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Goswami S, Singer SW, Simmons BA, Awasthi D. Optimization of electroporation method and promoter evaluation for type-1 methanotroph, Methylotuvimicrobium alcaliphilum. Front Bioeng Biotechnol 2024; 12:1412410. [PMID: 38812915 PMCID: PMC11133525 DOI: 10.3389/fbioe.2024.1412410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 04/26/2024] [Indexed: 05/31/2024] Open
Abstract
Methanotrophic bacteria are promising hosts for methane bioconversion to biochemicals or bioproducts. However, due to limitations associated with long genetic manipulation timelines and, lack of choice in genetic tools required for strain engineering, methanotrophs are currently not employed for bioconversion technologies. In this study, a rapid and reproducible electroporation protocol is developed for type 1 methanotroph, Methylotuvimicrobium alcaliphilum using common laboratory solutions, analyzing optimal electroshock voltages and post-shock cell recovery time. Successful reproducibility of the developed method was achieved when different replicative plasmids were assessed on lab adapted vs. wild-type M. alcaliphilum strains (DASS vs. DSM19304). Overall, a ∼ 3-fold decrease in time is reported with use of electroporation protocol developed here, compared to conjugation, which is the traditionally employed approach. Additionally, an inducible (3-methyl benzoate) and a constitutive (sucrose phosphate synthase) promoter is characterized for their strength in driving gene expression.
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Affiliation(s)
- Shubhasish Goswami
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Steven W. Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Joint BioEnergy Institute, Emeryville, CA, United States
| | - Blake A. Simmons
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Joint BioEnergy Institute, Emeryville, CA, United States
| | - Deepika Awasthi
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Joint BioEnergy Institute, Emeryville, CA, United States
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2
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Muñoz-Gómez SA. The energetic costs of cellular complexity in evolution. Trends Microbiol 2024:S0966-842X(24)00003-9. [PMID: 38307786 DOI: 10.1016/j.tim.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/04/2024]
Abstract
The evolutionary history of cells has been marked by drastic increases in complexity. Some hypothesize that such cellular complexification requires a massive energy flux as the origin of new features is hypothetically more energetically costly than their evolutionary maintenance. However, it remains unclear how increases in cellular complexity demand more energy. I propose that the early evolution of new genes with weak functions imposes higher energetic costs by overexpression before their functions are evolutionarily refined. In the long term, the accumulation of new genes deviates resources away from growth and reproduction. Accrued cellular complexity further requires additional infrastructure for its maintenance. Altogether, this suggests that larger and more complex cells are defined by increased survival but lower reproductive capacity.
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3
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Arbel-Groissman M, Menuhin-Gruman I, Naki D, Bergman S, Tuller T. Fighting the battle against evolution: designing genetically modified organisms for evolutionary stability. Trends Biotechnol 2023; 41:1518-1531. [PMID: 37442714 DOI: 10.1016/j.tibtech.2023.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/10/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023]
Abstract
Synthetic biology has made significant progress in many areas, but a major challenge that has received limited attention is the evolutionary stability of synthetic constructs made of heterologous genes. The expression of these constructs in microorganisms, that is, production of proteins that are not necessary for the organism, is a metabolic burden, leading to a decrease in relative fitness and make the synthetic constructs unstable over time. This is a significant concern for the synthetic biology community, particularly when it comes to bringing this technology out of the laboratory. In this review, we discuss the issue of evolutionary stability in synthetic biology and review the available tools to address this challenge.
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Affiliation(s)
- Matan Arbel-Groissman
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Itamar Menuhin-Gruman
- School of Mathematical Sciences, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Doron Naki
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Shaked Bergman
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel; The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 6997801, Israel.
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4
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Feedforward growth rate control mitigates gene activation burden. Nat Commun 2022; 13:7054. [PMID: 36396941 PMCID: PMC9672102 DOI: 10.1038/s41467-022-34647-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 11/02/2022] [Indexed: 11/18/2022] Open
Abstract
Heterologous gene activation causes non-physiological burden on cellular resources that cells are unable to adjust to. Here, we introduce a feedforward controller that actuates growth rate upon activation of a gene of interest (GOI) to compensate for such a burden. The controller achieves this by activating a modified SpoT enzyme (SpoTH) with sole hydrolysis activity, which lowers ppGpp level and thus increases growth rate. An inducible RelA+ expression cassette further allows to precisely set the basal level of ppGpp, and thus nominal growth rate, in any bacterial strain. Without the controller, activation of the GOI decreased growth rate by more than 50%. With the controller, we could activate the GOI to the same level without growth rate defect. A cell strain armed with the controller in co-culture enabled persistent population-level activation of a GOI, which could not be achieved by a strain devoid of the controller. The feedforward controller is a tunable, modular, and portable tool that allows dynamic gene activation without growth rate defects for bacterial synthetic biology applications.
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5
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Sun ML, Shi TQ, Lin L, Ledesma-Amaro R, Ji XJ. Advancing Yarrowia lipolytica as a superior biomanufacturing platform by tuning gene expression using promoter engineering. BIORESOURCE TECHNOLOGY 2022; 347:126717. [PMID: 35031438 DOI: 10.1016/j.biortech.2022.126717] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Yarrowia lipolytica is recognized as an excellent non-conventional yeast in the field of biomanufacturing, where it is used as a host to produce oleochemicals, terpenes, organic acids, polyols and recombinant proteins. Consequently, metabolic engineering of this yeast is becoming increasingly popular to advance it as a superior biomanufacturing platform, of which promoters are the most basic elements for tuning gene expression. Endogenous promoters of Yarrowia lipolytica were reviewed, which are the basis for promoter engineering. The engineering strategies, such as hybrid promoter engineering, intron enhancement promoter engineering, and transcription factor-based inducible promoter engineering are described. Additionally, the applications of Yarrowia lipolytica promoter engineering to rationally reconstruct biosynthetic gene clusters and improve the genome-editing efficiency of the CRISPR-Cas systems were reviewed. Finally, research needs and future directions for promoter engineering are also discussed in this review.
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Affiliation(s)
- Mei-Li Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210046, People's Republic of China
| | - Lu Lin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China.
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6
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Fordjour E, Mensah EO, Hao Y, Yang Y, Liu X, Li Y, Liu CL, Bai Z. Toward improved terpenoids biosynthesis: strategies to enhance the capabilities of cell factories. BIORESOUR BIOPROCESS 2022; 9:6. [PMID: 38647812 PMCID: PMC10992668 DOI: 10.1186/s40643-022-00493-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/04/2022] [Indexed: 02/22/2023] Open
Abstract
Terpenoids form the most diversified class of natural products, which have gained application in the pharmaceutical, food, transportation, and fine and bulk chemical industries. Extraction from naturally occurring sources does not meet industrial demands, whereas chemical synthesis is often associated with poor enantio-selectivity, harsh working conditions, and environmental pollutions. Microbial cell factories come as a suitable replacement. However, designing efficient microbial platforms for isoprenoid synthesis is often a challenging task. This has to do with the cytotoxic effects of pathway intermediates and some end products, instability of expressed pathways, as well as high enzyme promiscuity. Also, the low enzymatic activity of some terpene synthases and prenyltransferases, and the lack of an efficient throughput system to screen improved high-performing strains are bottlenecks in strain development. Metabolic engineering and synthetic biology seek to overcome these issues through the provision of effective synthetic tools. This review sought to provide an in-depth description of novel strategies for improving cell factory performance. We focused on improving transcriptional and translational efficiencies through static and dynamic regulatory elements, enzyme engineering and high-throughput screening strategies, cellular function enhancement through chromosomal integration, metabolite tolerance, and modularization of pathways.
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Affiliation(s)
- Eric Fordjour
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Emmanuel Osei Mensah
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Yunpeng Hao
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Yankun Yang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Xiuxia Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Ye Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Chun-Li Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China.
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China.
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7
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McBride CD, Del Vecchio D. Predicting Composition of Genetic Circuits with Resource Competition: Demand and Sensitivity. ACS Synth Biol 2021; 10:3330-3342. [PMID: 34780149 DOI: 10.1021/acssynbio.1c00281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The design of genetic circuits typically relies on characterization of constituent modules in isolation to predict the behavior of modules' composition. However, it has been shown that the behavior of a genetic module changes when other modules are in the cell due to competition for shared resources. In order to engineer multimodule circuits that behave as intended, it is thus necessary to predict changes in the behavior of a genetic module when other modules load cellular resources. Here, we introduce two characteristics of circuit modules: the demand for cellular resources and the sensitivity to resource loading. When both are known for every genetic module in a circuit library, they can be used to predict any module's behavior upon addition of any other module to the cell. We develop an experimental approach to measure both characteristics for any circuit module using a resource sensor module. Using the measured resource demand and sensitivity for each module in a library, the outputs of the modules can be accurately predicted when they are inserted in the cell in arbitrary combinations. These resource competition characteristics may be used to inform the design of genetic circuits that perform as predicted despite resource competition.
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Affiliation(s)
- Cameron D. McBride
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02142, United States
| | - Domitilla Del Vecchio
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02142, United States
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8
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Santos-Navarro FN, Vignoni A, Boada Y, Picó J. RBS and Promoter Strengths Determine the Cell-Growth-Dependent Protein Mass Fractions and Their Optimal Synthesis Rates. ACS Synth Biol 2021; 10:3290-3303. [PMID: 34767708 PMCID: PMC8689641 DOI: 10.1021/acssynbio.1c00131] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Models of gene expression
considering host–circuit interactions
are relevant for understanding both the strategies and associated
trade-offs that cell endogenous genes have evolved and for the efficient
design of heterologous protein expression systems and synthetic genetic
circuits. Here, we consider a small-size model of gene expression
dynamics in bacterial cells accounting for host–circuit interactions
due to limited cellular resources. We define the cellular resources
recruitment strength as a key functional coefficient that explains
the distribution of resources among the host and the genes of interest
and the relationship between the usage of resources and cell growth.
This functional coefficient explicitly takes into account lab-accessible
gene expression characteristics, such as promoter and ribosome binding
site (RBS) strengths, capturing their interplay with the growth-dependent
flux of available free cell resources. Despite its simplicity, the
model captures the differential role of promoter and RBS strengths
in the distribution of protein mass fractions as a function of growth
rate and the optimal protein synthesis rate with remarkable fit to
the experimental data from the literature for Escherichia
coli. This allows us to explain why endogenous genes
have evolved different strategies in the expression space and also
makes the model suitable for model-based design of exogenous synthetic
gene expression systems with desired characteristics.
