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Mechanistic basis for understanding the dual activities of the bifunctional Azotobacter vinelandii mannuronan C-5 epimerase and alginate lyase AlgE7. Appl Environ Microbiol 2021; 88:e0183621. [PMID: 34878812 PMCID: PMC8824271 DOI: 10.1128/aem.01836-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The structure and functional properties of alginates are dictated by the monomer composition and molecular weight distribution. Mannuronan C-5-epimerases determine the monomer composition by catalyzing the epimerization of β-d-mannuronic acid (M) residues into α-l-guluronic acid (G) residues. The molecular weight is affected by alginate lyases, which catalyze a β-elimination mechanism that cleaves alginate chains. The reaction mechanisms for the epimerization and lyase reactions are similar, and some enzymes can perform both reactions. These dualistic enzymes share high sequence identity with mannuronan C-5-epimerases without lyase activity. The mechanism behind their activity and the amino acid residues responsible for it are still unknown. We investigate mechanistic determinants involved in the bifunctional epimerase and lyase activity of AlgE7 from Azotobacter vinelandii. Based on sequence analyses, a range of AlgE7 variants were constructed and subjected to activity assays and product characterization by nuclear magnetic resonance (NMR) spectroscopy. Our results show that calcium promotes lyase activity, whereas NaCl reduces the lyase activity of AlgE7. By using defined polymannuronan (polyM) and polyalternating alginate (polyMG) substrates, the preferred cleavage sites of AlgE7 were found to be M|XM and G|XM, where X can be either M or G. From the study of AlgE7 mutants, R148 was identified as an important residue for the lyase activity, and the point mutant R148G resulted in an enzyme with only epimerase activity. Based on the results obtained in the present study, we suggest a unified catalytic reaction mechanism for both epimerase and lyase activities where H154 functions as the catalytic base and Y149 functions as the catalytic acid. IMPORTANCE Postharvest valorization and upgrading of algal constituents are promising strategies in the development of a sustainable bioeconomy based on algal biomass. In this respect, alginate epimerases and lyases are valuable enzymes for tailoring the functional properties of alginate, a polysaccharide extracted from brown seaweed with numerous applications in food, medicine, and material industries. By providing a better understanding of the catalytic mechanism and of how the two enzyme actions can be altered by changes in reaction conditions, this study opens further applications of bacterial epimerases and lyases in the enzymatic tailoring of alginate polymers.
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Gaardløs M, Samsonov SA, Sletmoen M, Hjørnevik M, Sætrom GI, Tøndervik A, Aachmann FL. Insights into the roles of charged residues in substrate binding and mode of action of mannuronan C-5 epimerase AlgE4. Glycobiology 2021; 31:1616-1635. [PMID: 33822050 DOI: 10.1093/glycob/cwab025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/10/2021] [Indexed: 01/18/2023] Open
Abstract
Mannuronan C-5 epimerases catalyse the epimerization of monomer residues in the polysaccharide alginate, changing the physical properties of the biopolymer. The enzymes are utilized to tailor alginate to numerous biological functions by alginate-producing organisms. The underlying molecular mechanisms that control the processive movement of the epimerase along the substrate chain is still elusive. To study this, we have used an interdisciplinary approach combining molecular dynamics simulations with experimental methods from mutant studies of AlgE4, where initial epimerase activity and product formation were addressed with NMR spectroscopy, and characteristics of enzyme-substrate interactions were obtained with isothermal titration calorimetry and optical tweezers. Positive charges lining the substrate-binding groove of AlgE4 appear to control the initial binding of poly-mannuronate, and binding also seems to be mediated by both electrostatic and hydrophobic interactions. After the catalytic reaction, negatively charged enzyme residues might facilitate dissociation of alginate from the positive residues, working like electrostatic switches, allowing the substrate to translocate in the binding groove. Molecular simulations show translocation increments of two monosaccharide units before the next productive binding event resulting in MG-block formation, with the epimerase moving with its N-terminus towards the reducing end of the alginate chain. Our results indicate that the charge pair R343-D345 might be directly involved in conformational changes of a loop that can be important for binding and dissociation. The computational and experimental approaches used in this study complement each other, allowing for a better understanding of individual residues' roles in binding and movement along the alginate chains.
