1
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Dong Z, Li L, Du G, Zhang Y, Wang X, Li S, Xiang W. A previously unidentified sugar transporter for engineering of high-yield Streptomyces. Appl Microbiol Biotechnol 2024; 108:72. [PMID: 38194147 DOI: 10.1007/s00253-023-12964-9] [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: 08/28/2023] [Revised: 11/04/2023] [Accepted: 11/07/2023] [Indexed: 01/10/2024]
Abstract
Sugar transporters have significant contributions to regulate metabolic flux towards products and they are general potential targets for engineering of high-yield microbial cell factories. Streptomyces, well-known producers of natural product pharmaceuticals, contain an abundance of sugar transporters, while few of them are well characterized and applied. Here, we report a previously unidentified ATP-binding cassette (ABC) sugar transporter TP6568 found within a Streptomyces avermitilis transposon library, along with its key regulator GM006564. Subsequent in silico molecular docking and genetic experiments demonstrated that TP6568 possessed a broad substrate specificity. It could not only promote uptake of diverse monosaccharides and disaccharides, but also enhance the utilization of industrial carbon sources such as starch, sucrose, and dextrin. Constitutive overexpression of TP6568 resulted in decrease of residual total sugar by 36.16%, 39.04%, 38.40%, and 30.21% in engineered S. avermitilis S0, Streptomyces caniferus NEAU6, Streptomyces bingchenggensis BC-101-4, and Streptomyces roseosporus NRRL 11379 than their individual parent strain, respectively. Production of avermectin B1a, guvermectin, and milbemycin A3/A4 increased by 75.61%, 56.89%, and 41.13%, respectively. We then overexpressed TP6568 in combination with the regulator GM006564 in a high-yield strain S. avermitilis S45, and further fine-tuning of their overexpression levels boosted production of avermectin B1a by 50.97% to 7.02 g/L in the engineering strain. Our work demonstrates that TP6568 as a promising sugar transporter may have broad applications in construction of high-yield Streptomyces microbial cell factories for desirable natural product pharmaceuticals. KEY POINTS: • TP6568 from Streptomyces avermitilis was identified as a sugar transporter • TP6568 enhanced utilization of diverse industrially used sugars in Streptomyces • TP6568 is a useful transporter to construct high-yield Streptomyces cell factories.
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Affiliation(s)
- Zhuoxu Dong
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lei Li
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guozhong Du
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yanyan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiangjing Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China
| | - Shanshan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China.
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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2
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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.
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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
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3
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Fragoso-Jiménez JC, Gutierrez-Rios RM, Flores N, Martinez A, Lara AR, Delvigne F, Gosset G. Glucose consumption rate-dependent transcriptome profiling of Escherichia coli provides insight on performance as microbial factories. Microb Cell Fact 2022; 21:189. [PMID: 36100849 PMCID: PMC9472385 DOI: 10.1186/s12934-022-01909-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/27/2022] [Indexed: 11/21/2022] Open
Abstract
Background The modification of glucose import capacity is an engineering strategy that has been shown to improve the characteristics of Escherichia coli as a microbial factory. A reduction in glucose import capacity can have a positive effect on production strain performance, however, this is not always the case. In this study, E. coli W3110 and a group of four isogenic derivative strains, harboring single or multiple deletions of genes encoding phosphoenolpyruvate:sugar phosphotransferase system (PTS)-dependent transporters as well as non-PTS transporters were characterized by determining their transcriptomic response to reduced glucose import capacity. Results These strains were grown in bioreactors with M9 mineral salts medium containing 20 g/L of glucose, where they displayed specific growth rates ranging from 0.67 to 0.27 h−1, and specific glucose consumption rates (qs) ranging from 1.78 to 0.37 g/g h. RNA-seq analysis revealed a transcriptional response consistent with carbon source limitation among all the mutant strains, involving functions related to transport and metabolism of alternate carbon sources and characterized by a decrease in genes encoding glycolytic enzymes and an increase in gluconeogenic functions. A total of 107 and 185 genes displayed positive and negative correlations with qs, respectively. Functions displaying positive correlation included energy generation, amino acid biosynthesis, and sugar import. Conclusion Changes in gene expression of E. coli strains with impaired glucose import capacity could be correlated with qs values and this allowed an inference of the physiological state of each mutant. In strains with lower qs values, a gene expression pattern is consistent with energy limitation and entry into the stationary phase. This physiological state could explain why these strains display a lower capacity to produce recombinant protein, even when they show very low rates of acetate production. The comparison of the transcriptomes of the engineered strains employed as microbial factories is an effective approach for identifying favorable phenotypes with the potential to improve the synthesis of biotechnological products. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01909-y.