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Affiliation(s)
- Fernando N. Santos-Navarro
- Synthetic Biology and Biosystems Control Lab, Institut d’Automàtica i Informàtica Industrial, Universitat Politècnica de València, Camí de Vera S/N, 46022 Valencia, Spain
| | - Alejandro Vignoni
- Synthetic Biology and Biosystems Control Lab, Institut d’Automàtica i Informàtica Industrial, Universitat Politècnica de València, Camí de Vera S/N, 46022 Valencia, Spain
| | - Yadira Boada
- Synthetic Biology and Biosystems Control Lab, Institut d’Automàtica i Informàtica Industrial, Universitat Politècnica de València, Camí de Vera S/N, 46022 Valencia, Spain
| | - Jesús Picó
- Synthetic Biology and Biosystems Control Lab, Institut d’Automàtica i Informàtica Industrial, Universitat Politècnica de València, Camí de Vera S/N, 46022 Valencia, Spain
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9
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Chae YK, Kim H. Development of an Autoinducible Plasmid for Recombinant Protein Production. Protein Pept Lett 2021; 28:1398-1407. [PMID: 34749604 DOI: 10.2174/0929866528666211105113750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/09/2021] [Accepted: 09/01/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND The production of recombinant proteins in E. coli involves such factors as host strains, expression vectors, culture media, and induction methods. The typical procedure to produce heterologous proteins consists of the following: (1) insertion of the target gene into a suitable vector to construct an overexpression plasmid, (2) transformation of a strain specialized for protein production with the constructed plasmid DNA, (3) growth of the host in a suitable medium and induction of the protein production at a right moment, and (4) further growth to get the maximum yield. There are hurdles involved in each of these steps, and researchers have developed many materials or methods, which often require special recipes or procedures. OBJECTIVE To eliminate the special requirements for the recombinant protein production by using readily available materials. Also to save time and effort in the routine protein production work. METHOD We started with a vector capable of producing a target protein fused to the C-terminus of the maltose binding protein (MBP). The mCherry (red fluorescent protein) gene was fused to MBP. It acted as a reporter in the initial screening procedure. The original lethal gene (barnase) was replaced with sacB. We chose 3 stationary phase promoters, and made hybrids of them by mixing halves from each one. The T5 promoter was replaced with these stationary phase promoters or their hybrids. The best plasmid was selected by the color intensity of the cell pellet. MBP and GST genes were inserted in place of sacB, and their production yields were compared with the original plasmid in the conventional way of expression. RESULTS We constructed an expression plasmid with an autoinducible promoter working in a host that was not specially designed for protein production and in a TB medium which did not contain any secret ingredient, nor was difficult to prepare unlike Studier's defined medium. This plasmid also contains a color indicator which turns red when protein production is successful. We tested our system with the maltose binding protein (MBP) and the glutathione S-transferase (GST), and showed that both proteins were produced to a level comparable to what the commercial medium and/or the specialized strain yielded. CONCLUSION We developed a plasmid equipped with an autoinducible promoter, a hybrid of the two promoters which were activated at the stationary phase. This plasmid does not need a special E. coli strain nor a sophisticated nor an expensive medium. It produces an intense red (or pink) color, which can be used as an indicator of a successful production of the target protein and as a predictive measure of the amount of the produced target protein. We speculate that this plasmid will have its greatest advantage when growing cells at low temperatures which would inevitably take a long time. .
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Affiliation(s)
- Young Kee Chae
- Department of Chemistry, Sejong University, 209 Neungdong-Ro, Gwangjin-Gu, Seoul. Korea
| | - Hakbeom Kim
- Department of Chemistry, Sejong University, 209 Neungdong-Ro, Gwangjin-Gu, Seoul. Korea
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10
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Hyun J, Jun S, Lim H, Cho H, You SH, Ha SJ, Min JJ, Bang D. Engineered Attenuated Salmonella typhimurium Expressing Neoantigen Has Anticancer Effects. ACS Synth Biol 2021; 10:2478-2487. [PMID: 34525796 DOI: 10.1021/acssynbio.1c00097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Neoantigen vaccines are an immunotherapy strategy for treating cancer. The vaccine degrades quickly, so the strategy must include protection and precise targeting for immune cell stimulation. In this study, we engineered attenuated Salmonella typhimurium, which is highly infiltrative to tumors, to act as a carrier for Neoantigen peptide vaccine. Our system used a constitutive promoter vector, so that a single injection of Salmonella expressing Neoantigen could be used without requiring additional induction injections. In vivo experiments on bacteria-treated mice showed that Neoantigen expressed by the engineered carrier infiltrated tumors and resulted in suppressed tumor growth, higher survival rates and longer survival times, a relative increase of CD4 and CD8 T cells, and cytokine release. These results indicate that engineered Salmonella can be used as a carrier for Neoantigen immunotherapy.
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Affiliation(s)
- Jungheun Hyun
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
| | - Soyeong Jun
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hyeonseob Lim
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hyunjun Cho
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sung-Hwan You
- Laboratory of In Vivo Molecular Imaging, Institute for Molecular Imaging and Theranostics, Chonnam National University Hwasun Hospital, Jeonnam, 58128, Republic of Korea
| | - Sang-Jun Ha
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jung-Joon Min
- Laboratory of In Vivo Molecular Imaging, Institute for Molecular Imaging and Theranostics, Chonnam National University Hwasun Hospital, Jeonnam, 58128, Republic of Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
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11
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Myers KS, Noguera DR, Donohue TJ. Promoter Architecture Differences among Alphaproteobacteria and Other Bacterial Taxa. mSystems 2021; 6:e0052621. [PMID: 34254822 PMCID: PMC8407463 DOI: 10.1128/msystems.00526-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/17/2021] [Indexed: 11/20/2022] Open
Abstract
Much of our knowledge of bacterial transcription initiation has been derived from studying the promoters of Escherichia coli and Bacillus subtilis. Given the expansive diversity across the bacterial phylogeny, it is unclear how much of this knowledge can be applied to other organisms. Here, we report on bioinformatic analyses of promoter sequences of the primary σ factor (σ70) by leveraging publicly available transcription start site (TSS) sequencing data sets for nine bacterial species spanning five phyla. This analysis identifies previously unreported differences in the -35 and -10 elements of σ70-dependent promoters in several groups of bacteria. We found that Actinobacteria and Betaproteobacteria σ70-dependent promoters lack the TTG triad in their -35 element, which is predicted to be conserved across the bacterial phyla. In addition, the majority of the Alphaproteobacteria σ70-dependent promoters analyzed lacked the thymine at position -7 that is highly conserved in other phyla. Bioinformatic examination of the Alphaproteobacteria σ70-dependent promoters identifies a significant overrepresentation of essential genes and ones encoding proteins with common cellular functions downstream of promoters containing an A, C, or G at position -7. We propose that transcription of many σ70-dependent promoters in Alphaproteobacteria depends on the transcription factor CarD, which is an essential protein in several members of this phylum. Our analysis expands the knowledge of promoter architecture across the bacterial phylogeny and provides new information that can be used to engineer bacteria for use in medical, environmental, agricultural, and biotechnological processes. IMPORTANCE Transcription of DNA to RNA by RNA polymerase is essential for cells to grow, develop, and respond to stress. Understanding the process and control of transcription is important for health, disease, the environment, and biotechnology. Decades of research on a few bacteria have identified promoter DNA sequences that are recognized by the σ subunit of RNA polymerase. We used bioinformatic analyses to reveal previously unreported differences in promoter DNA sequences across the bacterial phylogeny. We found that many Actinobacteria and Betaproteobacteria promoters lack a sequence in their -35 DNA recognition element that was previously assumed to be conserved and that Alphaproteobacteria lack a thymine residue at position -7, also previously assumed to be conserved. Our work reports important new information about bacterial transcription, illustrates the benefits of studying bacteria across the phylogenetic tree, and proposes new lines of future investigation.
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Affiliation(s)
- Kevin S. Myers
- Wisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- Wisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Civil & Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Timothy J. Donohue
- Wisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
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12
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Stukenberg D, Hensel T, Hoff J, Daniel B, Inckemann R, Tedeschi JN, Nousch F, Fritz G. The Marburg Collection: A Golden Gate DNA Assembly Framework for Synthetic Biology Applications in Vibrio natriegens. ACS Synth Biol 2021; 10:1904-1919. [PMID: 34255476 DOI: 10.1021/acssynbio.1c00126] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Vibrio natriegens is known as the world's fastest growing organism with a doubling time of less than 10 min. This incredible growth speed empowers V. natriegens as a chassis for synthetic and molecular biology, potentially replacing E. coli in many applications. While first genetic parts have been built and tested for V. natriegens, a comprehensive toolkit containing well-characterized and standardized parts did not exist. To close this gap, we created the Marburg Collection-a highly flexible Golden Gate cloning toolbox optimized for the emerging chassis organism V. natriegens, containing 191 genetic parts. The Marburg Collection overcomes the paradigm of plasmid construction-integrating inserts into a backbone-by enabling the de novo assembly of plasmids from basic genetic parts. This allows users to select the plasmid replication origin and resistance part independently, which is highly advantageous when limited knowledge about the behavior of those parts in the target organism is available. Additional design highlights of the Marburg Collection are novel connector parts, which facilitate modular circuit assembly and, optionally, the inversion of individual transcription units to reduce transcriptional crosstalk in multigene constructs. To quantitatively characterize the genetic parts contained in the Marburg Collection in V. natriegens, we developed a reliable microplate reader measurement workflow for reporter experiments and overcame organism-specific challenges. We think the Marburg Collection with its thoroughly characterized parts will provide a valuable resource for the growing V. natriegens community.
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Affiliation(s)
- Daniel Stukenberg
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg 35032, Germany
- Max-Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Tobias Hensel
- Faculty of Chemistry, Philipps-Universität Marburg, Marburg 35032, Germany
| | - Josef Hoff
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg 35032, Germany
- Max-Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Benjamin Daniel
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg 35032, Germany
- Institute of Microbiology, ETH Zurich, Zürich 8093, Switzerland
| | - René Inckemann
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg 35032, Germany
- Max-Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Jamie N. Tedeschi
- School of Molecular Sciences, The University of Western Australia, Perth 6009, Australia
| | - Franziska Nousch
- Faculty of Chemistry, Philipps-Universität Marburg, Marburg 35032, Germany
| | - Georg Fritz
- School of Molecular Sciences, The University of Western Australia, Perth 6009, Australia
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13
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Wu Q, Fu J, Sun J, Wang X, Tang X, Lu W, Tan C, Li L, Deng X, Xu Q. A plant CitPITP1 protein-coding exon sequence serves as a promoter in bacteria. J Biotechnol 2021; 339:1-13. [PMID: 34298024 DOI: 10.1016/j.jbiotec.2021.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/17/2021] [Accepted: 07/18/2021] [Indexed: 11/19/2022]
Abstract
Genetic manipulation of plant genes in prokaryotes has been widely used in molecular biology, but the function of a DNA sequence is far from being fully known. Here, we discovered that a plant protein-coding gene containing the CRAL_TRIO domain serves as a promoter in bacteria. We firstly characterized CitPITP1 from Citrus, which contains the CRAL_TRIO domain, and identified a 64-bp sequence (key64) that is critical for prokaryotic promoter activity. In vitro experiments indicated that the bacterial RNA polymerase subunit RpoD specifically binds to key64. We then expanded our research to fungi, plant and animal species to identify key64-like sequences. Five such prokaryotic promoters were isolated from Amborella, Rice, Arabidopsis and Citrus. Two conserved motifs were identified, and mutation analysis indicated that the nucleotides at positions 7, 29 and 30 are crucial for key64-like transcription activity. We detected full-length recombinant CitPITP1 from E. coli, and visualized a CitPITP1-GFP fusion protein in plant cells, supporting the idea that CitPITP1 encodes a protein. However, although exon 4 of CitPITP1 contained key64, it did not demonstrate promoter activity in plants. Our study describes a new basal promoter, provides evidence for neofunction of gene elements across different kingdoms, and provides new knowledge for the modular design of promoters.
