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Zhang C, Wei G, Zhou N, Wang Y, Feng J, Wang X, Zhang A, Chen K. Systematic Engineering of Escherichia coli for Efficient Production of Pseudouridine from Glucose and Uracil. ACS Synth Biol 2024; 13:1303-1311. [PMID: 38529630 DOI: 10.1021/acssynbio.4c00028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
In this study, we proposed a biological approach to efficiently produce pseudouridine (Ψ) from glucose and uracil in vivo using engineered Escherichia coli. By screening host strains and core enzymes, E. coli MG1655 overexpressing Ψ monophosphate (ΨMP) glycosidase and ΨMP phosphatase was obtained, which displayed the highest Ψ concentration. Then, optimization of the RBS sequences, enhancement of ribose 5-phosphate supply in the cells, and overexpression of the membrane transport protein UraA were investigated. Finally, fed-batch fermentation of Ψ in a 5 L fermentor can reach 27.5 g/L with a yield of 89.2 mol % toward uracil and 25.6 mol % toward glucose within 48 h, both of which are the highest to date. In addition, the Ψ product with a high purity of 99.8% can be purified from the fermentation broth after crystallization. This work provides an efficient and environmentally friendly protocol for allowing for the possibility of Ψ bioproduction on an industrial scale.
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Affiliation(s)
- Chi Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Guoguang Wei
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Ning Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Yingying Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Jia Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Alei Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
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Xiong P, Nocek JM, Vura-Weis J, Lockard JV, Wasielewski MR, Hoffman BM. Faster interprotein electron transfer in a [myoglobin, b⁵] complex with a redesigned interface. Science 2010; 330:1075-8. [PMID: 21097931 DOI: 10.1126/science.1197054] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Direct measurements of electron transfer (ET) within a protein-protein complex with a redesigned interface formed by physiological partner proteins myoglobin (Mb) and cytochrome b(5) (b(5)) reveal interprotein ET rates comparable to those observed within the photosynthetic reaction center. Brownian dynamics simulations show that Mb in which three surface acid residues are mutated to lysine binds b(5) in an ensemble of configurations distributed around a reactive most-probable structure. Correspondingly, charge-separation ET from a photoexcited singlet zinc porphyrin incorporated within Mb to the heme of b(5) and the follow-up charge-recombination exhibit distributed kinetics, with median rate constants, k(f)(s) = 2.1 × 10(9) second(-1) and k(b)(s) = 4.3 × 10(10) second(-1), respectively. The latter approaches that for the initial step in photosynthetic charge separation, k = 3.3 × 10(11) second(-1).
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Affiliation(s)
- Peng Xiong
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA
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Patel AD, Nocek JM, Hoffman BM. Kinetic-dynamic model for conformational control of an electron transfer photocycle: mixed-metal hemoglobin hybrids. J Phys Chem B 2008; 112:11827-37. [PMID: 18717535 PMCID: PMC2672620 DOI: 10.1021/jp8054679] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
It is becoming increasingly clear that the transfer of an electron across a protein-protein interface is coupled to the dynamics of conformational conversion between and within ensembles of interface conformations. Electron transfer (ET) reactions in conformationally mobile systems provide a "clock" against which the rapidity of a dynamic process may be measured, and we here report a simple kinetic (master equation) model that self-consistently incorporates conformational dynamics into an ET photocycle comprised of a photoinitiated "forward" step and thermal return to ground. This kinetic/dynamic (KD) model assumes an ET complex exists as multiple interconverting conformations which partition into an ET-optimized (reactive; R) population and a less-reactive population ( S). We take the members of each population to be equivalent by constraining them to have the same conformational energy, the same average rate constant for conversion to members of the other population, and the same rate constants for forward and back ET. The result is a mapping of a complicated energy surface onto the simple "gating", two-well surface, but with rate constants that are defined microscopically. This model successfully describes the changes in the ET photocycle within the "predocked" mixed-metal hemoglobin (Hb) hybrid, [alpha(Zn), beta(Fe3+N 3 (-))], as conformational kinetics are modulated by variations in viscosity (eta = 1-15 cP; 20 degrees C). The description reveals how the conformational "routes" by which a hybrid progresses through a photocycle differ in different dynamic regimes. Even at eta = 1 cP, the populations are not in fast exchange, and ET involves a complex interplay between conformational and ET processes; at intermediate viscosities the hybrid exhibits "differential dynamics" in which the forward and back ET processes involve different initial ensembles of configurational substates; by eta = 15 cP, the slow-exchange limit is approached. Even at low viscosity, the ET-coupled motions are fairly slow, with rate constants of <10 (3) s (-1). Current ideas about Hb function lead to the testable hypothesis that ET in the hybrid may be coupled to allosteric fluctuations of the two [alpha 1, beta 2] dimers of Hb.
