1
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Nikolaev YA, Loiko NG, Demkina EV, Atroshchik EA, Konstantinov AI, Perminova IV, El’-Registan GI. Functional Activity of Humic Substances in Survival Prolongation of Populations of Hydrocarbon-Oxidizing Bacteria Acinetobacter junii. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720010105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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2
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Escalante DE, Aksan A. Role of Water Hydrogen Bonding on Transport of Small Molecules inside Hydrophobic Channels. J Phys Chem B 2019; 123:6673-6685. [PMID: 31310534 DOI: 10.1021/acs.jpcb.9b03060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We conducted a systematic analysis of water networking inside smooth hyperboloid hydrophobic structures (cylindrical, barrel, and hourglass shapes) to elucidate the role of water hydrogen bonding on the transport of small hydrophobic molecules (ligands). Through a series of molecular dynamics simulations, we established that a hydrogen-bonded network forming along the centerline resulted in a water exclusion zone adjacent to the walls. The size of the exclusion zone is a function of the geometry and the nonbonded interaction strength, defining the effective hydrophobicity of the structure. Exclusion of water molecules from this zone results in lower apparent viscosity, leading to acceleration of ligand transport up to 7 times faster than that measured in the bulk. Transport of ligands into and out of the hydrophobic structures was shown to be controlled by a single water molecule that capped the narrow regions in the structure. This mechanism provides physical insights into the behavior and role of water in the bottleneck regions of hydrophobic enzyme channels. These findings were then used in a sister publication [ Escalante , D. E. , Comput. Struct. Biotechnol. J. 2019 17 757 760 ] to develop a model that can accurately predict the transport of ligands along nanochannels of broad-substrate specificity enzymes.
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Affiliation(s)
- Diego E Escalante
- Department of Mechanical Engineering , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Alptekin Aksan
- Department of Mechanical Engineering , University of Minnesota , Minneapolis , Minnesota 55455 , United States.,BioTechnology Institute , University of Minnesota , St. Paul , Minnesota 55108 , United States
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3
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Escalante DE, Aksan A. Prediction of Ligand Transport along Hydrophobic Enzyme Nanochannels. Comput Struct Biotechnol J 2019; 17:757-760. [PMID: 31303980 PMCID: PMC6606821 DOI: 10.1016/j.csbj.2019.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/08/2019] [Accepted: 06/01/2019] [Indexed: 12/22/2022] Open
Abstract
Buried active sites of enzymes are connected to the bulk solvent through a network of hydrophobic channels. We developed a discretized model that can accurately predict ligand transport along hydrophobic channels up to six orders of magnitude faster than any other existing method. The non-dimensional nature of the model makes it applicable to any hydrophobic channel/ligand combination.
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Affiliation(s)
- Diego E. Escalante
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, United States
| | - Alptekin Aksan
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, United States
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, United States
- Corresponding author at: Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, United States.
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4
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Hochstein R, Zhang Q, Sadowsky MJ, Forbes VE. The deposit feeder Capitella teleta has a unique and relatively complex microbiome likely supporting its ability to degrade pollutants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 670:547-554. [PMID: 30909032 DOI: 10.1016/j.scitotenv.2019.03.255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/12/2019] [Accepted: 03/17/2019] [Indexed: 06/09/2023]
Abstract
Capitella teleta is a sediment-dwelling marine polychaete that is often found in high densities in association with organic matter and pollutants. While C. teleta has been reported to transform a variety of aromatic hydrocarbons, the mechanisms by which degradation occurs are unknown. Moreover, there is continuing debate on the role of host and microbiota in degradation activity. The aims of this study were to characterize the gut microbiome of C. teleta and to identify microbiota that could potentially play a role in degradation of organic matter and aromatic hydrocarbons. Sequencing analysis of the 16S rRNA genes from the intestinal tracts of adult worms revealed a unique microbiome that was distinct from that of the worm's sediment food source and fecal pellets. About 66% of the 775 identified OTUs from the C. teleta gut microbiome were found to be unique to the worm and displayed high inter-individual variability. The gut microbiome was dominated by members of the genera Arcobacter, Pseudoalteromonas, Methylobacterium, and Propionibacterium. Functional analyses of microbiota revealed that hydrocarbon treatment led to a proliferation of gene classes involved in chemoheterotrophy and aromatic compound degradation. Of the 18 most abundant taxa identified, 50% were members of genera containing hydrocarbon (PAH)-degrading members, including Acinetobacter, Thalassotalea, and Achromobacter. Data obtained in this study will be useful to understand the biology of this marine polychaete and to elucidate the role that gut bacteria play in worm catabolism and the transformation of sediment organic pollutants.
