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Tomaś N, Myszka K, Wolko Ł, Juzwa W. Global transcriptome analysis of Pseudomonas aeruginosa NT06 response to potassium chloride, sodium lactate, sodium citrate, and microaerophilic conditions in a fish ecosystem. FEMS Microbiol Lett 2024; 371:fnae043. [PMID: 38845372 DOI: 10.1093/femsle/fnae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 05/25/2024] [Accepted: 06/05/2024] [Indexed: 06/29/2024] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that recently has been increasingly isolated from foods, especially from minimally processed fish-based products. Those are preserved by the addition of sodium chloride (NaCl) and packaging in a modified atmosphere. However, the current trends of minimizing NaCl content may result in an increased occurrence of P. aeruginosa. NaCl can be replaced with potassium chloride (KCl) or sodium salts of organic acids. Herein, we examined the antimicrobial effects of KCl, sodium lactate (NaL), sodium citrate (NaC), and sodium acetate (NaA) against P. aeruginosa NT06 isolated from fish. Transcriptome response of cells grown in medium imitating a fish product supplemented with KCl and KCl/NaL/NaC and maintained under microaerophilic conditions was analysed. Flow cytometry analysis showed that treatment with KCl and KCl/NaL/NaC resulted in changed metabolic activity of cells. In response to KCl and KCl/NaL/NaC treatment, genes related to cell maintenance, stress response, quorum sensing, virulence, efflux pump, and metabolism were differentially expressed. Collectively, our results provide an improved understanding of the response of P. aeruginosa to NaCl alternative compounds that can be implemented in fish-based products and encourage further exploration of the development of effective methods to protect foods against the P. aeruginosa, underestimate foodborne bacteria.
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Affiliation(s)
- Natalia Tomaś
- Department of Biotechnology and Food Microbiology, Faculty of Food Science and Nutrition, Poznan University of Life Sciences, Wojska Polskiego 48, 60-637 Poznań, Poland
- Department of Human Nutrition and Dietotherapy, Faculty of Biological Sciences, University of Zielona Gora, Pałac Kalsk 67, 66-100 Sulechów, Poland
| | - Kamila Myszka
- Department of Biotechnology and Food Microbiology, Faculty of Food Science and Nutrition, Poznan University of Life Sciences, Wojska Polskiego 48, 60-637 Poznań, Poland
| | - Łukasz Wolko
- Department of Biochemistry and Biotechnology, Faculty of Agriculture, Horticulture and Bioengineering, Poznan University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Wojciech Juzwa
- Department of Biotechnology and Food Microbiology, Faculty of Food Science and Nutrition, Poznan University of Life Sciences, Wojska Polskiego 48, 60-637 Poznań, Poland
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Hussein M, Jasim R, Gocol H, Baker M, Thombare VJ, Ziogas J, Purohit A, Rao GG, Li J, Velkov T. Comparative Proteomics of Outer Membrane Vesicles from Polymyxin-Susceptible and Extremely Drug-Resistant Klebsiella pneumoniae. mSphere 2023; 8:e0053722. [PMID: 36622250 PMCID: PMC9942579 DOI: 10.1128/msphere.00537-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/06/2022] [Indexed: 01/10/2023] Open
Abstract
Outer membrane vesicles (OMVs) secreted by Gram-negative bacteria serve as transporters for the delivery of cargo such as virulence and antibiotic resistance factors. OMVs play a key role in the defense against membrane-targeting antibiotics such as the polymyxin B. Herein, we conducted comparative proteomics of OMVs from paired Klebsiella pneumoniae ATCC 700721 polymyxin-susceptible (polymyxin B MIC = 0.5 mg/L) and an extremely resistant (polymyxin B MIC ≥128 mg/L), following exposure to 2 mg/L of polymyxin B. Comparative profiling of the OMV subproteome of each strain revealed proteins from multiple perturbed pathways, particularly in the polymyxin-susceptible strain, including outer membrane assembly (lipopolysaccharide, O-antigen, and peptidoglycan biosynthesis), cationic antimicrobial peptide resistance, β-lactam resistance, and quorum sensing. In the polymyxin-susceptible strain, polymyxin B treatment reduced the expression of OMV proteins in the pathways related to adhesion, virulence, and the cell envelope stress responses, whereas, in the polymyxin-resistant strain, the proteins involved in LPS biosynthesis, RNA degradation, and nucleotide excision repair were significantly overexpressed in response to polymyxin B treatment. Intriguingly, the key polymyxin resistance enzymes 4-amino-4-deoxy-l-arabinose transferase and the PhoPQ two-component protein kinase were significantly downregulated in the OMVs of the polymyxin-susceptible strain. Additionally, a significant reduction in class A β-lactamase proteins was observed following polymyxin B treatment in the OMVs of both strains, particularly the OMVs of the polymyxin-susceptible strain. These findings shed new light on the OMV subproteome of extremely polymyxin resistant K. pneumoniae, which putatively may serve as active decoys to make the outer membrane more impervious to polymyxin attack. IMPORTANCE OMVs can help bacteria to fight antibiotics not only by spreading antibiotic resistance genes but also by acting as protective armor against antibiotics. By employing proteomics, we found that OMVs have a potential role in shielding K. pneumoniae and acting as decoys to polymyxin attack, through declining the export of proteins (e.g., 4-amino-4-deoxy-l-arabinose transferase) involved in polymyxin resistance. Furthermore, polymyxin B treatment of both strains leads to shedding of the OMVs with perturbed proteins involved in outer membrane remodeling (e.g., LPS biosynthesis) as well as pathogenic potential of K. pneumoniae (e.g., quorum sensing). The problematic extended spectrum beta-lactamases SHV and TEM were significantly reduced in both strains, suggesting that polymyxin B may act as a potentiator to sensitize the bacterium to β-lactam antibiotics. This study highlights the importance of OMVs as "molecular mules" for the intercellular transmission and delivery of resistance and cellular repair factors in the bacterial response to polymyxins.
