1
|
Vasilopoulou E, Chroumpi T, Skretas G. Escherichia coli strains with precise domain deletions in the ribonuclease RNase E can achieve greatly enhanced levels of membrane protein production. Protein Sci 2024; 33:e4864. [PMID: 38073126 PMCID: PMC10804669 DOI: 10.1002/pro.4864] [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: 07/26/2023] [Revised: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 01/26/2024]
Abstract
Escherichia coli is one of the most widely utilized hosts for production of recombinant membrane proteins (MPs). Bacterial MP production, however, is usually accompanied by severe toxicity and low-level volumetric accumulation. In previous work, we had discovered that co-expression of RraA, an inhibitor of the RNA-degrading activity of RNase E, can efficiently suppress the cytotoxicity associated with the MP overexpression process and, simultaneously, enhance significantly the cellular accumulation of membrane-incorporated recombinant MPs in bacteria. Based on this, we constructed the specialized MP-producing E. coli strain SuptoxR, which can achieve dramatically enhanced volumetric yields of well-folded recombinant MPs. Ιn the present work, we have investigated whether domain deletions in the E. coli RNase E, which exhibit reduced ribonucleolytic activity, can result in suppressed MP-induced toxicity and enhanced recombinant MP production, in a manner resembling the conditions of rraA overexpression in E. coli SuptoxR. We have found that some strains encoding specific RNase E truncation variants can achieve significantly enhanced levels of recombinant MP production. Among these, we have found a single RNase E variant strain, which can efficiently suppress MP-induced toxicity and achieve greatly enhanced levels of recombinant MP production for proteins of both prokaryotic and eukaryotic origin. Based on its properties, and in analogy to the original SuptoxR strain, we have termed this strain SuptoxRNE22. E. coli SuptoxRNE22 can perform better than commercially available bacterial strains, which are frequently utilized for recombinant MP production. We anticipate that SuptoxRNE22 will become a widely utilized host for recombinant MP production in bacteria.
Collapse
Affiliation(s)
- Eleni Vasilopoulou
- Institute for Bio‐innovationBiomedical Sciences Research Center “Alexander Fleming”VariGreece
- Institute of Chemical Biology, National Hellenic Research FoundationAthensGreece
- Department of Biochemistry and BiotechnologyUniversity of ThessalyLarisaGreece
| | - Tania Chroumpi
- Institute of Chemical Biology, National Hellenic Research FoundationAthensGreece
| | - Georgios Skretas
- Institute for Bio‐innovationBiomedical Sciences Research Center “Alexander Fleming”VariGreece
- Institute of Chemical Biology, National Hellenic Research FoundationAthensGreece
| |
Collapse
|
2
|
Wiull K, Hagen LH, Rončević J, Westereng B, Boysen P, Eijsink VGH, Mathiesen G. Antigen surface display in two novel whole genome sequenced food grade strains, Lactiplantibacillus pentosus KW1 and KW2. Microb Cell Fact 2024; 23:19. [PMID: 38212746 PMCID: PMC10782763 DOI: 10.1186/s12934-024-02296-2] [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: 12/14/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Utilization of commensal bacteria for delivery of medicinal proteins, such as vaccine antigens, is an emerging strategy. Here, we describe two novel food-grade strains of lactic acid bacteria, Lactiplantibacillus pentosus KW1 and KW2, as well as newly developed tools for using this relatively unexplored but promising bacterial species for production and surface-display of heterologous proteins. RESULTS Whole genome sequencing was performed to investigate genomic features of both strains and to identify native proteins enabling surface display of heterologous proteins. Basic characterization of the strains revealed the optimum growth temperatures for both strains to be 35-37 °C, with peak heterologous protein production at 33 °C (KW1) and 37 °C (KW2). Negative staining revealed that only KW1 produces closely bound exopolysaccharides. Production of heterologous proteins with the inducible pSIP-expression system enabled high expression in both strains. Exposure to KW1 and KW2 skewed macrophages toward the antigen presenting state, indicating potential adjuvant properties. To develop these strains as delivery vehicles, expression of the mycobacterial H56 antigen was fused to four different strain-specific surface-anchoring sequences. CONCLUSION All experiments that enabled comparison of heterologous protein production revealed KW1 to be the better recombinant protein production host. Use of the pSIP expression system enabled successful construction of L. pentosus strains for production and surface display of an antigen, underpinning the potential of these strains as novel delivery vehicles.
Collapse
Affiliation(s)
- Kamilla Wiull
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.
| | - Live Heldal Hagen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Jelena Rončević
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Bjørge Westereng
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Preben Boysen
- Faculty of Veterinary Medicine, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Geir Mathiesen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.
| |
Collapse
|
3
|
Cho S, Lee H, Han YH, Park TS, Seo SW, Park TH. Design of an effective small expression tag to enhance GPCR production in E. coli-based cell-free and whole cell expression systems. Protein Sci 2023; 32:e4839. [PMID: 37967042 PMCID: PMC10682694 DOI: 10.1002/pro.4839] [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: 08/29/2023] [Revised: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 11/17/2023]
Abstract
G protein-coupled receptors (GPCRs) play crucial roles in sensory, immune, and tumor metastasis processes, making them valuable targets for pharmacological and sensing applications in various industries. However, most GPCRs have low production yields in Escherichia coli (E. coli) expression systems. To overcome this limitation, we introduced AT10 tag, an effective fusion tag that could significantly enhance expression levels of various GPCRs in E. coli and its derived cell-free protein synthesis (CFPS) system. This AT10 tag consisted of an A/T-rich gene sequence designed via optimization of translation initiation rate. It is translated into a short peptide sequence of 10 amino acids at the N-terminus of GPCRs. Additionally, effector proteins could be utilized to suppress cytotoxicity caused by membrane protein expression, further boosting GPCR production in E. coli. Enhanced expression of various GPCRs using this AT10 tag is a promising approach for large-scale production of functional GPCRs in E. coli-based CFPS and whole cell systems, enabling their potential utilization across a wide range of industrial applications.