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Affiliation(s)
- Margrethe Gaardløs
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
| | | | - Marit Sletmoen
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
| | - Maya Hjørnevik
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
| | - Gerd Inger Sætrom
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
| | - Anne Tøndervik
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Richard Birkelands veg 3 B, N-7491 Trondheim, Norway
| | - Finn Lillelund Aachmann
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
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Impacts of biofilm on monochloramine decay in storm sewer systems: Direct reactions or AOB cometabolism. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Huang L, Li Z, Lou Y, Cao F, Zhang D, Li X. Recent Advances in Scanning Electrochemical Microscopy for Biological Applications. MATERIALS (BASEL, SWITZERLAND) 2018; 11:E1389. [PMID: 30096895 PMCID: PMC6119995 DOI: 10.3390/ma11081389] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/24/2018] [Accepted: 07/28/2018] [Indexed: 12/17/2022]
Abstract
Scanning electrochemical microscopy (SECM) is a chemical microscopy technique with high spatial resolution for imaging sample topography and mapping specific chemical species in liquid environments. With the development of smaller, more sensitive ultramicroelectrodes (UMEs) and more precise computer-controlled measurements, SECM has been widely used to study biological systems over the past three decades. Recent methodological breakthroughs have popularized SECM as a tool for investigating molecular-level chemical reactions. The most common applications include monitoring and analyzing the biological processes associated with enzymatic activity and DNA, and the physiological activity of living cells and other microorganisms. The present article first introduces the basic principles of SECM, followed by an updated review of the applications of SECM in biological studies on enzymes, DNA, proteins, and living cells. Particularly, the potential of SECM for investigating bacterial and biofilm activities is discussed.
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Affiliation(s)
- Luyao Huang
- Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China.
| | - Ziyu Li
- Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China.
| | - Yuntian Lou
- Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China.
| | - Fahe Cao
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China.
| | - Dawei Zhang
- Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China.
| | - Xiaogang Li
- Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China.
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Seghal Kiran G, Ramasamy P, Sekar S, Ramu M, Hassan S, Ninawe A, Selvin J. Synthetic biology approaches: Towards sustainable exploitation of marine bioactive molecules. Int J Biol Macromol 2018; 112:1278-1288. [DOI: 10.1016/j.ijbiomac.2018.01.149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 01/18/2018] [Accepted: 01/21/2018] [Indexed: 12/18/2022]
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Maestre JP, Wahman DG, Speitel GE. Monochloramine Cometabolism by Mixed-Culture Nitrifiers under Drinking Water Conditions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:6240-6248. [PMID: 27196729 DOI: 10.1021/acs.est.5b05641] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Chloramines are the second most used secondary disinfectant by United States water utilities. However, chloramination may promote nitrifying bacteria. Recently, monochloramine cometabolism by the pure culture ammonia-oxidizing bacteria, Nitrosomonas europaea, was shown to increase monochloramine demand. The current research investigated monochloramine cometabolism by nitrifying mixed cultures grown under more relevant drinking water conditions and harvested from sand-packed reactors before conducting suspended growth batch kinetic experiments. Four types of batch kinetic experiments were conducted: (1) positive controls to estimate ammonia kinetic parameters, (2) negative controls to account for biomass reactivity, (3) utilization associated product (UAP) controls to account for UAP reactivity, and (4) cometabolism experiments to estimate cometabolism kinetic parameters. Kinetic parameters were estimated in AQUASIM with a simultaneous fit to the experimental data. Cometabolism kinetics were best described by a first-order model. Monochloramine cometabolism kinetics were similar to those of ammonia metabolism, and monochloramine cometabolism accounted for 30% of the observed monochloramine loss. These results demonstrated that monochloramine cometabolism occurred in mixed cultures similar to those found in drinking water distribution systems; therefore, monochloramine cometabolism may be a significant contribution to monochloramine loss during nitrification episodes in drinking water distribution systems.
