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Ma TF, Yu XY, Xing CY, Fu HM, Duan HY, Chen YP. Impacts of sulfamethoxazole on heterotrophic nitrification-aerobic denitrification bacteria and its response strategies: Insights from physiology to proteomics. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2025; 379:124890. [PMID: 40056593 DOI: 10.1016/j.jenvman.2025.124890] [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: 12/16/2024] [Revised: 02/04/2025] [Accepted: 03/04/2025] [Indexed: 03/10/2025]
Abstract
The effects of sulfonamide antibiotics on heterotrophic nitrification-aerobic denitrification (HN-AD) and the response mechanisms of HN-AD bacteria are not fully understood. This study investigated the physiological changes and proteomic responses of the HN-AD bacteria Pseudomonas stutzeri (P. stutzeri) under varying concentrations of sulfamethoxazole (SMX). Results indicated that SMX inhibited the growth and HN-AD performance of P. stutzeri in a concentration-dependent manner. SMX exposure led to decreased motility, reduced electron transfer system activity, and diminished activities of key denitrifying enzymes, accompanied by increased levels of intracellular reactive oxygen species and compromised cell membrane integrity. Additionally, the production of extracellular polymeric substances and self-aggregation ability of P. stutzeri initially increased and then decreased with rising SMX concentrations. Proteomic analysis revealed that SMX primarily suppressed pathways involved in bacterial chemotaxis, ABC transporters, two-component systems, fatty acid metabolism, and nitrogen metabolism. In response, P. stutzeri upregulated pathways associated with starch and sucrose metabolism, carotenoid biosynthesis, styrene degradation, O-antigen nucleotide sugar biosynthesis, and the pentose phosphate pathway. These findings provide insights into the effects of sulfonamide antibiotics on HN-AD bacteria and their response mechanisms, offering references for the application of HN-AD processes in treating antibiotic-containing wastewater.
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Affiliation(s)
- Teng-Fei Ma
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing, 400067, China
| | - Xiao-Yao Yu
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing, 400067, China
| | - Chong-Yang Xing
- School of Environment and Resource, Chongqing Technology and Business University, Chongqing, 400067, China
| | - Hui-Min Fu
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing, 400067, China; Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Hao-Yang Duan
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing, 400067, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China.
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Daley SR, Gallanosa PM, Sparling R. Kinetic characterization of annotated glycolytic enzymes present in cellulose-fermenting Clostridium thermocellum suggests different metabolic roles. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:112. [PMID: 37438781 DOI: 10.1186/s13068-023-02362-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/27/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND The efficient production of sustainable biofuels is important for the reduction of greenhouse gas emissions. Clostridium thermocellum ATCC 27405 is a candidate for ethanol production from lignocellulosic biomass using consolidated bioprocessing. Fermentation of cellulosic biomass goes through an atypical glycolytic pathway in this thermophilic bacterium, with various glycolytic enzymes capable of utilizing different phosphate donors, including GTP and inorganic pyrophosphate (PPi), in addition to or in place of the usual ATP. C. thermocellum contains three annotated phosphofructokinases (PFK) genes, the expression of which have all been detected through proteomics and transcriptomics. Pfp (Cthe_0347) was previously characterized as pyrophosphate dependent with fructose-6-phosphate (F6P) as its substrate. RESULTS We now demonstrate that this enzyme can also phosphorylate sedoheptulose-7-phosphate (an intermediate in the pentose phosphate pathway), with the Vmax and Km of F6P being approximately 15 folds higher and 43 folds lower, respectively, in comparison to sedoheptulose-7-phosphate. Purified PfkA shows preference for GTP as the phosphate donor as opposed to ATP with a 12.5-fold difference in Km values while phosphorylating F6P. Allosteric regulation is a factor at play in PfkA activity, with F6P exhibiting positive cooperativity, and an apparent requirement for ammonium ions to attain maximal activity. Phosphoenolpyruvate and PPi were the only inhibitors for PfkA determined from the study, which corroborates what is known about enzymes from this subfamily. The activation or inhibition by these ligands lends support to the argument that glycolysis is regulated by metabolites such as PPi and NH4+ in the organism. PfkB, showed no activity with F6P, but had significant activity with fructose, while utilizing either ATP or GTP, making it a fructokinase. Rounding out the upper glycolysis pathway, the identity of the fructose-1,6-bisphosphate aldolase in the genome was verified and reported to have substantial activity with fructose-1,6-bisphosphate, in the presence of the divalent ion, Zn2+. CONCLUSION These findings along with previous proteomic data suggest that Pfp, plays a role in both glycolysis and the pentose phosphate pathway, while PfkA and PfkB may phosphorylate sugars in glycolysis but is responsible for sugar metabolism elsewhere under conditions outside of growth on sufficient cellobiose.