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Affiliation(s)
- Qingjiang Wu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430000, China
| | - Jialing Fu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430000, China
| | - Juan Sun
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430000, China
| | - Xia Wang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430000, China
| | - Xiaomei Tang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430000, China
| | - Wenjia Lu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430000, China
| | - Chen Tan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430000, China
| | - Li Li
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA; Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, 14853, USA
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430000, China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430000, China.
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14
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Gene Expression Space Shapes the Bioprocess Trade-Offs among Titer, Yield and Productivity. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11135859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Optimal gene expression is central for the development of both bacterial expression systems for heterologous protein production, and microbial cell factories for industrial metabolite production. Our goal is to fulfill industry-level overproduction demands optimally, as measured by the following key performance metrics: titer, productivity rate, and yield (TRY). Here we use a multiscale model incorporating the dynamics of (i) the cell population in the bioreactor, (ii) the substrate uptake and (iii) the interaction between the cell host and expression of the protein of interest. Our model predicts cell growth rate and cell mass distribution between enzymes of interest and host enzymes as a function of substrate uptake and the following main lab-accessible gene expression-related characteristics: promoter strength, gene copy number and ribosome binding site strength. We evaluated the differential roles of gene transcription and translation in shaping TRY trade-offs for a wide range of expression levels and the sensitivity of the TRY space to variations in substrate availability. Our results show that, at low expression levels, gene transcription mainly defined TRY, and gene translation had a limited effect; whereas, at high expression levels, TRY depended on the product of both, in agreement with experiments in the literature.
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15
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Rational engineering strategies for achieving high-yield, high-quality and high-stability of natural product production in actinomycetes. Metab Eng 2021; 67:198-215. [PMID: 34166765 DOI: 10.1016/j.ymben.2021.06.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/30/2021] [Accepted: 06/19/2021] [Indexed: 12/11/2022]
Abstract
Actinomycetes are recognized as excellent producers of microbial natural products, which have a wide range of applications, especially in medicine, agriculture and stockbreeding. The three main indexes of industrialization (titer, purity and stability) must be taken into overall consideration in the manufacturing process of natural products. Over the past decades, synthetic biology techniques have expedited the development of industrially competitive strains with excellent performances. Here, we summarize various rational engineering strategies for upgrading the performance of industrial actinomycetes, which include enhancing the yield of natural products, eliminating the by-products and improving the genetic stability of engineered strains. Furthermore, the current challenges and future perspectives for optimizing the industrial strains more systematically through combinatorial engineering strategies are also discussed.
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16
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Morschett H, Tenhaef N, Hemmerich J, Herbst L, Spiertz M, Dogan D, Wiechert W, Noack S, Oldiges M. Robotic integration enables autonomous operation of laboratory scale stirred tank bioreactors with model-driven process analysis. Biotechnol Bioeng 2021; 118:2759-2769. [PMID: 33871051 DOI: 10.1002/bit.27795] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/14/2021] [Accepted: 04/10/2021] [Indexed: 12/19/2022]
Abstract
Given its geometric similarity to large-scale production plants and the excellent possibilities for precise process control and monitoring, the classic stirred tank bioreactor (STR) still represents the gold standard for bioprocess development at a laboratory scale. However, compared to microbioreactor technologies, bioreactors often suffer from a low degree of process automation and deriving key performance indicators (KPIs) such as specific rates or yields often requires manual sampling and sample processing. A widely used parallelized STR setup was automated by connecting it to a liquid handling system and controlling it with a custom-made process control system. This allowed for the setup of a flexible modular platform enabling autonomous operation of the bioreactors without any operator present. Multiple unit operations like automated inoculation, sampling, sample processing and analysis, and decision making, for example for automated induction of protein production were implemented to achieve such functionality. The data gained during application studies was used for fitting of bioprocess models to derive relevant KPIs being in good agreement with literature. By combining the capabilities of STRs with the flexibility of liquid handling systems, this platform technology can be applied to a multitude of different bioprocess development pipelines at laboratory scale.
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Affiliation(s)
- Holger Morschett
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Niklas Tenhaef
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Johannes Hemmerich
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Laura Herbst
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Markus Spiertz
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Deniz Dogan
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Computational Systems Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
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17
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Gupta JK, Srivastava S. The Effect of Promoter and RBS Combination on the Growth and Glycogen Productivity of Sodium-Dependent Bicarbonate Transporter (SbtA) Overexpressing Synechococcus sp. PCC 7002 Cells. Front Microbiol 2021; 12:607411. [PMID: 33927699 PMCID: PMC8076525 DOI: 10.3389/fmicb.2021.607411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/22/2021] [Indexed: 12/20/2022] Open
Abstract
Sodium dependent bicarbonate transporter, SbtA is a high-affinity, inducible bicarbonate transporter in cyanobacterial cells. Our previous work has shown that overexpression of this transporter can significantly increase growth and glycogen accumulation in Synechococcus sp. PCC 7002 cells. In this work, we have tested the effect of two different RBS sequences (RBS1: GGAGGA and RBS2: AGGAGA) and three different promoters (PcpcB, PcpcB560, and PrbcL2) on the growth and glycogen production in SbtA-overexpressing Synechococcus sp. PCC 7002 cells. Our results show that PcpcB or PcpcB560 were more effective than PrbcL2 in increasing the growth and glycogen content. The choice of RBS sequence had relatively minor effect, though RBS2 was more effective than RBS1. The transformant E, with PcpcB560 and RBS2, showed the highest growth. The biomass after 5 days of growth on air or 1% CO2 was increased by about 90% in the strain E compared to PCC 7002 cells. All transformants overexpressing SbtA had higher glycogen content. However, growing the cells with bubbling of 1% CO2 did not increase cellular glycogen content any further. The strain E had about 80% higher glycogen content compared to WT PCC 7002 cells. Therefore, the glycogen productivity of the strain E grown with air-bubbling was about 2.5-fold that of the WT PCC 7002 cells grown similarly. Additionally, some of the transformants had higher chlorophyll content while all the transformants had higher carotenoid content compared to the PCC 7002 cells, suggesting interaction between carbon transport and pigment levels. Thus, this work shows that the choice of photosynthetic promoters and RBSs sequences can impact growth and glycogen accumulation in SbtA-overexpressing cells.
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Affiliation(s)
- Jai Kumar Gupta
- Systems Biology for Biofuels Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Shireesh Srivastava
- Systems Biology for Biofuels Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India.,Department of Biotechnology-International Centre for Genetic Engineering and Biotechnology (DBT-ICGEB), Centre for Advanced Bioenergy Research, New Delhi, India
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18
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Abstract
It is generally recognized that proteins constitute the key cellular component in shaping microbial phenotypes. Due to limited cellular resources and space, optimal allocation of proteins is crucial for microbes to facilitate maximum proliferation rates while allowing a flexible response to environmental changes. To account for the growth condition-dependent proteome in the constraint-based metabolic modeling of Escherichia coli, we consolidated a coarse-grained protein allocation approach with the explicit consideration of enzymatic constraints on reaction fluxes. Besides representing physiologically relevant wild-type phenotypes and flux distributions, the resulting protein allocation model (PAM) advances the predictability of the metabolic responses to genetic perturbations. A main driver of mutant phenotypes was ascribed to inherited regulation patterns in protein distribution among metabolic enzymes. Moreover, the PAM correctly reflected metabolic responses to an augmented protein burden imposed by the heterologous expression of green fluorescent protein. In summary, we were able to model the effects of important and frequently applied metabolic engineering approaches on microbial metabolism. Therefore, we want to promote the integration of protein allocation constraints into classical constraint-based models to foster their predictive capabilities and application for strain analysis and engineering purposes. IMPORTANCE Predictive metabolic models are important, e.g., for generating biological knowledge and designing microbes with superior performance for target compound production. Yet today’s whole-cell models either show insufficient predictive capabilities or are computationally too expensive to be applied to metabolic engineering purposes. By linking the inherent genotype-phenotype relationship to a complete representation of the proteome, the PAM advances the accuracy of simulated phenotypes and intracellular flux distributions of E. coli. Being equally computationally lightweight as classical stoichiometric models and allowing for the application of established in silico tools, the PAM and related simulation approaches will foster the use of a model-driven metabolic research. Applications range from the investigation of mechanisms of microbial evolution to the determination of optimal strain design strategies in metabolic engineering, thus supporting basic scientists and engineers alike.
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19
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Kastenhofer J, Rajamanickam V, Libiseller-Egger J, Spadiut O. Monitoring and control of E. coli cell integrity. J Biotechnol 2021; 329:1-12. [PMID: 33485861 DOI: 10.1016/j.jbiotec.2021.01.009] [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] [Received: 09/11/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/15/2022]
Abstract
Soluble expression of recombinant proteins in E. coli is often done by translocation of the product across the inner membrane (IM) into the periplasm, where it is retained by the outer membrane (OM). While the integrity of the IM is strongly coupled to viability and impurity release, a decrease in OM integrity (corresponding to increased "leakiness") leads to accumulation of product in the extracellular space, strongly impacting the downstream process. Whether leakiness is desired or not, differential monitoring and control of IM and OM integrity are necessary for an efficient E. coli bioprocess in compliance with the guidelines of Quality by Design and Process Analytical Technology. In this review, we give an overview of relevant monitoring tools, summarize the research on factors affecting E. coli membrane integrity and provide a brief discussion on how the available monitoring technology can be implemented in real-time control of E. coli cultivations.
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Affiliation(s)
- Jens Kastenhofer
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Gumpendorfer Strasse 1a, 1060, Vienna, Austria
| | - Vignesh Rajamanickam
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Gumpendorfer Strasse 1a, 1060, Vienna, Austria
| | - Julian Libiseller-Egger
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Gumpendorfer Strasse 1a, 1060, Vienna, Austria
| | - Oliver Spadiut
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.