Collapse
Affiliation(s)
- Seongyeon Cho
- School of Chemical and Biological Engineering, Institute of Chemical ProcessSeoul National UniversitySeoulRepublic of Korea
| | - Haein Lee
- School of Chemical and Biological Engineering, Institute of Chemical ProcessSeoul National UniversitySeoulRepublic of Korea
| | - Yong Hee Han
- Interdisciplinary Program in BioengineeringSeoul National UniversitySeoulRepublic of Korea
| | - Tae Shin Park
- Receptech Research Institute, Receptech Inc.SiheungRepublic of Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Institute of Chemical ProcessSeoul National UniversitySeoulRepublic of Korea
- Interdisciplinary Program in BioengineeringSeoul National UniversitySeoulRepublic of Korea
| | - Tai Hyun Park
- School of Chemical and Biological Engineering, Institute of Chemical ProcessSeoul National UniversitySeoulRepublic of Korea
- Interdisciplinary Program in BioengineeringSeoul National UniversitySeoulRepublic of Korea
- Department of Nutritional Science and Food ManagementEwha Womans UniversitySeoulRepublic of Korea
| |
Collapse
|
4
|
Zhang MF, Xie WL, Chen C, Li CX, Xu JH. Computational redesign of taxane-10β-hydroxylase for de novo biosynthesis of a key paclitaxel intermediate. Appl Microbiol Biotechnol 2023; 107:7105-7117. [PMID: 37736790 DOI: 10.1007/s00253-023-12784-x] [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: 06/22/2023] [Revised: 08/27/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023]
Abstract
Paclitaxel (Taxol®) is the most popular anticancer diterpenoid predominantly present in Taxus. The core skeleton of paclitaxel is highly modified, but researches on the cytochrome P450s involved in post-modification process remain exceedingly limited. Herein, the taxane-10β-hydroxylase (T10βH) from Taxus cuspidata, which is the third post-modification enzyme that catalyzes the conversion of taxadiene-5α-yl-acetate (T5OAc) to taxadiene-5α-yl-acetoxy-10β-ol (T10OH), was investigated in Escherichia coli by combining computation-assisted protein engineering and metabolic engineering. The variant of T10βH, M3 (I75F/L226K/S345V), exhibited a remarkable 9.5-fold increase in protein expression, accompanied by respective 1.3-fold and 2.1-fold improvements in turnover frequency (TOF) and total turnover number (TTN). Upon integration into the engineered strain, the variant M3 resulted in a substantial enhancement in T10OH production from 0.97 to 2.23 mg/L. Ultimately, the titer of T10OH reached 3.89 mg/L by fed-batch culture in a 5-L bioreactor, representing the highest level reported so far for the microbial de novo synthesis of this key paclitaxel intermediate. This study can serve as a valuable reference for further investigation of other P450s associated with the artificial biosynthesis of paclitaxel and other terpenoids. KEY POINTS: • The T10βH from T. cuspidata was expressed and engineered in E. coli unprecedentedly. • The expression and activity of T10βH were improved through protein engineering. • De novo biosynthesis of T10OH was achieved in E. coli with a titer of 3.89 mg/L.
Collapse
Affiliation(s)
- Mei-Fang Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Wen-Liang Xie
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Cheng Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Chun-Xiu Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| |
Collapse
|
5
|
Chen JP, Gong JS, Su C, Li H, Xu ZH, Shi JS. Improving the soluble expression of difficult-to-express proteins in prokaryotic expression system via protein engineering and synthetic biology strategies. Metab Eng 2023; 78:99-114. [PMID: 37244368 DOI: 10.1016/j.ymben.2023.05.007] [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] [Received: 04/09/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023]
Abstract
Solubility and folding stability are key concerns for difficult-to-express proteins (DEPs) restricted by amino acid sequences and superarchitecture, resolved by the precise distribution of amino acids and molecular interactions as well as the assistance of the expression system. Therefore, an increasing number of tools are available to achieve efficient expression of DEPs, including directed evolution, solubilization partners, chaperones, and affluent expression hosts, among others. Furthermore, genome editing tools, such as transposons and CRISPR Cas9/dCas9, have been developed and expanded to construct engineered expression hosts capable of efficient expression ability of soluble proteins. Accounting for the accumulated knowledge of the pivotal factors in the solubility and folding stability of proteins, this review focuses on advanced technologies and tools of protein engineering, protein quality control systems, and the redesign of expression platforms in prokaryotic expression systems, as well as advances of the cell-free expression technologies for membrane proteins production.
Collapse
Affiliation(s)
- Jin-Ping Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jin-Song Gong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China.
| | - Chang Su
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
| | - Heng Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
| | - Zheng-Hong Xu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| |
Collapse
|
6
|
Kruth S, Nett M. Aurachins, Bacterial Antibiotics Interfering with Electron Transport Processes. Antibiotics (Basel) 2023; 12:1067. [PMID: 37370386 DOI: 10.3390/antibiotics12061067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Aurachins are farnesylated quinolone alkaloids of bacterial origin and excellent inhibitors of the respiratory chain in pro- and eukaryotes. Therefore, they have become important tool compounds for the investigation of electron transport processes and they also serve as lead structures for the development of antibacterial and antiprotozoal drugs. Especially aurachin D proved to be a valuable starting point for structure-activity relationship studies. Aurachin D is a selective inhibitor of the cytochrome bd oxidase, which has received increasing attention as a target for the treatment of infectious diseases caused by mycobacteria. Moreover, aurachin D possesses remarkable activities against Leishmania donovani, the causative agent of leishmaniasis. Aurachins are naturally produced by myxobacteria of the genus Stigmatella as well as by some Streptomyces and Rhodococcus strains. The recombinant production of these antibiotics turned out to be challenging due to their complex biosynthesis and their inherent toxicity. Recently, the biotechnological production of aurachin D was established in E. coli with a titer which is higher than previously reported from natural producer organisms.
Collapse
Affiliation(s)
- Sebastian Kruth
- Laboratory of Technical Biology, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
| | - Markus Nett
- Laboratory of Technical Biology, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
| |
Collapse
|
7
|
Cui D, Liu L, Sun L, Lin X, Lin L, Zhang C. Genome-wide analysis reveals Hsf1 maintains high transcript abundance of target genes controlled by strong constitutive promoter in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:72. [PMID: 37118827 PMCID: PMC10141939 DOI: 10.1186/s13068-023-02322-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/16/2023] [Indexed: 04/30/2023]
Abstract
BACKGROUND In synthetic biology, the strength of promoter elements is the basis for precise regulation of target gene transcription levels, which in turn increases the yield of the target product. However, the results of many researches proved that excessive transcription levels of target genes actually reduced the yield of the target product. This phenomenon has been found in studies using different microorganisms as chassis cells, thus, it becomes a bottleneck problem to improve the yield of the target product. RESULTS In this study, promoters PGK1p and TDH3p with different strengths were used to regulate the transcription level of alcohol acetyl transferase encoding gene ATF1. The results demonstrated that the strong promoter TDH3p decreased the production of ethyl acetate. The results of Real-time PCR proved that the transcription level of ATF1 decreased rapidly under the control of TDH3p, and the unfolded protein reaction was activated, which may be the reason for the abnormal production caused by the strong promoter. RNA-sequencing analysis showed that the overexpression of differential gene HSP30 increased the transcriptional abundance of ATF1 gene and production of ethyl acetate. Interestingly, deletion of the heat shock protein family (e.g., Hsp26, Hsp78, Hsp82) decreased the production of ethyl acetate, suggesting that the Hsp family was also involved in the regulation of ATF1 gene transcription. Furthermore, the results proved that the Hsf1, an upstream transcription factor of Hsps, had a positive effect on alleviating the unfolded protein response and that overexpression of Hsf1 reprogramed the pattern of ATF1 gene transcript levels. The combined overexpression of Hsf1 and Hsps further increased the production of ethyl acetate. In addition, kinase Rim15 may be involved in this regulatory pathway. Finally, the regulation effect of Hsf1 on recombinant strains constructed by other promoters was verified, which confirmed the universality of the strategy. CONCLUSIONS Our results elucidated the mechanism by which Rim15-Hsf1-Hsps pathway reconstructed the repression of high transcription level stress and increased the production of target products, thereby providing new insights and application strategies for the construction of recombinant strains in synthetic biology.
