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Wang X, Marchisio MA. Synthetic polycistronic sequences in eukaryotes. Synth Syst Biotechnol 2021; 6:254-261. [PMID: 34584993 PMCID: PMC8449083 DOI: 10.1016/j.synbio.2021.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/18/2022] Open
Abstract
The need for co-ordinate, high-level, and stable expression of multiple genes is essential for the engineering of biosynthetic circuits and metabolic pathways. This work outlines the functionality and design of IRES- and 2 A-peptide-based constructs by comparing different strategies for co-expression in polycistronic vectors. In particular, 2 A sequences are small peptides, mostly derived from viral polyproteins, that mediate a ribosome-skipping event such that several, different, separate proteins can be generated from a single open reading frame. When applied to metabolic engineering and synthetic gene circuits, 2 A peptides permit to achieve co-regulated and reliable expression of various genes in eukaryotic cells.
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Affiliation(s)
- Xuekun Wang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, 300072, Tianjin, China
| | - Mario Andrea Marchisio
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, 300072, Tianjin, China
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2
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Novikova LA, Yovkova V, Luzikov VN, Barth G, Mauersberger S. Recombinant Yarrowia lipolytica strains for the heterologous expression of multi-component enzyme systems: Expression of mammalian steroidogenic proteins. J Biotechnol 2021; 339:42-52. [PMID: 34333044 DOI: 10.1016/j.jbiotec.2021.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 06/15/2021] [Accepted: 07/24/2021] [Indexed: 11/25/2022]
Abstract
New Yarrowia lipolytica strains for the co-expression of steroidogenic mammalian proteins were obtained in this study. For this purpose, a two-step approach for constructing recombinant strains that permits the simple introduction of several expression cassettes encoding heterologous proteins into the yeast genome was successfully applied. This study tested two series of integrative multi-copy expression vectors containing cDNAs for the mature forms of P450scc system components (cytochrome P450scc (CYP11A1), adrenodoxin reductase, adrenodoxin, or fused adrenodoxin-P450scc) or for P45017α (CYP17A1) under the control of the isocitrate lyase promoter pICL1, which were constructed using the basic plasmids p64PT or p67PT (rDNA or the long terminal repeat (LTR) zeta of Ylt1 as integration targeting sequences and ura3d4 as a multi-copy selection marker). This study demonstrated the integration of up to three expression vectors containing different heterologous cDNA via their simultaneous transformation into haploid recipient strains. Additionally, further combinations of the different expression cassettes in one strain were obtained by subsequent diploidisation using selected haploid multi-copy transformants. Thus, recombinant strains containing three to five different expression cassettes were obtained, as demonstrated by Southern blotting. Expression of P450scc system proteins was identified by western blotting. The presented method for recombinant strain construction is a useful tool for the heterologous expression of multi-component enzyme systems in Y. lipolytica.
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Affiliation(s)
- Ludmila A Novikova
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1/40, 119991, Moscow, Russia.
| | - Venelina Yovkova
- Institute of Microbiology, Dresden University of Technology, Hedda Vogel, 01062, Dresden, Germany
| | - Valentin N Luzikov
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1/40, 119991, Moscow, Russia
| | - Gerold Barth
- Institute of Microbiology, Dresden University of Technology, Hedda Vogel, 01062, Dresden, Germany
| | - Stephan Mauersberger
- Institute of Microbiology, Dresden University of Technology, Hedda Vogel, 01062, Dresden, Germany
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Efimova VS, Isaeva LV, Orekhov PS, Bozdaganyan ME, Rubtsov MA, Novikova LA. Using a viral 2A peptide-based strategy to reconstruct the bovine P450scc steroidogenic system in S. cerevisiae: Bovine P450scc system expression using 2A peptides. J Biotechnol 2020; 325:186-195. [PMID: 33157198 DOI: 10.1016/j.jbiotec.2020.10.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/23/2020] [Accepted: 10/24/2020] [Indexed: 12/12/2022]
Abstract
Cytochrome P450scc system performs the first rate-limiting stage of steroidogenesis in mammals. The bovine P450scc system was reconstructed in Saccharomyces cerevisiae, using a foot-and-mouth disease virus 2A peptide (F2A)-based construct, to co-express cytochrome P450scc, adrenodoxin (Adx), and adrenodoxin reductase (AdR). During the translation of the self-processing fusion protein P450scc-F2A-Adx-F2A-AdR, the first and the second linkers are cleaved with different efficiencies (96 % and 11 %, respectively), resulting in the unbalanced expression of individual proteins. The low cleavage efficiency and the relative Adx and AdR protein levels were increased through replacing the second F2A peptide with different sequences and changing the order of Adx and AdR. The P450scc, AdR, and Adx sequences located upstream of the F2A affected F2A processing, to various degrees. Moreover, using molecular dynamics (MD) simulations, we showed that the 2A peptide fused to the C-terminus of Adx formed the steric hindrance during enzymatic complex formation, resulting in the reduction of catalytic activity. Thus, the functional activity of the reconstructed P450scc system was determined not only by the efficiency of 2A peptides but also by the overall sequence of the expressed 2A-polyprotein. Our results can be applied to the development of 2A-based co-translation strategies, to produce other multicomponent protein systems.