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Affiliation(s)
- Maytham Hussein
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Raad Jasim
- Department of Pharmacology, College of Pharmacy, University of Babylon, Iraq
| | - Hakan Gocol
- Department of Biochemistry and Pharmacology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Mark Baker
- Discipline of Biological Sciences, Priority Research Centre in Reproductive Biology, Faculty of Science and IT, University of Newcastle, Callaghan, New South Wales, Australia
| | - Varsha J. Thombare
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - James Ziogas
- Department of Biochemistry and Pharmacology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Aayush Purohit
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Gauri G. Rao
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jian Li
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Tony Velkov
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria, Australia
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Joo H, Eom H, Cho Y, Rho M, Song WJ. Discovery and Characterization of Polymyxin-Resistance Genes pmrE and pmrF from Sediment and Seawater Microbiome. Microbiol Spectr 2023; 11:e0273622. [PMID: 36602384 PMCID: PMC9927302 DOI: 10.1128/spectrum.02736-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Polymyxins are the last-line antibiotics used to treat Gram-negative pathogens. Thus, the discovery and biochemical characterization of the resistance genes against polymyxins are urgently needed for diagnosis, treatment, and novel antibiotic design. Herein, we report novel polymyxin-resistance genes identified from sediment and seawater microbiome. Despite their low sequence identity against the known pmrE and pmrF, they show in vitro activities in UDP-glucose oxidation and l-Ara4N transfer to undecaprenyl phosphate, respectively, which occur as the part of lipid A modification that leads to polymyxin resistance. The expression of pmrE and pmrF also showed substantially high MICs in the presence of vanadate ions, indicating that they constitute polymyxin resistomes. IMPORTANCE Polymyxins are one of the last-resort antibiotics. Polymyxin resistance is a severe threat to combat multidrug-resistant pathogens. Thus, up-to-date identification and understanding of the related genes are crucial. Herein, we performed structure-guided sequence and activity analysis of five putative polymyxin-resistant metagenomes. Despite relatively low sequence identity to the previously reported polymyxin-resistance genes, at least four out of five discovered genes show reactivity essential for lipid A modification and polymyxin resistance, constituting antibiotic resistomes.
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Affiliation(s)
- Hwanjin Joo
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Hyunuk Eom
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Youna Cho
- Department of Computer Science, Hanyang University, Seoul, Republic of Korea
| | - Mina Rho
- Department of Computer Science, Hanyang University, Seoul, Republic of Korea
- Department of Biomedical Informatics, Hanyang University, Seoul, Republic of Korea
| | - Woon Ju Song
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
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Cesur MF, Siraj B, Uddin R, Durmuş S, Çakır T. Network-Based Metabolism-Centered Screening of Potential Drug Targets in Klebsiella pneumoniae at Genome Scale. Front Cell Infect Microbiol 2020; 9:447. [PMID: 31993376 PMCID: PMC6970976 DOI: 10.3389/fcimb.2019.00447] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 12/12/2019] [Indexed: 01/28/2023] Open
Abstract
Klebsiella pneumoniae is an opportunistic bacterial pathogen leading to life-threatening nosocomial infections. Emergence of highly resistant strains poses a major challenge in the management of the infections by healthcare-associated K. pneumoniae isolates. Thus, despite intensive efforts, the current treatment strategies remain insufficient to eradicate such infections. Failure of the conventional infection-prevention and treatment efforts explicitly indicates the requirement of new therapeutic approaches. This prompted us to systematically analyze the K. pneumoniae metabolism to investigate drug targets. Genome-scale metabolic networks (GMNs) facilitating the systematic analysis of the metabolism are promising platforms. Thus, we used a GMN of K. pneumoniae MGH 78578 to determine putative targets through gene- and metabolite-centric approaches. To develop more realistic infection models, we performed the bacterial growth simulations within different host-mimicking media, using an improved biomass formation reaction. We selected more suitable targets based on several property-based prioritization procedures. KdsA was identified as the high-ranked putative target satisfying most of the target prioritization criteria specified under the gene-centric approach. Through a structure-based virtual screening protocol, we identified potential KdsA inhibitors. In addition, the metabolite-centric approach extended the drug target list based on synthetic lethality. This revealed the importance of combined metabolic analyses for a better understanding of the metabolism. To our knowledge, this is the first comprehensive effort on the investigation of the K. pneumoniae metabolism for drug target prediction through the constraint-based analysis of its GMN in conjunction with several bioinformatic approaches. This study can guide the researchers for the future drug designs by providing initial findings regarding crucial components of the Klebsiella metabolism.
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Affiliation(s)
- Müberra Fatma Cesur
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Turkey
| | - Bushra Siraj
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Saliha Durmuş
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Turkey
| | - Tunahan Çakır
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Turkey
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Han PP, Yao SY, Guo RJ, Shen SG, Yan RR, Tan ZL, Jia SR. The relationship between monosaccharide composition of extracellular polysaccharide and activities of related enzymes in Nostoc flagelliforme under different culture conditions. Carbohydr Polym 2017; 174:111-119. [PMID: 28821034 DOI: 10.1016/j.carbpol.2017.05.093] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/05/2017] [Accepted: 05/30/2017] [Indexed: 10/19/2022]
Abstract
The relationship between monosaccharide composition of Nostoc flagelliforme extracellular polysaccharide (EPS) and activities of EPS synthesis enzymes under various carbon sources, nitrogen sources and light culture condition was investigated. Culture conditions showed significant influences on both monosaccharide composition and related enzyme activities. Under both carbon and nitrogen sources conditions, mannose mole percentage was increased with the increase of initial mole ratio of C/N and positively related to fructose-1, 6-bisphosphatase activity, and glucuronic acid and galactose mole percentages were positively correlated with UDP-glucose dehydrogenase, while arabinose and rhamnose mole percentages were negatively associated with UDP-glucose pyrophosphorylase. Different correlation between monosaccharide composition and enzymes activity from carbon and nitrogen sources conditions was found under light condition. These findings will be helpful to establish a novel fermentation process aimed to produce the N. flagelliforme EPS with desired monosaccharide composition.
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Affiliation(s)
- Pei-Pei Han
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Shun-Yu Yao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Rong-Jun Guo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Shi-Gang Shen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Rong-Rong Yan
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Zhi-Lei Tan
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Shi-Ru Jia
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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Analysis of Shigella flexneri Resistance, Biofilm Formation, and Transcriptional Profile in Response to Bile Salts. Infect Immun 2017; 85:IAI.01067-16. [PMID: 28348056 DOI: 10.1128/iai.01067-16] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 03/23/2017] [Indexed: 01/07/2023] Open
Abstract
The Shigella species cause millions of cases of watery or bloody diarrhea each year, mostly in children in developing countries. While many aspects of Shigella colonic cell invasion are known, crucial gaps in knowledge regarding how the bacteria survive, transit, and regulate gene expression prior to infection remain. In this study, we define mechanisms of resistance to bile salts and build on previous research highlighting induced virulence in Shigella flexneri strain 2457T following exposure to bile salts. Typical growth patterns were observed within the physiological range of bile salts; however, growth was inhibited at higher concentrations. Interestingly, extended periods of exposure to bile salts led to biofilm formation, a conserved phenotype that we observed among members of the Enterobacteriaceae Characterization of S. flexneri 2457T biofilms determined that both bile salts and glucose were required for formation, dispersion was dependent upon bile salts depletion, and recovered bacteria displayed induced adherence to HT-29 cells. RNA-sequencing analysis verified an important bile salt transcriptional profile in S. flexneri 2457T, including induced drug resistance and virulence gene expression. Finally, functional mutagenesis identified the importance of the AcrAB efflux pump and lipopolysaccharide O-antigen synthesis for bile salt resistance. Our data demonstrate that S. flexneri 2457T employs multiple mechanisms to survive exposure to bile salts, which may have important implications for multidrug resistance. Furthermore, our work confirms that bile salts are important physiological signals to activate S. flexneri 2457T virulence. This work provides insights into how exposure to bile likely regulates Shigella survival and virulence during host transit and subsequent colonic infection.