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20
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Choi BH, Hwang HJ, Lee JE, Oh SH, Hwang JS, Lee BY, Lee PC. Microbial Production of Retinyl Palmitate and Its Application as a Cosmeceutical. Antioxidants (Basel) 2020; 9:antiox9111130. [PMID: 33202630 PMCID: PMC7698207 DOI: 10.3390/antiox9111130] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 01/07/2023] Open
Abstract
Chemically synthesized retinyl palmitate has been widely used in the cosmetic and biotechnology industry. In this study, we aimed to demonstrate the microbial production of retinyl palmitate and the benefits of microbial retinyl palmitate in skin physiology. A heterologous retinyl palmitate biosynthesis pathway was reconstructed in metabolically engineered Escherichia coli using synthetic expression modules from Pantoea agglomerans, Salinibacter ruber, and Homo sapiens. High production of retinyl palmitate (69.96 ± 2.64 mg/L) was obtained using a fed-batch fermentation process. Moreover, application of purified microbial retinyl palmitate to human foreskin HS68 fibroblasts led to increased cellular retinoic acid-binding protein 2 (CRABP2) mRNA level [1.7-fold (p = 0.001) at 100 μg/mL], acceleration of cell proliferation, and enhancement of procollagen synthesis [111% (p < 0.05) at 100 μg/mL], strongly indicating an anti-ageing-related effect of this substance. These results would pave the way for large-scale production of retinyl palmitate in microbial systems and represent the first evidence for the application of microbial retinyl palmitate as a cosmeceutical.
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Affiliation(s)
- Bo Hyun Choi
- Department of Molecular Science and Technology, Ajou University, World cup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do 16499, Korea; (B.H.C.); (H.J.H.); (S.H.O.); (B.Y.L.)
| | - Hee Jin Hwang
- Department of Molecular Science and Technology, Ajou University, World cup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do 16499, Korea; (B.H.C.); (H.J.H.); (S.H.O.); (B.Y.L.)
| | - Ji Eun Lee
- Department of Genetic Engineering & Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Korea; (J.E.L.); (J.S.H.)
| | - Soon Hwan Oh
- Department of Molecular Science and Technology, Ajou University, World cup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do 16499, Korea; (B.H.C.); (H.J.H.); (S.H.O.); (B.Y.L.)
| | - Jae Sung Hwang
- Department of Genetic Engineering & Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Korea; (J.E.L.); (J.S.H.)
| | - Bun Yeoul Lee
- Department of Molecular Science and Technology, Ajou University, World cup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do 16499, Korea; (B.H.C.); (H.J.H.); (S.H.O.); (B.Y.L.)
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology, Ajou University, World cup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do 16499, Korea; (B.H.C.); (H.J.H.); (S.H.O.); (B.Y.L.)
- Correspondence: ; Tel.: +82-31-219-2461
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21
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Kastenhofer J, Rettenbacher L, Feuchtenhofer L, Mairhofer J, Spadiut O. Inhibition of E. coli Host RNA Polymerase Allows Efficient Extracellular Recombinant Protein Production by Enhancing Outer Membrane Leakiness. Biotechnol J 2020; 16:e2000274. [PMID: 32915502 DOI: 10.1002/biot.202000274] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/27/2020] [Indexed: 12/20/2022]
Abstract
With the growing interest in continuous cultivation of Escherichia coli, secretion of product to the medium is not only a benefit, but a necessity in future bioprocessing. In this study, it is shown that induced decoupling of growth and heterologous gene expression in the E. coli X-press strain (derived from BL21(DE3)) facilitates extracellular recombinant protein production. The effect of the process parameters temperature and specific glucose consumption rate (qS ) on growth, productivity, lysis and leakiness, is investigated, to find the parameter space allowing extracellular protein production. Two model proteins are used, Protein A (SpA) and a heavy-chain single-domain antibody (VHH), and performance is compared to the industrial standard strain BL21(DE3). It is shown that inducible growth repression in the X-press strain greatly mitigates the effect of metabolic burden under different process conditions. Furthermore, temperature and qS are used to control productivity and leakiness. In the X-press strain, extracellular SpA and VHH titer reach up to 349 and 19.6 mg g-1 , respectively, comprising up to 90% of the total soluble product, while keeping cell lysis at a minimum. The findings demonstrate that the X-press strain constitutes a valuable host for extracellular production of recombinant protein with E. coli.
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Affiliation(s)
- Jens Kastenhofer
- TU Wien, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Institute of Chemical, Gumpendorfer Strasse 1a, Vienna, 1060, Austria
| | - Lukas Rettenbacher
- TU Wien, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Institute of Chemical, Gumpendorfer Strasse 1a, Vienna, 1060, Austria
| | | | | | - Oliver Spadiut
- TU Wien, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Institute of Chemical, Gumpendorfer Strasse 1a, Vienna, 1060, Austria
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22
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A quantitative method for proteome reallocation using minimal regulatory interventions. Nat Chem Biol 2020; 16:1026-1033. [PMID: 32661378 DOI: 10.1038/s41589-020-0593-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 06/15/2020] [Indexed: 12/22/2022]
Abstract
Engineering resource allocation in biological systems is an ongoing challenge. Organisms allocate resources for ensuring survival, reducing the productivity of synthetic biology functions. Here we present a new approach for engineering the resource allocation of Escherichia coli by rationally modifying its transcriptional regulatory network. Our method (ReProMin) identifies the minimal set of genetic interventions that maximizes the savings in cell resources. To this end, we categorized transcription factors according to the essentiality of its targets and we used proteomic data to rank them. We designed the combinatorial removal of transcription factors that maximize the release of resources. Our resulting strain containing only three mutations, theoretically releasing 0.5% of its proteome, had higher proteome budget, increased production of an engineered metabolic pathway and showed that the regulatory interventions are highly specific. This approach shows that combining proteomic and regulatory data is an effective way of optimizing strains using conventional molecular methods.
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23
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de Siqueira GMV, Silva-Rocha R, Guazzaroni ME. Turning the Screw: Engineering Extreme pH Resistance in Escherichia coli through Combinatorial Synthetic Operons. ACS Synth Biol 2020; 9:1254-1262. [PMID: 32438805 DOI: 10.1021/acssynbio.0c00089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adoption of microorganisms as platforms for sustainable biobased production requires host cells to be able to withstand harsh conditions, usually very distant from those in which these organisms are naturally adapted to thrive. However, novel survival mechanisms unearthed by the study of microbiomes from extreme habitats may be exploited to enhance microbial robustness under the strict conditions needed for different industrial appplications. In this work, synthetic biology approaches were used to engineer enhanced acidic resistance in Escherichia coli through the characterization of a collection of unique operons composed of combinatorial assemblies of three novel genes from an extreme environment and three synthetic ribosome binding sites. The results here presented illustrate the efficacy of combining different metagenomic genes for resistance in synthetic operons, as expression of these gene clusters increased hundred-fold the survival percentage of cells exposed to an acidic shock in minimal media at pH 1.9 under aerobic conditions.
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Affiliation(s)
- Guilherme M. V. de Siqueira
- Departamento de Bioquı́mica, Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Ribeirão Preto, SP 14049-900, Brasil
| | - Rafael Silva-Rocha
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Ribeirão Preto, SP 14049-900, Brasil
| | - María-Eugenia Guazzaroni
- Departamento de Biologia, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto (FFCLRP-USP), Ribeirão Preto, SP 14040-901, Brasil
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24
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Kemble H, Eisenhauer C, Couce A, Chapron A, Magnan M, Gautier G, Le Nagard H, Nghe P, Tenaillon O. Flux, toxicity, and expression costs generate complex genetic interactions in a metabolic pathway. SCIENCE ADVANCES 2020; 6:eabb2236. [PMID: 32537514 PMCID: PMC7269641 DOI: 10.1126/sciadv.abb2236] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 03/31/2020] [Indexed: 05/31/2023]
Abstract
Our ability to predict the impact of mutations on traits relevant for disease and evolution remains severely limited by the dependence of their effects on the genetic background and environment. Even when molecular interactions between genes are known, it is unclear how these translate to organism-level interactions between alleles. We therefore characterized the interplay of genetic and environmental dependencies in determining fitness by quantifying ~4000 fitness interactions between expression variants of two metabolic genes, starting from various environmentally modulated expression levels. We detect a remarkable variety of interactions dependent on initial expression levels and demonstrate that they can be quantitatively explained by a mechanistic model accounting for catabolic flux, metabolite toxicity, and expression costs. Complex fitness interactions between mutations can therefore be predicted simply from their simultaneous impact on a few connected molecular phenotypes.
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Affiliation(s)
- Harry Kemble
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
- Laboratory of Biochemistry (LBC), Chimie Biologie et Innovation, ESPCI Paris, PSL University, CNRS, 75005 Paris, France
| | | | - Alejandro Couce
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | - Audrey Chapron
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
| | - Mélanie Magnan
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
| | - Gregory Gautier
- Centre de Recherche sur l'Inflammation, INSERM, UMRS 1149, 75018 Paris, France
- Laboratoire d’Excellence INFLAMEX, Université de Paris, Sorbonne Paris Cité, 75018 Paris, France
| | - Hervé Le Nagard
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
| | - Philippe Nghe
- Laboratory of Biochemistry (LBC), Chimie Biologie et Innovation, ESPCI Paris, PSL University, CNRS, 75005 Paris, France
| | - Olivier Tenaillon
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
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25
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Nikam VS, Nikam S, Sydykov A, Ahlbrecht K, Morty RE, Seeger W, Voswinckel R. Implication of in vivo circulating fibrocytes ablation in experimental pulmonary hypertension murine model. Br J Pharmacol 2020; 177:2974-2990. [PMID: 32060903 DOI: 10.1111/bph.15025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 11/26/2019] [Accepted: 01/23/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND AND PURPOSE Recruitment and involvement of bone-/blood-derived circulating fibrocytes (CF) in the promotion of fibrotic tissue remodelling processes have been shown. However, their direct contribution to pathological changes is not clear. The present study investigates the causal role of CF in the pathogenesis of pulmonary hypertension (PH). EXPERIMENTAL APPROACH For selective ablation of CF, we applied the suicidal gene strategy with herpes simplex virus thymidine kinase (HSV-TK) and ganciclovir. The transgenic mice were generated, having HSV-TK-GFP transgene under the collagen 1 promoter. To selectively target CF, HSV-TK-GFP+ bone marrow transplanted into irradiated wild type mice. These chimera mice were subjected to hypoxia for PH induction and ganciclovir for CF ablation. KEY RESULTS In vivo CF ablation reduced right ventricular hypertrophy and vascular remodelling with reduced total collagen content. We quantified the CF recruited in the perivascular area and arterial wall of small pulmonary arteries. There was significant recruitment of CF in the lung in response to hypoxia. The characterization of CF showed the expression of CD45 and collagen1 (GFP) along with α-smooth muscle actin (αSMA). CONCLUSION AND IMPLICATIONS Our data demonstrated that CF ablation has a potential impact on right ventricular hypertrophy and vascular remodelling in the setting of experimental pulmonary hypertension induced by hypoxia. The beneficial effects may be related to the direct contribution of fibrocytes or its paracrine effect on other resident cell types. Thus, clinical manipulation of CF may represent a novel therapeutic approach to ameliorate the disease state in pulmonary hypertension.