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Affiliation(s)
- Rebecca Hochstein
- Department of Ecology, Evolution, and Behavior, University of Minnesota, United States of America; BioTechnology Institute, University of Minnesota, United States of America
| | - Qian Zhang
- BioTechnology Institute, University of Minnesota, United States of America
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, United States of America; Department of Soil, Water and Climate, University of Minnesota, United States of America; Department of Plant and Microbial Biology, University of Minnesota, United States of America.
| | - Valery E Forbes
- Department of Ecology, Evolution, and Behavior, University of Minnesota, United States of America.
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5
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Schwab M, Bergonzi C, Sakkos J, Staley C, Zhang Q, Sadowsky MJ, Aksan A, Elias M. Signal Disruption Leads to Changes in Bacterial Community Population. Front Microbiol 2019; 10:611. [PMID: 30984139 PMCID: PMC6449428 DOI: 10.3389/fmicb.2019.00611] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/11/2019] [Indexed: 01/02/2023] Open
Abstract
The disruption of bacterial signaling (quorum quenching) has been proven to be an innovative approach to influence the behavior of bacteria. In particular, lactonase enzymes that are capable of hydrolyzing the N-acyl homoserine lactone (AHL) molecules used by numerous bacteria, were reported to inhibit biofilm formation, including those of freshwater microbial communities. However, insights and tools are currently lacking to characterize, understand and explain the effects of signal disruption on complex microbial communities. Here, we produced silica capsules containing an engineered lactonase that exhibits quorum quenching activity. Capsules were used to design a filtration cartridge to selectively degrade AHLs from a recirculating bioreactor. The growth of a complex microbial community in the bioreactor, in the presence or absence of lactonase, was monitored over a 3-week period. Dynamic population analysis revealed that signal disruption using a quorum quenching lactonase can effectively reduce biofilm formation in the recirculating bioreactor system and that biofilm inhibition is concomitant to drastic changes in the composition, diversity and abundance of soil bacterial communities within these biofilms. Effects of the quorum quenching lactonase on the suspension community also affected the microbial composition, suggesting that effects of signal disruption are not limited to biofilm populations. This unexpected finding is evidence for the importance of signaling in the competition between bacteria within communities. This study provides foundational tools and data for the investigation of the importance of AHL-based signaling in the context of complex microbial communities.