Collapse
Affiliation(s)
- Danyao Cui
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Ling Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Lijing Sun
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Xue Lin
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Liangcai Lin
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| | - Cuiying Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| |
Collapse
|
8
|
Guidi C, De Wannemaeker L, De Baets J, Demeester W, Maertens J, De Paepe B, De Mey M. Dynamic feedback regulation for efficient membrane protein production using a small RNA-based genetic circuit in Escherichia coli. Microb Cell Fact 2022; 21:260. [PMID: 36522655 PMCID: PMC9753035 DOI: 10.1186/s12934-022-01983-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Membrane proteins (MPs) are an important class of molecules with a wide array of cellular functions and are part of many metabolic pathways. Despite their great potential-as therapeutic drug targets or in microbial cell factory optimization-many challenges remain for efficient and functional expression in a host such as Escherichia coli. RESULTS A dynamically regulated small RNA-based circuit was developed to counter membrane stress caused by overexpression of different MPs. The best performing small RNAs were able to enhance the maximum specific growth rate with 123%. On culture level, the total MP production was increased two-to three-fold compared to a system without dynamic control. This strategy not only improved cell growth and production of the studied MPs, it also suggested the potential use for countering metabolic burden in general. CONCLUSIONS A dynamically regulated feedback circuit was developed that can sense metabolic stress caused by, in casu, the overexpression of an MP and responds to it by balancing the metabolic state of the cell and more specifically by downregulating the expression of the MP of interest. This negative feedback mechanism was established by implementing and optimizing simple-to-use genetic control elements based on post-transcriptional regulation: small non-coding RNAs. In addition to membrane-related stress when the MP accumulated in the cytoplasm as aggregates, the sRNA-based feedback control system was still effective for improving cell growth but resulted in a decreased total protein production. This result suggests promiscuity of the MP sensor for more than solely membrane stress.
Collapse
Affiliation(s)
- Chiara Guidi
- Centre for Synthetic Biology, Ghent University, 9000, Ghent, Belgium
| | | | - Jasmine De Baets
- Centre for Synthetic Biology, Ghent University, 9000, Ghent, Belgium
| | - Wouter Demeester
- Centre for Synthetic Biology, Ghent University, 9000, Ghent, Belgium
| | - Jo Maertens
- Centre for Synthetic Biology, Ghent University, 9000, Ghent, Belgium
| | - Brecht De Paepe
- Centre for Synthetic Biology, Ghent University, 9000, Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology, Ghent University, 9000, Ghent, Belgium.
| |
Collapse
|
9
|
Kruth S, Schibajew L, Nett M. Biocatalytic production of the antibiotic aurachin D in Escherichia coli. AMB Express 2022; 12:138. [DOI: 10.1186/s13568-022-01478-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022] Open
Abstract
Abstract
Aurachin D is a potent inhibitor of cytochrome bd oxidases, which are potential targets in the treatment of infectious diseases. In this study, our aim was to improve the biocatalytic production of aurachin D from a quinolone precursor molecule with recombinant Escherichia coli cells expressing the biosynthesis enzyme AuaA. In order to achieve a high-level production of this membrane-bound farnesyltransferase in E. coli, the expression of the auaA gene was translationally coupled to an upstream cistron in accordance with a bicistronic design (BCD) strategy. Screening of various BCD elements led to the identification of optimized auaA expression cassettes, which increased the aurachin D titer in E. coli up to 29-fold in comparison to T7-mediated expression. This titer could be further raised by codon optimization of auaA and by introducing the mevalonate pathway into the production strain. The latter measure was intended to improve the availability of farnesyl pyrophosphate, which is needed as a cosubstrate for the AuaA-catalyzed reaction. In sum, the described efforts resulted in a strain producing aurachin D with a titer that is 424 times higher than that obtained with the original, non-optimized expression host.
Graphical Abstract
Collapse
|
10
|
Vasilopoulou E, Giannakopoulou A, Kapsalis C, Michou M, Michoglou-Sergiou A, Kolisis FN, Skretas G. Second-Generation Escherichia coli SuptoxR Strains for High-Level Recombinant Membrane Protein Production. ACS Synth Biol 2022; 11:2599-2609. [PMID: 35922033 PMCID: PMC9397408 DOI: 10.1021/acssynbio.1c00598] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Escherichia coli is one of the most widely utilized hosts for recombinant protein production, including that of membrane proteins (MPs). We have recently engineered a specialized E. coli strain for enhanced recombinant MP production, termed SuptoxR. By appropriately co-expressing the effector gene rraA, SuptoxR can suppress the high toxicity, which is frequently observed during the MP-overexpression process, and, at the same time, enhance significantly the cellular accumulation of membrane-incorporated and properly folded recombinant MP. The combination of these two beneficial effects results in dramatically enhanced volumetric yields for various prokaryotic and eukaryotic MPs. Here, we engineered second-generation SuptoxR strains with further improved properties, so that they can achieve even higher levels of recombinant MP production. We searched for naturally occurring RraA variants with similar or improved MP toxicity-suppressing and production-promoting effects to that of the native E. coli RraA of the original SuptoxR strain. We found that the RraA proteins from Proteus mirabilis and Providencia stuartii can be even more potent enhancers of MP productivity than the E. coli RraA. By exploiting these two newly identified RraAs, we constructed two second-generation SuptoxR strains, termed SuptoxR2.1 and SuptoxR2.2, whose MP-production capabilities often surpass those of the original SuptoxR significantly. SuptoxR2.1 and SuptoxR2.2 are expected to become widely useful expression hosts for recombinant MP production in bacteria.
Collapse
Affiliation(s)
- Eleni Vasilopoulou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece.,Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Larisa 41500, Greece
| | - Artemis Giannakopoulou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
| | - Charalampos Kapsalis
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
| | - Myrsini Michou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece.,Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Larisa 41500, Greece
| | | | - Fragiskos N Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens 15772, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
| |
Collapse
|
11
|
Sun Y, Chen Z, Wang G, Lv H, Mao Y, Ma K, Wang Y. De novo production of versatile oxidized kaurene diterpenes in Escherichia coli. Metab Eng 2022; 73:201-213. [DOI: 10.1016/j.ymben.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/24/2022] [Accepted: 08/01/2022] [Indexed: 10/16/2022]
|
12
|
Selenourea for Experimental Phasing of Membrane Protein Crystals Grown in Lipid Cubic Phase. CRYSTALS 2022. [DOI: 10.3390/cryst12070976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Heavy-atom soaking has been a major method for experimental phasing, but it has been difficult for membrane proteins, partly owing to the lack of available sites in the scarce soluble domain for non-invasive heavy-metal binding. The lipid cubic phase (LCP) has proven to be a successful method for membrane protein crystallization, but experimental phasing with LCP-grown crystals remains difficult, and so far, only 68 such structures were phased experimentally. Here, the selenourea was tested as a soaking reagent for the single-wavelength anomalous dispersion (SAD) phasing of crystals grown in LCP. Using a single crystal, the structure of the glycerol 3-phosphate acyltransferase (PlsY, ~21 kDa), a very hydrophobic enzyme with 80% membrane-embedded residues, was solved. Remarkably, a total of 15 Se sites were found in the two monomers of PlsY, translating to one selenourea-binding site per every six residues in the accessible extramembrane protein. Structure analysis reveals that surface-exposed selenourea sites are mostly contributed by mainchain amides and carbonyls. This low-specificity binding pattern may explain its high loading ratio. Importantly, both the crystal diffraction quality and the LCP integrity were unaffected by selenourea soaking. Taken together, selenourea presents a promising and generally useful reagent for heavy-atom soaking of membrane protein crystals grown in LCP.