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Affiliation(s)
- Vandana S Nikam
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Sandeep Nikam
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Akyl Sydykov
- Department of Internal Medicine, University of Giessen Lung Centre, University Hospital Giessen and Marburg, Giessen, Germany
| | - Katrin Ahlbrecht
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany.,Department of Internal Medicine, University of Giessen Lung Centre, University Hospital Giessen and Marburg, Giessen, Germany
| | - Rory E Morty
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Werner Seeger
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany.,Department of Internal Medicine, University of Giessen Lung Centre, University Hospital Giessen and Marburg, Giessen, Germany
| | - Robert Voswinckel
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany.,Department of Internal Medicine, University of Giessen Lung Centre, University Hospital Giessen and Marburg, Giessen, Germany
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26
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Faber MS, Wrenbeck EE, Azouz LR, Steiner PJ, Whitehead TA. Impact of In Vivo Protein Folding Probability on Local Fitness Landscapes. Mol Biol Evol 2020; 36:2764-2777. [PMID: 31400199 DOI: 10.1093/molbev/msz184] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
It is incompletely understood how biophysical properties like protein stability impact molecular evolution and epistasis. Epistasis is defined as specific when a mutation exclusively influences the phenotypic effect of another mutation, often at physically interacting residues. In contrast, nonspecific epistasis results when a mutation is influenced by a large number of nonlocal mutations. As most mutations are pleiotropic, the in vivo folding probability-governed by basal protein stability-is thought to determine activity-enhancing mutational tolerance, implying that nonspecific epistasis is dominant. However, evidence exists for both specific and nonspecific epistasis as the prevalent factor, with limited comprehensive data sets to support either claim. Here, we use deep mutational scanning to probe how in vivo enzyme folding probability impacts local fitness landscapes. We computationally designed two different variants of the amidase AmiE with statistically indistinguishable catalytic efficiencies but lower probabilities of folding in vivo compared with wild-type. Local fitness landscapes show slight alterations among variants, with essentially the same global distribution of fitness effects. However, specific epistasis was predominant for the subset of mutations exhibiting positive sign epistasis. These mutations mapped to spatially distinct locations on AmiE near the initial mutation or proximal to the active site. Intriguingly, the majority of specific epistatic mutations were codon dependent, with different synonymous codons resulting in fitness sign reversals. Together, these results offer a nuanced view of how protein folding probability impacts local fitness landscapes and suggest that transcriptional-translational effects are as important as stability in determining evolutionary outcomes.
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Affiliation(s)
- Matthew S Faber
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI
| | - Emily E Wrenbeck
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI
| | - Laura R Azouz
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI
| | - Paul J Steiner
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO
| | - Timothy A Whitehead
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI.,Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO.,E.E.W. Ginkgo Bioworks, L.R.A. McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX
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27
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Production of Lysostaphin by Nonproprietary Method Utilizing a Promoter from Toxin–Antitoxin System. Mol Biotechnol 2019; 61:774-782. [DOI: 10.1007/s12033-019-00203-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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28
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DeLorenzo DM, Moon TS. Construction of Genetic Logic Gates Based on the T7 RNA Polymerase Expression System in Rhodococcus opacus PD630. ACS Synth Biol 2019; 8:1921-1930. [PMID: 31362487 DOI: 10.1021/acssynbio.9b00213] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Rhodococcus opacus PD630 (R. opacus) is a nonmodel, Gram-positive bacterium that holds promise as a biological catalyst for the conversion of lignocellulosic biomass to value-added products. In particular, it demonstrates both a high tolerance for and an ability to consume inhibitory lignin-derived aromatics, generates large quantities of lipids, exhibits a relatively rapid growth rate, and has a growing genetic toolbox for engineering. However, the availability of genetic parts for tunable, high-activity gene expression is still limited in R. opacus. Furthermore, genetic logic circuits for sophisticated gene regulation have never been demonstrated in Rhodococcus spp. To address these shortcomings, two inducible T7 RNA polymerase-based expression systems were implemented for the first time in R. opacus and applied to the construction of AND and NAND genetic logic gates. Additionally, three isopropyl β-d-1-thiogalactopyranoside (IPTG)-inducible promoters were created by inserting LacI binding sites into newly characterized constitutive promoters. Furthermore, four novel aromatic sensors for 4-hydroxybenzoic acid, vanillic acid, sodium benzoate, and guaiacol were developed, expanding the gene expression toolbox. Finally, the T7 RNA polymerase platform was combined with a synthetic IPTG-inducible promoter to create an IMPLY logic gate. Overall, this work represents the first demonstration of a heterologous RNA polymerase system and synthetic genetic logic in R. opacus, enabling complex and tunable gene regulation in this promising nonmodel host for bioproduction.
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Affiliation(s)
- Drew M. DeLorenzo
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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29
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Jansen R, Tenhaef N, Moch M, Wiechert W, Noack S, Oldiges M. FeedER: a feedback-regulated enzyme-based slow-release system for fed-batch cultivation in microtiter plates. Bioprocess Biosyst Eng 2019; 42:1843-1852. [PMID: 31399865 PMCID: PMC6800402 DOI: 10.1007/s00449-019-02180-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 07/23/2019] [Indexed: 11/09/2022]
Abstract
With the advent of modern genetic engineering methods, microcultivation systems have become increasingly important tools for accelerated strain phenotyping and bioprocess engineering. While these systems offer sophisticated capabilities to screen batch processes, they lack the ability to realize fed-batch processes, which are used more frequently in industrial bioprocessing. In this study, a novel approach to realize a feedback-regulated enzyme-based slow-release system (FeedER), allowing exponential fed-batch for microscale cultivations, was realized by extending our existing Mini Pilot Plant technology with a customized process control system. By continuously comparing the experimental growth rates with predefined set points, the automated dosage of Amyloglucosidase enzyme for the cleavage of dextrin polymers into d-glucose monomers is triggered. As a prerequisite for stable fed-batch operation, a constant pH is maintained by automated addition of ammonium hydroxide. We show the successful application of FeedER to study fed-batch growth of different industrial model organisms including Corynebacterium glutamicum, Pichia pastoris, and Escherichia coli. Moreover, the comparative analysis of a C. glutamicum GFP producer strain, cultivated under microscale batch and fed-batch conditions, revealed two times higher product yields under slow growing fed-batch operation. In summary, FeedER enables to run 48 parallel fed-batch experiments in an automated and miniaturized manner, and thereby accelerates industrial bioprocess development at the screening stage.
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Affiliation(s)
- Roman Jansen
- Forschungszentrum Jülich, Institute of Bio- and Geosciences, Biotechnology (IBG-1), Jülich, Germany
| | - Niklas Tenhaef
- Forschungszentrum Jülich, Institute of Bio- and Geosciences, Biotechnology (IBG-1), Jülich, Germany.,Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Matthias Moch
- Forschungszentrum Jülich, Institute of Bio- and Geosciences, Biotechnology (IBG-1), Jülich, Germany
| | - Wolfgang Wiechert
- Forschungszentrum Jülich, Institute of Bio- and Geosciences, Biotechnology (IBG-1), Jülich, Germany.,RWTH Aachen University, Computational Systems Biotechnology (AVT.CSB), Aachen, Germany
| | - Stephan Noack
- Forschungszentrum Jülich, Institute of Bio- and Geosciences, Biotechnology (IBG-1), Jülich, Germany.,Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Marco Oldiges
- Forschungszentrum Jülich, Institute of Bio- and Geosciences, Biotechnology (IBG-1), Jülich, Germany. .,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany.
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30
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Abstract
Systemic Salmonella enterica infections are a major cause of mortality worldwide and are becoming increasingly untreatable. Recent single-cell data from a mouse model of typhoid fever show that the host immune system actually eradicates many Salmonella cells, while other Salmonella organisms thrive at the same time in the same tissue, causing lethal disease progression. The surviving Salmonella cells have highly heterogeneous metabolism, growth rates, and exposure to various stresses. Emerging evidence suggests that similarly heterogeneous host-pathogen encounters might be a key feature of many infectious diseases. This heterogeneity offers fascinating opportunities for research and application. If we understand the mechanisms that determine the disparate local outcomes, we might be able to develop entirely novel strategies for infection control by broadening successful host antimicrobial attacks and closing permissive niches in which pathogens can thrive. This review describes suitable technologies, a current working model of heterogeneous host-Salmonella interactions, the impact of diverse Salmonella subsets on antimicrobial chemotherapy, and major open questions and challenges.
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31
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Wrenbeck EE, Bedewitz MA, Klesmith JR, Noshin S, Barry CS, Whitehead TA. An Automated Data-Driven Pipeline for Improving Heterologous Enzyme Expression. ACS Synth Biol 2019; 8:474-481. [PMID: 30721031 DOI: 10.1021/acssynbio.8b00486] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes are the ultimate entities responsible for chemical transformations in natural and engineered biosynthetic pathways. However, many natural enzymes suffer from suboptimal functional expression due to poor intrinsic protein stability. Further, stability enhancing mutations often come at the cost of impaired function. Here we demonstrate an automated protein engineering strategy for stabilizing enzymes while retaining catalytic function using deep mutational scanning coupled to multiple-filter based screening and combinatorial mutagenesis. We validated this strategy by improving the functional expression of a Type III polyketide synthase from the Atropa belladonna biosynthetic pathway for tropane alkaloids. The best variant had a total of 8 mutations with over 25-fold improved activity over wild-type in E. coli cell lysates, an improved melting temperature of 11.5 ± 0.6 °C, and only minimal reduction in catalytic efficiency. We show that the multiple-filter approach maintains acceptable sensitivity with homology modeling structures up to 4 Å RMS. Our results highlight an automated protein engineering tool for improving the stability and solubility of difficult to express enzymes, which has impact for biotechnological applications.