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Affiliation(s)
- Michael Schwab
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Celine Bergonzi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Jonathan Sakkos
- Department of Mechanical Engineering, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Christopher Staley
- Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Department of Surgery, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Qian Zhang
- Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Department of Soil, Water, and Climate, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Michael J Sadowsky
- Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Department of Soil, Water, and Climate, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Alptekin Aksan
- Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Department of Mechanical Engineering, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Mikael Elias
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States
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6
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OleA Glu117 is key to condensation of two fatty-acyl coenzyme A substrates in long-chain olefin biosynthesis. Biochem J 2017; 474:3871-3886. [PMID: 29025976 DOI: 10.1042/bcj20170642] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/08/2017] [Accepted: 10/10/2017] [Indexed: 12/23/2022]
Abstract
In the interest of decreasing dependence on fossil fuels, microbial hydrocarbon biosynthesis pathways are being studied for renewable, tailored production of specialty chemicals and biofuels. One candidate is long-chain olefin biosynthesis, a widespread bacterial pathway that produces waxy hydrocarbons. Found in three- and four-gene clusters, oleABCD encodes the enzymes necessary to produce cis-olefins that differ by alkyl chain length, degree of unsaturation, and alkyl chain branching. The first enzyme in the pathway, OleA, catalyzes the Claisen condensation of two fatty acyl-coenzyme A (CoA) molecules to form a β-keto acid. In this report, the mechanistic role of Xanthomonas campestris OleA Glu117 is investigated through mutant enzymes. Crystal structures were determined for each mutant as well as their complex with the inhibitor cerulenin. Complemented by substrate modeling, these structures suggest that Glu117 aids in substrate positioning for productive carbon-carbon bond formation. Analysis of acyl-CoA substrate hydrolysis shows diminished activity in all mutants. When the active site lacks an acidic residue in the 117 position, OleA cannot form condensed product, demonstrating that Glu117 has a critical role upstream of the essential condensation reaction. Profiling of pH dependence shows that the apparent pKa for Glu117 is affected by mutagenesis. Taken together, we propose that Glu117 is the general base needed to prime condensation via deprotonation of the second, non-covalently bound substrate during turnover. This is the first example of a member of the thiolase superfamily of condensing enzymes to contain an active site base originating from the second monomer of the dimer.
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7
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Sakkos JK, Mutlu BR, Wackett LP, Aksan A. Adsorption and Biodegradation of Aromatic Chemicals by Bacteria Encapsulated in a Hydrophobic Silica Gel. ACS APPLIED MATERIALS & INTERFACES 2017; 9:26848-26858. [PMID: 28719174 DOI: 10.1021/acsami.7b06791] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
An adsorbent silica biogel material was developed via silica gel encapsulation of Pseudomonas sp. NCIB 9816-4, a bacterium that degrades a broad spectrum of aromatic pollutants. The adsorbent matrix was synthesized using silica precursors methyltrimethoxysilane and tetramethoxysilane to maximize the adsorption capacity of the matrix while maintaining a highly networked and porous microstructure. The encapsulated bacteria enhanced the removal rate and capacity of the matrix for an aromatic chemical mixture. Repeated use of the material over four cycles was conducted to demonstrate that the removal capacity could be maintained with combined adsorption and biodegradation. The silica biogel can thus be used extensively without the need for disposal, as a result of continuous biodegradation by the encapsulated bacteria. However, an inverse trend was observed with the ratio of biodegradation to adsorption as a function of log Kow, suggesting increasing mass-transport limitation for the most hydrophobic chemicals used (log Kow > 4).
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Affiliation(s)
| | | | - Lawrence P Wackett
- The BioTechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
| | - Alptekin Aksan
- The BioTechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
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8
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Fang Y, Zhang LS, Wang J, Zhou Y, Ye BC. Identification of the di-n-butyl phthalate-biodegrading strains and the biodegradation pathway in strain LMB-1. APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s000368381703005x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Escalante DE, Aukema KG, Wackett LP, Aksan A. Simulation of the Bottleneck Controlling Access into a Rieske Active Site: Predicting Substrates of Naphthalene 1,2-Dioxygenase. J Chem Inf Model 2017; 57:550-561. [PMID: 28170277 DOI: 10.1021/acs.jcim.6b00469] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Naphthalene 1,2-dioxygenase (NDO) has been computationally understudied despite the extensive experimental knowledge obtained for this enzyme, including numerous crystal structures and over 100 demonstrated substrates. In this study, we have developed a substrate prediction model that moves away from the traditional active-site-centric approach to include the energetics of substrate entry into the active site. By comparison with experimental data, the accuracy of the model for predicting substrate oxidation is 92%, with a positive predictive value of 93% and a negative predictive value of 98%. Also, the present analysis has revealed that the amino acid residues that provided the largest energetic barrier for compounds entering the active site are residues F224, L227, P234, and L235. In addition, F224 is proposed to play a role in controlling ligand entrance via π-π stacking stabilization as well as providing stabilization via T-shaped π-π interactions once the ligand has reached the active-site cavity. Overall, we present a method capable of being scaled to computationally discover thousands of substrates of NDO, and we present parameters to be used for expanding the prediction method to other members of the Rieske non-heme iron oxygenase family.