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Han PP, Yao SY, Guo RJ, Yan RR, Wu YK, Shen SG, Jia SR. Influence of culture conditions on extracellular polysaccharide production and the activities of enzymes involved in the polysaccharide synthesis of Nostoc flagelliforme. RSC Adv 2017. [DOI: 10.1039/c7ra07982f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Important enzymes influencing the production ofNostoc flagelliformeEPS were investigated under different culture conditions.
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Affiliation(s)
- Pei-pei Han
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
| | - Shun-yu Yao
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
| | - Rong-jun Guo
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
| | - Rong-rong Yan
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
| | - Yi-kai Wu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
| | - Shi-gang Shen
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
| | - Shi-ru Jia
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
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8
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Weyler C, Bureik M, Heinzle E. Selective oxidation of UDP-glucose to UDP-glucuronic acid using permeabilized Schizosaccharomyces pombe expressing human UDP-glucose 6-dehydrogenase. Biotechnol Lett 2015; 38:477-81. [PMID: 26582015 DOI: 10.1007/s10529-015-1995-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/03/2015] [Indexed: 10/22/2022]
Abstract
OBJECTIVES To use permeabilized cells of the fission yeast, Schizosaccharomyces pombe, that expresses human UDP-glucose 6-dehydrogenase (UGDH, EC 1.1.1.22), for the production of UDP-glucuronic acid from UDP-glucose. RESULTS In cell extracts no activity was detected. Therefore, cells were permeabilized with 0.3 % (v/v) Triton X-100. After washing away all low molecular weight metabolites, the permeabilized cells were directly used as whole cell biocatalyst. Substrates were 5 mM UDP-glucose and 10 mM NAD(+). Divalent cations were not added to the reaction medium as they promoted UDP-glucose hydrolysis. With this reaction system 5 mM UDP-glucose were converted into 5 mM UDP-glucuronic acid within 3 h. CONCLUSIONS Recombinant permeabilized cells of S. pombe can be used to synthesize UDP-glucuronic acid with 100 % yield and selectivity.
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Affiliation(s)
- Christian Weyler
- Biochemical Engineering Institute, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany
| | - Matthias Bureik
- School of Pharmaceutical Science and Technology (SPST), Tianjin University, Building 24, 92 Weijin Road, Nankai District, Tianjin, 300072, People's Republic of China
| | - Elmar Heinzle
- Biochemical Engineering Institute, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany.
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Singh S, Michalska K, Bigelow L, Endres M, Kharel MK, Babnigg G, Yennamalli RM, Bingman CA, Joachimiak A, Thorson JS, Phillips GN. Structural Characterization of CalS8, a TDP-α-D-Glucose Dehydrogenase Involved in Calicheamicin Aminodideoxypentose Biosynthesis. J Biol Chem 2015; 290:26249-58. [PMID: 26240141 DOI: 10.1074/jbc.m115.673459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Indexed: 11/06/2022] Open
Abstract
Classical UDP-glucose 6-dehydrogenases (UGDHs; EC 1.1.1.22) catalyze the conversion of UDP-α-d-glucose (UDP-Glc) to the key metabolic precursor UDP-α-d-glucuronic acid (UDP-GlcA) and display specificity for UDP-Glc. The fundamental biochemical and structural study of the UGDH homolog CalS8 encoded by the calicheamicin biosynthetic gene is reported and represents one of the first studies of a UGDH homolog involved in secondary metabolism. The corresponding biochemical characterization of CalS8 reveals CalS8 as one of the first characterized base-permissive UGDH homologs with a >15-fold preference for TDP-Glc over UDP-Glc. The corresponding structure elucidations of apo-CalS8 and the CalS8·substrate·cofactor ternary complex (at 2.47 and 1.95 Å resolution, respectively) highlight a notably high degree of conservation between CalS8 and classical UGDHs where structural divergence within the intersubunit loop structure likely contributes to the CalS8 base permissivity. As such, this study begins to provide a putative blueprint for base specificity among sugar nucleotide-dependent dehydrogenases and, in conjunction with prior studies on the base specificity of the calicheamicin aminopentosyltransferase CalG4, provides growing support for the calicheamicin aminopentose pathway as a TDP-sugar-dependent process.
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Affiliation(s)
- Shanteri Singh
- From the Center for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, Lexington, Kentucky 40536-0596
| | - Karolina Michalska
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Lance Bigelow
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Michael Endres
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Madan K Kharel
- the School of Pharmacy, University of Maryland Eastern Shore, Princess Anne, Maryland 21853
| | - Gyorgy Babnigg
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Ragothaman M Yennamalli
- the Department of BioSciences, Department of Chemistry, Rice University, Houston, Texas 77005
| | - Craig A Bingman
- the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, and
| | - Andrzej Joachimiak
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Jon S Thorson
- From the Center for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, Lexington, Kentucky 40536-0596,
| | - George N Phillips
- the Department of BioSciences, Department of Chemistry, Rice University, Houston, Texas 77005 the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, and
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Peng L, Qiao S, Xu Z, Guan F, Ding Z, Gu Z, Zhang L, Shi G. Effects of culture conditions on monosaccharide composition of Ganoderma lucidum exopolysaccharide and on activities of related enzymes. Carbohydr Polym 2015; 133:104-9. [PMID: 26344261 DOI: 10.1016/j.carbpol.2015.07.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 07/06/2015] [Accepted: 07/07/2015] [Indexed: 11/29/2022]
Abstract
We investigated the relationship between monosaccharide composition of Ganoderma lucidum exopolysaccharide (EPS) and activities of EPS synthesis enzymes under various culture temperatures and initial pH values. The mole percentages of three major EPS monosaccharides, glucose, galactose and mannose, varied depending on culture conditions and the resulting EPS displayed differing anti-tumor activities. In nine tested enzymes, higher enzyme activities were correlated with higher temperature and lower initial pH. Altered mole percentages of galactose and mannose under various culture conditions were associated with activities of α-phosphoglucomutase (PGM) and phosphoglucose isomerase (PGI), respectively, and that of mannose was also associated with phosphomannose isomerase (PMI) activity only under various pH. Our findings suggest that mole percentages of G. lucidum EPS monosaccharides can be manipulated by changes of culture conditions that affect enzyme activities, and that novel fermentation strategies based on this approach may enhance production and biological activity of EPS.