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Affiliation(s)
| | | | | | - Syeda Noshin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
| | | | - Timothy A. Whitehead
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80305, United States
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32
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Palazzotto E, Tong Y, Lee SY, Weber T. Synthetic biology and metabolic engineering of actinomycetes for natural product discovery. Biotechnol Adv 2019; 37:107366. [PMID: 30853630 DOI: 10.1016/j.biotechadv.2019.03.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 12/15/2022]
Abstract
Actinomycetes are one of the most valuable sources of natural products with industrial and medicinal importance. After more than half a century of exploitation, it has become increasingly challenging to find novel natural products with useful properties as the same known compounds are often repeatedly re-discovered when using traditional approaches. Modern genome mining approaches have led to the discovery of new biosynthetic gene clusters, thus indicating that actinomycetes still harbor a huge unexploited potential to produce novel natural products. In recent years, innovative synthetic biology and metabolic engineering tools have greatly accelerated the discovery of new natural products and the engineering of actinomycetes. In the first part of this review, we outline the successful application of metabolic engineering to optimize natural product production, focusing on the use of multi-omics data, genome-scale metabolic models, rational approaches to balance precursor pools, and the engineering of regulatory genes and regulatory elements. In the second part, we summarize the recent advances of synthetic biology for actinomycetal metabolic engineering including cluster assembly, cloning and expression, CRISPR/Cas9 technologies, and chassis strain development for natural product overproduction and discovery. Finally, we describe new advances in reprogramming biosynthetic pathways through polyketide synthase and non-ribosomal peptide synthetase engineering. These new developments are expected to revitalize discovery and development of new natural products with medicinal and other industrial applications.
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Affiliation(s)
- Emilia Palazzotto
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Yaojun Tong
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Sang Yup Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark; Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology, 34141 Daejeon, Republic of Korea.
| | - Tilmann Weber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark.
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33
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Circuit-Host Coupling Induces Multifaceted Behavioral Modulations of a Gene Switch. Biophys J 2019; 114:737-746. [PMID: 29414718 DOI: 10.1016/j.bpj.2017.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/12/2017] [Accepted: 12/01/2017] [Indexed: 12/30/2022] Open
Abstract
Quantitative modeling of gene circuits is fundamentally important to synthetic biology, as it offers the potential to transform circuit engineering from trial-and-error construction to rational design and, hence, facilitates the advance of the field. Currently, typical models regard gene circuits as isolated entities and focus only on the biochemical processes within the circuits. However, such a standard paradigm is getting challenged by increasing experimental evidence suggesting that circuits and their host are intimately connected, and their interactions can potentially impact circuit behaviors. Here we systematically examined the roles of circuit-host coupling in shaping circuit dynamics by using a self-activating gene switch as a model circuit. Through a combination of deterministic modeling, stochastic simulation, and Fokker-Planck equation formalism, we found that circuit-host coupling alters switch behaviors across multiple scales. At the single-cell level, it slows the switch dynamics in the high protein production regime and enlarges the difference between stable steady-state values. At the population level, it favors cells with low protein production through differential growth amplification. Together, the two-level coupling effects induce both quantitative and qualitative modulations of the switch, with the primary component of the effects determined by the circuit's architectural parameters. This study illustrates the complexity and importance of circuit-host coupling in modulating circuit behaviors, demonstrating the need for a new paradigm-integrated modeling of the circuit-host system-for quantitative understanding of engineered gene networks.
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34
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Hemmerich J, Moch M, Jurischka S, Wiechert W, Freudl R, Oldiges M. Combinatorial impact of Sec signal peptides fromBacillus subtilisand bioprocess conditions on heterologous cutinase secretion byCorynebacterium glutamicum. Biotechnol Bioeng 2018; 116:644-655. [DOI: 10.1002/bit.26873] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 09/11/2018] [Accepted: 10/26/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Johannes Hemmerich
- Forschungszentrum JülichInstitute of Bio‐ and Geosciences—Biotechnology (IBG‐1)Jülich Germany
- Bioeconomy Science Center (BioSC)c/o Forschungszentrum JülichJülich Germany
| | - Matthias Moch
- Forschungszentrum JülichInstitute of Bio‐ and Geosciences—Biotechnology (IBG‐1)Jülich Germany
| | - Sarah Jurischka
- Forschungszentrum JülichInstitute of Bio‐ and Geosciences—Biotechnology (IBG‐1)Jülich Germany
- Bioeconomy Science Center (BioSC)c/o Forschungszentrum JülichJülich Germany
| | - Wolfgang Wiechert
- Forschungszentrum JülichInstitute of Bio‐ and Geosciences—Biotechnology (IBG‐1)Jülich Germany
- Bioeconomy Science Center (BioSC)c/o Forschungszentrum JülichJülich Germany
- Computational Systems Biotechnology (AVT.CSB)RWTH Aachen UniversityAachen Germany
| | - Roland Freudl
- Forschungszentrum JülichInstitute of Bio‐ and Geosciences—Biotechnology (IBG‐1)Jülich Germany
- Bioeconomy Science Center (BioSC)c/o Forschungszentrum JülichJülich Germany
| | - Marco Oldiges
- Forschungszentrum JülichInstitute of Bio‐ and Geosciences—Biotechnology (IBG‐1)Jülich Germany
- Bioeconomy Science Center (BioSC)c/o Forschungszentrum JülichJülich Germany
- Institute of BiotechnologyRWTH Aachen UniversityAachen Germany
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35
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Mühlmann MJ, Forsten E, Noack S, Büchs J. Prediction of recombinant protein production by Escherichia coli derived online from indicators of metabolic burden. Biotechnol Prog 2018; 34:1543-1552. [PMID: 30248250 DOI: 10.1002/btpr.2704] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/23/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND The oxygen transfer rate (OTR) and the biomass concentration are two important parameters describing a microbial fermentation. It has been shown before that from the course of these parameters over time information on metabolic burden during heterologous protein production can be obtained. While online monitoring in large fermenters is ubiquitously established, it is still not a common practice in small-scale cultures. Nevertheless, several techniques like the Respiration Activity MOnitoring System (RAMOS) device for online monitoring of the OTR in shake flasks and the BioLector device for measuring scattered light (ScL) representing biomass in microtiter plates have been developed. RESULTS A new microtiter plate-based method is presented that reveals how online derived ScL signals can be transformed into signals that are proportional to the courses of OTR over time for Escherichia coli. The transformed signal is obtained by simply taking the first derivative of ScL (dScL/dt). The proportionality of both parameters is successfully validated for the strains E. coli BL21(DE3) and Tuner(DE3) expressing cellulases and the fluorescent protein FbFP, respectively. Relative amounts of produced heterologous proteins are predicted exclusively based on the course of the transformed ScL signal. A variety of induction conditions with varying inducer concentration and induction time were investigated with this method. CONCLUSION The presented method based on ScL measurement allows for high-throughput online determination of signals proportional to OTR courses. They enable the interpretation of physiological states and offer the possibility to predict the recombinant protein production in E. coli. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:1543-1552, 2018.
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Affiliation(s)
- Martina Julia Mühlmann
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, Aachen, 52074, Germany
| | - Eva Forsten
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, Aachen, 52074, Germany
| | - Saskia Noack
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, Aachen, 52074, Germany
| | - Jochen Büchs
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, Aachen, 52074, Germany
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36
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Liljeruhm J, Funk SK, Tietscher S, Edlund AD, Jamal S, Wistrand-Yuen P, Dyrhage K, Gynnå A, Ivermark K, Lövgren J, Törnblom V, Virtanen A, Lundin ER, Wistrand-Yuen E, Forster AC. Engineering a palette of eukaryotic chromoproteins for bacterial synthetic biology. J Biol Eng 2018; 12:8. [PMID: 29760772 PMCID: PMC5946454 DOI: 10.1186/s13036-018-0100-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/23/2018] [Indexed: 01/14/2023] Open
Abstract
Background Coral reefs are colored by eukaryotic chromoproteins (CPs) that are homologous to green fluorescent protein. CPs differ from fluorescent proteins (FPs) by intensely absorbing visible light to give strong colors in ambient light. This endows CPs with certain advantages over FPs, such as instrument-free detection uncomplicated by ultra-violet light damage or background fluorescence, efficient Förster resonance energy transfer (FRET) quenching, and photoacoustic imaging. Thus, CPs have found utility as genetic markers and in teaching, and are attractive for potential cell biosensor applications in the field. Most near-term applications of CPs require expression in a different domain of life: bacteria. However, it is unclear which of the eukaryotic CP genes might be suitable and how best to assay them. Results Here, taking advantage of codon optimization programs in 12 cases, we engineered 14 CP sequences (meffRed, eforRed, asPink, spisPink, scOrange, fwYellow, amilGFP, amajLime, cjBlue, meffBlue, aeBlue, amilCP, tsPurple and gfasPurple) into a palette of Escherichia coli BioBrick plasmids. BioBricks comply with synthetic biology’s most widely used, simplified, cloning standard. Differences in color intensities, maturation times and fitness costs of expression were compared under the same conditions, and visible readout of gene expression was quantitated. A surprisingly large variation in cellular fitness costs was found, resulting in loss of color in some overnight liquid cultures of certain high-copy-plasmid-borne CPs, and cautioning the use of multiple CPs as markers in competition assays. We solved these two problems by integrating pairs of these genes into the chromosome and by engineering versions of the same CP with very different colors. Conclusion Availability of 14 engineered CP genes compared in E. coli, together with chromosomal mutants suitable for competition assays, should simplify and expand CP study and applications. There was no single plasmid-borne CP that combined all of the most desirable features of intense color, fast maturation and low fitness cost, so this study should help direct future engineering efforts. Electronic supplementary material The online version of this article (10.1186/s13036-018-0100-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Josefine Liljeruhm
- 1Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Saskia K Funk
- 1Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Sandra Tietscher
- 1Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Anders D Edlund
- 1Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,2iGEM Uppsala, Uppsala University, Uppsala, Sweden
| | - Sabri Jamal
- 2iGEM Uppsala, Uppsala University, Uppsala, Sweden
| | | | - Karl Dyrhage
- 2iGEM Uppsala, Uppsala University, Uppsala, Sweden
| | - Arvid Gynnå
- 1Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,2iGEM Uppsala, Uppsala University, Uppsala, Sweden
| | | | - Jessica Lövgren
- 3Biology Education Centre at Uppsala University, Uppsala, Sweden
| | - Viktor Törnblom
- 3Biology Education Centre at Uppsala University, Uppsala, Sweden
| | - Anders Virtanen
- 1Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Erik R Lundin
- 2iGEM Uppsala, Uppsala University, Uppsala, Sweden.,4Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Erik Wistrand-Yuen
- 4Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Anthony C Forster
- 1Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,5Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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37
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Mühlmann M, Forsten E, Noack S, Büchs J. Optimizing recombinant protein expression via automated induction profiling in microtiter plates at different temperatures. Microb Cell Fact 2017; 16:220. [PMID: 29183374 PMCID: PMC5706349 DOI: 10.1186/s12934-017-0832-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/21/2017] [Indexed: 02/06/2023] Open
Abstract
Background Escherichia coli (E. coli) is the most abundant expression host for recombinant proteins. The production efficiency is dependent on a multitude of parameters. Therefore, high-throughput applications have become an increasingly frequent technique to investigate the main factors. Within this study, the effects of temperature, induction time and inducer concentration on the metabolic state and the product formation were extensively examined. Induction profiling of E. coli Tuner(DE3) pRhotHi-2-EcFbFP was performed in 48-well Flowerplates and standard 96-well plates using a robotic platform. In parallel shake flask cultivations, the respiration activity of the microorganisms was analyzed. Therefore, two online-monitoring systems were applied: the BioLector for microtiter plates and the RAMOS-device for shake flasks. The impact of different induction conditions on biomass and product formation as well as on the oxygen transfer rate was surveyed. Results Different optimal induction conditions were obtained for temperatures of 28, 30, 34, and 37 °C. The best inducer concentrations were determined to be between 0.05 and 0.1 mM IPTG for all investigated temperatures. This is 10–20 times lower than conventional guidelines suggest. The induction time was less relevant when the correct inducer concentration was chosen. Furthermore, there was a stronger impact on growth and respiration activity at higher temperatures. This indicated a higher metabolic burden. Therefore, lower IPTG concentrations were advantageous at elevated temperatures. Very similar results were obtained in standard 96-well plates. Conclusion Two online-monitoring systems were successfully used to investigate the optimal induction conditions for the E. coli Tuner(DE3) pRhotHi-2-EcFbFP strain (lacY deletion mutant) at four different temperatures. The experimental effort was reduced to a minimum by integrating a liquid handling robot. To reach the maximum product formation, a detailed induction analysis was necessary. Whenever the cultivation temperature was changed, the induction conditions have to be adapted. Due to the experimental options provided by the BioLector technology, it was found that the higher the cultivation temperature, the lower the inducer concentration that has to be applied. Electronic supplementary material The online version of this article (10.1186/s12934-017-0832-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martina Mühlmann
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Eva Forsten
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Saskia Noack
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Jochen Büchs
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany.