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Affiliation(s)
- Vera S Efimova
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1/40, Moscow, 119991, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1/12, Moscow, 119991, Russia
| | - Ludmila V Isaeva
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1/40, Moscow, 119991, Russia
| | - Philipp S Orekhov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1/12, Moscow, 119991, Russia; Department of Biochemistry, Institute for Translational Medicine and Biotechnology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Bolshaya Pirogovskaya st. 2, Moscow, 119991 Russia; Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow, 141701, Russia
| | - Marine E Bozdaganyan
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1/12, Moscow, 119991, Russia; Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow, 141701, Russia; N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Kosygina st. 4, Moscow, 119991, Russia
| | - Mikhail A Rubtsov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1/12, Moscow, 119991, Russia; Department of Biochemistry, Institute for Translational Medicine and Biotechnology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Bolshaya Pirogovskaya st. 2, Moscow, 119991 Russia
| | - Ludmila A Novikova
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1/40, Moscow, 119991, Russia.
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Hofmann A, Falk J, Prangemeier T, Happel D, Köber A, Christmann A, Koeppl H, Kolmar H. A tightly regulated and adjustable CRISPR-dCas9 based AND gate in yeast. Nucleic Acids Res 2019; 47:509-520. [PMID: 30476163 PMCID: PMC6326796 DOI: 10.1093/nar/gky1191] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 11/19/2018] [Indexed: 02/07/2023] Open
Abstract
The robust and precise on and off switching of one or more genes of interest, followed by expression or repression is essential for many biological circuits as well as for industrial applications. However, many regulated systems published to date influence the viability of the host cell, show high basal expression or enable only the overexpression of the target gene without the possibility of fine regulation. Herein, we describe an AND gate designed to overcome these limitations by combining the advantages of three well established systems, namely the scaffold RNA CRISPR/dCas9 platform that is controlled by Gal10 as a natural and by LexA-ER-AD as heterologous transcription factor. We hence developed a predictable and modular, versatile expression control system. The selection of a reporter gene set up combining a gene of interest (GOI) with a fluorophore by the ribosomal skipping T2A sequence allows to adapt the system to any gene of interest without losing reporter function. In order to obtain a better understanding of the underlying principles and the functioning of our system, we backed our experimental findings with the development of a mathematical model and single-cell analysis.
