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Franco A, Chukwubuikem A, Meiners C, Rosenbaum MA. Exploring phenazine electron transfer interaction with elements of the respiratory pathways of Pseudomonas putida and Pseudomonas aeruginosa. Bioelectrochemistry 2024; 157:108636. [PMID: 38181591 DOI: 10.1016/j.bioelechem.2023.108636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/20/2023] [Accepted: 12/23/2023] [Indexed: 01/07/2024]
Abstract
Pseudomonas aeruginosa phenazines contribute to survival under microaerobic and anaerobic conditions by extracellular electron discharge to regulate cellular redox balances. This electron discharge is also attractive to be used for bioelectrochemical applications. However, elements of the respiratory pathways that interact with phenazines are not well understood. Five terminal oxidases are involved in the aerobic electron transport chain (ETC) of Pseudomonas putida and P. aeruginosa. The latter bacterium also includes four reductases that allow for denitrification. Here, we explored if phenazine-1-carboxylic acid interacts with those elements to enhance anodic electron discharge and drive bacterial growth in oxygen-limited conditions. Bioelectrochemical evaluations of terminal oxidase-deficient mutants of both Pseudomonas strains and P. aeruginosa with stimulated denitrification pathways indicated no direct beneficial interaction of phenazines with ETC elements for extracellular electron discharge. However, the single usage of the Cbb3-2 oxidase increased phenazine production, electron discharge, and cell growth. Assays with purified periplasmic cytochromes NirM and NirS indicated that pyocyanin acts as their electron donor. We conclude that phenazines play an important role in electron transfer to, between, and from terminal oxidases under oxygen-limiting conditions and their modulation might enhance EET. However, the phenazine-anode interaction cannot replace oxygen respiration to deliver energy for biomass formation.
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Affiliation(s)
- Angel Franco
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Anthony Chukwubuikem
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstr. 11a, 07745 Jena, Germany; Faculty of Biological Sciences, Friedrich Schiller University (FSU), Fürstengraben 1, 07743 Jena, Germany
| | - Carina Meiners
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstr. 11a, 07745 Jena, Germany; Faculty of Biological Sciences, Friedrich Schiller University (FSU), Fürstengraben 1, 07743 Jena, Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstr. 11a, 07745 Jena, Germany; Faculty of Biological Sciences, Friedrich Schiller University (FSU), Fürstengraben 1, 07743 Jena, Germany.
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Pucelik S, Becker M, Heyber S, Wöhlbrand L, Rabus R, Jahn D, Härtig E. The blue light-dependent LOV-protein LdaP of Dinoroseobacter shibae acts as antirepressor of the PpsR repressor, regulating photosynthetic gene cluster expression. Front Microbiol 2024; 15:1351297. [PMID: 38404597 PMCID: PMC10890935 DOI: 10.3389/fmicb.2024.1351297] [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: 12/06/2023] [Accepted: 01/17/2024] [Indexed: 02/27/2024] Open
Abstract
In the marine α-proteobacterium Dinoroseobacter shibae more than 40 genes of the aerobic anoxygenic photosynthesis are regulated in a light-dependent manner. A genome-wide screen of 5,605 clones from a D. shibae transposon library for loss of pigmentation and changes in bacteriochlorophyll absorbance identified 179 mutant clones. The gene encoding the LOV-domain containing protein Dshi_1135 was identified by its colorless phenotype. The mutant phenotype was complemented by the expression of a Dshi_1135-strep fusion protein in trans. The recombinantly produced and chromatographically purified Dshi_1135 protein was able to undergo a blue light-induced photocycle mediated by bound FMN. Transcriptome analyses revealed an essential role for Dshi_1135 in the light-dependent expression of the photosynthetic gene cluster. Interactomic studies identified the repressor protein PpsR as an interaction partner of Dshi_1135. The physical contact between PpsR and the Dshi_1135 protein was verified in vivo using the bacterial adenylate cyclase-based two-hybrid system. In addition, the antirepressor function of the Dshi_1135 protein was demonstrated in vivo testing of a bchF-lacZ reporter gene fusion in a heterologous Escherichia coli-based host system. We therefore propose to rename the Dshi_1135 protein to LdaP (light-dependent antirepressor of PpsR). Using the bacterial two-hybrid system, it was also shown that cobalamin (B12) is essential for the interaction of the antirepressor PpaA with PpsR. A regulatory model for the photosynthetic gene cluster in D. shibae was derived, including the repressor PpsR, the light-dependent antirepressor LdaP and the B12-dependent antirepressor PpaA.
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Affiliation(s)
- Saskia Pucelik
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Miriam Becker
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Steffi Heyber
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Lars Wöhlbrand
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Elisabeth Härtig
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
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Kaleta MF, Sauer K. MoaB1 Homologs Contribute to Biofilm Formation and Motility by Pseudomonas aeruginosa and Escherichia coli. J Bacteriol 2023; 205:e0000423. [PMID: 37098964 PMCID: PMC10210980 DOI: 10.1128/jb.00004-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/27/2023] [Indexed: 04/27/2023] Open
Abstract
moaB homologs, encoding the molybdopterin biosynthetic protein B1, have been reported to be expressed under anoxic conditions and during biofilm growth in various microorganisms; however, little is known about MoaB's function. Here, we demonstrate that in Pseudomonas aeruginosa, MoaB1 (PA3915) contributes to biofilm-related phenotypes. Specifically, moaB1 expression is induced in biofilms, and insertional inactivation of moaB1 reduced biofilm biomass accumulation and pyocyanin production while enhancing swarming motility, and pyoverdine abundance without affecting attachment, swimming motility, or c-di-GMP levels. Inactivation of the highly conserved E. coli homolog of moaB1, moaBEc, likewise coincided with reduced biofilm biomass accumulation. In turn, heterologous expression of moaBEc restored biofilm formation and swarming motility by the P. aeruginosa moaB1 mutant to wild-type levels. Moreover, MoaB1 was found to interact with other conserved biofilm-associated proteins, PA2184 and PA2146, as well as the sensor-kinase SagS. However, despite the interaction, MoaB1 failed to restore SagS-dependent expression of brlR encoding the transcriptional regulator BrlR, and inactivation of moaB1 or moaBEc had no effect on the antibiotic susceptibility phenotype of biofilms formed by P. aeruginosa and E. coli, respectively. While our findings did not establish a link between MoaB1 and molybdenum cofactor biosynthesis, they suggest that MoaB1 homologs contribute to biofilm-associated phenotypes across species boundaries, possibly hinting at the existence of a previously undescribed conserved biofilm pathway. IMPORTANCE Proteins contributing to the biogenesis of molybdenum cofactors have been characterized; however, the role of the molybdopterin biosynthetic protein B1 (MoaB1) has remained elusive, and solid evidence to support its role in biosynthesis of molybdenum cofactor is lacking. Here, we demonstrate that, in Pseudomonas aeruginosa, MoaB1 (PA3915) contributes to biofilm-related phenotypes in a manner that does not support a role of MoaB1 in the biosynthesis of molybdenum cofactors.
