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Teixeira RM, Sakamoto IK, Motteran F, Camargo FP, Varesche MBA. Removal of nonylphenol ethoxylate surfactant in batch reactors: emphasis on methanogenic potential and microbial community characterization under optimized conditions. ENVIRONMENTAL TECHNOLOGY 2024; 45:1343-1357. [PMID: 36352347 DOI: 10.1080/09593330.2022.2143287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
ABSTRACTNonylphenol ethoxylate (NPE) is an endocrine-disrupting chemical that has bioaccumulative, persistent and toxic characteristics in different environmental matrices and is difficult to remove in sewage treatment plants. In this study, the effects of the initial concentration of NPE (0.2 ± 0.03 - 3.0 ± 0.02 mg. L-1) and ethanol (73.9 ± 5.0-218.6 ± 10.6 mg. L-1) were investigated using factorial design. Assays were carried out in anaerobic batch reactors, using the Zinder basal medium, yeast extract (200 mg. L-1), vitamin solution and sodium bicarbonate (10% v/v). The optimal conditions were 218.56 mg.L-1 of ethanol and 1596.51 µg.L-1 of NPE, with 92% and 88% of NPE and organic matter removal, respectively, and methane yield (1689.8 ± 59.6 mmol) after 450 h of operation. In this condition, bacteria potentially involved in the degradation of this surfactant were identified in greater relative abundance, such as Acetoanaerobium (1.68%), Smithella (1.52%), Aminivibrio (0.91%), Petrimonas (0.57%) and Enterobacter (0.47%), as well as archaea Methanobacterium and Methanoregula, mainly involved in hydrogenotrophic pathway.
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Affiliation(s)
- Rômulo Mota Teixeira
- Department of Hydraulic Engineering and Sanitation, São Carlos School of Engineering (EESC), University of São Paulo (USP), São Paulo, Brazil
| | - Isabel Kimiko Sakamoto
- Department of Hydraulic Engineering and Sanitation, São Carlos School of Engineering (EESC), University of São Paulo (USP), São Paulo, Brazil
| | - Fabrício Motteran
- Department of Civil and Environmental Engineering, Federal University of Pernambuco, Recife, Brazil
| | - Franciele Pereira Camargo
- Department of Hydraulic Engineering and Sanitation, São Carlos School of Engineering (EESC), University of São Paulo (USP), São Paulo, Brazil
| | - Maria Bernadete Amâncio Varesche
- Department of Hydraulic Engineering and Sanitation, São Carlos School of Engineering (EESC), University of São Paulo (USP), São Paulo, Brazil
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Wang J, Anderson K, Yang E, He L, Lidstrom ME. Enzyme engineering and in vivo testing of a formate reduction pathway. Synth Biol (Oxf) 2021; 6:ysab020. [PMID: 34651085 PMCID: PMC8511477 DOI: 10.1093/synbio/ysab020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 07/08/2021] [Accepted: 08/04/2021] [Indexed: 11/13/2022] Open
Abstract
Formate is an attractive feedstock for sustainable microbial production of fuels and chemicals, but its potential is limited by the lack of efficient assimilation pathways. The reduction of formate to formaldehyde would allow efficient downstream assimilation, but no efficient enzymes are known for this transformation. To develop a 2-step formate reduction pathway, we screened natural variants of acyl-CoA synthetase (ACS) and acylating aldehyde dehydrogenase (ACDH) for activity on one-carbon substrates and identified active and highly expressed homologs of both enzymes. We then performed directed evolution, increasing ACDH-specific activity by 2.5-fold and ACS lysate activity by 5-fold. To test for the in vivo activity of our pathway, we expressed it in a methylotroph which can natively assimilate formaldehyde. Although the enzymes were active in cell extracts, we could not detect formate assimilation into biomass, indicating that further improvement will be required for formatotrophy. Our work provides a foundation for further development of a versatile pathway for formate assimilation.