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Affiliation(s)
- Ami D Patel
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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Ullmann GM, Kloppmann E, Essigke T, Krammer EM, Klingen AR, Becker T, Bombarda E. Investigating the mechanisms of photosynthetic proteins using continuum electrostatics. PHOTOSYNTHESIS RESEARCH 2008; 97:33-53. [PMID: 18478354 DOI: 10.1007/s11120-008-9306-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Accepted: 04/10/2008] [Indexed: 05/26/2023]
Abstract
Computational methods based on continuum electrostatics are widely used in theoretical biochemistry to analyze the function of proteins. Continuum electrostatic methods in combination with quantum chemical and molecular mechanical methods can help to analyze even very complex biochemical systems. In this article, applications of these methods to proteins involved in photosynthesis are reviewed. After giving a short introduction to the basic concepts of the continuum electrostatic model based on the Poisson-Boltzmann equation, we describe the application of this approach to the docking of electron transfer proteins, to the comparison of isofunctional proteins, to the tuning of absorption spectra, to the analysis of the coupling of electron and proton transfer, to the analysis of the effect of membrane potentials on the energetics of membrane proteins, and to the kinetics of charge transfer reactions. Simulations as those reviewed in this article help to analyze molecular mechanisms on the basis of the structure of the protein, guide new experiments, and provide a better and deeper understanding of protein functions.
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Affiliation(s)
- G Matthias Ullmann
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstr. 30, BGI, Bayreuth 95447, Germany.
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Hoffman BM, Celis LM, Cull DA, Patel AD, Seifert JL, Wheeler KE, Wang J, Yao J, Kurnikov IV, Nocek JM. Differential influence of dynamic processes on forward and reverse electron transfer across a protein-protein interface. Proc Natl Acad Sci U S A 2005; 102:3564-9. [PMID: 15738411 PMCID: PMC553314 DOI: 10.1073/pnas.0408767102] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We propose that the forward and reverse halves of a flash-induced protein-protein electron transfer (ET) photocycle should exhibit differential responses to dynamic interconversion of configurations when the most stable configuration is not the most reactive, because the reactants exist in different initial configurations: the flash-photoinitiated forward ET process begins with the protein partners in an equilibrium ensemble of configurations, many of which have little or no reactivity, whereas the reactant of the thermal back ET (the charge-separated intermediate) is formed in a nonequilibrium, "activated" protein configuration. We report evidence for this proposal in measurements on (i) mixed-metal hemoglobin hybrids, (ii) the complex between cytochrome c peroxidase and cytochrome c, and (iii and iv) the complexes of myoglobin and isolated hemoglobin alpha-chains with cytochrome b(5). For all three systems, forward and reverse ET does respond differently to modulation of dynamic processes; further, the response to changes in viscosity is different for each system.
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Affiliation(s)
- Brian M Hoffman
- Department of Chemistry, Northwestern University, 2145 North Sheridan Road, Evanston, IL 60208-3113, USA.
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Affiliation(s)
- David B Rorabacher
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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Jeuken LJC. Conformational reorganisation in interfacial protein electron transfer. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1604:67-76. [PMID: 12765764 DOI: 10.1016/s0005-2728(03)00026-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Protein-protein electron transfer (ET) plays an essential role in all redox chains. Earlier studies which used cross-linking and increased solution viscosity indicated that the rate of many ET reactions is limited (i.e., gated) by conformational reorientations at the surface interface. These results are later supported by structural studies using NMR and molecular modelling. New insights into conformational gating have also come from electrochemical experiments in which proteins are noncovalently adsorbed on the electrode surface. These systems have the advantage that it is relatively easy to vary systematically the driving force and electronic coupling. In this review we summarize the current knowledge obtained from these electrochemical experiments and compare it with some of the results obtained for protein-protein ET.
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Effects of pH on kinetics of the structural rearrangement that gates the electron-transfer reaction between zinc cytochrome c and plastocyanin: Analysis of protonation states in a diprotein complex. JOURNAL OF THE SERBIAN CHEMICAL SOCIETY 2003. [DOI: 10.2298/jsc0305327c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Electron transfer from zinc cytochrome c to copper(II)plastocyanin in the electrostatically- stabilized complex [Crnogorac MM, Shen C, Young S Hansson O, Kostic NM (1996) Biochemistry 35, 16465?74]. We study this rearrangement in four complexes Zncyt/pc(II), which zinc cytochrome c makes with the wild-type form and the single mutants Asp42Asn, Glu59Gln, and Glu60Gln of plastocyanin. The rate constant for the rearrangement, kF differs for the four forms of plastocyanin but is independent of pH from 5.4 to 9.0 in all four cases. That kF is affected by the single mutations but not by pH changes suggests that the residues Asp 42, Glu59, and Glu60 in the wild-type plastocyanin remain deprotonated (i.e., as anions) within the Zncyt/pc(II) complex throughout the pH range examined. This fact agrees with the notion that loss of salt bridges in the initial (redox-inactive) configuration of the complex is compensated by formation of new salt bridges in the rearranged (redox-active) configuration.
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Tremain SM, Kostić NM. Fate of the excited triplet state of zinc cytochrome c in the presence of iron(III), iron(II), iron-free, and heme-free forms of cytochrome c. Inorganica Chim Acta 2000. [DOI: 10.1016/s0020-1693(00)00012-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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