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Affiliation(s)
- Matthew F. Kaleta
- Department of Biological Sciences, Binghamton University, Binghamton, New York, USA
- Binghamton Biofilm Research Center, Binghamton University, Binghamton, New York, USA
| | - Karin Sauer
- Department of Biological Sciences, Binghamton University, Binghamton, New York, USA
- Binghamton Biofilm Research Center, Binghamton University, Binghamton, New York, USA
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Hu C, Sun X, Zhang L, Wang H, Dong L, Li S. Long-term stability of reactor microbiome through bioaugmentation with Alcaligenes aquatilis AS1 promotes nitrogen removal of piggery wastewater. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 330:117146. [PMID: 36586372 DOI: 10.1016/j.jenvman.2022.117146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Bioaugmentation is considered as an attractive method for nitrogen removal in water treatment, but its effectiveness in actual high-strength piggery wastewater has not been adequately verified and the mechanism of bioaugmentation in actual wastewater treatment system is not very clear especially from the perspectives of microbial communities and functional genes. This study investigated the mechanisms of a heterotrophic nitrifying-aerobic denitrifying strain Alcaligenes aquatilis AS1 in the bioaugmentation of continuous biological nitrogen removal of actual piggery wastewater at laboratory scale. The addition of strain AS1 significantly improved the nitrogen removal efficiency (more than 95% of NH4+-N and 75% of TN were removed) and raised the activated sludge resistance to shock loading. AS1 addition also significantly shifted the microbiota structure and interactions among microbial networks were enhanced to obtain the stable bacterial communities. Moreover, strain AS1 achieved effective proliferation and long-term colonization in activated sludge with a relative abundance of genus Alcaligenes more than 70% during the whole operation process and played a dominant role in biological nitrogen removal, while different genera were respectively enriched and involved in pollutants removal at different stages in the control group. In addition, the abundances of most functional genes involved in carbon (C) degradation, carbon fixation and nitrogen (N), phosphorus (P), sulfur (S) cycling in activated sludge were significantly increased in reactor AS1, indicating that strain AS1 not only relied on its unique C and N metabolic activities, but also recruited microorganisms with diverse functions to jointly remove pollutants in wastewater, which could be a common bioaugmentation mechanism in open reactors. This study proves the promising application prospect of strain AS1 in the treatment of high-strength piggery wastewater and shows great importance for guiding bioaugmentation application of functional strains in practical wastewater treatment systems.
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Affiliation(s)
- Chengcheng Hu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianyun Sun
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Long Zhang
- Shandong Jinniu Group Co., Ltd., Jinan, 250001, China
| | - Hongzhi Wang
- Xinjiang Herun Water Industry Co., Ltd., Urumqi, 830000, China
| | - Liang Dong
- Xinjiang Herun Water Industry Co., Ltd., Urumqi, 830000, China
| | - Shaojie Li
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation. Commun Biol 2023; 6:165. [PMID: 36765199 PMCID: PMC9918512 DOI: 10.1038/s42003-023-04540-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
Pseudomonas aeruginosa is one of the leading causes of hospital-acquired infections. To decipher the metabolic mechanisms associated with virulence and antibiotic resistance, we have developed an updated genome-scale model (GEM) of P. aeruginosa. The model (iSD1509) is an extensively curated, three-compartment, and mass-and-charge balanced BiGG model containing 1509 genes, the largest gene content for any P. aeruginosa GEM to date. It is the most accurate with prediction accuracies as high as 92.4% (gene essentiality) and 93.5% (substrate utilization). In iSD1509, we newly added a recently discovered pathway for ubiquinone-9 biosynthesis which is required for anaerobic growth. We used a modified iSD1509 to demonstrate the role of virulence factor (phenazines) in the pathogen survival within biofilm/oxygen-limited condition. Further, the model can mechanistically explain the overproduction of a drug susceptibility biomarker in the P. aeruginosa mutants. Finally, we use iSD1509 to demonstrate the drug potentiation by metabolite supplementation, and elucidate the mechanisms behind the phenotype, which agree with experimental results.
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Ruparel FJ, Shah SK, Patel JH, Thakkar NR, Gajera GN, Kothari VO. Network analysis for identifying potential anti-virulence targets from whole transcriptome of Pseudomonas aeruginosa and Staphylococcus aureus exposed to certain anti-pathogenic polyherbal formulations. Drug Target Insights 2023; 17:58-69. [PMID: 37275512 PMCID: PMC10238913 DOI: 10.33393/dti.2022.2595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 05/10/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Antimicrobial resistance (AMR) is a serious global threat. Identification of novel antibacterial targets is urgently warranted to help antimicrobial drug discovery programs. This study attempted identification of potential targets in two important pathogens Pseudomonas aeruginosa and Staphylococcus aureus. Methods Transcriptomes of P. aeruginosa and S. aureus exposed to two different quorum-modulatory polyherbal formulations were subjected to network analysis to identify the most highly networked differentially expressed genes (hubs) as potential anti-virulence targets. Results Genes associated with denitrification and sulfur metabolism emerged as the most important targets in P. aeruginosa. Increased buildup of nitrite (NO2) in P. aeruginosa culture exposed to the polyherbal formulation Panchvalkal was confirmed through in vitro assay too. Generation of nitrosative stress and inducing sulfur starvation seemed to be effective anti-pathogenic strategies against this notorious gram-negative pathogen. Important targets identified in S. aureus were the transcriptional regulator sarA, immunoglobulin-binding protein Sbi, serine protease SplA, the saeR/S response regulator system, and gamma-hemolysin components hlgB and hlgC. Conclusion Further validation of the potential targets identified in this study is warranted through appropriate in vitro and in vivo assays in model hosts. Such validated targets can prove vital to many antibacterial drug discovery programs globally.