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Affiliation(s)
- Juan Carlos Fragoso-Jiménez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México
| | - Rosa María Gutierrez-Rios
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México
| | - Noemí Flores
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México
| | - Alfredo Martinez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México
| | - Alvaro R Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Ciudad de Mexico, México
| | - Frank Delvigne
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI) Gembloux Agro‑Bio Tech, University of Liège, Gembloux, Belgium
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México.
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4
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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.
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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
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5
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Bruni R, Laguerre A, Kaminska A, McSweeney S, Hendrickson WA, Liu Q. High-throughput cell-free screening of eukaryotic membrane protein expression in lipidic mimetics. Protein Sci 2022; 31:639-651. [PMID: 34910339 PMCID: PMC8862427 DOI: 10.1002/pro.4259] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 12/16/2022]
Abstract
Membrane proteins play essential roles in cellular function and metabolism. Nonetheless, biophysical and structural studies of membrane proteins are impeded by the difficulty of their expression in and purification from heterologous cell-based systems. As an alternative to these cell-based systems, cell-free protein synthesis has proven to be an exquisite method for screening membrane protein targets in a variety of lipidic mimetics. Here we report a high-throughput screening workflow and apply it to screen 61 eukaryotic membrane protein targets. For each target, we tested its expression in lipidic mimetics: two detergents, two liposomes, and two nanodiscs. We show that 35 membrane proteins (57%) can be expressed in a soluble fraction in at least one of the mimetics with the two detergents performing significantly better than nanodiscs and liposomes, in that order. Using the established cell-free workflow, we studied the production and biophysical assays for mitochondrial pyruvate carrier (MPC) complexes. Our studies show that the complexes produced in cell-free are functionally competent in complex formation and substrate binding. Our results highlight the utility of using cell-free systems for screening and production of eukaryotic membrane proteins.
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Affiliation(s)
- Renato Bruni
- Center on Membrane Protein Production and Analysis (COMPPÅ)New York Structural Biology CenterNew YorkNew YorkUSA
| | - Aisha Laguerre
- Center on Membrane Protein Production and Analysis (COMPPÅ)New York Structural Biology CenterNew YorkNew YorkUSA,Present address:
Roche DiagnosticsSanta ClaraCaliforniaUSA
| | - Anna‐Maria Kaminska
- Center on Membrane Protein Production and Analysis (COMPPÅ)New York Structural Biology CenterNew YorkNew YorkUSA,Present address:
New York Blood CenterNew YorkNew YorkUSA
| | | | - Wayne A. Hendrickson
- Center on Membrane Protein Production and Analysis (COMPPÅ)New York Structural Biology CenterNew YorkNew YorkUSA,Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
| | - Qun Liu
- NSLS‐II, Brookhaven National LaboratoryUptonNew YorkUSA,Biology DepartmentBrookhaven National LaboratoryUptonNew YorkUSA
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6
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Petrovskaya LE, Ziganshin RH, Kryukova EA, Zlobinov AV, Gapizov SS, Shingarova LN, Mironov VA, Lomakina GY, Dolgikh DA, Kirpichnikov MP. Increased Synthesis of a Magnesium Transporter MgtA During Recombinant Autotransporter Expression in Escherichia coli. Appl Biochem Biotechnol 2021; 193:3672-3703. [PMID: 34351586 DOI: 10.1007/s12010-021-03634-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/19/2021] [Indexed: 12/01/2022]
Abstract
Overproduction of the membrane proteins in Escherichia coli cells is a common approach to obtain sufficient material for their functional and structural studies. However, the efficiency of this process can be limited by toxic effects which decrease the viability of the host and lead to low yield of the product. During the expression of the esterase autotransporter AT877 from Psychrobacter cryohalolentis K5T, we observed significant growth inhibition of the C41(DE3) cells in comparison with the same cells producing other recombinant proteins. Induction of AT877 synthesis also resulted in the elevated expression of a magnesium transporter MgtA and decreased ATP content of the cells. To characterize the response to overexpression of the autotransporter in bacterial cells, we performed a comparative analysis of their proteomic profile by mass spectrometry. According to the obtained data, E. coli cells which synthesize AT877 experience complex stress condition presumably associated with secretion apparatus overloading and improper localization of the recombinant protein. Several response pathways were shown to be activated by AT877 overproduction including Cpx, PhoP/PhoQ, Psp, and σE The obtained results open new opportunities for optimization of the recombinant membrane protein expression in E. coli for structural studies and biotechnological applications.