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Affiliation(s)
- Lin Peng
- Key Laboratory of Carbohydrate Chemistry & Biotechnology Ministry of Education, & School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Shuangkui Qiao
- Key Laboratory of Carbohydrate Chemistry & Biotechnology Ministry of Education, & School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
| | - Zhenghong Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Feng Guan
- Key Laboratory of Carbohydrate Chemistry & Biotechnology Ministry of Education, & School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhongyang Ding
- Key Laboratory of Carbohydrate Chemistry & Biotechnology Ministry of Education, & School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China.
| | - Zhenghua Gu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
| | - Liang Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
| | - Guiyang Shi
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
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Two UDP-glucuronic acid decarboxylases involved in the biosynthesis of a bacterial exopolysaccharide in Paenibacillus elgii. Appl Microbiol Biotechnol 2015; 99:3127-39. [PMID: 25573472 DOI: 10.1007/s00253-014-6362-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 12/20/2014] [Accepted: 12/23/2014] [Indexed: 12/11/2022]
Abstract
Xylose is described as a component of bacterial exopolysaccharides in only a limited number of bacterial strains. A bacterial strain, Paenibacillus elgii, B69 was shown to be efficient in producing a xylose-containing exopolysaccharide. Sequence analysis was performed to identify the genes encoding the uridine diphosphate (UDP)-glucuronic acid decarboxylase required for the synthesis of UDP-xylose, the precursor of the exopolysaccharide. Two sequences, designated as Peuxs1 and Peuxs2, were found as the candidate genes for such enzymes. The activities of the UDP-glucuronic acid decarboxylases were proven by heterologous expression and real-time nuclear magnetic resonance analysis. The intracellular activity and effect of these genes on the synthesis of exopolysaccharide were further investigated by developing a thymidylate synthase based knockout system. This system was used to substitute the conventional antibiotic resistance gene system in P. elgii, a natural multi-antibiotic resistant strain. Results of intracellular nucleotide sugar analysis showed that the intracellular UDP-xylose and UDP-glucuronic acid levels were affected in Peuxs1 or Peuxs2 knockout strains. The knockout of either Peuxs1 or Peuxs2 reduced the polysaccharide production and changed the monosaccharide ratio. No polysaccharide was found in the Peuxs1/Peuxs2 double knockout strain. Our results show that P. elgii can be efficient in forming UDP-xylose, which is then used for the synthesis of xylose-containing exopolysaccharide.
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12
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Zimaro T, Thomas L, Marondedze C, Garavaglia BS, Gehring C, Ottado J, Gottig N. Insights into xanthomonas axonopodis pv. citri biofilm through proteomics. BMC Microbiol 2013; 13:186. [PMID: 23924281 PMCID: PMC3750573 DOI: 10.1186/1471-2180-13-186] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 08/02/2013] [Indexed: 11/28/2022] Open
Abstract
Background Xanthomonas axonopodis pv. citri (X. a. pv. citri) causes citrus canker that can result in defoliation and premature fruit drop with significant production losses worldwide. Biofilm formation is an important process in bacterial pathogens and several lines of evidence suggest that in X. a. pv. citri this process is a requirement to achieve maximal virulence since it has a major role in host interactions. In this study, proteomics was used to gain further insights into the functions of biofilms. Results In order to identify differentially expressed proteins, a comparative proteomic study using 2D difference gel electrophoresis was carried out on X. a. pv. citri mature biofilm and planktonic cells. The biofilm proteome showed major variations in the composition of outer membrane proteins and receptor or transport proteins. Among them, several porins and TonB-dependent receptor were differentially regulated in the biofilm compared to the planktonic cells, indicating that these proteins may serve in maintaining specific membrane-associated functions including signaling and cellular homeostasis. In biofilms, UDP-glucose dehydrogenase with a major role in exopolysaccharide production and the non-fimbrial adhesin YapH involved in adherence were over-expressed, while a polynucleotide phosphorylase that was demonstrated to negatively control biofilm formation in E. coli was down-regulated. In addition, several proteins involved in protein synthesis, folding and stabilization were up-regulated in biofilms. Interestingly, some proteins related to energy production, such as ATP-synthase were down-regulated in biofilms. Moreover, a number of enzymes of the tricarboxylic acid cycle were differentially expressed. In addition, X. a. pv. citri biofilms also showed down-regulation of several antioxidant enzymes. The respective gene expression patterns of several identified proteins in both X. a. pv. citri mature biofilm and planktonic cells were evaluated by quantitative real-time PCR and shown to consistently correlate with those deduced from the proteomic study. Conclusions Differentially expressed proteins are enriched in functional categories. Firstly, proteins that are down-regulated in X. a. pv. citri biofilms are enriched for the gene ontology (GO) terms ‘generation of precursor metabolites and energy’ and secondly, the biofilm proteome mainly changes in ‘outer membrane and receptor or transport’. We argue that the differentially expressed proteins have a critical role in maintaining a functional external structure as well as enabling appropriate flow of nutrients and signals specific to the biofilm lifestyle.
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Affiliation(s)
- Tamara Zimaro
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR-CONICET), Ocampo y Esmeralda, Rosario, Santa Fe, Argentina
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13
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Mainprize IL, Bean JD, Bouwman C, Kimber MS, Whitfield C. The UDP-glucose dehydrogenase of Escherichia coli K-12 displays substrate inhibition by NAD that is relieved by nucleotide triphosphates. J Biol Chem 2013; 288:23064-74. [PMID: 23792965 DOI: 10.1074/jbc.m113.486613] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
UDP-glucose dehydrogenase (Ugd) generates UDP-glucuronic acid, an important precursor for the production of many hexuronic acid-containing bacterial surface glycostructures. In Escherichia coli K-12, Ugd is important for biosynthesis of the environmentally regulated exopolysaccharide known as colanic acid, whereas in other E. coli isolates, the same enzyme is required for production of the constitutive group 1 capsular polysaccharides, which act as virulence determinants. Recent studies have implicated tyrosine phosphorylation in the activation of Ugd from E. coli K-12, although it is not known if this is a feature shared by bacterial Ugd proteins. The activities of Ugd from E. coli K-12 and from the group 1 capsule prototype (serotype K30) were compared. Surprisingly, for both enzymes, site-directed Tyr → Phe mutants affecting the previously proposed phosphorylation site retained similar kinetic properties to the wild-type protein. Purified Ugd from E. coli K-12 had significant levels of NAD substrate inhibition, which could be alleviated by the addition of ATP and several other nucleotide triphosphates. Mutations in a previously identified UDP-glucuronic acid allosteric binding site decreased the binding affinity of the nucleotide triphosphate. Ugd from E. coli serotype K30 was not inhibited by NAD, but its activity still increased in the presence of ATP.