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Affiliation(s)
- Steve R Daley
- Department of Microbiology, University of Manitoba, 213 Buller Building, Winnipeg, MB, R3T 2N2, Canada
| | - Patricia Mae Gallanosa
- Department of Microbiology, University of Manitoba, 213 Buller Building, Winnipeg, MB, R3T 2N2, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, 213 Buller Building, Winnipeg, MB, R3T 2N2, Canada.
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Sánchez-Moreno I, Trachtmann N, Ilhan S, Hélaine V, Lemaire M, Guérard-Hélaine C, Sprenger GA. 2-Ketogluconate Kinase from Cupriavidus necator H16: Purification, Characterization, and Exploration of Its Substrate Specificity. Molecules 2019; 24:molecules24132393. [PMID: 31261738 PMCID: PMC6651773 DOI: 10.3390/molecules24132393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 06/21/2019] [Accepted: 06/27/2019] [Indexed: 11/30/2022] Open
Abstract
We have cloned, overexpressed, purified, and characterized a 2-ketogluconate kinase (2-dehydrogluconokinase, EC 2.7.1.13) from Cupriavidus necator (Ralstonia eutropha) H16. Exploration of its substrate specificity revealed that three ketoacids (2-keto-3-deoxy-d-gluconate, 2-keto-d-gulonate, and 2-keto-3-deoxy-d-gulonate) with structures close to the natural substrate (2-keto-d-gluconate) were successfully phosphorylated at an efficiency lower than or comparable to 2-ketogluconate, as depicted by the measured kinetic constant values. Eleven aldo and keto monosaccharides of different chain lengths and stereochemistries were also assayed but not found to be substrates. 2-ketogluconate-6-phosphate was synthesized at a preparative scale and was fully characterized for the first time.
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Affiliation(s)
- Israel Sánchez-Moreno
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Natalia Trachtmann
- University of Stuttgart, Institute of Microbiology, D-70569 Stuttgart, Germany
| | - Sibel Ilhan
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
- University of Stuttgart, Institute of Microbiology, D-70569 Stuttgart, Germany
| | - Virgil Hélaine
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Marielle Lemaire
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Christine Guérard-Hélaine
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France.
| | - Georg A Sprenger
- University of Stuttgart, Institute of Microbiology, D-70569 Stuttgart, Germany.
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Hu FZ, Król JE, Tsai CHS, Eutsey RA, Hiller LN, Sen B, Ahmed A, Hillman T, Buchinsky FJ, Nistico L, Dice B, Longwell M, Horsey E, Ehrlich GD. Deletion of genes involved in the ketogluconate metabolism, Entner-Doudoroff pathway, and glucose dehydrogenase increase local and invasive virulence phenotypes in Streptococcus pneumoniae. PLoS One 2019; 14:e0209688. [PMID: 30620734 PMCID: PMC6324787 DOI: 10.1371/journal.pone.0209688] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/10/2018] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pneumoniae displays increased resistance to antibiotic therapy following biofilm formation. A genome-wide search revealed that SP 0320 and SP 0675 (respectively annotated as 5-keto-D-gluconate-5-reductase and glucose dehydrogenase) contain the highest degree of homology to CsgA of Myxococcus xanthus, a signaling factor that promotes cell aggregation and biofilm formation. Single and double SP 0320 and SP 0675 knockout mutants were created in strain BS72; however, no differences were observed in the biofilm-forming phenotypes of mutants compared to the wild type strain. Using the chinchilla model of otitis media and invasive disease, all three mutants exhibited greatly increased virulence compared to the wild type strain (increased pus formation, tympanic membrane rupture, mortality rates). The SP 0320 gene is located in an operon with SP 0317, SP 0318 and SP 0319, which we bioinformatically annotated as being part of the Entner-Doudoroff pathway. Deletion of SP 0317 also resulted in increased mortality in chinchillas; however, mutations in SP 0318 and SP 0319 did not alter the virulence of bacteria compared to the wild type strain. Complementing the SP 0317, SP 0320 and SP 0675 mutant strains reversed the virulence phenotype. We prepared recombinant SP 0317, SP 0318, SP 0320 and SP 0675 proteins and confirmed their functions. These data reveal that disruption of genes involved in the degradation of ketogluconate, the Entner-Doudoroff pathway, and glucose dehydrogenase significantly increase the virulence of bacteria in vivo; two hypothetical models involving virulence triggered by reduced in carbon-flux through the glycolytic pathways are presented.
