobically Induced sRNA PaiI Affects Denitrification in Pseudomonas aeruginosa PA14. Front Microbiol 2017; 8:2312. [PMID: 29218039 PMCID: PMC5703892 DOI: 10.3389/fmicb.2017.02312] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/08/2017] [Indexed: 01/08/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that can thrive by anaerobic respiration in the lungs of cystic fibrosis patients using nitrate as terminal electron acceptor. Here, we report the identification and characterization of the small RNA PaiI in the P. aeruginosa strain 14 (PA14). PaiI is anaerobically induced in the presence of nitrate and depends on the two-component system NarXL. Our studies revealed that PaiI is required for efficient denitrification affecting the conversion of nitrite to nitric oxide. In the absence of PaiI anaerobic growth was impaired on glucose, which can be reconciled with a decreased uptake of the carbon source under these conditions. The importance of PaiI for anaerobic growth is further underlined by the observation that a paiI deletion mutant was impaired in growth in murine tumors.
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Affiliation(s)
- Muralidhar Tata
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Fabian Amman
- Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Vinay Pawar
- Institute of Immunology, Hannover Medical School, Hannover, Germany.,Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany
| | | | - Siegfried Weiss
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany.,Institute of Molecular Bacteriology, Twincore, Center for Experimental and Clinical Infection Research, Hannover, Germany
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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