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Affiliation(s)
- Iain L Mainprize
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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14
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Wei Q, Tarighi S, Dötsch A, Häussler S, Müsken M, Wright VJ, Cámara M, Williams P, Haenen S, Boerjan B, Bogaerts A, Vierstraete E, Verleyen P, Schoofs L, Willaert R, De Groote VN, Michiels J, Vercammen K, Crabbé A, Cornelis P. Phenotypic and genome-wide analysis of an antibiotic-resistant small colony variant (SCV) of Pseudomonas aeruginosa. PLoS One 2011; 6:e29276. [PMID: 22195037 PMCID: PMC3240657 DOI: 10.1371/journal.pone.0029276] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 11/23/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Small colony variants (SCVs) are slow-growing bacteria, which often show increased resistance to antibiotics and cause latent or recurrent infections. It is therefore important to understand the mechanisms at the basis of this phenotypic switch. METHODOLOGY/PRINCIPAL FINDINGS One SCV (termed PAO-SCV) was isolated, showing high resistance to gentamicin and to the cephalosporine cefotaxime. PAO-SCV was prone to reversion as evidenced by emergence of large colonies with a frequency of 10(-5) on media without antibiotics while it was stably maintained in presence of gentamicin. PAO-SCV showed a delayed growth, defective motility, and strongly reduced levels of the quorum sensing Pseudomonas quinolone signal (PQS). Whole genome expression analysis further suggested a multi-layered antibiotic resistance mechanism, including simultaneous over-expression of two drug efflux pumps (MexAB-OprM, MexXY-OprM), the LPS modification operon arnBCADTEF, and the PhoP-PhoQ two-component system. Conversely, the genes for the synthesis of PQS were strongly down-regulated in PAO-SCV. Finally, genomic analysis revealed the presence of mutations in phoP and phoQ genes as well as in the mexZ gene encoding a repressor of the mexXY and mexAB-oprM genes. Only one mutation occurred only in REV, at nucleotide 1020 of the tufA gene, a paralog of tufB, both encoding the elongation factor Tu, causing a change of the rarely used aspartic acid codon GAU to the more common GAC, possibly causing an increase of tufA mRNA translation. High expression of phoP and phoQ was confirmed for the SCV variant while the revertant showed expression levels reduced to wild-type levels. CONCLUSIONS By combining data coming from phenotypic, gene expression and proteome analysis, we could demonstrate that resistance to aminoglycosides in one SCV mutant is multifactorial including overexpression of efflux mechanisms, LPS modification and is accompanied by a drastic down-regulation of the Pseudomonas quinolone signal quorum sensing system.
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Affiliation(s)
- Qing Wei
- Research Group Microbiology, VIB Department of Structural Biology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Saeed Tarighi
- Research Group Microbiology, VIB Department of Structural Biology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Andreas Dötsch
- Chronic Pseudomonas Infections, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Susanne Häussler
- Chronic Pseudomonas Infections, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Twincore, Center for Experimental and Clinical Infection Research, Helmholtz Center for Infection Research and the Medical School Hannover, Hannover, Germany
| | - Mathias Müsken
- Chronic Pseudomonas Infections, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Twincore, Center for Experimental and Clinical Infection Research, Helmholtz Center for Infection Research and the Medical School Hannover, Hannover, Germany
| | - Victoria J. Wright
- School of Molecular Medical Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Miguel Cámara
- School of Molecular Medical Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Paul Williams
- School of Molecular Medical Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Steven Haenen
- Functional Genomics and Proteomics, Faculty of Sciences, K.U. Leuven, Leuven, Belgium
| | - Bart Boerjan
- Functional Genomics and Proteomics, Faculty of Sciences, K.U. Leuven, Leuven, Belgium
| | - Annelies Bogaerts
- Functional Genomics and Proteomics, Faculty of Sciences, K.U. Leuven, Leuven, Belgium
| | - Evy Vierstraete
- Functional Genomics and Proteomics, Faculty of Sciences, K.U. Leuven, Leuven, Belgium
| | - Peter Verleyen
- Functional Genomics and Proteomics, Faculty of Sciences, K.U. Leuven, Leuven, Belgium
| | - Liliane Schoofs
- Functional Genomics and Proteomics, Faculty of Sciences, K.U. Leuven, Leuven, Belgium
| | - Ronnie Willaert
- Structural Biology Brussels, VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Jan Michiels
- Centre of Microbial and Plant Genetics, K.U. Leuven, Heverlee, Belgium
| | - Ken Vercammen
- Research Group Microbiology, VIB Department of Structural Biology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Aurélie Crabbé
- The Biodesign Institute, Center for Infectious Diseases and Vaccinology, Arizona State University, Tempe, Arizona, United States of America
| | - Pierre Cornelis
- Research Group Microbiology, VIB Department of Structural Biology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- * E-mail:
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15
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Broach B, Gu X, Bar-Peled M. Biosynthesis of UDP-glucuronic acid and UDP-galacturonic acid in Bacillus cereus subsp. cytotoxis NVH 391-98. FEBS J 2011; 279:100-12. [PMID: 22023070 DOI: 10.1111/j.1742-4658.2011.08402.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The food borne pathogen Bacillus cereus produces uronic acid-containing glycans that are secreted in a shielding biofilm environment, and certain alkaliphilic Bacillus deposit uronate-glycan polymers in the cell wall when adapting to alkaline environments. The source of these acidic sugars is unknown and, in the present study, we describe the functional identification of an operon in Bacillus cerues subsp. cytotoxis NVH 391-98 that comprises genes involved in the synthesis of UDP-uronic acids in Bacillus spp. Within the operon, a UDP-glucose 6-dehydrogenase converts UDP-glucose in the presence of NAD(+) to UDP-glucuronic acid and NADH, and a UDP-GlcA 4-epimerase (UGlcAE) converts UDP-glucuronic acid to UDP-galacturonic acid. Interestingly, in vitro, both enzymes can utilize the TDP-sugar forms as well, albeit at lower catalytic efficiency. Unlike most of the very few bacterial 4-epimerases that have been characterized, which are promiscuous, the B. cereus UGlcAE enzyme is very specific and cannot use UDP-glucose, UDP-N-acetylglucosamine, UDP-N-acetylglucosaminuronic acid or UDP-xylose as substrates. Size exclusion chromatography suggests that UGlcAE is active as a monomer, unlike the dimeric form of plant enzymes; the Bacillus UDP-glucose 6-dehydrogenase is also found as a monomer. Phylogenic analysis further suggests that the Bacillus UGlcAE may have evolved separately from other bacterial and plant epimerases. Our results provide insight into the formation and function of uronic acid-containing glycans in the lifecycle of B. cereus and related species containing homologous operons, as well as a basis for determining the importance of these acidic glycans. We also discuss the ability to target UGlcAE as a drug candidate.
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Affiliation(s)
- Bryan Broach
- Complex Carbohydrate Research Center (CCRC), University of Georgia, Athens, GA 30602, USA
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16
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Loutet SA, Valvano MA. Extreme antimicrobial peptide and polymyxin B resistance in the genus Burkholderia. Front Cell Infect Microbiol 2011; 1:6. [PMID: 22919572 PMCID: PMC3417367 DOI: 10.3389/fcimb.2011.00006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 07/12/2011] [Indexed: 12/12/2022] Open
Abstract
Cationic antimicrobial peptides and polymyxins are a group of naturally occurring antibiotics that can also possess immunomodulatory activities. They are considered a new source of antibiotics for treating infections by bacteria that are resistant to conventional antibiotics. Members of the genus Burkholderia, which includes various human pathogens, are inherently resistant to antimicrobial peptides. The resistance is several orders of magnitude higher than that of other Gram-negative bacteria such as Escherichia coli, Salmonella enterica, or Pseudomonas aeruginosa. This review summarizes our current understanding of antimicrobial peptide and polymyxin B resistance in the genus Burkholderia. These bacteria possess major and minor resistance mechanisms that will be described in detail. Recent studies have revealed that many other emerging Gram-negative opportunistic pathogens may also be inherently resistant to antimicrobial peptides and polymyxins and we propose that Burkholderia sp. are a model system to investigate the molecular basis of the resistance in extremely resistant bacteria. Understanding resistance in these types of bacteria will be important if antimicrobial peptides come to be used regularly for the treatment of infections by susceptible bacteria because this may lead to increased resistance in the species that are currently susceptible and may also open up new niches for opportunistic pathogens with high inherent resistance.