Collapse
|
13
|
Wireless portable bioelectronic nose device for multiplex monitoring toward food freshness/spoilage. Biosens Bioelectron 2022; 215:114551. [PMID: 35839622 DOI: 10.1016/j.bios.2022.114551] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/22/2022] [Accepted: 07/05/2022] [Indexed: 01/07/2023]
Abstract
Monitoring food freshness/spoilage is important to ensure food quality and safety. Current methods of food quality monitoring are mostly time-consuming and labor intensive processes that require massive analytical equipment. In this study, we developed a portable bioelectronic nose (BE-nose) integrated with trace amine-associated receptor (TAAR) nanodiscs (NDs), allowing food quality monitoring via the detection of food spoilage indicators, including the biogenic amines cadaverine (CV) and putrescine (PT). The olfactory receptors TAAR13c and TAAR13d, which have specific affinities for CV and PT, were produced and successfully reconstituted in ND structures. TAAR13 NDs BE-nose-based side-gated field-effect transistor (SG-FET) system was constructed by utilizing a graphene micropattern (GM) into which two types of olfactory NDs (TAAR13c ND and TAAR13d ND) were introduced, and this system showed ultrahigh sensitivity for a limit of detection (LOD) of 1 fM for CV and PT. Moreover, the binding affinities between the TAAR13 NDs and the indicators were confirmed by a tryptophan fluorescence quenching assay and biosimulations, in which the specific binding site was confirmed. Gas-phase indicators were detected by the TAAR13 NDs BE-nose platform, and the LODs for CV and PT were confirmed to be 26.48 and 7.29 ppb, respectively. In addition, TAAR13 NDs BE-nose was fabricated with commercial gas sensors as a portable platform for the measurement of NH3 and H2S, multiplexed monitoring was achieved with similar performance, and the change ratio of the indicators was observed in a real sample. The integration of commercial gas sensors on a BE-nose enhanced the accuracy and reliability for the quality monitoring of real food samples. These results indicate that the portable TAAR13 NDs BE-nose can be used to monitor CV and PT over a wide range of concentrations, therefore, the electronic nose platform can be utilized for monitoring the freshness/spoilage step in various foods.
Collapse
|
14
|
Ding X, Zheng Z, Zhao G, Wang L, Wang H, Yang Q, Zhang M, Li L, Wang P. Bottom-up synthetic biology approach for improving the efficiency of menaquinone-7 synthesis in Bacillus subtilis. Microb Cell Fact 2022; 21:101. [PMID: 35643569 PMCID: PMC9148487 DOI: 10.1186/s12934-022-01823-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/13/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Menaquinone-7 (MK-7), which is associated with complex and tightly regulated pathways and redox imbalances, is produced at low titres in Bacillus subtilis. Synthetic biology provides a rational engineering principle for the transcriptional optimisation of key enzymes and the artificial creation of cofactor regeneration systems without regulatory interference. This holds great promise for alleviating pathway bottlenecks and improving the efficiency of carbon and energy utilisation.
Results
We used a bottom-up synthetic biology approach for the synthetic redesign of central carbon and to improve the adaptability between material and energy metabolism in MK-7 synthesis pathways. First, the rate-limiting enzymes, 1-deoxyxylulose-5-phosphate synthase (DXS), isopentenyl-diphosphate delta-isomerase (Fni), 1-deoxyxylulose-5-phosphate reductase (DXR), isochorismate synthase (MenF), and 3-deoxy-7-phosphoheptulonate synthase (AroA) in the MK-7 pathway were sequentially overexpressed. Promoter engineering and fusion tags were used to overexpress the key enzyme MenA, and the titre of MK-7 was 39.01 mg/L. Finally, after stoichiometric calculation and optimisation of the cofactor regeneration pathway, we constructed two NADPH regeneration systems, enhanced the endogenous cofactor regeneration pathway, and introduced a heterologous NADH kinase (Pos5P) to increase the availability of NADPH for MK-7 biosynthesis. The strain expressing pos5P was more efficient in converting NADH to NADPH and had excellent MK-7 synthesis ability. Following three Design-Build-Test-Learn cycles, the titre of MK-7 after flask fermentation reached 53.07 mg/L, which was 4.52 times that of B. subtilis 168. Additionally, the artificially constructed cofactor regeneration system reduced the amount of NADH-dependent by-product lactate in the fermentation broth by 9.15%. This resulted in decreased energy loss and improved carbon conversion.
Conclusions
In summary, a "high-efficiency, low-carbon, cofactor-recycling" MK-7 synthetic strain was constructed, and the strategy used in this study can be generally applied for constructing high-efficiency synthesis platforms for other terpenoids, laying the foundation for the large-scale production of high-value MK-7 as well as terpenoids.
Collapse
|
15
|
Level of hM4D(Gi) DREADD Expression Determines Inhibitory and Neurotoxic Effects in the Hippocampus. eNeuro 2021; 8:ENEURO.0105-21.2021. [PMID: 34620623 PMCID: PMC8570686 DOI: 10.1523/eneuro.0105-21.2021] [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: 03/16/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
Selective neuromodulation using designer receptors exclusively activated by designer drugs (DREADDs) has become an increasingly important research tool, as well as an emerging therapeutic approach. However, the safety profile of DREADD expression is unknown. Here, different titers of adeno-associated viral (AAV) vector were administered in an attempt to vary total expression levels of the inhibitory DREADD hM4D(Gi) in excitatory hippocampal neurons. Male Sprague Dawley rats were injected with AAV2/7 encoding DREADD-mCherry, DREADD, or mCherry. Pronounced neuronal loss and neuroinflammatory reactions were observed after transduction with the high titer DREADD AAV, which also resulted in the highest DREADD expression levels. No such effects were observed in the mCherry control group, despite an equally high titer, nor in conditions where lower viral vector titers were injected. In the high titer DREADD conditions, dentate gyrus (DG) evoked potentials were inhibited on clozapine-induced activation of hM4D(Gi), while in low titer conditions DG evoked potentials were enhanced. Recordings of single neuronal activity nevertheless indicated a reduction in spontaneous firing of granule cell layer neurons. Our results indicate that prolonged, high levels of DREADD expression can have neurotoxic effects and that chemogenetic suppression of excitatory hippocampal neurons can paradoxically enhance DG evoked potentials.
Collapse
|
16
|
Tran KM, Lee HM, Thai TD, Shen J, Eyun SI, Na D. Synthetically engineered microbial scavengers for enhanced bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2021; 419:126516. [PMID: 34218189 DOI: 10.1016/j.jhazmat.2021.126516] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Microbial bioremediation has gained attention as a cheap, efficient, and sustainable technology to manage the increasing environmental pollution. Since microorganisms in nature are not evolved to degrade pollutants, there is an increasing demand for developing safer and more efficient pollutant-scavengers for enhanced bioremediation. In this review, we introduce the strategies and technologies developed in the field of synthetic biology and their applications to the construction of microbial scavengers with improved efficiency of biodegradation while minimizing the impact of genetically engineered microbial scavengers on ecosystems. In addition, we discuss recent achievements in the biodegradation of fastidious pollutants, greenhouse gases, and microplastics using engineered microbial scavengers. Using synthetic microbial scavengers and multidisciplinary technologies, toxic pollutants could be more easily eliminated, and the environment could be more efficiently recovered.