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Affiliation(s)
- Jue Wang
- Department of Chemical Engineering, University of Washington, Seattle, DC, USA
| | - Karl Anderson
- Department of Chemical Engineering, University of Washington, Seattle, DC, USA
| | - Ellen Yang
- Department of Chemical Engineering, University of Washington, Seattle, DC, USA
| | - Lian He
- Department of Chemical Engineering, University of Washington, Seattle, DC, USA
| | - Mary E Lidstrom
- Department of Chemical Engineering, University of Washington, Seattle, DC, USA
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Liang H, Ma X, Ning W, Liu Y, Sinskey AJ, Stephanopoulos G, Zhou K. Constructing an ethanol utilization pathway in Escherichia coli to produce acetyl-CoA derived compounds. Metab Eng 2020; 65:223-231. [PMID: 33248272 DOI: 10.1016/j.ymben.2020.11.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 10/30/2020] [Accepted: 11/15/2020] [Indexed: 01/05/2023]
Abstract
Engineering microbes to utilize non-conventional substrates could create short and efficient pathways to convert substrate into product. In this study, we designed and constructed a two-step heterologous ethanol utilization pathway (EUP) in Escherichia coli by using acetaldehyde dehydrogenase (encoded by ada) from Dickeya zeae and alcohol dehydrogenase (encoded by adh2) from Saccharomyces cerevisiae. This EUP can convert ethanol into acetyl-CoA without ATP consumption, and generate two molecules of NADH per molecule of ethanol. We optimized the expression of these two genes and found that ethanol consumption could be improved by expressing them in a specific order (ada-adh2) with a constitutive promoter (PgyrA). The engineered E. coli strain with EUP consumed approximately 8 g/L of ethanol in 96 h when it was used as sole carbon source. Subsequently, we combined EUP with the biosynthesis of polyhydroxybutyrate (PHB), a biodegradable polymer derived from acetyl-CoA. The engineered E. coli strain carrying EUP and PHB biosynthetic pathway produced 1.1 g/L of PHB from 10 g/L of ethanol and 1 g/L of aspartate family amino acids in 96 h. We also engineered a E. coli strain to produce 24 mg/L of prenol in an ethanol-containing medium, supporting the feasibility of converting ethanol into different classes of acetyl-CoA derived compounds.
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Affiliation(s)
- Hong Liang
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
| | - Xiaoqiang Ma
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore
| | - Wenbo Ning
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
| | - Yurou Liu
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
| | - Anthony J Sinskey
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore; Department of Biology, Massachusetts Institute of Technology, United States
| | - Gregory Stephanopoulos
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore; Department of Chemical Engineering, Massachusetts Institute of Technology, United States.
| | - Kang Zhou
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore.
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Wenk S, Schann K, He H, Rainaldi V, Kim S, Lindner SN, Bar-Even A. An "energy-auxotroph" Escherichia coli provides an in vivo platform for assessing NADH regeneration systems. Biotechnol Bioeng 2020; 117:3422-3434. [PMID: 32658302 DOI: 10.1002/bit.27490] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/01/2020] [Accepted: 07/09/2020] [Indexed: 12/18/2022]
Abstract
An efficient in vivo regeneration of the primary cellular resources NADH and ATP is vital for optimizing the production of value-added chemicals and enabling the activity of synthetic pathways. Currently, such regeneration routes are tested and characterized mainly in vitro before being introduced into the cell. However, in vitro measurements could be misleading as they do not reflect enzyme activity under physiological conditions. Here, we construct an in vivo platform to test and compare NADH regeneration systems. By deleting dihydrolipoyl dehydrogenase in Escherichia coli, we abolish the activity of pyruvate dehydrogenase and 2-ketoglutarate dehydrogenase. When cultivated on acetate, the resulting strain is auxotrophic to NADH and ATP: acetate can be assimilated via the glyoxylate shunt but cannot be oxidized to provide the cell with reducing power and energy. This strain can, therefore, serve to select for and test different NADH regeneration routes. We exemplify this by comparing several NAD-dependent formate dehydrogenases and methanol dehydrogenases. We identify the most efficient enzyme variants under in vivo conditions and pinpoint optimal feedstock concentrations that maximize NADH biosynthesis while avoiding cellular toxicity. Our strain thus provides a useful platform for comparing and optimizing enzymatic systems for cofactor regeneration under physiological conditions.