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Affiliation(s)
- Lada E Petrovskaya
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia.
| | - Rustam H Ziganshin
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
| | - Elena A Kryukova
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
- Emanuel Institute of Biochemical Physics, Kosygina str., 4, Moscow, 119334, Russia
| | - Alexander V Zlobinov
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
| | - Sultan Sh Gapizov
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
- Emanuel Institute of Biochemical Physics, Kosygina str., 4, Moscow, 119334, Russia
- Department of Biology, M. V. Lomonosov Moscow State University, Leninskie gory, 1, Moscow, 119234, Russia
| | - Lyudmila N Shingarova
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
| | - Vasiliy A Mironov
- Roche Diagnostics Rus LLC, Letnikovskaya str. 2/2, Moscow, 115114, Russia
| | - Galina Yu Lomakina
- Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory, 1/3, Moscow, 119991, Russia
- Bauman Moscow State Technical University, Baumanskaya 2-ya, 5/1, Moscow, 105005, Russia
| | - Dmitriy A Dolgikh
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
- Emanuel Institute of Biochemical Physics, Kosygina str., 4, Moscow, 119334, Russia
- Department of Biology, M. V. Lomonosov Moscow State University, Leninskie gory, 1, Moscow, 119234, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin & Ovchinnikov Institute of Bioorganic , Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
- Department of Biology, M. V. Lomonosov Moscow State University, Leninskie gory, 1, Moscow, 119234, Russia
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7
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Escherichia coli as a platform microbial host for systems metabolic engineering. Essays Biochem 2021; 65:225-246. [PMID: 33956149 DOI: 10.1042/ebc20200172] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/19/2022]
Abstract
Bio-based production of industrially important chemicals and materials from non-edible and renewable biomass has become increasingly important to resolve the urgent worldwide issues including climate change. Also, bio-based production, instead of chemical synthesis, of food ingredients and natural products has gained ever increasing interest for health benefits. Systems metabolic engineering allows more efficient development of microbial cell factories capable of sustainable, green, and human-friendly production of diverse chemicals and materials. Escherichia coli is unarguably the most widely employed host strain for the bio-based production of chemicals and materials. In the present paper, we review the tools and strategies employed for systems metabolic engineering of E. coli. Next, representative examples and strategies for the production of chemicals including biofuels, bulk and specialty chemicals, and natural products are discussed, followed by discussion on materials including polyhydroxyalkanoates (PHAs), proteins, and nanomaterials. Lastly, future perspectives and challenges remaining for systems metabolic engineering of E. coli are discussed.
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8
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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.
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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
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9
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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.
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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
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10
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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.
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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
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11
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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.
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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.