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Affiliation(s)
- Anja Hofmann
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Johannes Falk
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - Tim Prangemeier
- Department of Electrical Engineering and Information Technology, Technische Universität Darmstadt, 64283 Darmstadt, Germany
| | - Dominic Happel
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Adrian Köber
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Andreas Christmann
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Heinz Koeppl
- Department of Electrical Engineering and Information Technology, Technische Universität Darmstadt, 64283 Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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Analysis of In Vivo Activity of the Bovine Cholesterol Hydroxylase/Lyase System Proteins Expressed in Escherichia coli. Mol Biotechnol 2019; 61:261-273. [PMID: 30729436 DOI: 10.1007/s12033-019-00158-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The cholesterol hydroxylase/lyase (CHL) system, located in the mitochondria of the mammalian adrenal cortex cells, consists of cytochrome P450scc (CYP11A1), adrenodoxin (Adx), and adrenodoxin reductase (AdR) and performs the first stage of the steroidogenesis: AdR and Adx enable the electron transfer between NADPH and cytochrome P450scc, and P450scc catalyzes the conversion of cholesterol into pregnenolone. CHL system was reconstructed in Escherichia coli using the polycistronic plasmid pTrc99A/CHL. In E. coli cells, the recombinant proteins form the catalytically active system. CHL activity towards 22R-hydroxycholesterol was 4.0 ± 1.3 nmol pregnenolone/h per 1 mg homogenate protein. The alteration of the order of heterologous cDNAs in the expression cassette from AdR-Adx-P450scc to P450scc-Adx-AdR results in alteration of stoichiometric ratio P450scc/Adx/AdR from 1:1.45:4.2 to 1:1.67:0.98; the former ratio is more optimal for the functioning of the cytochrome P450scc. The application of modified cDNA of Adx (AdxS112W) does not increase the CHL activity; however, the introduction of the second copy of AdxS112W gene into the expression cassette increases both the expression level of АdxS112W and the CHL activity in comparison with P450scc/АdxS112W/AdR system. In vivo activity of the CHL system in bacteria is limited by the substrate uptake by bacterial cells: it varied in the range of 0.05-0.62 mg pregnenolone/l resting cell suspension per 1-day cultivation, depending on the type and concentration of permeabilizing agents in the medium. The obtained results contribute to the knowledge of CHL system functioning in living bacteria.
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Glyakina AV, Strizhov NI, Karpov MV, Dovidchenko NV, Matkarimov BT, Isaeva LV, Efimova VS, Rubtsov MA, Novikova LA, Donova MV, Galzitskaya OV. Ile351, Leu355 and Ile461 residues are essential for catalytic activity of bovine cytochrome P450scc (CYP11A1). Steroids 2019; 143:80-90. [PMID: 30641046 DOI: 10.1016/j.steroids.2019.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/28/2018] [Accepted: 01/07/2019] [Indexed: 11/23/2022]
Abstract
Cytochrome P450scc (CYP11A1) is a mammalian mitochondrial enzyme which catalyzes cholesterol side chain cleavage to form pregnenolone. Along with cholesterol, some other steroids including sterols with a branched side chain like β-sitosterol are the substrates for the enzyme, but the activity towards β-sitosterol is rather low. Modification of the catalytic site conformation could provide more effective β-sitosterol bioconversion by the enzyme. This study was aimed to find out the amino acid residues substitution of which could modify the conformation of the active site providing possible higher enzyme activity towards β-sitosterol. After structural and bioinformatics analysis three amino acid residues I351, L355, I461 were chosen. Molecular dynamics simulations of P450scc evidenced the stability of the wild type, double (I351A/L355A) and triple (I351A/L355A/I461A) mutants. Mutant variants of cDNA encoding P450scc with the single, double and triple mutations were obtained by site-directed mutagenesis. However, the experimental data indicate that the introduced single mutations Ile351A, Leu355A and Ile461A dramatically decrease the target catalytic activity of CYP11A1, and no activity was observed for double and triple mutants obtained. Therefore, isoleucine residues 351 and 461, and leucine residue 355 are important for the cytochrome P450scc functioning towards sterols both with unbranched (cholesterol) and branched (sitosterol) side chains.
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Affiliation(s)
- Anna V Glyakina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia; Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Nicolai I Strizhov
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; Pharmins, Ltd., R&D, 142290 Pushchino, Moscow Region, Russia
| | - Mikhail V Karpov
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; Pharmins, Ltd., R&D, 142290 Pushchino, Moscow Region, Russia
| | - Nikita V Dovidchenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | | | - Ludmila V Isaeva
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/40, 119234 Moscow, Russia
| | - Vera S Efimova
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia
| | - Mikhail A Rubtsov
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia; Department of Biochemistry, Institute of Translational Medicine and Biotechnology, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Ludmila A Novikova
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/40, 119234 Moscow, Russia
| | - Marina V Donova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; Pharmins, Ltd., R&D, 142290 Pushchino, Moscow Region, Russia.
