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Huong KH, Orita I, Fukui T. Microaerobic insights into production of polyhydroxyalkanoates containing 3-hydroxyhexanoate via native reverse β-oxidation from glucose in Ralstonia eutropha H16. Microb Cell Fact 2024; 23:21. [PMID: 38221622 PMCID: PMC10788006 DOI: 10.1186/s12934-024-02294-4] [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: 10/17/2023] [Accepted: 01/01/2024] [Indexed: 01/16/2024] Open
Abstract
BACKGROUND Ralstonia eutropha H16, a facultative chemolitoautotroph, is an important workhorse for bioindustrial production of useful compounds such as polyhydroxyalkanoates (PHAs). Despite the extensive studies to date, some of its physiological properties remain not fully understood. RESULTS This study demonstrated that the knallgas bacterium exhibited altered PHA production behaviors under slow-shaking condition, as compared to its usual aerobic condition. One of them was a notable increase in PHA accumulation, ranging from 3.0 to 4.5-fold in the mutants lacking of at least two NADPH-acetoacetyl-CoA reductases (PhaB1, PhaB3 and/or phaB2) when compared to their respective aerobic counterpart, suggesting the probable existence of (R)-3HB-CoA-providing route(s) independent on PhaBs. Interestingly, PHA production was still considerably high even with an excess nitrogen source under this regime. The present study further uncovered the conditional activation of native reverse β-oxidation (rBOX) allowing formation of (R)-3HHx-CoA, a crucial precursor for poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) [P(3HB-co-3HHx)], solely from glucose. This native rBOX led to the natural incorporation of 3.9 mol% 3HHx in a triple phaB-deleted mutant (∆phaB1∆phaB1∆phaB2-C2). Gene deletion experiments elucidated that the native rBOX was mediated by previously characterized (S)-3HB-CoA dehydrogenases (PaaH1/Had), β-ketothiolase (BktB), (R)-2-enoyl-CoA hydratase (PhaJ4a), and unknown crotonase(s) and reductase(s) for crotonyl-CoA to butyryl-CoA conversion prior to elongation. The introduction of heterologous enzymes, crotonyl-CoA carboxylase/reductase (Ccr) and ethylmalonyl-CoA decarboxylase (Emd) along with (R)-2-enoyl-CoA hydratase (PhaJ) aided the native rBOX, resulting in remarkably high 3HHx composition (up to 37.9 mol%) in the polyester chains under the low-aerated condition. CONCLUSION These findings shed new light on the robust characteristics of Ralstonia eutropha H16 and have the potential for the development of new strategies for practical P(3HB-co-3HHx) copolyesters production from sugars under low-aerated conditions.
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Affiliation(s)
- Kai-Hee Huong
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan
| | - Izumi Orita
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan.
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Schmitt FJ, Mehmood AS, Tüting C, Phan HT, Reisdorf J, Rieder F, Ghane Golmohamadi F, Verma R, Kastritis PL, Laufer J. Effect of Molecular Dynamics and Internal Water Contact on the Photophysical Properties of Red pH-Sensitive Proteins. Biochemistry 2024; 63:82-93. [PMID: 38085825 DOI: 10.1021/acs.biochem.3c00444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The pH dependence of the absorption and (time-resolved) fluorescence of two red-shifted fluorescent proteins, mCardinal and mNeptune, was investigated. Decay-associated spectra were measured following fluorescence excitation at 470 nm in PBS buffer with a pH that ranged from 5.5 to 8.0. The fluorescence of both proteins shows two different decay components. mCardinal exhibits an increase in the long-lived fluorescence component with acidification from 1.34 ns at pH 8.0 to 1.62 ns at pH 5.5. An additional fast decay component with 0.64 ns at pH 8.0 up to 1.1 ns at pH 5.5 was found to be blue-shifted compared to the long-lived component. The fluorescence lifetime of mNeptune is insensitive to pH. DAS of mCardinal were simulated assuming a coupled two-level system to describe the 1S state of the chromophore within two different conformations of the protein. MD simulations were conducted to correlate the experimentally observed pH-induced change in the lifetime in mCardinal with its molecular properties. While the chromophores of both protein variants are stabilized by the same number of hydrogen bonds, it was found that the chromophore in mCardinal exhibits more water contacts compared to mNeptune. In mCardinal, interaction between the chromophore and Glu-145 is reduced as compared to mNeptune, but interaction with Thr-147 which is Ser-147 in mNeptune is stronger in mCardinal. Therefore, the dynamics of the excited-state proton transfer (ESPT) might be different in mCardinal and mNeptune. The pH dependency of ESPT is suggested as a key mechanism for pH sensitivity.