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Affiliation(s)
- Diego E Escalante
- Department of Mechanical Engineering, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Kelly G Aukema
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota , Minneapolis, Minnesota 55455, United States.,BioTechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
| | - Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota , Minneapolis, Minnesota 55455, United States.,BioTechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
| | - Alptekin Aksan
- Department of Mechanical Engineering, University of Minnesota , Minneapolis, Minnesota 55455, United States.,BioTechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
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10
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Aukema KG, Escalante DE, Maltby MM, Bera AK, Aksan A, Wackett LP. In Silico Identification of Bioremediation Potential: Carbamazepine and Other Recalcitrant Personal Care Products. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:880-888. [PMID: 27977154 DOI: 10.1021/acs.est.6b04345] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Emerging contaminants are principally personal care products not readily removed by conventional wastewater treatment and, with an increasing reliance on water recycling, become disseminated in drinking water supplies. Carbamazepine, a widely used neuroactive pharmaceutical, increasingly escapes wastewater treatment and is found in potable water. In this study, a mechanism is proposed by which carbamazepine resists biodegradation, and a previously unknown microbial biodegradation was predicted computationally. The prediction identified biphenyl dioxygenase from Paraburkholderia xenovorans LB400 as the best candidate enzyme for metabolizing carbamazepine. The rate of degradation described here is 40 times greater than the best reported rates. The metabolites cis-10,11-dihydroxy-10,11-dihydrocarbamazepine and cis-2,3-dihydroxy-2,3-dihydrocarbamazepine were demonstrated with the native organism and a recombinant host. The metabolites are considered nonharmful and mitigate the generation of carcinogenic acridine products known to form when advanced oxidation methods are used in water treatment. Other recalcitrant personal care products were subjected to prediction by the Pathway Prediction System and tested experimentally with P. xenovorans LB400. It was shown to biodegrade structurally diverse compounds. Predictions indicated hydrolase or oxygenase enzymes catalyzed the initial reactions. This study highlights the potential for using the growing body of enzyme-structural and genomic information with computational methods to rapidly identify enzymes and microorganisms that biodegrade emerging contaminants.
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Affiliation(s)
- Kelly G Aukema
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Diego E Escalante
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Meghan M Maltby
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Asim K Bera
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Alptekin Aksan
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
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11
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Identification of a novel oxygenase capable of regiospecific hydroxylation of d-limonene into (+)-trans-carveol. Tetrahedron 2016. [DOI: 10.1016/j.tet.2015.12.061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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12
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Mutlu BR, Sakkos JK, Yeom S, Wackett LP, Aksan A. Silica ecosystem for synergistic biotransformation. Sci Rep 2016; 6:27404. [PMID: 27264916 PMCID: PMC4893658 DOI: 10.1038/srep27404] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/18/2016] [Indexed: 01/07/2023] Open
Abstract
Synergistical bacterial species can perform more varied and complex transformations of chemical substances than either species alone, but this is rarely used commercially because of technical difficulties in maintaining mixed cultures. Typical problems with mixed cultures on scale are unrestrained growth of one bacterium, which leads to suboptimal population ratios, and lack of control over bacterial spatial distribution, which leads to inefficient substrate transport. To address these issues, we designed and produced a synthetic ecosystem by co-encapsulation in a silica gel matrix, which enabled precise control of the microbial populations and their microenvironment. As a case study, two greatly different microorganisms: Pseudomonas sp. NCIB 9816 and Synechococcus elongatus PCC 7942 were encapsulated. NCIB 9816 can aerobically biotransform over 100 aromatic hydrocarbons, a feat useful for synthesis of higher value commodity chemicals or environmental remediation. In our system, NCIB 9816 was used for biotransformation of naphthalene (a model substrate) into CO2 and the cyanobacterium PCC 7942 was used to provide the necessary oxygen for the biotransformation reactions via photosynthesis. A mathematical model was constructed to determine the critical cell density parameter to maximize oxygen production, and was then used to maximize the biotransformation rate of the system.