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.
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Efimova VS, Isaeva LV, Labudina AA, Tashlitsky VN, Rubtsov MA, Novikova LA. Polycistronic expression of the mitochondrial steroidogenic P450scc system in the HEK293T cell line. J Cell Biochem 2018; 120:3124-3136. [DOI: 10.1002/jcb.27577] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 08/08/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Vera S. Efimova
- Department of Molecular Biology Faculty of Biology, M.V. Lomonosov Moscow State University Moscow Russia
- LIA LFR2O (LIA French‐Russian Cancer Research Laboratory) Villejuif France – Moscow Russia
| | - Ludmila V. Isaeva
- Department of Molecular Basis on Ontogenesis A.N. Belozersky Institute of Physico‐Chemical Biology, M.V. Lomonosov Moscow State University Moscow Russia
| | - Anastasia A. Labudina
- Department of Molecular Biology Faculty of Biology, M.V. Lomonosov Moscow State University Moscow Russia
| | - Vadim N. Tashlitsky
- Division of Chemistry of Natural Compounds Faculty of Chemistry, M.V. Lomonosov Moscow State University Moscow Russia
| | - Mikhail A. Rubtsov
- Department of Molecular Biology Faculty of Biology, M.V. Lomonosov Moscow State University Moscow Russia
- LIA LFR2O (LIA French‐Russian Cancer Research Laboratory) Villejuif France – Moscow Russia
- Department of Biochemistry I.M. Sechenov First Moscow State Medical University (Sechenov University) 119991 Moscow Russia
- Institute of Translational Medicine and Biotechnology I.M. Sechenov First Moscow State Medical University (Sechenov University) Moscow Russia
| | - Ludmila A. Novikova
- Department of Molecular Basis on Ontogenesis A.N. Belozersky Institute of Physico‐Chemical Biology, M.V. Lomonosov Moscow State University Moscow Russia
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Geib E, Brock M. ATNT: an enhanced system for expression of polycistronic secondary metabolite gene clusters in Aspergillus niger. Fungal Biol Biotechnol 2017; 4:13. [PMID: 29270299 PMCID: PMC5735947 DOI: 10.1186/s40694-017-0042-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/12/2017] [Indexed: 11/16/2022] Open
Abstract
Background Fungi are treasure chests for yet unexplored natural products. However, exploitation of their real potential remains difficult as a significant proportion of biosynthetic gene clusters appears silent under standard laboratory conditions. Therefore, elucidation of novel products requires gene activation or heterologous expression. For heterologous gene expression, we previously developed an expression platform in Aspergillus niger that is based on the transcriptional regulator TerR and its target promoter PterA. Results In this study, we extended this system by regulating expression of terR by the doxycycline inducible Tet-on system. Reporter genes cloned under the control of the target promoter PterA remained silent in the absence of doxycycline, but were strongly expressed when doxycycline was added. Reporter quantification revealed that the coupled system results in about five times higher expression rates compared to gene expression under direct control of the Tet-on system. As production of secondary metabolites generally requires the expression of several biosynthetic genes, the suitability of the self-cleaving viral peptide sequence P2A was tested in this optimised expression system. P2A allowed polycistronic expression of genes required for Asp-melanin formation in combination with the gene coding for the red fluorescent protein tdTomato. Gene expression and Asp-melanin formation was prevented in the absence of doxycycline and strongly induced by addition of doxycycline. Fluorescence studies confirmed the correct subcellular localisation of the respective enzymes. Conclusion This tightly regulated but strongly inducible expression system enables high level production of secondary metabolites most likely even those with toxic potential. Furthermore, this system is compatible with polycistronic gene expression and, thus, suitable for the discovery of novel natural products. Electronic supplementary material The online version of this article (10.1186/s40694-017-0042-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elena Geib
- Fungal Genetics and Biology, School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Matthias Brock
- Fungal Genetics and Biology, School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
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