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Affiliation(s)
- Juan P Maestre
- University of Texas at Austin , Department of Civil, Architectural and Environmental Engineering, 301 East Dean Keeton Street, Stop C2100, Austin, Texas 78712, United States
| | - David G Wahman
- United States Environmental Protection Agency , Office of Research and Development, Cincinnati, Ohio 45268, United States
| | - Gerald E Speitel
- University of Texas at Austin , Department of Civil, Architectural and Environmental Engineering, 301 East Dean Keeton Street, Stop C2100, Austin, Texas 78712, United States
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Ding X, Behbahani M, Gruden C, Seo Y. Characterization and evaluation of phosphate microsensors to monitor internal phosphorus loading in Lake Erie sediments. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2015; 160:193-200. [PMID: 26156193 DOI: 10.1016/j.jenvman.2015.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 06/01/2015] [Accepted: 06/05/2015] [Indexed: 06/04/2023]
Abstract
Monitoring phosphate concentration is very important to prevent and control eutrophication in natural waters. In this study, cobalt-based microsensors were modified, characterized, and tested to monitor internal soluble phosphorous (SRP) loading in lakes with improved detection limits. The effectiveness of surface modification on the performance of a cobalt-based microelectrode was fully examined by determining detection limit, response time, selectivity, interference with ions (sulfate, nitrate, and nitrite) and dissolved oxygen (DO). To assess their performance, phosphate sensors were applied to sediment samples collected from Lake Erie. SRP loading from sediments was determined under different DO conditions. After increasing the phosphate sensing area and modifying the surface, phosphate microsensors showed an increased detection limit of up to 10(-8) M concentration of phosphate ion. The phosphate microsensor also showed its ability to measure sediment SRP profiling without disturbing sediment structure, and diffusion coefficients of phosphate in sediment could be determined under both oxic and anoxic conditions. Modified phosphate sensors showed improved sensitivity and could be applied to both water and sediment samples with high spatial resolution; however, signal interferences (especially with oxygen) required consideration during sample analysis. Overall, obtained results showed that phosphate microsensors can be an effective tool for measurement of phosphate in lake water and sediment samples for SRP monitoring.
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Affiliation(s)
- Xue Ding
- Department of Civil Engineering, University of Toledo, Toledo, OH, USA
| | - Mohsen Behbahani
- Department of Civil Engineering, University of Toledo, Toledo, OH, USA
| | - Cyndee Gruden
- Department of Civil Engineering, University of Toledo, Toledo, OH, USA
| | - Youngwoo Seo
- Department of Civil Engineering, University of Toledo, Toledo, OH, USA; Department of Chemical and Environmental Engineering, University of Toledo, Toledo, OH, USA.
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Jang A, Szabo J, Hosni AA, Coughlin M, Bishop PL. Measurement of chlorine dioxide penetration in dairy process pipe biofilms during disinfection. Appl Microbiol Biotechnol 2006; 72:368-76. [PMID: 16397769 DOI: 10.1007/s00253-005-0274-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Revised: 11/22/2005] [Accepted: 11/27/2005] [Indexed: 10/25/2022]
Abstract
Biofilms are considered a significant health risk in the food and dairy industries because they can harbor pathogens, and direct contact with them can lead to food contamination. Biofilm control is often performed using strong oxidizing agents like chlorine and peracetic acid. Although chlorine dioxide (ClO2) is being used increasingly to control microbiological growth in a number of different industries, not much is known about disinfection in biofilms using chlorine dioxide. In this study, a microelectrode originally made for chlorine detection was modified to measure the profiles of chlorine dioxide in biofilm as a function of depth into the biofilm. In addition, discarded microelectrodes proved useful for in situ direct measurement of biofilm thicknesses. The chlorine dioxide microelectrode had a linear response when calibrated up to a ClO2 concentration of 0.4 mM. ClO2 profiles showed depletion of disinfectant at 100 microm in the biofilm depth, indicating that ClO2 may not reach bacteria in a biofilm thicker than this using a 25 mg/l solution.
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Affiliation(s)
- Am Jang
- Department of Civil and Environmental Engineering, University of Cincinnati, Cincinnati, OH 45221-0071, USA
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Junter GA, Coquet L, Vilain S, Jouenne T. Immobilized-cell physiology: current data and the potentialities of proteomics. Enzyme Microb Technol 2002. [DOI: 10.1016/s0141-0229(02)00073-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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