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38
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Wrenbeck EE, Azouz LR, Whitehead TA. Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded. Nat Commun 2017; 8:15695. [PMID: 28585537 PMCID: PMC5467163 DOI: 10.1038/ncomms15695] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 04/20/2017] [Indexed: 01/17/2023] Open
Abstract
Our lack of total understanding of the intricacies of how enzymes behave has constrained our ability to robustly engineer substrate specificity. Furthermore, the mechanisms of natural evolution leading to improved or novel substrate specificities are not wholly defined. Here we generate near-comprehensive single-mutation fitness landscapes comprising >96.3% of all possible single nonsynonymous mutations for hydrolysis activity of an amidase expressed in E. coli with three different substrates. For all three selections, we find that the distribution of beneficial mutations can be described as exponential, supporting a current hypothesis for adaptive molecular evolution. Beneficial mutations in one selection have essentially no correlation with fitness for other selections and are dispersed throughout the protein sequence and structure. Our results further demonstrate the dependence of local fitness landscapes on substrate identity and provide an example of globally distributed sequence-specificity determinants for an enzyme. Systematically understanding the sequence determinants to substrate specificity for enzymes has implications in areas from evolutionary biology to biocatalysis. Here, Whitehead and colleagues generate and analyse near-comprehensive single-mutation fitness landscapes for an amidase with three different substrates.
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Affiliation(s)
- Emily E Wrenbeck
- Department of Chemical Engineering and Materials Science, Michigan State University, Engineering Building, 428 S. Shaw Lane, Room 2100, East Lansing, Michigan 48824, USA
| | - Laura R Azouz
- Department of Chemical Engineering and Materials Science, Michigan State University, Engineering Building, 428 S. Shaw Lane, Room 2100, East Lansing, Michigan 48824, USA
| | - Timothy A Whitehead
- Department of Chemical Engineering and Materials Science, Michigan State University, Engineering Building, 428 S. Shaw Lane, Room 2100, East Lansing, Michigan 48824, USA.,Department of Biosystems and Agricultural Engineering, Michigan State University, Farrall Hall, 524 S. Shaw Lane, Room 216, East Lansing, Michigan 48824, USA
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Wang H, Ling MH, Chua TK, Poh CL. Two cellular resource‐based models linking growth and parts characteristics aids the study and optimisation of synthetic gene circuits. ENGINEERING BIOLOGY 2017. [DOI: 10.1049/enb.2017.0005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Huijuan Wang
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore 637459 Singapore
| | - Maurice H.T. Ling
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore 637459 Singapore
| | - Tze Kwang Chua
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore 637459 Singapore
| | - Chueh Loo Poh
- Department of Biomedical Engineering National University of Singapore Singapore 117583 Singapore
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40
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Marschall L, Sagmeister P, Herwig C. Tunable recombinant protein expression in E. coli: promoter systems and genetic constraints. Appl Microbiol Biotechnol 2017; 101:501-512. [PMID: 27999902 PMCID: PMC5566544 DOI: 10.1007/s00253-016-8045-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 11/26/2016] [Accepted: 11/29/2016] [Indexed: 12/11/2022]
Abstract
Tuning of transcription is a promising strategy to overcome challenges associated with a non-suitable expression rate like outgrowth of segregants, inclusion body formation, metabolic burden and inefficient translocation. By adjusting the expression rate-even on line-to purposeful levels higher product titres and more cost-efficient production processes can be achieved by enabling culture long-term stability and constant product quality. Some tunable systems are registered for patents or already commercially available. Within this contribution, we discuss the induction mechanisms of various Escherichia coli inherent promoter systems with respect to their tunability and review studies using these systems for expression tuning. According to the current level of knowledge, some promoter systems were successfully used for expression tuning, and in some cases, analytical evidence on single-cell level is still pending. However, only a few studies using tunable strains apply a suitable process control strategy. So far, expression tuning has only gathered little attention, but we anticipate that expression tuning harbours great potential for enabling and optimizing the production of a broad spectrum of products in E. coli.
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Affiliation(s)
- Lukas Marschall
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Vienna, Austria
| | | | - Christoph Herwig
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Vienna, Austria.
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Vienna University of Technology, Gumpendorferstrasse 1a/166-4, A-1060, Vienna, Austria.
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41
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Frumkin I, Schirman D, Rotman A, Li F, Zahavi L, Mordret E, Asraf O, Wu S, Levy SF, Pilpel Y. Gene Architectures that Minimize Cost of Gene Expression. Mol Cell 2016; 65:142-153. [PMID: 27989436 DOI: 10.1016/j.molcel.2016.11.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/10/2016] [Accepted: 11/01/2016] [Indexed: 11/30/2022]
Abstract
Gene expression burdens cells by consuming resources and energy. While numerous studies have investigated regulation of expression level, little is known about gene design elements that govern expression costs. Here, we ask how cells minimize production costs while maintaining a given protein expression level and whether there are gene architectures that optimize this process. We measured fitness of ∼14,000 E. coli strains, each expressing a reporter gene with a unique 5' architecture. By comparing cost-effective and ineffective architectures, we found that cost per protein molecule could be minimized by lowering transcription levels, regulating translation speeds, and utilizing amino acids that are cheap to synthesize and that are less hydrophobic. We then examined natural E. coli genes and found that highly expressed genes have evolved more forcefully to minimize costs associated with their expression. Our study thus elucidates gene design elements that improve the economy of protein expression in natural and heterologous systems.
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Affiliation(s)
- Idan Frumkin
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Dvir Schirman
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Aviv Rotman
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Fangfei Li
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Liron Zahavi
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ernest Mordret
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Omer Asraf
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Song Wu
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Sasha F Levy
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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42
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Kowalsky CA, Whitehead TA. Determination of binding affinity upon mutation for type I dockerin-cohesin complexes from Clostridium thermocellum and Clostridium cellulolyticum using deep sequencing. Proteins 2016; 84:1914-1928. [PMID: 27699856 DOI: 10.1002/prot.25175] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 09/05/2016] [Accepted: 09/27/2016] [Indexed: 12/27/2022]
Abstract
The comprehensive sequence determinants of binding affinity for type I cohesin toward dockerin from Clostridium thermocellum and Clostridium cellulolyticum was evaluated using deep mutational scanning coupled to yeast surface display. We measured the relative binding affinity to dockerin for 2970 and 2778 single point mutants of C. thermocellum and C. cellulolyticum, respectively, representing over 96% of all possible single point mutants. The interface ΔΔG for each variant was reconstructed from sequencing counts and compared with the three independent experimental methods. This reconstruction results in a narrow dynamic range of -0.8-0.5 kcal/mol. The computational software packages FoldX and Rosetta were used to predict mutations that disrupt binding by more than 0.4 kcal/mol. The area under the curve of receiver operator curves was 0.82 for FoldX and 0.77 for Rosetta, showing reasonable agreements between predictions and experimental results. Destabilizing mutations to core and rim positions were predicted with higher accuracy than support positions. This benchmark dataset may be useful for developing new computational prediction tools for the prediction of the mutational effect on binding affinities for protein-protein interactions. Experimental considerations to improve precision and range of the reconstruction method are discussed. Proteins 2016; 84:1914-1928. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Caitlin A Kowalsky
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, 48824
| | - Timothy A Whitehead
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, 48824
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, Michigan, 48824
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43
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Haarmeyer CN, Smith MD, Chundawat SPS, Sammond D, Whitehead TA. Insights into cellulase-lignin non-specific binding revealed by computational redesign of the surface of green fluorescent protein. Biotechnol Bioeng 2016; 114:740-750. [DOI: 10.1002/bit.26201] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 09/09/2016] [Accepted: 10/10/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Carolyn N. Haarmeyer
- Department of Chemical Engineering and Materials Science; Michigan State University; East Lansing Michigan 48824
| | - Matthew D. Smith
- Department of Chemical Engineering and Materials Science; Michigan State University; East Lansing Michigan 48824
| | - Shishir P. S Chundawat
- Great Lakes Bioenergy Research Center (GLBRC); Michigan State University; East Lansing Michigan
- Department of Chemical and Biochemical Engineering; Rutgers; The State University of New Jersey; Piscataway New Jersey
| | - Deanne Sammond
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - Timothy A. Whitehead
- Department of Chemical Engineering and Materials Science; Michigan State University; East Lansing Michigan 48824
- Department of Biosystems and Agricultural Engineering; Michigan State University; East Lansing Michigan 48824
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44
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Plasmid-based one-pot saturation mutagenesis. Nat Methods 2016; 13:928-930. [PMID: 27723752 DOI: 10.1038/nmeth.4029] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 09/09/2016] [Indexed: 01/12/2023]
Abstract
Deep mutational scanning is a foundational tool for addressing the functional consequences of large numbers of mutants, but a more efficient and accessible method for construction of user-defined mutagenesis libraries is needed. Here we present nicking mutagenesis, a robust, single-day, one-pot saturation mutagenesis method performed on routinely prepped plasmid dsDNA. The method can be used to produce comprehensive or single- or multi-site saturation mutagenesis libraries.