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12
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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
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13
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Jia B, Jeon CO. High-throughput recombinant protein expression in Escherichia coli: current status and future perspectives. Open Biol 2017; 6:rsob.160196. [PMID: 27581654 PMCID: PMC5008019 DOI: 10.1098/rsob.160196] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/03/2016] [Indexed: 12/26/2022] Open
Abstract
The ease of genetic manipulation, low cost, rapid growth and number of previous studies have made Escherichia coli one of the most widely used microorganism species for producing recombinant proteins. In this post-genomic era, challenges remain to rapidly express and purify large numbers of proteins for academic and commercial purposes in a high-throughput manner. In this review, we describe several state-of-the-art approaches that are suitable for the cloning, expression and purification, conducted in parallel, of numerous molecules, and we discuss recent progress related to soluble protein expression, mRNA folding, fusion tags, post-translational modification and production of membrane proteins. Moreover, we address the ongoing efforts to overcome various challenges faced in protein expression in E. coli, which could lead to an improvement of the current system from trial and error to a predictable and rational design.
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Affiliation(s)
- Baolei Jia
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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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.
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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.
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15
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Gialama D, Kostelidou K, Michou M, Delivoria DC, Kolisis FN, Skretas G. Development of Escherichia coli Strains That Withstand Membrane Protein-Induced Toxicity and Achieve High-Level Recombinant Membrane Protein Production. ACS Synth Biol 2017; 6:284-300. [PMID: 27797488 DOI: 10.1021/acssynbio.6b00174] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Membrane proteins perform critical cellular functions in all living organisms and constitute major targets for drug discovery. Escherichia coli has been the most popular overexpression host for membrane protein biochemical/structural studies. Bacterial production of recombinant membrane proteins, however, is typically hampered by poor cellular accumulation and severe toxicity for the host, which leads to low final biomass and minute volumetric yields. In this work, we aimed to rewire the E. coli protein-producing machinery to withstand the toxicity caused by membrane protein overexpression in order to generate engineered bacterial strains with the ability to achieve high-level membrane protein production. To achieve this, we searched for bacterial genes whose coexpression can suppress membrane protein-induced toxicity and identified two highly potent effectors: the membrane-bound DnaK cochaperone DjlA, and the inhibitor of the mRNA-degrading activity of the E. coli RNase E, RraA. E. coli strains coexpressing either djlA or rraA, termed SuptoxD and SuptoxR, respectively, accumulated markedly higher levels of final biomass and produced dramatically enhanced yields for a variety of prokaryotic and eukaryotic recombinant membrane proteins. In all tested cases, either SuptoxD, or SuptoxR, or both, outperformed the capabilities of commercial strains frequently utilized for recombinant membrane protein production purposes.
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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
| | - Kalliopi Kostelidou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens 11635, Greece
| | - Myrsini Michou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens 11635, 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
| | - Fragiskos N. Kolisis
- Laboratory
of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens 15780, Greece
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens 11635, Greece
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16
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Lee YJ, Lee R, Lee SH, Yim SS, Jeong KJ. Enhanced secretion of recombinant proteins via signal recognition particle (SRP)-dependent secretion pathway by deletion of rrsE in Escherichia coli. Biotechnol Bioeng 2016; 113:2453-61. [PMID: 27111103 DOI: 10.1002/bit.25997] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/07/2016] [Accepted: 04/21/2016] [Indexed: 12/29/2022]
Abstract
Although signal recognition particle (SRP)-dependent secretion pathway, which is characterized by co-translational translocation, helps prevent cytoplasmic aggregation of proteins before secretion, its limited capacity for the protein secretion is a major hurdle for utilizing the pathway as an attractive route for secretory production of recombinant proteins. Therefore, we developed an Escherichia coli mutant, whose efficiency of secretion via the SRP pathway was dramatically increased. First, we developed a novel FACS-based screening system by combining a periplasmic display system (PECS) and direct fluorescent labeling with the organoarsenic compound, FlAsH-EDT2 . With this screening system, transposon-insertion library of E. coli was screened, and then we isolated mutants which exhibited higher protein production through the SRP pathway than the parental strain. From the genetic analysis, we found that all isolated mutants had the same mutation-disruption of the 16S rRNA gene (rrsE). The positive effect of rrsE deficiency on protein secretion via the SRP pathway was successfully demonstrated using various model proteins including endogenous SRP-dependent proteins, antibodies, and G protein-coupled receptor. For the large-scale production of IgG and GPCR, we performed fed-batch cultivation with the rrsE-deficient mutant, and very high yields of IgG (0.4 g/L) and GPCR (1.4 g/L) were obtained. Biotechnol. Bioeng. 2016;113: 2453-2461. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Yong Jae Lee
- Department of Chemical and Biomolecular Engineering (BK21 Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Roojin Lee
- Department of Chemical and Biomolecular Engineering (BK21 Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Se Hwa Lee
- Department of Chemical and Biomolecular Engineering (BK21 Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Sung Sun Yim
- Department of Chemical and Biomolecular Engineering (BK21 Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering (BK21 Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea. .,KAIST Institute for the BioCentury, Yuseong-gu, Daejeon, Republic of Korea.