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Affiliation(s)
- Feny J Ruparel
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Siddhi K Shah
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Jhanvi H Patel
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Nidhi R Thakkar
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Gemini N Gajera
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Vijay O Kothari
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
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7
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Ruparel FJ, Shah SK, Patel JH, Thakkar NR, Gajera GN, Kothari VO. Network analysis for identifying potential anti-virulence targets from whole transcriptome of Pseudomonas aeruginosa and Staphylococcus aureus exposed to certain anti-pathogenic polyherbal formulations. Drug Target Insights 2023; 17:58-69. [PMID: 37275512 PMCID: PMC10238913 DOI: 10.33393/dti.2023.2595] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 05/10/2023] [Indexed: 03/07/2024] Open
Abstract
Introduction Antimicrobial resistance (AMR) is a serious global threat. Identification of novel antibacterial targets is urgently warranted to help antimicrobial drug discovery programs. This study attempted identification of potential targets in two important pathogens Pseudomonas aeruginosa and Staphylococcus aureus. Methods Transcriptomes of P. aeruginosa and S. aureus exposed to two different quorum-modulatory polyherbal formulations were subjected to network analysis to identify the most highly networked differentially expressed genes (hubs) as potential anti-virulence targets. Results Genes associated with denitrification and sulfur metabolism emerged as the most important targets in P. aeruginosa. Increased buildup of nitrite (NO2) in P. aeruginosa culture exposed to the polyherbal formulation Panchvalkal was confirmed through in vitro assay too. Generation of nitrosative stress and inducing sulfur starvation seemed to be effective anti-pathogenic strategies against this notorious gram-negative pathogen. Important targets identified in S. aureus were the transcriptional regulator sarA, immunoglobulin-binding protein Sbi, serine protease SplA, the saeR/S response regulator system, and gamma-hemolysin components hlgB and hlgC. Conclusion Further validation of the potential targets identified in this study is warranted through appropriate in vitro and in vivo assays in model hosts. Such validated targets can prove vital to many antibacterial drug discovery programs globally.
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Affiliation(s)
- Feny J Ruparel
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Siddhi K Shah
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Jhanvi H Patel
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Nidhi R Thakkar
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Gemini N Gajera
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
| | - Vijay O Kothari
- Institute of Science, Nirma University, Ahmedabad - India
- FJR, NRT, and GNG contributed equally
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Abstract
Pf4 is a filamentous bacteriophage integrated as a prophage into the genome of Pseudomonas aeruginosa PAO1. Pf4 virions can be produced without killing P. aeruginosa. However, cell lysis can occur during superinfection when Pf virions successfully infect a host lysogenized by a Pf superinfective variant. We have previously shown that infection of P. aeruginosa PAO1 with a superinfective Pf4 variant abolished twitching motility and altered biofilm architecture. More precisely, most of the cells embedded into the biofilm were showing a filamentous morphology, suggesting the activation of the cell envelope stress response involving both AlgU and SigX extracytoplasmic function sigma factors. Here, we show that Pf4 variant infection results in a drastic dysregulation of 3,360 genes representing about 58% of P. aeruginosa genome; of these, 70% of the virulence factors encoding genes show a dysregulation. Accordingly, Pf4 variant infection (termed Pf4*) causes in vivo reduction of P. aeruginosa virulence and decreased production of N-acyl-homoserine lactones and 2-alkyl-4-quinolones quorum-sensing molecules and related virulence factors, such as pyocyanin, elastase, and pyoverdine. In addition, the expression of genes involved in metabolism, including energy generation and iron homeostasis, was affected, suggesting further relationships between virulence and central metabolism. Altogether, these data show that Pf4 phage variant infection results in complex network dysregulation, leading to reducing acute virulence in P. aeruginosa. This study contributes to the comprehension of the bacterial response to filamentous phage infection. IMPORTANCE Filamentous bacteriophages can become superinfective and infect P. aeruginosa, even though they are inserted in the genome as lysogens. Despite this productive infection, growth of the host is only mildly affected, allowing the study of the interaction between the phage and the host, which is not possible in the case of lytic phages killing rapidly their host. Here, we demonstrate by transcriptome and phenotypic analysis that the infection by a superinfective filamentous phage variant causes a massive disruption in gene expression, including those coding for virulence factors and metabolic pathways.
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Nitrite Promotes ROS Production to Potentiate Cefoperazone-Sulbactam-Mediated Elimination to Lab-Evolved and Clinical-Evolved Pseudomonas aeruginosa. Microbiol Spectr 2022; 10:e0232721. [PMID: 35863024 PMCID: PMC9430864 DOI: 10.1128/spectrum.02327-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cefoperazone-sulbactam (SCF)-resistant Pseudomonas aeruginosa poses a big challenge in the use of SCF to treat infection caused by the pathogen. We have recently shown exogenous nitrite-enabled killing of naturally and artificially evolved Pseudomonas aeruginosa strains (AP-RCLIN-EVO and AP-RLAB-EVO, respectively) by SCF. However, the underlying mechanism is unknown. Here, reprogramming metabolomics was adopted to investigate how nitrite enhanced the SCF-mediated killing efficacy. Nitrite-reprogrammed metabolome displayed an activated pyruvate cycle (P cycle), which was confirmed by elevated activity of pyruvate dehydrogenase (PDH), α-ketoglutarate dehydrogenase, succinate dehydrogenase, and malate dehydrogenase. The activated P cycle provided NADH for the electron transport chain and thereby increased reactive oxygen species (ROS), which potentiated SCF to kill AP-RCLIN-EVO and AP-RLAB-EVO. The nitrite-enabled killing of AP-RCLIN-EVO and AP-RLAB-EVO by SCF was inhibited by PDH inhibitor furfural and ROS scavenger N-Acetyl-L-cysteine but promoted by ROS promoter Fe3+. SCF alone could not induce ROS, but SCF-mediated killing efficacy was enhanced by ROS. In addition, the present study demonstrated that nitrite repressed antioxidants, which were partly responsible for the elevated ROS. These results reveal a nitrite-reprogrammed metabolome mechanism by which AP-RCLIN-EVO and AP-RLAB-EVO sensitivity to SCF is elevated. IMPORTANCE Antibiotic-resistant Pseudomonas aeruginosa has become a real concern in hospital-acquired infections, especially in critically ill and immunocompromised patients. Understanding antibiotic resistance mechanisms and developing novel control measures are highly appreciated. We have recently shown that a reduced nitrite-dependent NO biosynthesis contributes to cefoperazone-sulbactam (SCF) resistance, which is reverted by exogenous nitrite, in both naturally and artificially evolved P. aeruginosa strains (AP-RCLIN-EVO and AP-RLAB-EVO, respectively). However, the mechanism is unknown. The present study reports that the nitrite-enabled killing of AP-RCLIN-EVO and AP-RLAB-EVO by SCF is attributed to the promoted production of reactive oxygen species (ROS). Nitrite activates the pyruvate cycle to generate NADH for the electron transport chain, which in turn promotes ROS generation. Nitrite-potentiated SCF-mediated killing is decreased by pyruvate dehydrogenase inhibitor furfural and ROS scavenger N-Acetyl-L-cysteine but increased by ROS promoter Fe3+. Furthermore, SCF-mediated killing is promoted by H2O2 in a dose-dependent manner. In addition, the combination of nitrite and H2O2 greatly enhances SCF-mediated killing. These results not only disclose a nitrite-ROS-potentiated SCF-mediated killing, but also show SCF-mediated killing is dependent upon ROS.