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Affiliation(s)
- Sebastian Wenk
- Systems and Synthetic Metabolism Lab, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Karin Schann
- Systems and Synthetic Metabolism Lab, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Hai He
- Systems and Synthetic Metabolism Lab, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Vittorio Rainaldi
- Systems and Synthetic Metabolism Lab, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Seohyoung Kim
- Systems and Synthetic Metabolism Lab, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Steffen N Lindner
- Systems and Synthetic Metabolism Lab, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Arren Bar-Even
- Systems and Synthetic Metabolism Lab, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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Song JY, Park JS, Kang CD, Cho HY, Yang D, Lee S, Cho KM. Introduction of a bacterial acetyl-CoA synthesis pathway improves lactic acid production in Saccharomyces cerevisiae. Metab Eng 2015; 35:38-45. [PMID: 26384570 DOI: 10.1016/j.ymben.2015.09.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 08/06/2015] [Accepted: 09/08/2015] [Indexed: 11/19/2022]
Abstract
Acid-tolerant Saccharomyces cerevisiae was engineered to produce lactic acid by expressing heterologous lactate dehydrogenase (LDH) genes, while attenuating several key pathway genes, including glycerol-3-phosphate dehydrogenase1 (GPD1) and cytochrome-c oxidoreductase2 (CYB2). In order to increase the yield of lactic acid further, the ethanol production pathway was attenuated by disrupting the pyruvate decarboxylase1 (PDC1) and alcohol dehydrogenase1 (ADH1) genes. Despite an increase in lactic acid yield, severe reduction of the growth rate and glucose consumption rate owing to the absence of ADH1 caused a considerable decrease in the overall productivity. In Δadh1 cells, the levels of acetyl-CoA, a key precursor for biologically applicable components, could be insufficient for normal cell growth. To increase the cellular supply of acetyl-CoA, we introduced bacterial acetylating acetaldehyde dehydrogenase (A-ALD) enzyme (EC 1.2.1.10) genes into the lactic acid-producing S. cerevisiae. Escherichia coli-derived A-ALD genes, mhpF and eutE, were expressed and effectively complemented the attenuated acetaldehyde dehydrogenase (ALD)/acetyl-CoA synthetase (ACS) pathway in the yeast. The engineered strain, possessing a heterologous acetyl-CoA synthetic pathway, showed an increased glucose consumption rate and higher productivity of lactic acid fermentation. The production of lactic acid was reached at 142g/L with production yield of 0.89g/g and productivity of 3.55gL(-1)h(-1) under fed-batch fermentation in bioreactor. This study demonstrates a novel approach that improves productivity of lactic acid by metabolic engineering of the acetyl-CoA biosynthetic pathway in yeast.
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Affiliation(s)
- Ji-Yoon Song
- Biomaterials Laboratory, Material Research Center, Samsung Advanced Institute of Technology, Gyeonggi-do, Republic of Korea
| | - Joon-Song Park
- Biomaterials Laboratory, Material Research Center, Samsung Advanced Institute of Technology, Gyeonggi-do, Republic of Korea
| | - Chang Duk Kang
- Biomaterials Laboratory, Material Research Center, Samsung Advanced Institute of Technology, Gyeonggi-do, Republic of Korea
| | - Hwa-Young Cho
- Biomaterials Laboratory, Material Research Center, Samsung Advanced Institute of Technology, Gyeonggi-do, Republic of Korea
| | - Dongsik Yang
- Biomaterials Laboratory, Material Research Center, Samsung Advanced Institute of Technology, Gyeonggi-do, Republic of Korea
| | - Seunghyun Lee
- Biomaterials Laboratory, Material Research Center, Samsung Advanced Institute of Technology, Gyeonggi-do, Republic of Korea
| | - Kwang Myung Cho
- Biomaterials Laboratory, Material Research Center, Samsung Advanced Institute of Technology, Gyeonggi-do, Republic of Korea.
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Kim S, Clomburg JM, Gonzalez R. Synthesis of medium-chain length (C6-C10) fuels and chemicals via β-oxidation reversal in Escherichia coli. J Ind Microbiol Biotechnol 2015; 42:465-75. [PMID: 25645093 DOI: 10.1007/s10295-015-1589-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/14/2015] [Indexed: 11/30/2022]
Abstract
The recently engineered reversal of the β-oxidation cycle has been proposed as a potential platform for the efficient synthesis of longer chain (C ≥ 4) fuels and chemicals. Here, we demonstrate the utility of this platform for the synthesis of medium-chain length (C6-C10) products through the manipulation of key components of the pathway. Deletion of endogenous thioesterases provided a clean background in which the expression of various thiolase and termination components, along with required core enzymes, resulted in the ability to alter the chain length distribution and functionality of target products. This approach enabled the synthesis of medium-chain length carboxylic acids and primary alcohols from glycerol, a low-value feedstock. The use of BktB as the thiolase component with thioesterase TesA' as the termination enzyme enabled the synthesis of about 1.3 g/L C6-C10 saturated carboxylic acids. Tailoring of product formation to primary alcohol synthesis was achieved with the use of various acyl-CoA reductases. The combination of AtoB and FadA as the thiolase components with the alcohol-forming acyl-CoA reductase Maqu2507 from M. aquaeolei resulted in the synthesis of nearly 0.3 g/L C6-C10 alcohols. These results further demonstrate the versatile nature of a β-oxidation reversal, and highlight several key aspects and control points that can be further manipulated to fine-tune the synthesis of various fuels and chemicals.