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17
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Jo M, Jung ST. Engineering therapeutic antibodies targeting G-protein-coupled receptors. Exp Mol Med 2016; 48:e207. [PMID: 26846450 PMCID: PMC4892866 DOI: 10.1038/emm.2015.105] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 09/21/2015] [Indexed: 12/16/2022] Open
Abstract
G-protein–coupled receptors (GPCRs) are one of the most attractive therapeutic target classes because of their critical roles in intracellular signaling and their clinical relevance to a variety of diseases, including cancer, infection and inflammation. However, high conformational variability, the small exposed area of extracellular epitopes and difficulty in the preparation of GPCR antigens have delayed both the isolation of therapeutic anti-GPCR antibodies as well as studies on the structure, function and biochemical mechanisms of GPCRs. To overcome the challenges in generating highly specific anti-GPCR antibodies with enhanced efficacy and safety, various forms of antigens have been successfully designed and employed for screening with newly emerged systems based on laboratory animal immunization and high-throughput-directed evolution.
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Affiliation(s)
- Migyeong Jo
- Department of Bio and Nano Chemistry, Kookmin University, Seoul, Korea
| | - Sang Taek Jung
- Department of Bio and Nano Chemistry, Kookmin University, Seoul, Korea
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18
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Hattab G, Warschawski DE, Moncoq K, Miroux B. Escherichia coli as host for membrane protein structure determination: a global analysis. Sci Rep 2015; 5:12097. [PMID: 26160693 PMCID: PMC4498379 DOI: 10.1038/srep12097] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/11/2015] [Indexed: 11/13/2022] Open
Abstract
The structural biology of membrane proteins (MP) is hampered by the difficulty in producing and purifying them. A comprehensive analysis of protein databases revealed that 213 unique membrane protein structures have been obtained after production of the target protein in E. coli. The primary expression system used was the one based on the T7 RNA polymerase, followed by the arabinose and T5 promoter based expression systems. The C41λ(DE3) and C43λ(DE3) bacterial mutant hosts have contributed to 28% of non E. coli membrane protein structures. A large scale analysis of expression protocols demonstrated a preference for a combination of bacterial host-vector together with a bimodal distribution of induction temperature and of inducer concentration. Altogether our analysis provides a set of rules for the optimal use of bacterial expression systems in membrane protein production.