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Affiliation(s)
- Slade A Loutet
- Centre for Human Immunology, University of Western Ontario London, Ontario, Canada
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17
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Loutet SA, Valvano MA. Extreme antimicrobial Peptide and polymyxin B resistance in the genus burkholderia. Front Microbiol 2011; 2:159. [PMID: 21811491 PMCID: PMC3143681 DOI: 10.3389/fmicb.2011.00159] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 07/12/2011] [Indexed: 01/04/2023] Open
Abstract
Cationic antimicrobial peptides and polymyxins are a group of naturally occurring antibiotics that can also possess immunomodulatory activities. They are considered a new source of antibiotics for treating infections by bacteria that are resistant to conventional antibiotics. Members of the genus Burkholderia, which includes various human pathogens, are inherently resistant to antimicrobial peptides. The resistance is several orders of magnitude higher than that of other Gram-negative bacteria such as Escherichia coli, Salmonella enterica, or Pseudomonas aeruginosa. This review summarizes our current understanding of antimicrobial peptide and polymyxin B resistance in the genus Burkholderia. These bacteria possess major and minor resistance mechanisms that will be described in detail. Recent studies have revealed that many other emerging Gram-negative opportunistic pathogens may also be inherently resistant to antimicrobial peptides and polymyxins and we propose that Burkholderia sp. are a model system to investigate the molecular basis of the resistance in extremely resistant bacteria. Understanding resistance in these types of bacteria will be important if antimicrobial peptides come to be used regularly for the treatment of infections by susceptible bacteria because this may lead to increased resistance in the species that are currently susceptible and may also open up new niches for opportunistic pathogens with high inherent resistance.
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Affiliation(s)
- Slade A Loutet
- Centre for Human Immunology, University of Western Ontario London, ON, Canada
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18
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Structure of Burkholderia cepacia UDP-glucose dehydrogenase (UGD) BceC and role of Tyr10 in final hydrolysis of UGD thioester intermediate. J Bacteriol 2011; 193:3978-87. [PMID: 21602353 DOI: 10.1128/jb.01076-10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Members of the Burkholderia cepacia complex (BCC) are serious respiratory pathogens in immunocompromised individuals and in patients with cystic fibrosis (CF). They are exceptionally resistant to many antimicrobial agents and have the capacity to spread between patients, leading to a decline in lung function and necrotizing pneumonia. BCC members often express a mucoid phenotype associated with the secretion of the exopolysaccharide (EPS) cepacian. There is much evidence supporting the fact that cepacian is a major virulence factor of BCC. UDP-glucose dehydrogenase (UGD) is responsible for the NAD-dependent 2-fold oxidation of UDP-glucose (UDP-Glc) to UDP-glucuronic acid (UDP-GlcA), which is a key step in cepacian biosynthesis. Here, we report the structure of BceC, determined at 1.75-Å resolution. Mutagenic studies were performed on the active sites of UGDs, and together with the crystallographic structures, they elucidate the molecular mechanism of this family of sugar nucleotide-modifying enzymes. Superposition with the structures of human and other bacterial UGDs showed an active site with high structural homology. This family contains a strictly conserved tyrosine residue (Y10 in BceC; shown in italics) within the glycine-rich motif (GXGYXG) of its N-terminal Rossmann-like domain. We constructed several BceC Y10 mutants, revealing only residual dehydrogenase activity and thus highlighting the importance of this conserved residue in the catalytic activity of BceC. Based on the literature of the UGD/GMD nucleotide sugar 6-dehydrogenase family and the kinetic and structural data we obtained for BceC, we determined Y10 as a key catalytic residue in a UGD rate-determining step, the final hydrolysis of the enzymatic thioester intermediate.
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Skultety L, Hajduch M, Flores-Ramirez G, Miernyk JA, Ciampor F, Toman R, Sekeyova Z. Proteomic comparison of virulent phase I and avirulent phase II of Coxiella burnetii, the causative agent of Q fever. J Proteomics 2011; 74:1974-84. [PMID: 21616182 DOI: 10.1016/j.jprot.2011.05.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 04/20/2011] [Accepted: 05/09/2011] [Indexed: 01/06/2023]
Abstract
Coxiella burnetii, a category B biological warfare agent, causes multiple outbreaks of the zoonotic disease Q fever world-wide, each year. The virulent phase I and avirulent phase II variants of the Nine Mile RSA 493 and 439 strains of C. burnetii were propagated in embryonated hen eggs and then purified by centrifugation through Renografin gradients. Total protein fractions were isolated from each phase and subjected to analysis by one-dimensional electrophoresis plus tandem mass spectrometry. A total of 235 and 215 non-redundant proteins were unambiguously identified from the phase I and II cells, respectively. Many of these proteins had not been previously reported in proteomic studies of C. burnetii. The newly identified proteins should provide additional insight into the pathogenesis of Q fever. Several of the identified proteins are involved in the biosynthesis and metabolism of components of the extracellular matrix. Forty-four of the proteins have been annotated as having distinct roles in the pathogenesis or survival of C. burnetii within the harsh phagolysosomal environment. We propose that nine enzymes specifically involved with lipopolysaccharide biosynthesis and metabolism, and that are distinctively present in phase I cells, are virulence-associated proteins.
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Affiliation(s)
- Ludovit Skultety
- Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia.