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Affiliation(s)
- Franz-Josef Schmitt
- Institute of Physics, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 3, 06120 Halle, Saale, Germany
| | - Amna Shah Mehmood
- Institute of Physics, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 3, 06120 Halle, Saale, Germany
| | - Christian Tüting
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06120 Halle, Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle, Saale, Germany
| | - Hoang Trong Phan
- Institute of Physics, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 3, 06120 Halle, Saale, Germany
- INM-Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
| | - Judith Reisdorf
- Institute of Physics, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 3, 06120 Halle, Saale, Germany
| | - Fabian Rieder
- Institute of Physics, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 3, 06120 Halle, Saale, Germany
| | - Farzin Ghane Golmohamadi
- Institute of Physics, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 3, 06120 Halle, Saale, Germany
| | | | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06120 Halle, Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle, Saale, Germany
| | - Jan Laufer
- Institute of Physics, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 3, 06120 Halle, Saale, Germany
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The development of NAD+-dependent dehydrogenase screen-printed biosensor based on enzyme and nanoporous gold co-catalytic strategy. Biosens Bioelectron 2022; 211:114376. [DOI: 10.1016/j.bios.2022.114376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 01/20/2023]
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Hu J, Tang H, Wang YZ, Yang C, Gao MT, Tsang YF, Li J. Effect of dissolved solids released from biochar on soil microbial metabolism. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:598-608. [PMID: 35332912 DOI: 10.1039/d2em00036a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Dissolved solids released from biochar (DSRB), including organic and inorganic compounds, may affect the role of biochar as a soil amendment. In this study, the effects of DSRB on soil microbe metabolism, especially CO2 fixation, were evaluated in liquid soil extract. DSRB were found to be released in large amounts (289.05 mg L-1 at 1 hour) from biochar over a short period of time before their rate of release slowed to a gradual pace. They increased the microbial biomass and provided energy and reducing power to microbes, while reducing their metabolic output of extracellular proteins and polysaccharides. DSRB inputs led to the redistribution of metabolic flux in soil microorganisms and an increased organic carbon content in the short term. This content gradually decreased as it was utilized. DSRB did not improve microbial CO2 fixation but, rather, enhanced its release, while promoting specific soil microorganism genera, including Cupriavidus, Flavisolibacter, and Pseudoxanthomonas. These heterotrophic genera may compete with autotrophic microorganisms for nutrients but have positive synergistic relationships with autotrophs during CO2 fixation. These results demonstrated that reducing the DSRB in biochar can improve its role as a soil amendment by enhancing soil carbon storage and CO2 fixation capabilities.
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Affiliation(s)
- Jiajun Hu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Han Tang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Ya Zhu Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Chen Yang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China.
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Min-Tian Gao
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Yiu Fai Tsang
- Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong, China
| | - Jixiang Li
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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Olavarria K, Pijman YO, Cabrera R, van Loosdrecht MCM, Wahl SA. Engineering an acetoacetyl-CoA reductase from Cupriavidus necator toward NADH preference under physiological conditions. Sci Rep 2022; 12:3757. [PMID: 35260659 PMCID: PMC8904767 DOI: 10.1038/s41598-022-07663-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/21/2022] [Indexed: 11/09/2022] Open
Abstract
The coupling of PHB generation with NADH reoxidation is required to generate PHB as a fermentation product. A fundamental trait to accomplish this feature is to express a functional NADH-preferring acetoacetyl-CoA reductase, engaged in PHB accumulation. One way to obtain such a reductase is by engineering the cofactor preference of the acetoacetyl-CoA reductase encoded by the phaB1 gene from Cupriavidus necator (AARCn1). Aiming to have a deeper understanding of the structural determinants of the cofactor preference in AARCn1, and to obtain an NADH-preferring acetoacetyl-CoA reductase derived from this protein, some engineered enzymes were expressed, purified and kinetically characterized, together with the parental AARCn1. One of these engineered enzymes, Chimera 5, experimentally showed a selectivity ratio ((kcat/KM)NADH/(kcat/KM)NADPH) ≈ 18, which is 160 times higher than the selectivity ratio experimentally observed in the parental AARCn1. A thermodynamic-kinetic approach was employed to estimate the cofactor preference and flux capacity of Chimera 5 under physiological conditions. According to this approach, Chimera 5 could prefer NADH over NADPH between 25 and 150 times. Being a derivative of AARCn1, Chimera 5 should be readily functional in Escherichia coli and C. necator. Moreover, with the expected expression level, its activity should be enough to sustain PHB accumulation fluxes similar to the fluxes previously observed in these biotechnologically relevant cell factories.