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Affiliation(s)
- Baris R Mutlu
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jonathan K Sakkos
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sujin Yeom
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.,BioTechnology Institute, University of Minnesota, St Paul, MN 55108, USA
| | - Alptekin Aksan
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, USA.,BioTechnology Institute, University of Minnesota, St Paul, MN 55108, USA
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13
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Kane AL, Al-Shayeb B, Holec PV, Rajan S, Le Mieux NE, Heinsch SC, Psarska S, Aukema KG, Sarkar CA, Nater EA, Gralnick JA. Toward Bioremediation of Methylmercury Using Silica Encapsulated Escherichia coli Harboring the mer Operon. PLoS One 2016; 11:e0147036. [PMID: 26761437 PMCID: PMC4712050 DOI: 10.1371/journal.pone.0147036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/28/2015] [Indexed: 11/18/2022] Open
Abstract
Mercury is a highly toxic heavy metal and the ability of the neurotoxin methylmercury to biomagnify in the food chain is a serious concern for both public and environmental health globally. Because thousands of tons of mercury are released into the environment each year, remediation strategies are urgently needed and prompted this study. To facilitate remediation of both organic and inorganic forms of mercury, Escherichia coli was engineered to harbor a subset of genes (merRTPAB) from the mercury resistance operon. Protein products of the mer operon enable transport of mercury into the cell, cleavage of organic C-Hg bonds, and subsequent reduction of ionic mercury to the less toxic elemental form, Hg(0). E. coli containing merRTPAB was then encapsulated in silica beads resulting in a biological-based filtration material. Performing encapsulation in aerated mineral oil yielded silica beads that were smooth, spherical, and similar in diameter. Following encapsulation, E. coli containing merRTPAB retained the ability to degrade methylmercury and performed similarly to non-encapsulated cells. Due to the versatility of both the engineered mercury resistant strain and silica bead technology, this study provides a strong foundation for use of the resulting biological-based filtration material for methylmercury remediation.
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Affiliation(s)
- Aunica L. Kane
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, United States of America
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, Minneapolis, Minnesota, United States of America
| | - Basem Al-Shayeb
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, United States of America
| | - Patrick V. Holec
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, United States of America
| | - Srijay Rajan
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, United States of America
| | - Nicholas E. Le Mieux
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, United States of America
| | - Stephen C. Heinsch
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, United States of America
| | - Sona Psarska
- Department of Soil, Water, and Climate, University of Minnesota-Twin Cities, St. Paul, Minnesota, United States of America
| | - Kelly G. Aukema
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, United States of America
| | - Casim A. Sarkar
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, United States of America
- Department of Biomedical Engineering, University of Minnesota-Twin Cities, Minneapolis, Minnesota, United States of America
| | - Edward A. Nater
- Department of Soil, Water, and Climate, University of Minnesota-Twin Cities, St. Paul, Minnesota, United States of America
| | - Jeffrey A. Gralnick
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, United States of America
- Department of Microbiology and Immunology, University of Minnesota-Twin Cities, Minneapolis, Minnesota, United States of America
- * E-mail:
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14
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Sakkos JK, Kieffer DP, Mutlu BR, Wackett LP, Aksan A. Engineering of a silica encapsulation platform for hydrocarbon degradation using Pseudomonas sp. NCIB 9816-4. Biotechnol Bioeng 2015; 113:513-21. [PMID: 26332745 DOI: 10.1002/bit.25821] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/13/2015] [Accepted: 08/23/2015] [Indexed: 11/07/2022]
Abstract
Industrial application of encapsulated bacteria for biodegradation of hydrocarbons in water requires mechanically stable materials. A silica gel encapsulation method was optimized for Pseudomonas sp. NCIB 9816-4, a bacterium that degrades more than 100 aromatic hydrocarbons. The design process focused on three aspects: (i) mechanical property enhancement; (ii) gel cytocompatibility; and (iii) reduction of the diffusion barrier in the gel. Mechanical testing indicated that the compressive strength at failure (σf ) and elastic modulus (E) changed linearly with the amount of silicon alkoxide used in the gel composition. Measurement of naphthalene biodegradation by encapsulated cells indicated that the gel maintained cytocompatibility at lower levels of alkoxide. However, significant loss in activity was observed due to methanol formation during hydrolysis at high alkoxide concentrations, as measured by FTIR spectroscopy. The silica gel with the highest amount of alkoxide (without toxicity from methanol) had a biodegradation rate of 285 ± 42 nmol/L-s, σf = 652 ± 88 kPa, and E = 15.8 ± 2.0 MPa. Biodegradation was sustained for 1 month before it dropped below 20% of the initial rate. In order to improve the diffusion through the gel, polyvinyl alcohol (PVA) was used as a porogen and resulted in a 48 ± 19% enhancement in biodegradation, but it impacted the mechanical properties negatively. This is the first report studying how the silica composition affects biodegradation of naphthalene by Pseudomonas sp. NCIB 9816-4 and establishes a foundation for future studies of aromatic hydrocarbon biodegradation for industrial application.