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20
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Chen YY, Ko TP, Lin CH, Chen WH, Wang AHJ. Conformational change upon product binding to Klebsiella pneumoniae UDP-glucose dehydrogenase: a possible inhibition mechanism for the key enzyme in polymyxin resistance. J Struct Biol 2011; 175:300-10. [PMID: 21536136 DOI: 10.1016/j.jsb.2011.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Revised: 03/22/2011] [Accepted: 04/14/2011] [Indexed: 10/18/2022]
Abstract
Cationic modification of lipid A with 4-amino-4-deoxy-L-arabinopyranose (L-Ara4N) allows the pathogen Klebsiella pneumoniae to resist the antibiotic polymyxin and other cationic antimicrobial peptides. UDP-glucose dehydrogenase (Ugd) catalyzes the NAD⁺-dependent twofold oxidation of UDP-glucose (UPG) to produce UDP-glucuronic acid (UGA), a requisite precursor in the biosynthesis of L-Ara4N and bacterial exopolysaccharides. Here we report five crystal structures of K. pneumoniae Ugd (KpUgd) in its apo form, in complex with UPG, UPG/NADH, two UGA molecules, and finally with a C-terminal His₆-tag. The UGA-complex structure differs from the others by a 14° rotation of the N-terminal domain toward the C-terminal domain, and represents a closed enzyme conformation. It also reveals that the second UGA molecule binds to a pre-existing positively charged surface patch away from the active site. The enzyme is thus inactivated by moving the catalytically important residues C253, K256 and D257 from their original positions. Kinetic data also suggest that KpUgd has multiple binding sites for UPG, and that UGA is a competitive inhibitor. The conformational changes triggered by UGA binding to the allosteric site can be exploited in designing potent inhibitors.
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Affiliation(s)
- Ying-Yin Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
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Loutet SA, Mussen LE, Flannagan RS, Valvano MA. A two-tier model of polymyxin B resistance in Burkholderia cenocepacia. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:278-285. [PMID: 23761261 DOI: 10.1111/j.1758-2229.2010.00222.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Burkholderia cenocepacia is an environmental bacterium causing serious human opportunistic infections and is extremely resistant to multiple antibiotics including antimicrobial peptides, such as polymyxin B (PmB). Extreme antibiotic resistance is attributed to outer membrane impermeability ('intrinsic' resistance). Previous work showed that production of full-length lipopolysaccharide (LPS) prevents surface binding of PmB. We hypothesized that two tiers of resistance mechanisms rendering different thresholds of PmB resistance exist in B. cenocepacia. To test this notion, candidate genes were mutated in two isogenic strains expressing full-length LPS or truncated LPS devoid of heptose ('heptoseless LPS') respectively. We uncovered various proteins required for PmB resistance only in the strain with heptoseless LPS. These proteins are not involved in preventing PmB binding to whole cells or permeabilization of the outer membrane. Our results support a two-tier model of PmB resistance in B. cenocepacia. One tier sets a very high threshold mediated by the LPS and the outer membrane permeability barrier. The second tier sets a lower threshold that may play a role in PmB resistance only when outer membrane permeability is compromised. This model may be of general applicability to understanding the high antimicrobial peptide resistance of environmental opportunistic pathogens.
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Affiliation(s)
- Slade A Loutet
- Centre for Human Immunology, Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada N6A 5C1 Department of Medicine, University of Western Ontario, London, ON, Canada N6A 5C1
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22
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UDP-glucose dehydrogenase: structure and function of a potential drug target. Biochem Soc Trans 2011; 38:1378-85. [PMID: 20863317 DOI: 10.1042/bst0381378] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Biosynthesis of the glycosaminoglycan precursor UDP-α-D-glucuronic acid occurs through a 2-fold oxidation of UDP-α-D-glucose that is catalysed by UGDH (UDP-α-D-glucose 6-dehydrogenase). Structure-function relationships for UGDH and proposals for the enzymatic reaction mechanism are reviewed in the present paper, and structure-based sequence comparison is used for subclassification of UGDH family members. The eukaryotic group of enzymes (UGDH-II) utilize an extended C-terminal domain for the formation of complex homohexameric assemblies. The comparably simpler oligomerization behaviour of the prokaryotic group of enzymes (UGDH-I), in which dimeric forms prevail, is traced back to the lack of relevant intersubunit contacts and trimmings within the C-terminal region. The active site of UGDH contains a highly conserved cysteine residue, which plays a key role in covalent catalysis. Elevated glycosaminoglycan formation is implicated in a variety of human diseases, including the progression of tumours. The inhibition of synthesis of UDP-α-D-glucuronic acid using UGDH antagonists might therefore be a useful strategy for therapy.
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Kiley TB, Stanley-Wall NR. Post-translational control of Bacillus subtilis biofilm formation mediated by tyrosine phosphorylation. Mol Microbiol 2010; 78:947-63. [DOI: 10.1111/j.1365-2958.2010.07382.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wang TP, Pan YR, Fu CY, Chang HY. Down-regulation of UDP-glucose dehydrogenase affects glycosaminoglycans synthesis and motility in HCT-8 colorectal carcinoma cells. Exp Cell Res 2010; 316:2893-902. [PMID: 20691680 DOI: 10.1016/j.yexcr.2010.07.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 06/23/2010] [Accepted: 07/24/2010] [Indexed: 01/13/2023]
Abstract
UDP-glucose dehydrogenase (UGDH) catalyzes oxidation of UDP-glucose to yield UDP-glucuronic acid, a precursor of hyaluronic acid (HA) and other glycosaminoglycans (GAGs) in extracellular matrix. Although association of extracellular matrix with cell proliferation and migration has been well documented, the importance of UGDH in these behaviors is not clear. Using UGDH-specific small interference RNA to treat HCT-8 colorectal carcinoma cells, a decrease in both mRNA and protein levels of UGDH, as well as the cellular UDP-glucuronic acid and GAG production was observed. Treatment of HCT-8 cells with either UGDH-specific siRNA or HA synthesis inhibitor 4-methylumbelliferone effectively delayed cell aggregation into multicellular spheroids and impaired cell motility in both three-dimensional collagen gel and transwell migration assays. The reduction in cell aggregation and migration rates could be restored by addition of exogenous HA. These results indicate that UGDH can regulate cell motility through the production of GAG. The enzyme may be a potential target for therapeutic intervention of colorectal cancers.
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Affiliation(s)
- Tsung-Pao Wang
- Institute of Molecular Medicine, National Tsing Hua University, Hsin Chu, Taiwan, Republic of China
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Characterization of UDP-glucose dehydrogenase and UDP-glucose pyrophosphorylase mutants of Proteus mirabilis: defectiveness in polymyxin B resistance, swarming, and virulence. Antimicrob Agents Chemother 2010; 54:2000-9. [PMID: 20160049 DOI: 10.1128/aac.01384-09] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Proteus mirabilis is known to be highly resistant to the action of polymyxin B (PB). However, the mechanism underlying PB resistance is not clear. In this study, we used Tn5 transposon mutagenesis to identify genes that may affect PB resistance in P. mirabilis. Two genes, ugd and galU, which may encode UDP-glucose dehydrogenase (Ugd) and UDP-glucose pyrophosphorylase (GalU), respectively, were identified. Knockout mutants of ugd and galU were found to be extremely sensitive to PB, presumably because of alterations in lipopolysaccharide (LPS) structure and cell surface architecture in these mutants. These mutants were defective in swarming, expressed lower levels of virulence factor hemolysin, and had lower cell invasion ability. Complementation of the ugd or galU mutant with the full-length ugd or galU gene, respectively, led to the restoration of wild-type phenotypic traits. Interestingly, we found that the expression of Ugd and GalU was induced by PB through RppA, a putative response regulator of the bacterial two-component system that we identified previously. Mutation in either ugd or galU led to activation of RpoE, an extracytoplasmic function sigma factor that has been shown to be activated by protein misfolding and alterations in cell surface structure in other bacteria. Activation of RpoE or RpoE overexpression was found to cause inhibition of FlhDC and hemolysin expression. To our knowledge, this is the first report describing the roles and regulation of Ugd and GalU in P. mirabilis.