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Affiliation(s)
- Fen Z. Hu
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States of America
- Department of Otolaryngology-Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA, United States of America
- * E-mail: (FZH); (GDE)
| | - Jarosław E. Król
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States of America
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - Chen Hsuan Sherry Tsai
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - Rory A. Eutsey
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Luisa N. Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Bhaswati Sen
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States of America
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - Azad Ahmed
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States of America
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - Todd Hillman
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, PA, United States of America
| | - Farrel J. Buchinsky
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, PA, United States of America
| | - Laura Nistico
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, PA, United States of America
| | - Bethany Dice
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, PA, United States of America
| | - Mark Longwell
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, PA, United States of America
| | - Edward Horsey
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, PA, United States of America
| | - Garth D. Ehrlich
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States of America
- Department of Otolaryngology-Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA, United States of America
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States of America
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States of America
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, PA, United States of America
- * E-mail: (FZH); (GDE)
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Nishiyama R, Inoue A, Ojima T. Identification of 2-keto-3-deoxy-d-Gluconate Kinase and 2-keto-3-deoxy-d-Phosphogluconate Aldolase in an Alginate-Assimilating Bacterium, Flavobacterium sp. Strain UMI-01. Mar Drugs 2017; 15:md15020037. [PMID: 28216576 PMCID: PMC5334617 DOI: 10.3390/md15020037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/26/2017] [Accepted: 02/08/2017] [Indexed: 01/21/2023] Open
Abstract
Recently, we identified an alginate-assimilating gene cluster in the genome of Flavobacterium sp. strain UMI-01, a member of Bacteroidetes. Alginate lyase genes and a 4-deoxy-l-erythro-5-hexoseulose uronic acid (DEH) reductase gene in the cluster have already been characterized; however, 2-keto-3-deoxy-d-gluconate (KDG) kinase and 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase genes, i.e., flkin and flald, still remained uncharacterized. The amino acid sequences deduced from flkin and flald showed low identities with those of corresponding enzymes of Saccharophagus degradans 2-40T, a member of Proteobacteria (Kim et al., Process Biochem., 2016). This led us to consider that the DEH-assimilating enzymes of Bacteroidetes species are somewhat deviated from those of Proteobacteria species. Thus, in the present study, we first assessed the characteristics in the primary structures of KDG kinase and KDG aldolase of the strain UMI-01, and then investigated the enzymatic properties of recombinant enzymes, recFlKin and recFlAld, expressed by an Escherichia coli expression system. Multiple-sequence alignment among KDG kinases and KDG aldolases from several Proteobacteria and Bacteroidetes species indicated that the strain UMI-01 enzymes showed considerably low sequence identities (15%-25%) with the Proteobacteria enzymes, while they showed relatively high identities (47%-68%) with the Bacteroidetes enzymes. Phylogenetic analyses for these enzymes indicated the distant relationship between the Proteobacteria enzymes and the Bacteroidetes enzymes, i.e., they formed distinct clusters in the phylogenetic tree. recFlKin and recFlAld produced with the genes flkin and flald, respectively, were confirmed to show KDG kinase and KDPG aldolase activities. Namely, recFlKin produced 1.7 mM KDPG in a reaction mixture containing 2.5 mM KDG and 2.5 mM ATP in a 90-min reaction, while recFlAld produced 1.2 mM pyruvate in the reaction mixture containing 5 mM KDPG at the equilibrium state. An in vitro alginate-metabolizing system constructed from recFlKin, recFlAld, and previously reported alginate lyases and DEH reductase of the strain UMI-01 could convert alginate to pyruvate and glyceraldehyde-3-phosphate with an efficiency of 38%.
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Affiliation(s)
- Ryuji Nishiyama
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
| | - Akira Inoue
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
| | - Takao Ojima
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
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