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Cao X, Zhao B, Wu Y, Huang J, Wang H, Sun X, Li S. Characterization of Alcaligenes aquatilis as a novel member of heterotrophic nitrifier-aerobic denitrifier and its performance in treating piggery wastewater. BIORESOURCE TECHNOLOGY 2022; 354:127176. [PMID: 35439558 DOI: 10.1016/j.biortech.2022.127176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
A novel strain AS1 with heterotrophic nitrifying-aerobic denitrifying capacity in the species of Alcaligenes aquatilis was isolated from the aerobic activated sludge. It showed a great capability of ammonia removal, and the aerobic metabolic pathways to yield gaseous-nitrogen by hydroxylamine oxidation and nitrite denitrification were proposed. AS1 could efficiently remove ammonia under a wide range of environmental conditions, including the ratio of chemical oxygen demand to total nitrogen: 15-30, pH: 6-10, NaCl: 0-60 g/L, shaking speed of 0-180 rpm, and succinate, acetate, or citrate as carbon source. In the treatment of actual piggery wastewater, 95.3%, 95.1% and 84.9% of NH4+-N was removed by AS1 when the initial ammonia concentration was 500, 1300, and 2000 mg/L, respectively, with the maximum NH4+-N removal rate of 30.5 mg/L/h and 569.7 mg/L/d. Furthermore, plate colony-counting showed that AS1 achieved an efficient proliferation. These results imply the application potential of AS1 in treating high-ammonia wastewater.
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Affiliation(s)
- Xianhe Cao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Binhan Zhao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongming Wu
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang 330096, China
| | - Jun Huang
- Shandong Jinniu Group Company Limited, Jinan 250001, China
| | - Hongzhi Wang
- Xinjiang Herun Water Industry Company Limited, Urumqi 830000, China
| | - Xianyun Sun
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shaojie Li
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang 330096, China.
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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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Salas A, Cabrera JJ, Jiménez-Leiva A, Mesa S, Bedmar EJ, Richardson DJ, Gates AJ, Delgado MJ. Bacterial nitric oxide metabolism: Recent insights in rhizobia. Adv Microb Physiol 2021; 78:259-315. [PMID: 34147187 DOI: 10.1016/bs.ampbs.2021.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nitric oxide (NO) is a reactive gaseous molecule that has several functions in biological systems depending on its concentration. At low concentrations, NO acts as a signaling molecule, while at high concentrations, it becomes very toxic due to its ability to react with multiple cellular targets. Soil bacteria, commonly known as rhizobia, have the capacity to establish a N2-fixing symbiosis with legumes inducing the formation of nodules in their roots. Several reports have shown NO production in the nodules where this gas acts either as a signaling molecule which regulates gene expression, or as a potent inhibitor of nitrogenase and other plant and bacteria enzymes. A better understanding of the sinks and sources of NO in rhizobia is essential to protect symbiotic nitrogen fixation from nitrosative stress. In nodules, both the plant and the microsymbiont contribute to the production of NO. From the bacterial perspective, the main source of NO reported in rhizobia is the denitrification pathway that varies significantly depending on the species. In addition to denitrification, nitrate assimilation is emerging as a new source of NO in rhizobia. To control NO accumulation in the nodules, in addition to plant haemoglobins, bacteroids also contribute to NO detoxification through the expression of a NorBC-type nitric oxide reductase as well as rhizobial haemoglobins. In the present review, updated knowledge about the NO metabolism in legume-associated endosymbiotic bacteria is summarized.
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Affiliation(s)
- Ana Salas
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Juan J Cabrera
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrea Jiménez-Leiva
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Socorro Mesa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrew J Gates
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - María J Delgado
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain.
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13
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Tosha T, Yamagiwa R, Sawai H, Shiro Y. NO Dynamics in Microbial Denitrification System. CHEM LETT 2021. [DOI: 10.1246/cl.200629] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Takehiko Tosha
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Raika Yamagiwa
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hitomi Sawai
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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14
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Balasubramaniam A, Adi P, Tra My DT, Keshari S, Sankar R, Chen CL, Huang CM. Repurposing INCI-registered compounds as skin prebiotics for probiotic Staphylococcus epidermidis against UV-B. Sci Rep 2020; 10:21585. [PMID: 33299009 PMCID: PMC7725810 DOI: 10.1038/s41598-020-78132-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/12/2020] [Indexed: 12/16/2022] Open
Abstract
Repurposing existing compounds for new indications may facilitate the discovery of skin prebiotics which have not been well defined. Four compounds that have been registered by the International Nomenclature of Cosmetic Ingredients (INCI) were included to study their abilities to induce the fermentation of Staphylococcusepidermidis (S. epidermidis), a bacterial species abundant in the human skin. Liquid coco-caprylate/caprate (LCC), originally used as an emollient, effectively initiated the fermentation of S. epidermidis ATCC 12228, produced short-chain fatty acids (SCFAs), and provoked robust electricity. Application of LCC plus electrogenic S. epidermidis ATCC 12228 on mouse skin significantly reduced ultraviolet B (UV-B)-induced injuries which were evaluated by the formation of 4-hydroxynonenal (4-HNE), cyclobutane pyrimidine dimers (CPD), and skin lesions. A S. epidermidis S2 isolate with low expressions of genes encoding pyruvate dehydrogenase (pdh), and phosphate acetyltransferase (pta) was found to be poorly electrogenic. The protective action of electrogenic S. epidermidis against UV-B-induced skin injuries was considerably suppressed when mouse skin was applied with LCC in combination with a poorly electrogenic S. epidermidis S2 isolate. Exploring new indication of LCC for promoting S. epidermidis against UV-B provided an example of repurposing INCI-registered compounds as skin prebiotics.
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Affiliation(s)
- Arun Balasubramaniam
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Prakoso Adi
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Do Thi Tra My
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Sunita Keshari
- Department of Life Sciences, National Central University, Taoyuan, Taiwan
| | - Raman Sankar
- Institute of Physics, Academia Sinica, Nankang, Taipei, Taiwan
| | - Chien-Lung Chen
- Division of Nephrology, Landseed International Hospital, Taoyuan, Taiwan
| | - Chun-Ming Huang
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan.