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King JD, Kocíncová D, Westman EL, Lam JS. Review: Lipopolysaccharide biosynthesis in Pseudomonas aeruginosa. Innate Immun 2009; 15:261-312. [PMID: 19710102 DOI: 10.1177/1753425909106436] [Citation(s) in RCA: 225] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas aeruginosa causes serious nosocomial infections, and an important virulence factor produced by this organism is lipopolysaccharide (LPS). This review summarizes knowledge about biosynthesis of all three structural domains of LPS - lipid A, core oligosaccharide, and O polysaccharides. In addition, based on similarities with other bacterial species, this review proposes new hypothetical pathways for unstudied steps in the biosynthesis of P. aeruginosa LPS. Lipid A biosynthesis is discussed in relation to Escherichia coli and Salmonella, and the biosyntheses of core sugar precursors and core oligosaccharide are summarised. Pseudomonas aeruginosa attaches a Common Polysaccharide Antigen and O-Specific Antigen polysaccharides to lipid A-core. Both forms of O polysaccharide are discussed with respect to their independent synthesis mechanisms. Recent advances in understanding O-polysaccharide biosynthesis since the last major review on this subject, published nearly a decade ago, are highlighted. Since P. aeruginosa O polysaccharides contain unusual sugars, sugar-nucleotide biosynthesis pathways are reviewed in detail. Knowledge derived from detailed studies in the O5, O6 and O11 serotypes is applied to predict biosynthesis pathways of sugars in poorly-studied serotypes, especially O1, O4, and O13/O14. Although further work is required, a full understanding of LPS biosynthesis in P. aeruginosa is almost within reach.
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Affiliation(s)
- Jerry D King
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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Contributions of two UDP-glucose dehydrogenases to viability and polymyxin B resistance of Burkholderia cenocepacia. Microbiology (Reading) 2009; 155:2029-2039. [DOI: 10.1099/mic.0.027607-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Burkholderia cenocepacia is highly resistant to antimicrobial peptides and we hypothesized that the conversion of UDP-glucose to UDP-glucuronic acid, a reaction catalysed by the enzyme UDP-glucose dehydrogenase (Ugd) would be important for this resistance. The genome of B. cenocepacia contains three predicted ugd genes: ugdBCAL2946
, ugdBCAM0855
and ugdBCAM2034
, all of which were individually inactivated. Only inactivation of ugdBCAL2946
resulted in increased sensitivity to polymyxin B and this sensitivity could be overcome when either ugdBCAL2946
or ugdBCAM0855
but not ugdBCAM2034
was expressed from plasmids. The growth of a conditional ugdBCAL2946
mutant, created in the ΔugdBCAM0855
background, was significantly impaired under non-permissive conditions. Growth could be rescued by either ugdBCAL2946
or ugdBCAM0855
expressed in trans, but not by ugdBCAM2034
. Biochemical analysis of the purified, recombinant forms of UgdBCAL2946 and UgdBCAM0855 revealed that they are soluble homodimers with similar in vitro Ugd activity and comparable kinetic constants for their substrates UDP-glucose and NAD+. Purified UgdBCAM2034 showed no in vitro Ugd activity. Real-time PCR analysis showed that the expression of ugdBCAL2946
was 5.4- and 135-fold greater than that of ugdBCAM0855
and ugdBCAM2034
, respectively. Together, these data indicate that the combined activity of UgdBCAL2946 and UgdBCAM0855 is essential for the survival of B. cenocepacia but only the most highly expressed ugd gene, ugdBCAL2946
, is required for polymyxin B resistance.
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Identification of amino acid residues important for the phosphomannose isomerase activity of PslB in Pseudomonas aeruginosa PAO1. FEBS Lett 2008; 582:3479-83. [PMID: 18801364 DOI: 10.1016/j.febslet.2008.09.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 09/09/2008] [Accepted: 09/09/2008] [Indexed: 11/20/2022]
Abstract
Phosphomannose isomerase (PMI) plays a pivotal role in biosynthesis of GDP-mannose, an important precursor of many polysaccharides. We demonstrate in this study that Pseudomonas aeruginosa pslB encodes a protein with GDP-mannose pyrophosphorylase/PMI dual activities. The PMI activity is Co2+-dependent and could be inhibited by GDP-mannose in a competitive manner. Furthermore, the activity could be inactivated by 2,3-butanedione suggesting the presence of a catalytic Arg residue. Site-specific mutations at R373, R472, R479, E410, H411, N433 and E458 increase the KM approximately 8-20-fold. The PMI activity of PslB was completely diminished with a R408K or R408A, reflecting the importance of this residue in catalysis. Overall, these results provide a basis for understanding the catalytic mechanism of PMI.
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Granja AT, Popescu A, Marques AR, Sá-Correia I, Fialho AM. Biochemical characterization and phylogenetic analysis of UDP-glucose dehydrogenase from the gellan gum producer Sphingomonas elodea ATCC 31461. Appl Microbiol Biotechnol 2007; 76:1319-27. [PMID: 17668199 DOI: 10.1007/s00253-007-1112-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Revised: 07/03/2007] [Accepted: 07/04/2007] [Indexed: 10/23/2022]
Abstract
Sphingomonas elodea ATCC 31461 synthesizes in high yield the exopolysaccharide gellan, which is a water-soluble gelling agent with many applications. In this study, we describe the cloning and sequence analysis of the ugdG gene, encoding a UDP-glucose dehydrogenase (47.2 kDa; UDPG-DH; EC 1.1.1.22), required for the synthesis of the gellan gum precursor UDP-glucuronic acid. UgdG protein shows homology to members of the UDP-glucose/GDP-mannose dehydrogenase superfamily. The Neighbor-Joining method was used to determine phylogenetic relationships among prokaryotic and eukaryotic UDPG-DHs. UgdG from S. elodea and UDPG-DHs from Novosphingobium, Zymomonas, Agrobacterium, and Caulobacter species form a divergent phylogenetic group with a close evolutionary relationship with eukaryotic UDPG-DHs. The ugdG gene was recombinantly expressed in Escherichia coli with and N-terminal 6-His tag and purified for biochemical characterization. The enzyme has an optimum temperature and pH of 37 degrees C and 8.7, respectively. The estimated apparent K(m) values for UDP-glucose and NAD(+) were 0.87 and 0.4 mM, respectively. DNA sequencing of chromosomal regions adjacent to ugdG gene and sequence similarity studies suggests that this gene maps together with others presumably involved in the biosynthesis of S. elodea cell wall polysaccharides.
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Affiliation(s)
- Ana Teresa Granja
- IBB - Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
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