Collapse
Affiliation(s)
- Kha Mong Tran
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Thi Duc Thai
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Junhao Shen
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea.
| |
Collapse
|
17
|
Tailoring the evolution of BL21(DE3) uncovers a key role for RNA stability in gene expression toxicity. Commun Biol 2021; 4:963. [PMID: 34385596 PMCID: PMC8361080 DOI: 10.1038/s42003-021-02493-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Gene expression toxicity is an important biological phenomenon and a major bottleneck in biotechnology. Escherichia coli BL21(DE3) is the most popular choice for recombinant protein production, and various derivatives have been evolved or engineered to facilitate improved yield and tolerance to toxic genes. However, previous efforts to evolve BL21, such as the Walker strains C41 and C43, resulted only in decreased expression strength of the T7 system. This reveals little about the mechanisms at play and constitutes only marginal progress towards a generally higher producing cell factory. Here, we restrict the solution space for BL21(DE3) to evolve tolerance and isolate a mutant strain Evo21(DE3) with a truncation in the essential RNase E. This suggests that RNA stability plays a central role in gene expression toxicity. The evolved rne truncation is similar to a mutation previously engineered into the commercially available BL21Star(DE3), which challenges the existing assumption that this strain is unsuitable for expressing toxic proteins. We isolated another dominant mutation in a presumed substrate binding site of RNase E that improves protein production further when provided as an auxiliary plasmid. This makes it easy to improve other BL21 variants and points to RNases as prime targets for cell factory optimisation.
Collapse
|
18
|
Guo H, Xu N, Prell M, Königs H, Hermanns-Sachweh B, Lüscher B, Kappes F. Bacterial Growth Inhibition Screen (BGIS): harnessing recombinant protein toxicity for rapid and unbiased interrogation of protein function. FEBS Lett 2021; 595:1422-1437. [PMID: 33704777 DOI: 10.1002/1873-3468.14072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022]
Abstract
In two proof-of-concept studies, we established and validated the Bacterial Growth Inhibition Screen (BGIS), which explores recombinant protein toxicity in Escherichia coli as a largely overlooked and alternative means for basic characterization of functional eukaryotic protein domains. By applying BGIS, we identified an unrecognized RNA-interacting domain in the DEK oncoprotein (this study) and successfully combined BGIS with random mutagenesis as a screening tool for loss-of-function mutants of the DNA modulating domain of DEK [1]. Collectively, our findings shed new light on the phenomenon of recombinant protein toxicity in E. coli. Given the easy and rapid implementation and wide applicability, BGIS will extend the repertoire of basic methods for the identification, analysis and unbiased manipulation of proteins.
Collapse
Affiliation(s)
- Haihong Guo
- Institute for Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Germany
| | - Nengwei Xu
- Department of Biological Sciences, Suzhou Dushu Lake Science and Education Innovation District, Suzhou Industrial Park, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Malte Prell
- Institute for Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Germany
| | - Hiltrud Königs
- Institute of Pathology, Medical School, RWTH Aachen University, Germany
| | | | - Bernhard Lüscher
- Institute for Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Germany
| | - Ferdinand Kappes
- Institute for Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Germany
- Department of Biological Sciences, Suzhou Dushu Lake Science and Education Innovation District, Suzhou Industrial Park, Xi'an Jiaotong-Liverpool University, Suzhou, China
| |
Collapse
|
19
|
Ahmed MS, Lauersen KJ, Ikram S, Li C. Efflux Transporters' Engineering and Their Application in Microbial Production of Heterologous Metabolites. ACS Synth Biol 2021; 10:646-669. [PMID: 33751883 DOI: 10.1021/acssynbio.0c00507] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metabolic engineering of microbial hosts for the production of heterologous metabolites and biochemicals is an enabling technology to generate meaningful quantities of desired products that may be otherwise difficult to produce by traditional means. Heterologous metabolite production can be restricted by the accumulation of toxic products within the cell. Efflux transport proteins (transporters) provide a potential solution to facilitate the export of these products, mitigate toxic effects, and enhance production. Recent investigations using knockout lines, heterologous expression, and expression profiling of transporters have revealed candidates that can enhance the export of heterologous metabolites from microbial cell systems. Transporter engineering efforts have revealed that some exhibit flexible substrate specificity and may have broader application potentials. In this Review, the major superfamilies of efflux transporters, their mechanistic modes of action, selection of appropriate efflux transporters for desired compounds, and potential transporter engineering strategies are described for potential applications in enhancing engineered microbial metabolite production. Future studies in substrate recognition, heterologous expression, and combinatorial engineering of efflux transporters will assist efforts to enhance heterologous metabolite production in microbial hosts.
Collapse
Affiliation(s)
- Muhammad Saad Ahmed
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology (BIT), Beijing 100081, P. R. China
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Abid Majeed Road, The Mall, Rawalpindi 46000, Pakistan
| | - Kyle J. Lauersen
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Sana Ikram
- Beijing Higher Institution Engineering Research Center for Food Additives and Ingredients, Beijing Technology & Business University (BTBU), Beijing 100048, P. R. China
| | - Chun Li
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology (BIT), Beijing 100081, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
| |
Collapse
|
20
|
Michou M, Delivoria DC, Skretas G. High-level Production of Recombinant Membrane Proteins Using the Engineered Escherichia coli Strains SuptoxD and SuptoxR. Bio Protoc 2020; 10:e3710. [PMID: 33659374 DOI: 10.21769/bioprotoc.3710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/25/2020] [Accepted: 06/21/2020] [Indexed: 11/02/2022] Open
Abstract
We have previously described the development of two specialized Escherichia coli strains for high-level recombinant membrane protein (MP) production. These engineered strains, termed SuptoxD and SuptoxR, are capable of suppressing the cytotoxicity caused by MP overexpression and of producing greatly enhanced MP yields. Here, we present a Bio-protocol that describes gene overexpression and culturing conditions that maximize the accumulation of membrane-integrated and well-folded recombinant MPs in these strains.
Collapse
Affiliation(s)
- Myrsini Michou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece.,Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Larisa 41500, Greece
| | - Dafni C Delivoria
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
| |
Collapse
|
21
|
A novel knock out strategy to enhance recombinant protein expression in Escherichia coli. Microb Cell Fact 2020; 19:148. [PMID: 32703203 PMCID: PMC7376861 DOI: 10.1186/s12934-020-01407-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022] Open
Abstract
Background The expression of recombinant proteins triggers a stress response which downregulates key metabolic pathway genes leading to a decline in cellular health and feedback inhibition of both growth and protein expression. Instead of individually upregulating these downregulated genes or improving transcription rates by better vector design, an innovative strategy would be to block this stress response thereby ensuring a sustained level of protein expression. Results We postulated that the genes which are commonly up-regulated post induction may play the role of signalling messengers in mounting the cellular stress response. We identified those genes which have no known downstream regulatees and created knock outs which were then tested for GFP expression. Many of these knock outs showed significantly higher expression levels which was also sustained for longer periods. The highest product yield (Yp/x) was observed in a BW25113ΔcysJ knock out (Yp/x 0.57) and BW25113ΔelaA (Yp/x 0.49), whereas the Yp/x of the control W3110 strain was 0.08 and BW25113 was 0.16. Double knock out combinations were then created from the ten best performing single knock outs leading to a further enhancement in expression levels. Out of 45 double knock outs created, BW25113ΔelaAΔyhbC (Yp/x 0.7) and BW25113ΔcysJΔyhbC (Yp/x 0.64) showed the highest increase in product yield compared to the single gene mutant strains. We confirmed the improved performance of these knock outs by testing and obtaining higher levels of recombinant asparaginase expression, a system better suited for analysing sustained expression since it gets exported to the extracellular medium. Conclusion Creating key knock outs to block the CSR and enhance expression is a radically different strategy that can be synergistically combined with traditional methods of improving protein yields thus helping in the design of superior host platforms for protein expression.