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15
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Mechanisms controlling bacterial infection in myeloid cells under hypoxic conditions. Cell Mol Life Sci 2020; 78:1887-1907. [PMID: 33125509 PMCID: PMC7966188 DOI: 10.1007/s00018-020-03684-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 09/08/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022]
Abstract
Various factors of the tissue microenvironment such as the oxygen concentration influence the host-pathogen interaction. During the past decade, hypoxia-driven signaling via hypoxia-inducible factors (HIF) has emerged as an important factor that affects both the pathogen and the host. In this chapter, we will review the current knowledge of this complex interplay, with a particular emphasis given to the impact of hypoxia and HIF on the inflammatory and antimicrobial activity of myeloid cells, the bacterial responses to hypoxia and the containment of bacterial infections under oxygen-limited conditions. We will also summarize how low oxygen concentrations influence the metabolism of neutrophils, macrophages and dendritic cells. Finally, we will discuss the consequences of hypoxia and HIFα activation for the invading pathogen, with a focus on Pseudomonas aeruginosa, Mycobacterium tuberculosis, Coxiella burnetii, Salmonella enterica and Staphylococcus aureus. This includes a description of the mechanisms and microbial factors, which the pathogens use to sense and react to hypoxic conditions.
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16
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Vo CDT, Michaud J, Elsen S, Faivre B, Bouveret E, Barras F, Fontecave M, Pierrel F, Lombard M, Pelosi L. The O 2-independent pathway of ubiquinone biosynthesis is essential for denitrification in Pseudomonas aeruginosa. J Biol Chem 2020; 295:9021-9032. [PMID: 32409583 PMCID: PMC7335794 DOI: 10.1074/jbc.ra120.013748] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/10/2020] [Indexed: 01/05/2023] Open
Abstract
Many proteobacteria, such as Escherichia coli, contain two main types of quinones: benzoquinones, represented by ubiquinone (UQ) and naphthoquinones, such as menaquinone (MK), and dimethyl-menaquinone (DMK). MK and DMK function predominantly in anaerobic respiratory chains, whereas UQ is the major electron carrier in the reduction of dioxygen. However, this division of labor is probably not very strict. Indeed, a pathway that produces UQ under anaerobic conditions in an UbiU-, UbiV-, and UbiT-dependent manner has been discovered recently in E. coli Its physiological relevance is not yet understood, because MK and DMK are also present in E. coli Here, we established that UQ9 is the major quinone of Pseudomonas aeruginosa and is required for growth under anaerobic respiration (i.e. denitrification). We demonstrate that the ORFs PA3911, PA3912, and PA3913, which are homologs of the E. coli ubiT, ubiV, and ubiU genes, respectively, are essential for UQ9 biosynthesis and, thus, for denitrification in P. aeruginosa These three genes here are called ubiTPa , ubiVPa , and ubiUPa We show that UbiVPa accommodates an iron-sulfur [4Fe-4S] cluster. Moreover, we report that UbiUPa and UbiTPa can bind UQ and that the isoprenoid tail of UQ is the structural determinant required for recognition by these two Ubi proteins. Since the denitrification metabolism of P. aeruginosa is believed to be important for the pathogenicity of this bacterium in individuals with cystic fibrosis, our results highlight that the O2-independent UQ biosynthetic pathway may represent a target for antibiotics development to manage P. aeruginosa infections.
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Affiliation(s)
- Chau-Duy-Tam Vo
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8229, PSL Research University, Sorbonne Université, Paris, France
| | - Julie Michaud
- CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Université Grenoble Alpes, Grenoble, France
| | - Sylvie Elsen
- Biology of Cancer and Infection, U1036 INSERM, CEA, Université Grenoble Alpes, ERL5261 CNRS, Grenoble, France
| | - Bruno Faivre
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8229, PSL Research University, Sorbonne Université, Paris, France
| | - Emmanuelle Bouveret
- SAMe Unit, Department of Microbiology, Institut Pasteur, Paris, France; IMM-UMR 2001 CNRS-Institut Pasteur, Paris, France
| | - Frédéric Barras
- SAMe Unit, Department of Microbiology, Institut Pasteur, Paris, France; IMM-UMR 2001 CNRS-Institut Pasteur, Paris, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8229, PSL Research University, Sorbonne Université, Paris, France
| | - Fabien Pierrel
- CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Université Grenoble Alpes, Grenoble, France
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8229, PSL Research University, Sorbonne Université, Paris, France.
| | - Ludovic Pelosi
- CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Université Grenoble Alpes, Grenoble, France.
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17
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Ferousi C, Majer SH, DiMucci IM, Lancaster KM. Biological and Bioinspired Inorganic N-N Bond-Forming Reactions. Chem Rev 2020; 120:5252-5307. [PMID: 32108471 PMCID: PMC7339862 DOI: 10.1021/acs.chemrev.9b00629] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.
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Affiliation(s)
- Christina Ferousi
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Sean H Majer
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Ida M DiMucci
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
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18
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Zhang X, Li S, Zheng S, Duan S. Impact of dissolved oxygen and loading rate on NH 3 oxidation and N 2 production mechanisms in activated sludge treatment of sewage. Microb Biotechnol 2020; 14:419-429. [PMID: 32488999 PMCID: PMC7936313 DOI: 10.1111/1751-7915.13599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 01/19/2023] Open
Abstract
Microaerobic activated sludge (MAS) is a one-stage process operated at 0.5-1.0 mg l-1 dissolved oxygen (DO) aiming at simultaneous nitrification and denitrification. We used molecular techniques and a comprehensive nitrogen (N)-transformation activity test to investigate the dominant NH3 -oxidizing and N2 -producing mechanism as well as the dominant ammonia-oxidizing bacteria (AOB) species in sludge samples individually collected from an MAS system and a conventional anoxic/oxic (A/O) system; both systems were operated at a normal loading rate (i.e. 1.0 kg chemical oxygen demand (COD) m-3 day-1 and 0.1 kg NH4 + -N m-3 day-1 ) in our previous studies. The DO levels in both systems (aerobic: conventional A/O system; microaerobic: MAS system) did not affect the dominant NH3 -oxidizing mechanism or the dominant AOB species. This study further demonstrated the feasibility of a higher loading rate (i.e. 2.30 kg COD m-3 day-1 and 0.34 kg NH4 + -N m-3 day-1 ) with the MAS process during sewage treatment, which achieved a 40% reduction in aeration energy consumption than that obtained in the conventional A/O system. The increase in loading rates in the MAS system did not affect the dominant NH3 -oxidizing mechanism but did impact the dominant AOB species. Besides, N2 was predominantly produced by microaerobic denitrification in the MAS system at the two loading rates.