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Affiliation(s)
- Georges Hattab
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, CNRS, Univ Paris Diderot, Sorbonne Paris Cité, PSL research university, Paris, France
| | - Dror E Warschawski
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, CNRS, Univ Paris Diderot, Sorbonne Paris Cité, PSL research university, Paris, France
| | - Karine Moncoq
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, CNRS, Univ Paris Diderot, Sorbonne Paris Cité, PSL research university, Paris, France
| | - Bruno Miroux
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, CNRS, Univ Paris Diderot, Sorbonne Paris Cité, PSL research university, Paris, France
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19
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Bacterial-based membrane protein production. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:1739-49. [PMID: 24200679 DOI: 10.1016/j.bbamcr.2013.10.023] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 10/20/2013] [Accepted: 10/29/2013] [Indexed: 01/08/2023]
Abstract
Escherichia coli is by far the most widely used bacterial host for the production of membrane proteins. Usually, different strains, culture conditions and production regimes are screened for to design the optimal production process. However, these E. coli-based screening approaches often do not result in satisfactory membrane protein production yields. Recently, it has been shown that (i) E. coli strains with strongly improved membrane protein production characteristics can be engineered or selected for, (ii) many membrane proteins can be efficiently produced in E. coli-based cell-free systems, (iii) bacteria other than E. coli can be used for the efficient production of membrane proteins, and, (iv) membrane protein variants that retain functionality but are produced at higher yields than the wild-type protein can be engineered or selected for. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Recombinant polypeptide production in E. coli: towards a rational approach to improve the yields of functional proteins. Microb Cell Fact 2013; 12:101. [PMID: 24176192 PMCID: PMC3832250 DOI: 10.1186/1475-2859-12-101] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 10/30/2013] [Indexed: 11/16/2022] Open
Abstract
The development of complementary technologies enabled the successful production of recombinant polypeptides in bacteria and opened to biology researchers new avenues as obtaining suitable amounts of proteins necessary for their experimental work became easy, fast, and inexpensive. Nevertheless, the recombinant approach remained somehow unpredictable, since many constructs resisted to apparent production or accumulated as aggregates. Several factors and physical/chemical conditions that could improve the accumulation of native-like protein were identified. At the same time, it was acknowledged that the outcome of most of them was erratic and that almost any protein required its own specific optimized set of conditions to achieve its correct folding. The attempt to understand the critical points specific for recombinant protein production missed the goal of setting universally useful protocols, but contributed to the increase of the rate of success by proposing always new empiric combinations. Nevertheless, the results published in the recent literature allow for a better comprehension of some key mechanisms controlling protein production in E. coli and could enable the elaboration of rational methodologies for improving the quantitative and qualitative features of the produced polypeptides. This result will be achieved when the identification of the limiting step that impairs the accomplishment of the native folding for any single construct will become straightforward. This minireview will discuss how factors such as the expression rate, the folding machinery, and the secretion efficiency may impact the final protein yields.
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21
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Skretas G, Kolisis FN. Combinatorial approaches for inverse metabolic engineering applications. Comput Struct Biotechnol J 2013; 3:e201210021. [PMID: 24688681 PMCID: PMC3962077 DOI: 10.5936/csbj.201210021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 02/11/2013] [Accepted: 02/17/2013] [Indexed: 11/22/2022] Open
Abstract
Traditional metabolic engineering analyzes biosynthetic and physiological pathways, identifies bottlenecks, and makes targeted genetic modifications with the ultimate goal of increasing the production of high-value products in living cells. Such efforts have led to the development of a variety of organisms with industrially relevant properties. However, there are a number of cellular phenotypes important for research and the industry for which the rational selection of cellular targets for modification is not easy or possible. In these cases, strain engineering can be alternatively carried out using “inverse metabolic engineering”, an approach that first generates genetic diversity by subjecting a population of cells to a particular mutagenic process, and then utilizes genetic screens or selections to identify the clones exhibiting the desired phenotype. Given the availability of an appropriate screen for a particular property, the success of inverse metabolic engineering efforts usually depends on the level and quality of genetic diversity which can be generated. Here, we review classic and recently developed combinatorial approaches for creating such genetic diversity and discuss the use of these methodologies in inverse metabolic engineering applications.
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Affiliation(s)
- Georgios Skretas
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N Kolisis
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens - Zografou Campus, Athens, Greece
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22
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Optimizing Membrane Protein Overexpression in the Escherichia coli strain Lemo21(DE3). J Mol Biol 2012; 423:648-59. [DOI: 10.1016/j.jmb.2012.07.019] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 07/20/2012] [Accepted: 07/24/2012] [Indexed: 11/19/2022]
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23
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Kang J, Gu P, Wang Y, Li Y, Yang F, Wang Q, Qi Q. Engineering of an N-acetylneuraminic acid synthetic pathway in Escherichia coli. Metab Eng 2012; 14:623-9. [DOI: 10.1016/j.ymben.2012.09.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 08/27/2012] [Accepted: 09/04/2012] [Indexed: 10/27/2022]
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