Collapse
|
22
|
Zhu Y, Zhou C, Wang Y, Li C. Transporter Engineering for Microbial Manufacturing. Biotechnol J 2020; 15:e1900494. [PMID: 32298528 DOI: 10.1002/biot.201900494] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/30/2020] [Indexed: 01/08/2023]
Abstract
Microbes play an important role in biotransformation and biosynthesis of biofuels, natural products, and polymers. Therefore, microbial manufacturing has been widely used in medicine, industry, and agriculture. However, common strategies including enzyme engineering, pathway optimization, and host engineering are generally inadequate to obtain an efficient microbial production system. Transporter engineering provides an alternative strategy to promote the transmembrane transfer of substrates, intermediates, and final products in microbial cells and thus enhances production by alleviating feedback inhibition and cytotoxicity caused by final products. According to the current studies in transport engineering, native transporters usually have low expression and poor transportation ability, resulting in inefficient transport processes and microbial production. In this review, current approaches for transporter mining, characterization, and verification are comprehensively summarized. Practical approaches to enhance the transport system in engineered cells, such as balancing transporter overexpression and cell growth, and evolution of native transporters are discussed. Furthermore, the applications of transporter engineering in microbial manufacturing, including enhancement of substrate utilization, concentration of metabolic flux to the target pathway, and acceleration of efflux and recovery of products, demonstrate its outstanding advantages and promising prospects.
Collapse
Affiliation(s)
- Ying Zhu
- Department of Biochemical Engineering, Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Chen Zhou
- Department of Biochemical Engineering, Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Ying Wang
- Department of Biochemical Engineering, Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Chun Li
- Department of Biochemical Engineering, Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| |
Collapse
|
23
|
Michou M, Stergios A, Skretas G. SuptoxD2.0: A second-generation engineered Escherichia coli strain achieving further enhanced levels of recombinant membrane protein production. Biotechnol Bioeng 2020; 117:2434-2445. [PMID: 32383198 DOI: 10.1002/bit.27378] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 11/10/2022]
Abstract
The bacterium Escherichia coli is among the most popular hosts for recombinant protein production, including that of membrane proteins (MPs). We have recently generated the specialized MP-producing E. coli strain SuptoxD, which upon co-expression of the effector gene djlA, is capable of alleviating two major bottlenecks in bacterial recombinant MP production: it suppresses the toxicity that frequently accompanies the MP-overexpression process and it markedly increases the cellular accumulation of membrane incorporated and properly folded recombinant MP. Combined, these two positive effects result in dramatically enhanced volumetric yields for various recombinant MPs of both prokaryotic and eukaryotic origin. Based on the observation that djlA is found in the genomes of various pathogenic bacteria, the aim of the present work was to investigate (a) whether other naturally occurring DjlA variants can exert the MP toxicity-suppressing and production-promoting effects similarly to the E. coli DjlA and (b) if we can identify a DjlA variant whose efficiency surpasses that of the E. coli DjlA of SuptoxD. We report that a quite surprisingly broad variety of homologous DjlA proteins exert beneficial effects on recombinant MP when overexpressed in E. coli. Furthermore, we demonstrate that the Salmonella enterica DjlA is an even more potent enhancer of MP productivity compared with the E. coli DjlA of SuptoxD. Based on this, we constructed a second-generation SuptoxD strain, termed SuptoxD2.0, whose MP-production capabilities surpass significantly those of the original SuptoxD, and we anticipate that SuptoxD2.0 will become a broadly utilized expression host for recombinant MP production in bacteria.
Collapse
Affiliation(s)
- Myrsini Michou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.,Department of Biochemistry and Biotechnology, University of Thessaly, Larisa, Greece
| | - Angelos Stergios
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.,Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| |
Collapse
|
24
|
Michou M, Kapsalis C, Pliotas C, Skretas G. Optimization of Recombinant Membrane Protein Production in the Engineered Escherichia coli Strains SuptoxD and SuptoxR. ACS Synth Biol 2019; 8:1631-1641. [PMID: 31243979 DOI: 10.1021/acssynbio.9b00120] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Membrane proteins (MPs) execute a wide variety of critical biological functions in all living organisms and constitute approximately half of current targets for drug discovery. As in the case of soluble proteins, the bacterium Escherichia coli has served as a very popular overexpression host for biochemical/structural studies of membrane proteins as well. Bacterial recombinant membrane protein production, however, is typically hampered by poor cellular accumulation and severe toxicity for the host, which leads to low levels of final biomass and minute volumetric yields. In previous work, we generated the engineered E. coli strains SuptoxD and SuptoxR, which upon coexpression of the effector genes djlA or rraA, respectively, can suppress the cytotoxicity caused by MP overexpression and produce enhanced MP yields. Here, we systematically looked for gene overexpression and culturing conditions that maximize the accumulation of membrane-integrated and well-folded recombinant MPs in these strains. We have found that, under optimal conditions, SuptoxD and SuptoxR achieve greatly enhanced recombinant production for a variety of MP, irrespective of their archaeal, eubacterial, or eukaryotic origin. Furthermore, we demonstrate that the use of these engineered strains enables the production of well-folded recombinant MPs of high quality and at high yields, which are suitable for functional and structural studies. We anticipate that SuptoxD and SuptoxR will become broadly utilized expression hosts for recombinant MP production in bacteria.
Collapse
Affiliation(s)
- Myrsini Michou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
- Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Larisa 41500, Greece
| | - Charalampos Kapsalis
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY169ST, United Kingdom
| | - Christos Pliotas
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY169ST, United Kingdom
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
| |
Collapse
|
25
|
Claassens NJ, Finger-Bou M, Scholten B, Muis F, de Groot JJ, de Gier JW, de Vos WM, van der Oost J. Bicistronic Design-Based Continuous and High-Level Membrane Protein Production in Escherichia coli. ACS Synth Biol 2019; 8:1685-1690. [PMID: 31264406 PMCID: PMC6646956 DOI: 10.1021/acssynbio.9b00101] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Escherichia coli has been widely used as a platform microorganism for both membrane protein production and cell factory engineering. The current methods to produce membrane proteins in this organism require the induction of target gene expression and often result in unstable, low yields. Here, we present a method combining a constitutive promoter with a library of bicistronic design (BCD) elements, which enables inducer-free, tuned translation initiation for optimal protein production. Our system mediates stable, constitutive production of bacterial membrane proteins at yields that outperform those obtained with E. coli Lemo21(DE3), the current gold standard for bacterial membrane protein production. We envisage that the continuous, fine-tunable, and high-level production of membrane proteins by our method will greatly facilitate their study and their utilization in engineering cell factories.