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45
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Song Y, Nikoloff JM, Fu G, Chen J, Li Q, Xie N, Zheng P, Sun J, Zhang D. Promoter Screening from Bacillus subtilis in Various Conditions Hunting for Synthetic Biology and Industrial Applications. PLoS One 2016; 11:e0158447. [PMID: 27380260 PMCID: PMC4933340 DOI: 10.1371/journal.pone.0158447] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 06/16/2016] [Indexed: 11/24/2022] Open
Abstract
The use of Bacillus subtilis in synthetic biology and metabolic engineering is highly desirable to take advantage of the unique metabolic pathways present in this organism. To do this, an evaluation of B. subtilis’ intrinsic biological parts is required to determine the best strategies to accurately regulate metabolic circuits and expression of target proteins. The strengths of promoter candidates were evaluated by measuring relative fluorescence units of a green fluorescent protein reporter, integrated into B. subtilis’ chromosome. A total of 84 predicted promoter sequences located upstream of different classes of proteins including heat shock proteins, cell-envelope proteins, and proteins resistant against toxic metals (based on similarity) and other kinds of genes were tested. The expression levels measured ranged from 0.0023 to 4.53-fold of the activity of the well-characterized strong promoter P43. No significant shifts were observed when strains, carrying different promoter candidates, were cultured at high temperature or in media with ethanol, but some strains showed increased activity when cultured under high osmotic pressure. Randomly selected promoter candidates were tested and found to activate transcription of thermostable β-galactosidase (bgaB) at a similar level, implying the ability of these sequences to function as promoter elements in multiple genetic contexts. In addition, selected promoters elevated the final production of both cytoplasmic bgaB and secreted protein α-amylase to about fourfold and twofold, respectively. The generated data allows a deeper understanding of B. subtilis’ metabolism and will facilitate future work to develop this organism for synthetic biology.
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Affiliation(s)
- Yafeng Song
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jonas M Nikoloff
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Gang Fu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jingqi Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Qinggang Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Nengzhong Xie
- National Engineering Research Center for Non-food Biorefinery, State Key Laboratory of Non-food Biomass Energy and Enzyme Technology, Nanning 5300074, P. R. China
- Guangxi Biomass Industrialization Engineering Institute, Guangxi Academy of Sciences, Nanning 530007, P. R. China
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
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O’Brien EJ, Utrilla J, Palsson BO. Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments. PLoS Comput Biol 2016; 12:e1004998. [PMID: 27351952 PMCID: PMC4924638 DOI: 10.1371/journal.pcbi.1004998] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/25/2016] [Indexed: 12/14/2022] Open
Abstract
The costs and benefits of protein expression are balanced through evolution. Expression of un-utilized protein (that have no benefits in the current environment) incurs a quantifiable fitness costs on cellular growth rates; however, the magnitude and variability of un-utilized protein expression in natural settings is unknown, largely due to the challenge in determining environment-specific proteome utilization. We address this challenge using absolute and global proteomics data combined with a recently developed genome-scale model of Escherichia coli that computes the environment-specific cost and utility of the proteome on a per gene basis. We show that nearly half of the proteome mass is unused in certain environments and accounting for the cost of this unused protein expression explains >95% of the variance in growth rates of Escherichia coli across 16 distinct environments. Furthermore, reduction in unused protein expression is shown to be a common mechanism to increase cellular growth rates in adaptive evolution experiments. Classification of the unused protein reveals that the unused protein encodes several nutrient- and stress- preparedness functions, which may convey fitness benefits in varying environments. Thus, unused protein expression is the source of large and pervasive fitness costs that may provide the benefit of hedging against environmental change. An overarching endeavor in systems biology is to characterize and understand the allocation of an organism’s proteome. Common approaches to characterize proteome allocation are based on annotations of protein functions or transcriptional regulatory targets. Here, we develop a novel approach based on model-predicted proteome utilization. This approach reveals that in many environments, a large fraction of the proteome is unused. Unused protein expression is known to incur costs on organismal fitness. We show that changes in the allocation of the proteome to used versus unused fractions can account for the variability in growth rates observed across environments and is a common mechanism to increase growth rates in laboratory evolution experiments. We compare our approach to classify the proteome based on model-predicted utilization to more traditional approaches to reveal biological functions and transcriptional regulators underlying the expression of unused protein. Expression of these functions may reflect ecological trade-offs between growth, nutrient-readiness, and stress resistance.
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Affiliation(s)
- Edward J. O’Brien
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
- Bioinformatics and Systems Biology program, University of California, San Diego, La Jolla, California, United States of America
| | - Jose Utrilla
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
- Centro de Ciencias Genómicas. Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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47
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Marschall L, Sagmeister P, Herwig C. Tunable recombinant protein expression in E. coli: enabler for continuous processing? Appl Microbiol Biotechnol 2016; 100:5719-28. [PMID: 27170324 PMCID: PMC4957632 DOI: 10.1007/s00253-016-7550-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/11/2016] [Accepted: 04/13/2016] [Indexed: 02/06/2023]
Abstract
Tuning of transcription is a powerful process technological tool for efficient recombinant protein production in Escherichia coli. Many challenges such as product toxicity, formation of inclusion bodies, cell death, and metabolic burden are associated with non-suitable (too high or too low) levels of recombinant protein expression. Tunable expression systems allow adjusting the recombinant protein expression using process technological means. This enables to exploit the cell's metabolic capacities to a maximum. Within this article, we review genetic and process technological aspects of tunable expression systems in E. coli, providing a roadmap for the industrial exploitation of the reviewed technologies. We attempt to differentiate the term "expression tuning" from its inflationary use by providing a concise definition and highlight interesting fields of application for this versatile new technology. Dependent on the type of inducer (metabolizable or non-metabolizable), different process strategies are required in order to achieve tuning. To fully profit from the benefits of tunable systems, an independent control of growth rate and expression rate is indispensable. Being able to tackle problems such as long-term culture stability and constant product quality expression tuning is a promising enabler for continuous processing in biopharmaceutical production.
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Affiliation(s)
- Lukas Marschall
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Vienna, Austria
| | | | - Christoph Herwig
- Exputec GmbH, Vienna, Austria. .,Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Vienna University of Technology, Gumpendorferstraße 1a/166-4, 1060, Vienna, Austria.
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48
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Wandrey G, Bier C, Binder D, Hoffmann K, Jaeger KE, Pietruszka J, Drepper T, Büchs J. Light-induced gene expression with photocaged IPTG for induction profiling in a high-throughput screening system. Microb Cell Fact 2016; 15:63. [PMID: 27107964 PMCID: PMC4842301 DOI: 10.1186/s12934-016-0461-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/13/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Inducible expression systems are frequently used for the production of heterologous proteins. Achieving maximum product concentrations requires induction profiling, namely the optimization of induction time and inducer concentration. However, the respective experiments can be very laborious and time-consuming. In this work, a new approach for induction profiling is presented where induction in a microtiter plate based cultivation system (BioLector) is achieved by light using photocaged isopropyl β-D-1-thiogalactopyranoside (cIPTG). RESULTS A flavin mononucleotide-based fluorescent reporter protein (FbFP) was expressed using a T7-RNA-polymerase dependent E. coli expression system which required IPTG as inducer. High power UV-A irradiation was directed into a microtiter plate by light-emitting diodes placed above each well of a 48-well plate. Upon UV irradiation, IPTG is released (uncaged) and induces product formation. IPTG uncaging, formation of the fluorescent reporter protein and biomass growth were monitored simultaneously in up to four 48-well microtiter plates in parallel with an in-house constructed BioLector screening system. The amount of released IPTG can be gradually and individually controlled for each well by duration of UV-A exposure, irradiance and concentration of photocaged IPTG added at the start of the cultivation. A comparison of experiments with either optical or conventional IPTG induction shows that product formation and growth are equivalent. Detailed induction profiles revealed that for the strain and conditions used maximum product formation is reached for very early induction times and with just 6-8 s of UV-A irradiation or 60-80 µM IPTG. CONCLUSIONS Optical induction and online monitoring were successfully combined in a high-throughput screening system and the effect of optical induction with photocaged IPTG was shown to be equivalent to conventional induction with IPTG. In contrast to conventional induction, optical induction is less costly to parallelize, easy to automate, non-invasive and without risk of contamination. Therefore, light-induced gene expression with photocaged IPTG is a highly advantageous method for the efficient optimization of heterologous protein production and has the potential to replace conventional induction with IPTG.
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Affiliation(s)
- Georg Wandrey
- AVT-Biochemical Engineering, RWTH Aachen University, Worringerweg 1, Aachen, 52074, Germany
| | - Claus Bier
- Institute of Bioorganic Chemistry, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, 52426, Germany
| | - Dennis Binder
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, 52426, Germany
| | - Kyra Hoffmann
- AVT-Biochemical Engineering, RWTH Aachen University, Worringerweg 1, Aachen, 52074, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, 52426, Germany.,Institut für Bio- und Geowissenschaften (IBG-1: Biotechnologie), Forschungszentrum Jülich, Jülich, 52428, Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, 52426, Germany.,Institut für Bio- und Geowissenschaften (IBG-1: Biotechnologie), Forschungszentrum Jülich, Jülich, 52428, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, 52426, Germany
| | - Jochen Büchs
- AVT-Biochemical Engineering, RWTH Aachen University, Worringerweg 1, Aachen, 52074, Germany.
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49
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Abstract
A central challenge in the field of metabolic engineering is the efficient identification of a metabolic pathway genotype that maximizes specific productivity over a robust range of process conditions. Here we review current methods for optimizing specific productivity of metabolic pathways in living cells. New tools for library generation, computational analysis of pathway sequence-flux space, and high-throughput screening and selection techniques are discussed.
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Affiliation(s)
- Justin R Klesmith
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Timothy A Whitehead
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, USA; Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA
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50
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Fernandez-Rodriguez J, Yang L, Gorochowski TE, Gordon DB, Voigt CA. Memory and Combinatorial Logic Based on DNA Inversions: Dynamics and Evolutionary Stability. ACS Synth Biol 2015; 4:1361-72. [PMID: 26548807 DOI: 10.1021/acssynbio.5b00170] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Genetic memory can be implemented using enzymes that catalyze DNA inversions, where each orientation corresponds to a "bit". Here, we use two DNA invertases (FimE and HbiF) that reorient DNA irreversibly between two states with opposite directionality. First, we construct memory that is set by FimE and reset by HbiF. Next, we build a NOT gate where the input promoter drives FimE and in the absence of signal the reverse state is maintained by the constitutive expression of HbiF. The gate requires ∼3 h to turn on and off. The evolutionary stabilities of these circuits are measured by passaging cells while cycling function. The memory switch is stable over 400 h (17 days, 14 state changes); however, the gate breaks after 54 h (>2 days) due to continuous invertase expression. Genome sequencing reveals that the circuit remains intact, but the host strain evolves to reduce invertase expression. This work highlights the need to evaluate the evolutionary robustness and failure modes of circuit designs, especially as more complex multigate circuits are implemented.
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Affiliation(s)
- Jesus Fernandez-Rodriguez
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Lei Yang
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas E. Gorochowski
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - D. Benjamin Gordon
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Christopher A. Voigt
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
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