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Affiliation(s)
- Xueyu Zhang
- MOE Key Laboratory of Water and Sediment Sciences/State Key Lab of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Shida Li
- MOE Key Laboratory of Water and Sediment Sciences/State Key Lab of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Shaokui Zheng
- MOE Key Laboratory of Water and Sediment Sciences/State Key Lab of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Shoupeng Duan
- MOE Key Laboratory of Water and Sediment Sciences/State Key Lab of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
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19
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Ciemniecki JA, Newman DK. The Potential for Redox-Active Metabolites To Enhance or Unlock Anaerobic Survival Metabolisms in Aerobes. J Bacteriol 2020; 202:e00797-19. [PMID: 32071098 PMCID: PMC7221258 DOI: 10.1128/jb.00797-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Classifying microorganisms as "obligate" aerobes has colloquially implied death without air, leading to the erroneous assumption that, without oxygen, they are unable to survive. However, over the past few decades, more than a few obligate aerobes have been found to possess anaerobic energy conservation strategies that sustain metabolic activity in the absence of growth or at very low growth rates. Similarly, studies emphasizing the aerobic prowess of certain facultative aerobes have sometimes led to underrecognition of their anaerobic capabilities. Yet an inescapable consequence of the affinity both obligate and facultative aerobes have for oxygen is that the metabolism of these organisms may drive this substrate to scarcity, making anoxic survival an essential skill. To illustrate this, we highlight the importance of anaerobic survival strategies for Pseudomonas aeruginosa and Streptomyces coelicolor, representative facultative and obligate aerobes, respectively. Included among these strategies, we describe a role for redox-active secondary metabolites (RAMs), such as phenazines made by P. aeruginosa, in enhancing substrate-level phosphorylation. Importantly, RAMs are made by diverse bacteria, often during stationary phase in the absence of oxygen, and can sustain anoxic survival. We present a hypothesis for how RAMs may enhance or even unlock energy conservation pathways that facilitate the anaerobic survival of both RAM producers and nonproducers.
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Affiliation(s)
- John A Ciemniecki
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
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20
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Wang YH, Chen HH, Huang Z, Li XJ, Zhou N, Liu C, Jiang CY, Li DF, Liu SJ. PapA, a peptidoglycan-associated protein, interacts with OmpC and maintains cell envelope integrity. Environ Microbiol 2020; 23:600-612. [PMID: 32329167 DOI: 10.1111/1462-2920.15038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/21/2020] [Indexed: 01/26/2023]
Abstract
The bacterial cell envelope is critical to support and maintain cellular life. In Gram-negative bacterial cells, the outer membrane and the peptidoglycan layer are two important parts of the cell envelope and they harbour abundant proteins. Here, we report the identification and characterization of a previously unknown peptidoglycan-associated protein, PapA, from the Gram-negative Comamonas testosteroni. PapA bound peptidoglycan with its C-terminal domain and interacted with the outer-membrane porin OmpC. The PapA-OmpC complex riveted the outer membrane and the peptidoglycan layer, and played a role in maintaining cell envelope integrity. When papA was disrupted, the mutant CNB-1ΔpapA apparently had an outer membrane partly separated from the peptidoglycan layer. Phenotypically, the mutant CNB-1ΔpapA lost chemotactic responses and had longer lag-phase of growth, less flagellation and higher sensitivity to harsh environments. Totally, 1093 functionally unknown PapA homologues were identified from the public NR protein database and they were mainly distributed in Burkholderiales of Betaproteobacteria. Our finding provides a clue that the PapA homologous proteins might function as a rivet to maintain cell envelope integrity in those Gram-negative bacteria.
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Affiliation(s)
- Yun-Hao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Hong-He Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Zhou Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xiao-Jing Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Chang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - De-Feng Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.,Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.,Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
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21
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Nitrogen Removal Performance and Metabolic Pathways Analysis of a Novel Aerobic Denitrifying Halotolerant Pseudomonas balearica strain RAD-17. Microorganisms 2020; 8:microorganisms8010072. [PMID: 31906569 PMCID: PMC7022906 DOI: 10.3390/microorganisms8010072] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 12/21/2019] [Accepted: 12/24/2019] [Indexed: 11/17/2022] Open
Abstract
An aerobic denitrification strain, Pseudomonas balearica RAD-17, was identified and showed efficient inorganic nitrogen removal ability. The average NO3−-N, NO2−-N, and total ammonium nitrogen (TAN) removal rate (>95% removal efficiency) in a batch test was 6.22 mg/(L∙h), 6.30 mg/(L∙h), and 1.56 mg/(L∙h), respectively. Meanwhile, optimal incubate conditions were obtained through single factor experiments. For nitrogen removal pathways, the transcriptional results proved that respiratory nitrate reductases encoded by napA, which was primarily performed in aerobic denitrification and cell assimilation, were conducted by gluS and gluD genes for ammonium metabolism. In addition, adding the strain RAD-17 into actual wastewater showed obvious higher denitrification performance than in the no inoculum group (84.22% vs. 22.54%), and the maximum cell abundance achieved 28.5 ± 4.5% in a ratio of total cell numbers. Overall, the efficient nitrogen removal performance plus strong environmental fitness makes the strain RAD-17 a potential alternative for RAS (recirculating aquaculture system) effluent treatment.
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22
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Rinaldo S, Giardina G, Mantoni F, Paone A, Cutruzzolà F. Beyond nitrogen metabolism: nitric oxide, cyclic-di-GMP and bacterial biofilms. FEMS Microbiol Lett 2019; 365:4834012. [PMID: 29401255 DOI: 10.1093/femsle/fny029] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/31/2018] [Indexed: 12/18/2022] Open
Abstract
The nitrogen cycle pathways are responsible for the circulation of inorganic and organic N-containing molecules in nature. Among these pathways, those involving amino acids, N-oxides and in particular nitric oxide (NO) play strategic roles in the metabolism of microorganisms in natural environments and in host-pathogen interactions. Beyond their role in the N-cycle, amino acids and NO are also signalling molecules able to influence group behaviour in microorganisms and cell-cell communication in multicellular organisms, including humans. In this minireview, we summarise the role of these compounds in the homeostasis of the bacterial communities called biofilms, commonly found in environmental, industrial and medical settings. Biofilms are difficult to eradicate since they are highly resistant to antimicrobials and to the host immune system. We highlight the effect of amino acids such as glutamate, glutamine and arginine and of NO on the signalling pathways involved in the metabolism of 3',5'-cyclic diguanylic acid (c-di-GMP), a master regulator of motility, attachment and group behaviour in bacteria. The study of the metabolic routes involving these N-containing compounds represents an attractive topic to identify targets for biofilm control in both natural and medical settings.