Collapse
Affiliation(s)
- Nico J. Claassens
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Max Finger-Bou
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Bart Scholten
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Frederieke Muis
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jonas J. de Groot
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, FI-00014, Helsinki, Finland
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| |
Collapse
|
26
|
Pedro AQ, Queiroz JA, Passarinha LA. Smoothing membrane protein structure determination by initial upstream stage improvements. Appl Microbiol Biotechnol 2019; 103:5483-5500. [PMID: 31127356 PMCID: PMC7079970 DOI: 10.1007/s00253-019-09873-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 12/14/2022]
Abstract
Membrane proteins (MP) constitute 20–30% of all proteins encoded by the genome of various organisms and perform a wide range of essential biological functions. However, despite they represent the largest class of protein drug targets, a relatively small number high-resolution 3D structures have been obtained yet. Membrane protein biogenesis is more complex than that of the soluble proteins and its recombinant biosynthesis has been a major drawback, thus delaying their further structural characterization. Indeed, the major limitation in structure determination of MP is the low yield achieved in recombinant expression, usually coupled to low functionality, pinpointing the optimization target in recombinant MP research. Recently, the growing attention that have been dedicated to the upstream stage of MP bioprocesses allowed great advances, permitting the evolution of the number of MP solved structures. In this review, we analyse and discuss effective solutions and technical advances at the level of the upstream stage using prokaryotic and eukaryotic organisms foreseeing an increase in expression yields of correctly folded MP and that may facilitate the determination of their three-dimensional structure. A section on techniques used to protein quality control and further structure determination of MP is also included. Lastly, a critical assessment of major factors contributing for a good decision-making process related to the upstream stage of MP is presented.
Collapse
Affiliation(s)
- Augusto Quaresma Pedro
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-001, Covilhã, Portugal
- CICECO - Aveiro Institute of Materials, Department of Chemistry, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - João António Queiroz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-001, Covilhã, Portugal
| | - Luís António Passarinha
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-001, Covilhã, Portugal.
- UCIBIO@REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
| |
Collapse
|
27
|
Mathieu K, Javed W, Vallet S, Lesterlin C, Candusso MP, Ding F, Xu XN, Ebel C, Jault JM, Orelle C. Functionality of membrane proteins overexpressed and purified from E. coli is highly dependent upon the strain. Sci Rep 2019; 9:2654. [PMID: 30804404 PMCID: PMC6390180 DOI: 10.1038/s41598-019-39382-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/22/2019] [Indexed: 11/24/2022] Open
Abstract
Overexpression of correctly folded membrane proteins is a fundamental prerequisite for functional and structural studies. One of the most commonly used expression systems for the production of membrane proteins is Escherichia coli. While misfolded proteins typically aggregate and form inclusions bodies, membrane proteins that are addressed to the membrane and extractable by detergents are generally assumed to be properly folded. Accordingly, GFP fusion strategy is often used as a fluorescent proxy to monitor their expression and folding quality. Here we investigated the functionality of two different multidrug ABC transporters, the homodimer BmrA from Bacillus subtilis and the heterodimer PatA/PatB from Streptococcus pneumoniae, when produced in several E. coli strains with T7 expression system. Strikingly, while strong expression in the membrane of several strains could be achieved, we observed drastic differences in the functionality of these proteins. Moreover, we observed a general trend in which mild detergents mainly extract the population of active transporters, whereas a harsher detergent like Fos-choline 12 could solubilize transporters irrespective of their functionality. Our results suggest that the amount of T7 RNA polymerase transcripts may indirectly but notably impact the structure and activity of overexpressed membrane proteins, and advise caution when using GFP fusion strategy.
Collapse
Affiliation(s)
- Khadija Mathieu
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France
| | - Waqas Javed
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France.,Université Grenoble Alpes, CNRS, CEA, IBS, 38000, Grenoble, France
| | - Sylvain Vallet
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France
| | - Christian Lesterlin
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France
| | - Marie-Pierre Candusso
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France
| | - Feng Ding
- Department of Chemistry & Biochemistry, Old Dominion University, Norfolk, VA, 23529, USA
| | - Xiaohong Nancy Xu
- Department of Chemistry & Biochemistry, Old Dominion University, Norfolk, VA, 23529, USA
| | - Christine Ebel
- Université Grenoble Alpes, CNRS, CEA, IBS, 38000, Grenoble, France
| | - Jean-Michel Jault
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France.
| | - Cédric Orelle
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France.
| |
Collapse
|
28
|
Karyolaimos A, Ampah-Korsah H, Zhang Z, de Gier JW. Shaping Escherichia coli for recombinant membrane protein production. FEMS Microbiol Lett 2018; 365:5040224. [DOI: 10.1093/femsle/fny152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/18/2018] [Indexed: 12/29/2022] Open
Affiliation(s)
- Alexandros Karyolaimos
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Sv. Arrheniusväg 16C, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Henry Ampah-Korsah
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Sv. Arrheniusväg 16C, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Zhe Zhang
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Sv. Arrheniusväg 16C, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Sv. Arrheniusväg 16C, Stockholm University, SE-106 91, Stockholm, Sweden
| |
Collapse
|
29
|
Angius F, Ilioaia O, Amrani A, Suisse A, Rosset L, Legrand A, Abou-Hamdan A, Uzan M, Zito F, Miroux B. A novel regulation mechanism of the T7 RNA polymerase based expression system improves overproduction and folding of membrane proteins. Sci Rep 2018; 8:8572. [PMID: 29872064 PMCID: PMC5988807 DOI: 10.1038/s41598-018-26668-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 05/04/2018] [Indexed: 02/03/2023] Open
Abstract
Membrane protein (MP) overproduction is one of the major bottlenecks in structural genomics and biotechnology. Despite the emergence of eukaryotic expression systems, bacteria remain a cost effective and powerful tool for protein production. The T7 RNA polymerase (T7RNAP)-based expression system is a successful and efficient expression system, which achieves high-level production of proteins. However some foreign MPs require a fine-tuning of their expression to minimize the toxicity associated with their production. Here we report a novel regulation mechanism for the T7 expression system. We have isolated two bacterial hosts, namely C44(DE3) and C45(DE3), harboring a stop codon in the T7RNAP gene, whose translation is under the control of the basal nonsense suppressive activity of the BL21(DE3) host. Evaluation of hosts with superfolder green fluorescent protein (sfGFP) revealed an unprecedented tighter control of transgene expression with a marked accumulation of the recombinant protein during stationary phase. Analysis of a collection of twenty MP fused to GFP showed an improved production yield and quality of several bacterial MPs and of one human monotopic MP. These mutant hosts are complementary to the other existing T7 hosts and will increase the versatility of the T7 expression system.