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Affiliation(s)
- Seohyoung Kim
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, TX, 77005, USA
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Smith NE, Vrielink A, Attwood PV, Corry B. Binding and channeling of alternative substrates in the enzyme DmpFG: a molecular dynamics study. Biophys J 2014; 106:1681-90. [PMID: 24739167 DOI: 10.1016/j.bpj.2014.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 02/13/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022] Open
Abstract
DmpFG is a bifunctional enzyme comprised of an aldolase subunit, DmpG, and a dehydrogenase subunit, DmpF. The aldehyde intermediate produced by the aldolase is channeled directly through a buried molecular channel in the protein structure from the aldolase to the dehydrogenase active site. In this study, we have investigated the binding of a series of progressively larger substrates to the aldolase, DmpG, using molecular dynamics. All substrates investigated are easily accommodated within the active site, binding with free energy values comparable to the physiological substrate 4-hydroxy-2-ketovalerate. Subsequently, umbrella sampling was utilized to obtain free energy surfaces for the aldehyde intermediates (which would be generated from the aldolase reaction on each of these substrates) to move through the channel to the dehydrogenase DmpF. Small substrates were channeled with limited barriers in an energetically feasible process. We show that the barriers preventing bulky intermediates such as benzaldehyde from moving through the wild-type protein can be removed by selective mutation of channel-lining residues, demonstrating the potential for tailoring this enzyme to allow its use for the synthesis of specific chemical products. Furthermore, positions of transient escape routes in this flexible channel were determined.
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Affiliation(s)
- Natalie E Smith
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Alice Vrielink
- School of Chemistry and Biochemistry, University of Western Australia, Perth, Western Australia
| | - Paul V Attwood
- School of Chemistry and Biochemistry, University of Western Australia, Perth, Western Australia
| | - Ben Corry
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia.
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Smith NE, Tie WJ, Flematti GR, Stubbs KA, Corry B, Attwood PV, Vrielink A. Mechanism of the dehydrogenase reaction of DmpFG and analysis of inter-subunit channeling efficiency and thermodynamic parameters in the overall reaction. Int J Biochem Cell Biol 2013; 45:1878-85. [PMID: 23742989 DOI: 10.1016/j.biocel.2013.05.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 05/23/2013] [Accepted: 05/27/2013] [Indexed: 11/30/2022]
Abstract
The bifunctional, microbial enzyme DmpFG is comprised of two subunits: the aldolase, DmpG, and the dehydrogenase, DmpF. DmpFG is of interest due to its ability to channel substrates between the two spatially distinct active sites. While the aldolase is well studied, significantly less is known about the dehydrogenase. Steady-state kinetic measurements of the reverse reaction of DmpF confirmed that the dehydrogenase uses a ping-pong mechanism, with substrate inhibition by acetyl CoA indicating that NAD(+)/NADH and CoA/acetyl CoA bind to the same site in DmpF. The Km of DmpF for exogenous acetaldehyde as a substrate was 23.7 mM, demonstrating the necessity for the channel to deliver acetaldehyde directly from the aldolase to the dehydrogenase active site. A channeling assay on the bifunctional enzyme gave an efficiency of 93% indicating that less than 10% of the toxic acetaldehyde leaks out of the channel into the bulk media, prior to reaching the dehydrogenase active site. The thermodynamic activation parameters of the reactions catalyzed by the aldolase, the dehydrogenase and the DmpFG complex were determined. The Gibb's free energy of activation for the dehydrogenase reaction was lower than that obtained for the full DmpFG reaction, in agreement with the high kcat obtained for the dehydrogenase reaction in isolation. Furthermore, although both the DmpF and DmpG reactions occur with small, favorable entropies of activation, the full DmpFG reaction occurs with a negative entropy of activation. This supports the concept of allosteric structural communication between the two enzymes to coordinate their activities.
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Affiliation(s)
- Natalie E Smith
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA 6009, Australia
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