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Affiliation(s)
- Serena Rinaldo
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Federico Mantoni
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Alessio Paone
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesca Cutruzzolà
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
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23
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24
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Anupama R, Lulu S, Madhusmita R, Vino S, Mukherjee A, Babu S. Insights into the interaction of key biofilm proteins in Pseudomonas aeruginosa PAO1 with TiO 2 nanoparticle: An in silico analysis. J Theor Biol 2019; 462:12-25. [PMID: 30391649 DOI: 10.1016/j.jtbi.2018.10.057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 10/27/2022]
Abstract
Pseudomonas aeruginosa is a pathogenic biofilm forming bacteria which exist in wide range of environments such as water, soil and human body. In an earlier study, we used a system biology approach based analysis of biofilm forming genes of P. aeruginosa and their possible role in TiO2 nanoparticle binding. The major protein of P. aeruginosa targeted by TiO2 was found to be KatA, a major catalase required for H2O2 resistance and acute virulence and the direct interacting protein partners of KatA were found to be DnaK, Hfq, RpoA and RpoS. To understand the protein-protein physical interaction characteristic of these key proteins involved in biofilm related processes, homology modeling, docking and molecular dynamic simulation were performed. For all these proteins, physical and chemical properties, amino acid composition, nest and cleft analysis were performed using online tools. The interactions between TiO2NPs-KatA and four protein-protein complexes such as KatA-DnaK, KatA-Hfq, KatA-RpoA and KatA-RpoS were studied. Our results indicate that all four key proteins and TiO2NPs can have stable complexation with KatA. The study has given enough clues to understand the interaction of TiO2NPs with P. aeruginosa biofilm in natural environment. Further investigations could lead to development of TiO2NPs based therapeutic and sanitary interventions to combat this pathogenic bacterium.
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Affiliation(s)
- Rani Anupama
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Sajitha Lulu
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
| | - Rout Madhusmita
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Sundararajan Vino
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
| | - Amitava Mukherjee
- Centre for Nanobiotechnology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
| | - Subramanian Babu
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
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25
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Li H, Qin Y, Mao X, Zheng W, Luo G, Xu X, Zheng J. Silencing of cyt-c4 led to decrease of biofilm formation in Aeromonas hydrophila. Biosci Biotechnol Biochem 2018; 83:221-232. [PMID: 30304991 DOI: 10.1080/09168451.2018.1528543] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Aquaculture suffers from a number of diseases caused by Aeromonas hydrophila. Biofilm can protect bacteria from antibiotic therapy. To identify the genes those play crucial roles in A. hydrophila biofilm formation, a library of mini-Tn10 transposon insertion mutants of A. hydrophila B11 has been constructed, and 10 mutants were subjected to biofilm formation assay. The biofilm formation ability of mutant (B188) was significantly decreased compared with B11. The DNA sequence flanking the mini-Tn10 transposon inserted showed that an ORF of approximately 576 bp of the mutant strain B188 was inserted. This ORF putatively displays the highest identity (92%) with the cytochrome c4 gene (cyt-c4) of A. hydrophila subsp. hydrophila ATCC 7966. Silencing cyt-c4 led to deficiencies in biofilm formation, adhesion, drug resistance and pathogenicity of A. hydrophila, which suggests that cyt-c4 plays crucial role in the biofilm formation and virulence mechanisms of A. hydrophila. ABBREVIATIONS: GEN: gentamycin; SDZ: sulfadiazine; AK: amikacin; P: penicillin; CFP: cefoperazone; LEV: levofloxacin; MH: minocycline; FFC: florfenicol; TE: tetracycline; AMP: ampicillin; KAN: kanamycin; STR: streptomycin; SXT: sulfamethoxazole/trimethoprim; DO: doxycycline; OT: Oxytetracycline.
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Affiliation(s)
- Huiyao Li
- a Fisheries College , Jimei University , Xiamen , Fujian Province , China.,b Engineering Research Center of the Modern Technology for Eel Industry , Ministry of Education , Xiamen , P.R. China.,c Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment , Xiamen , Fujian Province , China
| | - Yingxue Qin
- a Fisheries College , Jimei University , Xiamen , Fujian Province , China.,b Engineering Research Center of the Modern Technology for Eel Industry , Ministry of Education , Xiamen , P.R. China.,c Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment , Xiamen , Fujian Province , China
| | - Xiuxiu Mao
- a Fisheries College , Jimei University , Xiamen , Fujian Province , China.,b Engineering Research Center of the Modern Technology for Eel Industry , Ministry of Education , Xiamen , P.R. China.,c Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment , Xiamen , Fujian Province , China
| | - Wanmei Zheng
- d SiChuan Agricultural University , Ya'an , Sichuan Province , China
| | - Gang Luo
- a Fisheries College , Jimei University , Xiamen , Fujian Province , China.,b Engineering Research Center of the Modern Technology for Eel Industry , Ministry of Education , Xiamen , P.R. China.,c Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment , Xiamen , Fujian Province , China
| | - Xiaojin Xu
- a Fisheries College , Jimei University , Xiamen , Fujian Province , China.,b Engineering Research Center of the Modern Technology for Eel Industry , Ministry of Education , Xiamen , P.R. China.,c Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment , Xiamen , Fujian Province , China
| | - Jiang Zheng
- a Fisheries College , Jimei University , Xiamen , Fujian Province , China.,b Engineering Research Center of the Modern Technology for Eel Industry , Ministry of Education , Xiamen , P.R. China.,c Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment , Xiamen , Fujian Province , China
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26
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Lemaire ON, Infossi P, Ali Chaouche A, Espinosa L, Leimkühler S, Giudici-Orticoni MT, Méjean V, Iobbi-Nivol C. Small membranous proteins of the TorE/NapE family, crutches for cognate respiratory systems in Proteobacteria. Sci Rep 2018; 8:13576. [PMID: 30206249 PMCID: PMC6134056 DOI: 10.1038/s41598-018-31851-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/23/2018] [Indexed: 01/18/2023] Open
Abstract
In this report, we investigate small proteins involved in bacterial alternative respiratory systems that improve the enzymatic efficiency through better anchorage and multimerization of membrane components. Using the small protein TorE of the respiratory TMAO reductase system as a model, we discovered that TorE is part of a subfamily of small proteins that are present in proteobacteria in which they play a similar role for bacterial respiratory systems. We reveal by microscopy that, in Shewanella oneidensis MR1, alternative respiratory systems are evenly distributed in the membrane contrary to what has been described for Escherichia coli. Thus, the better efficiency of the respiratory systems observed in the presence of the small proteins is not due to a specific localization in the membrane, but rather to the formation of membranous complexes formed by TorE homologs with their c-type cytochrome partner protein. By an in vivo approach combining Clear Native electrophoresis and fluorescent translational fusions, we determined the 4:4 stoichiometry of the complexes. In addition, mild solubilization of the cytochrome indicates that the presence of the small protein reinforces its anchoring to the membrane. Therefore, assembly of the complex induced by this small protein improves the efficiency of the respiratory system.