Collapse
Affiliation(s)
- Federica Angius
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Oana Ilioaia
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Amira Amrani
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Annabelle Suisse
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France.,Helen L. and Martin S. Kimmel Center at the Skirball Institute for Biomolecular Medicine and Department of Cell Biology, NYU School of Medicine, New York, USA
| | - Lindsay Rosset
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Amélie Legrand
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Abbas Abou-Hamdan
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France.,Institut de Biologie Intégrative de la Cellule, CNRS, Gif sur Yvette, France
| | - Marc Uzan
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Francesca Zito
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Bruno Miroux
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France.
| |
Collapse
|
30
|
Gao W, Yin J, Bao L, Wang Q, Hou S, Yue Y, Yao W, Gao X. Engineering Extracellular Expression Systems in Escherichia coli Based on Transcriptome Analysis and Cell Growth State. ACS Synth Biol 2018; 7:1291-1302. [PMID: 29668266 DOI: 10.1021/acssynbio.7b00400] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Escherichia coli extracellular expression systems have a number of advantages over other systems, such as lower pyrogen levels and a simple purification process. Various approaches, such as the generation of leaky mutants via chromosomal engineering, have been explored for this expression system. However, extracellular protein yields in leaky mutants are relatively low compared to that in intracellular expression systems and therefore need to be improved. In this work, we describe the construction, characterization, and mechanism of enhanced extracellular expression in Escherichia coli. On the basis of the localizations, functions, and transcription levels of cell envelope proteins, we systematically elucidated the effects of multiple gene deletions on cell growth and extracellular expression using modified CRISPR/Cas9-based genome editing and a FlAsH labeling assay. High extracellular yields of heterologous proteins of different sizes were obtained by screening multiple gene mutations. The enhancement of extracellular secretion was associated with the derepression of translation and translocation. This work utilized universal methods in the design of extracellular expression systems for genes not directly associated with protein synthesis that were used to generate strains with higher protein expression capability. We anticipate that extracellular expression systems may help to shed light on the poorly understood aspects of these secretion processes as well as to further assist in the construction of engineered prokaryotic cells for efficient extracellular production of heterologous proteins.
Collapse
Affiliation(s)
- Wen Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Jun Yin
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Lichen Bao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Qun Wang
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Shan Hou
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Yali Yue
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Wenbing Yao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Xiangdong Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| |
Collapse
|
31
|
Basler G, Thompson M, Tullman-Ercek D, Keasling J. A Pseudomonas putida efflux pump acts on short-chain alcohols. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:136. [PMID: 29760777 PMCID: PMC5946390 DOI: 10.1186/s13068-018-1133-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 04/28/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND The microbial production of biofuels is complicated by a tradeoff between yield and toxicity of many fuels. Efflux pumps enable bacteria to tolerate toxic substances by their removal from the cells while bypassing the periplasm. Their use for the microbial production of biofuels can help to improve cell survival, product recovery, and productivity. However, no native efflux pump is known to act on the class of short-chain alcohols, important next-generation biofuels, and it was considered unlikely that such an efflux pump exists. RESULTS We report that controlled expression of the RND-type efflux pump TtgABC from Pseudomonas putida DOT-T1E strongly improved cell survival in highly toxic levels of the next-generation biofuels n-butanol, isobutanol, isoprenol, and isopentanol. GC-FID measurements indicated active efflux of n-butanol when the pump is expressed. Conversely, pump expression did not lead to faster growth in media supplemented with low concentrations of n-butanol and isopentanol. CONCLUSIONS TtgABC is the first native efflux pump shown to act on multiple short-chain alcohols. Its controlled expression can be used to improve cell survival and increase production of biofuels as an orthogonal approach to metabolic engineering. Together with the increased interest in P. putida for metabolic engineering due to its flexible metabolism, high native tolerance to toxic substances, and various applications of engineering its metabolism, our findings endorse the strain as an excellent biocatalyst for the high-yield production of next-generation biofuels.
Collapse
Affiliation(s)
- Georg Basler
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA USA
- Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Mitchell Thompson
- Department of Plant & Microbial Biology, University of California, Berkeley, CA USA
- Joint BioEnergy Institute, Emeryville, CA USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL USA
- Center for Synthetic Biology, Northwestern University, Technological Institute B486, Evanston, USA
| | - Jay Keasling
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA USA
- Joint BioEnergy Institute, Emeryville, CA USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
- Novo Nordisk Foundation Center for Sustainability, Technical University of Denmark, Copenhagen, Denmark
| |
Collapse
|
32
|
Improving membrane protein expression and function using genomic edits. Sci Rep 2017; 7:13030. [PMID: 29026162 PMCID: PMC5638813 DOI: 10.1038/s41598-017-12901-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/08/2017] [Indexed: 11/08/2022] Open
Abstract
Expression of membrane proteins often leads to growth inhibition and perturbs central metabolism and this burden varies with the protein being overexpressed. There are also known strain backgrounds that allow greater expression of membrane proteins but that differ in efficacy across proteins. We hypothesized that for any membrane protein, it may be possible to identify a modified strain background where its expression can be accommodated with less burden. To directly test this hypothesis, we used a bar-coded transposon insertion library in tandem with cell sorting to assess genome-wide impact of gene deletions on membrane protein expression. The expression of five membrane proteins (CyoB, CydB, MdlB, YidC, and LepI) and one soluble protein (GST), each fused to GFP, was examined. We identified Escherichia coli mutants that demonstrated increased membrane protein expression relative to that in wild type. For two of the proteins (CyoB and CydB), we conducted functional assays to confirm that the increase in protein expression also led to phenotypic improvement in function. This study represents a systematic approach to broadly identify genetic loci that can be used to improve membrane protein expression, and our method can be used to improve expression of any protein that poses a cellular burden.
Collapse
|
33
|
Gialama D, Delivoria DC, Michou M, Giannakopoulou A, Skretas G. Functional Requirements for DjlA- and RraA-Mediated Enhancement of Recombinant Membrane Protein Production in the Engineered Escherichia coli Strains SuptoxD and SuptoxR. J Mol Biol 2017; 429:1800-1816. [PMID: 28501587 DOI: 10.1016/j.jmb.2017.05.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 04/30/2017] [Accepted: 05/04/2017] [Indexed: 12/17/2022]
Abstract
In previous work, we have generated the engineered Escherichia coli strains SuptoxD and SuptoxR, which upon co-expression of the effector genes djlA or rraA, respectively, are capable of suppressing the cytotoxicity caused by membrane protein (MP) overexpression and of producing dramatically enhanced yields for a variety of recombinant MPs of both prokaryotic and eukaryotic origin. Here, we investigated the functional requirements for DnaJ-like protein A (DjlA)- and regulator of ribonuclease activity A (RraA)-mediated enhancement of recombinant MP production in these strains and show that: (i) DjlA and RraA act independently, that is, the beneficial effects of each protein on recombinant MP production occur through a mechanism that does not involve the other, and in a non-additive manner; (ii) full-length and membrane-bound DjlA is required for exerting its beneficial effects on recombinant MP production in E. coli SuptoxD; (iii) the MP production-promoting properties of DjlA in SuptoxD involve the action of the molecular chaperone DnaK but do not rely on the activation of the regulation of capsular synthesis response, a well-established consequence of djlA overexpression; (iv) the observed RraA-mediated effects in E. coli SuptoxR involve the ribonucleolytic activity of RNase E, but not that of its paralogous ribonuclease RNase G; and (v) DjlA and RraA are unique among similar E. coli proteins in their ability to promote bacterial recombinant MP production. These observations provide important clues about the molecular requirements for suppressed toxicity and enhanced MP accumulation in SuptoxD/SuptoxR and will guide future studies aiming to decipher the exact mechanism of DjlA- and RraA-mediated enhancement of recombinant MP production in these strains.
Collapse
Affiliation(s)
- Dimitra Gialama
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, 11635, Greece; Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, 15780, Greece
| | - Dafni Chrysanthi Delivoria
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, 11635, Greece; Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, 15780, Greece
| | - Myrsini Michou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, 11635, Greece; Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, 41500, Greece
| | - Artemis Giannakopoulou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, 11635, Greece
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, 11635, Greece.
| |
Collapse
|