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Affiliation(s)
- Jonathan K Sakkos
- Department of Mechanical Engineering, University of Minnesota, 111 Church St SE, Minneapolis, Minnesota, 55455
| | - Daniel P Kieffer
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Baris R Mutlu
- Department of Mechanical Engineering, University of Minnesota, 111 Church St SE, Minneapolis, Minnesota, 55455
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota
| | - Lawrence P Wackett
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Alptekin Aksan
- Department of Mechanical Engineering, University of Minnesota, 111 Church St SE, Minneapolis, Minnesota, 55455.
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota.
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15
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Rivard BS, Rogers MS, Marell DJ, Neibergall MB, Chakrabarty S, Cramer CJ, Lipscomb JD. Rate-Determining Attack on Substrate Precedes Rieske Cluster Oxidation during Cis-Dihydroxylation by Benzoate Dioxygenase. Biochemistry 2015; 54:4652-64. [PMID: 26154836 DOI: 10.1021/acs.biochem.5b00573] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rieske dearomatizing dioxygenases utilize a Rieske iron-sulfur cluster and a mononuclear Fe(II) located 15 Å across a subunit boundary to catalyze O2-dependent formation of cis-dihydrodiol products from aromatic substrates. During catalysis, O2 binds to the Fe(II) while the substrate binds nearby. Single-turnover reactions have shown that one electron from each metal center is required for catalysis. This finding suggested that the reactive intermediate is Fe(III)-(H)peroxo or HO-Fe(V)═O formed by O-O bond scission. Surprisingly, several kinetic phases were observed during the single-turnover Rieske cluster oxidation. Here, the Rieske cluster oxidation and product formation steps of a single turnover of benzoate 1,2-dioxygenase are investigated using benzoate and three fluorinated analogues. It is shown that the rate constant for product formation correlates with the reciprocal relaxation time of only the fastest kinetic phase (RRT-1) for each substrate, suggesting that the slower phases are not mechanistically relevant. RRT-1 is strongly dependent on substrate type, suggesting a role for substrate in electron transfer from the Rieske cluster to the mononuclear iron site. This insight, together with the substrate and O2 concentration dependencies of RRT-1, indicates that a reactive species is formed after substrate and O2 binding but before electron transfer from the Rieske cluster. Computational studies show that RRT-1 is correlated with the electron density at the substrate carbon closest to the Fe(II), consistent with initial electrophilic attack by an Fe(III)-superoxo intermediate. The resulting Fe(III)-peroxo-aryl radical species would then readily accept an electron from the Rieske cluster to complete the cis-dihydroxylation reaction.
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Affiliation(s)
- Brent S Rivard
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Melanie S Rogers
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Daniel J Marell
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Matthew B Neibergall
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Sarmistha Chakrabarty
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christopher J Cramer
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D Lipscomb
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Aerobic biodegradation of organic compounds in hydraulic fracturing fluids. Biodegradation 2015; 26:271-87. [DOI: 10.1007/s10532-015-9733-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/19/2015] [Indexed: 10/23/2022]
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