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Affiliation(s)
- Olivier N Lemaire
- Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402, Marseille, France
| | - Pascale Infossi
- Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402, Marseille, France
| | - Amine Ali Chaouche
- Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402, Marseille, France
| | - Leon Espinosa
- Aix-Marseille Université, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402, Marseille, France
| | - Silke Leimkühler
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, 14476, Potsdam, Germany
| | - Marie-Thérèse Giudici-Orticoni
- Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402, Marseille, France
| | - Vincent Méjean
- Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402, Marseille, France
| | - Chantal Iobbi-Nivol
- Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402, Marseille, France.
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27
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Timmis K. Environmental microbiology - the next 20 years: bioconnectivity and meta'omics 2.0. Environ Microbiol 2018; 20:1949-1954. [PMID: 29750400 DOI: 10.1111/1462-2920.14236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kenneth Timmis
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
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28
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Buttet GF, Willemin MS, Hamelin R, Rupakula A, Maillard J. The Membrane-Bound C Subunit of Reductive Dehalogenases: Topology Analysis and Reconstitution of the FMN-Binding Domain of PceC. Front Microbiol 2018; 9:755. [PMID: 29740408 PMCID: PMC5928378 DOI: 10.3389/fmicb.2018.00755] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/04/2018] [Indexed: 12/15/2022] Open
Abstract
Organohalide respiration (OHR) is the energy metabolism of anaerobic bacteria able to use halogenated organic compounds as terminal electron acceptors. While the terminal enzymes in OHR, so-called reductive dehalogenases, are well-characterized, the identity of proteins potentially involved in electron transfer to the terminal enzymes remains elusive. Among the accessory genes identified in OHR gene clusters, the C subunit (rdhC) could well code for the missing redox protein between the quinol pool and the reductive dehalogenase, although it was initially proposed to act as transcriptional regulator. RdhC sequences are characterized by the presence of multiple transmembrane segments, a flavin mononucleotide (FMN) binding motif and two conserved CX3CP motifs. Based on these features, we propose a curated selection of RdhC proteins identified in general sequence databases. Beside the Firmicutes from which RdhC sequences were initially identified, the identified sequences belong to three additional phyla, the Chloroflexi, the Proteobacteria, and the Bacteriodetes. The diversity of RdhC sequences mostly respects the phylogenetic distribution, suggesting that rdhC genes emerged relatively early in the evolution of the OHR metabolism. PceC, the C subunit of the tetrachloroethene (PCE) reductive dehalogenase is encoded by the conserved pceABCT gene cluster identified in Dehalobacter restrictus PER-K23 and in several strains of Desulfitobacterium hafniense. Surfaceome analysis of D. restrictus cells confirmed the predicted topology of the FMN-binding domain (FBD) of PceC that is the exocytoplasmic face of the membrane. Starting from inclusion bodies of a recombinant FBD protein, strategies for successful assembly of the FMN cofactor and refolding were achieved with the use of the flavin-trafficking protein from D. hafniense TCE1. Mass spectrometry analysis and site-directed mutagenesis of rFBD revealed that threonine-168 of PceC is binding FMN covalently. Our results suggest that PceC, and more generally RdhC proteins, may play a role in electron transfer in the metabolism of OHR.
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Affiliation(s)
- Géraldine F Buttet
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
| | - Mathilde S Willemin
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
| | - Romain Hamelin
- Protein Core Facility, Faculty of Life Sciences, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
| | - Aamani Rupakula
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
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29
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Borrero-de Acuña JM, Timmis KN, Jahn M, Jahn D. Protein complex formation during denitrification by Pseudomonas aeruginosa. Microb Biotechnol 2017; 10:1523-1534. [PMID: 28857512 PMCID: PMC5658584 DOI: 10.1111/1751-7915.12851] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/18/2022] Open
Abstract
The most efficient means of generating cellular energy is through aerobic respiration. Under anaerobic conditions, several prokaryotes can replace oxygen by nitrate as final electron acceptor. During denitrification, nitrate is reduced via nitrite, NO and N2O to molecular nitrogen (N2) by four membrane‐localized reductases with the simultaneous formation of an ion gradient for ATP synthesis. These four multisubunit enzyme complexes are coupled in four electron transport chains to electron donating primary dehydrogenases and intermediate electron transfer proteins. Many components require membrane transport and insertion, complex assembly and cofactor incorporation. All these processes are mediated by fine‐tuned stable and transient protein–protein interactions. Recently, an interactomic approach was used to determine the exact protein–protein interactions involved in the assembly of the denitrification apparatus of Pseudomonas aeruginosa. Both subunits of the NO reductase NorBC, combined with the flavoprotein NosR, serve as a membrane‐localized assembly platform for the attachment of the nitrate reductase NarGHI, the periplasmic nitrite reductase NirS via its maturation factor NirF and the N2O reductase NosZ through NosR. A nitrate transporter (NarK2), the corresponding regulatory system NarXL, various nitrite (NirEJMNQ) and N2O reductase (NosFL) maturation proteins are also part of the complex. Primary dehydrogenases, ATP synthase, most enzymes of the TCA cycle, and the SEC protein export system, as well as a number of other proteins, were found to interact with the denitrification complex. Finally, a protein complex composed of the flagella protein FliC, nitrite reductase NirS and the chaperone DnaK required for flagella formation was found in the periplasm of P. aeruginosa. This work demonstrated that the interactomic approach allows for the identification and characterization of stable and transient protein–protein complexes and interactions involved in the assembly and function of multi‐enzyme complexes.
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Affiliation(s)
| | - Kenneth N Timmis
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, Braunschweig, Germany
| | - Martina Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, Braunschweig, Germany
| | - Dieter Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology BRICS, Technische Universität Braunschweig, Rebenring 56, Braunschweig, Germany
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