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Affiliation(s)
- Karel Olavarria
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands. .,Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6700 EH, Wageningen, The Netherlands.
| | - Yared O Pijman
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Ricardo Cabrera
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Región Metropolitana, Chile
| | - Mark C M van Loosdrecht
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - S Aljoscha Wahl
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
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Lee JK, Suh HN, Yoon SH, Lee KH, Ahn SY, Kim HJ, Kim SH. Non-Destructive Monitoring via Electrochemical NADH Detection in Murine Cells. BIOSENSORS 2022; 12:107. [PMID: 35200367 PMCID: PMC8869533 DOI: 10.3390/bios12020107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/25/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Nicotinamide adenine dinucleotide (NADH) is an important cofactor involved in metabolic redox reactions in living cells. The detection of NADH in living animal cells is a challenge. We developed a one-step monitoring method for NADH via an electrocatalytic reaction that uses a surface-modified, screen-printed electrode (SPE) having a redox active monolayer 4'-mercapto-N-phenlyquinone diamine (NPQD) formed by a self-assembled monolayer (SAM) of an aromatic thiol, 4-aminothiophenol (4-ATP). This electrode has a limit of detection (LOD) of 0.49 μM and a sensitivity of 0.0076 ± 0.0006 μM/μA in cell culture media, which indicates that it retains its selectivity. The applicability of this NADH sensor was demonstrated for the first time by cell viability monitoring via NADH-sensing in cell culture supernatants.
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Affiliation(s)
- Ju Kyung Lee
- Department of Medical IT Convergence, Kumoh National Institute of Technology, Gumi 39177, Korea;
| | - Han Na Suh
- Korea Institute of Toxicology, Jeongeup 56212, Korea; (H.N.S.); (S.H.Y.); (K.H.L.)
| | - Sung Hoon Yoon
- Korea Institute of Toxicology, Jeongeup 56212, Korea; (H.N.S.); (S.H.Y.); (K.H.L.)
- Department of Human and Environmental Toxicology, University of Science & Technology, Daejeon 34113, Korea
| | - Kyu Hong Lee
- Korea Institute of Toxicology, Jeongeup 56212, Korea; (H.N.S.); (S.H.Y.); (K.H.L.)
| | - Sae Young Ahn
- NDD Inc., Gumi 39253, Korea;
- Fuzbien Technology Institute, Rockville, MD 20850, USA
| | - Hyung Jin Kim
- Digital Health Care Research Center, Gumi Electronics and Information Technology Research Institute (GERI), Gumi 39253, Korea;
| | - Sang Hee Kim
- Department of Medical IT Convergence, Kumoh National Institute of Technology, Gumi 39177, Korea;
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Kostyuk AI, Panova AS, Kokova AD, Kotova DA, Maltsev DI, Podgorny OV, Belousov VV, Bilan DS. In Vivo Imaging with Genetically Encoded Redox Biosensors. Int J Mol Sci 2020; 21:E8164. [PMID: 33142884 PMCID: PMC7662651 DOI: 10.3390/ijms21218164] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
Redox reactions are of high fundamental and practical interest since they are involved in both normal physiology and the pathogenesis of various diseases. However, this area of research has always been a relatively problematic field in the context of analytical approaches, mostly because of the unstable nature of the compounds that are measured. Genetically encoded sensors allow for the registration of highly reactive molecules in real-time mode and, therefore, they began a new era in redox biology. Their strongest points manifest most brightly in in vivo experiments and pave the way for the non-invasive investigation of biochemical pathways that proceed in organisms from different systematic groups. In the first part of the review, we briefly describe the redox sensors that were used in vivo as well as summarize the model systems to which they were applied. Next, we thoroughly discuss the biological results obtained in these studies in regard to animals, plants, as well as unicellular eukaryotes and prokaryotes. We hope that this work reflects the amazing power of this technology and can serve as a useful guide for biologists and chemists who work in the field of redox processes.
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Affiliation(s)
- Alexander I. Kostyuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Anastasiya S. Panova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Aleksandra D. Kokova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Daria A. Kotova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Dmitry I. Maltsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Federal Center for Cerebrovascular Pathology and Stroke, 117997 Moscow, Russia
| | - Oleg V. Podgorny
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Vsevolod V. Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Federal Center for Cerebrovascular Pathology and Stroke, 117997 Moscow, Russia
- Institute for Cardiovascular Physiology, Georg August University Göttingen, D-37073 Göttingen, Germany
| | - Dmitry S. Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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