1
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Intelligent host engineering for metabolic flux optimisation in biotechnology. Biochem J 2021; 478:3685-3721. [PMID: 34673920 PMCID: PMC8589332 DOI: 10.1042/bcj20210535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Optimising the function of a protein of length N amino acids by directed evolution involves navigating a 'search space' of possible sequences of some 20N. Optimising the expression levels of P proteins that materially affect host performance, each of which might also take 20 (logarithmically spaced) values, implies a similar search space of 20P. In this combinatorial sense, then, the problems of directed protein evolution and of host engineering are broadly equivalent. In practice, however, they have different means for avoiding the inevitable difficulties of implementation. The spare capacity exhibited in metabolic networks implies that host engineering may admit substantial increases in flux to targets of interest. Thus, we rehearse the relevant issues for those wishing to understand and exploit those modern genome-wide host engineering tools and thinking that have been designed and developed to optimise fluxes towards desirable products in biotechnological processes, with a focus on microbial systems. The aim throughput is 'making such biology predictable'. Strategies have been aimed at both transcription and translation, especially for regulatory processes that can affect multiple targets. However, because there is a limit on how much protein a cell can produce, increasing kcat in selected targets may be a better strategy than increasing protein expression levels for optimal host engineering.
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2
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Amer M, Toogood H, Scrutton NS. Engineering nature for gaseous hydrocarbon production. Microb Cell Fact 2020; 19:209. [PMID: 33187524 PMCID: PMC7661322 DOI: 10.1186/s12934-020-01470-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 11/04/2020] [Indexed: 11/10/2022] Open
Abstract
The development of sustainable routes to the bio-manufacture of gaseous hydrocarbons will contribute widely to future energy needs. Their realisation would contribute towards minimising over-reliance on fossil fuels, improving air quality, reducing carbon footprints and enhancing overall energy security. Alkane gases (propane, butane and isobutane) are efficient and clean-burning fuels. They are established globally within the transportation industry and are used for domestic heating and cooking, non-greenhouse gas refrigerants and as aerosol propellants. As no natural biosynthetic routes to short chain alkanes have been discovered, de novo pathways have been engineered. These pathways incorporate one of two enzymes, either aldehyde deformylating oxygenase or fatty acid photodecarboxylase, to catalyse the final step that leads to gas formation. These new pathways are derived from established routes of fatty acid biosynthesis, reverse β-oxidation for butanol production, valine biosynthesis and amino acid degradation. Single-step production of alkane gases in vivo is also possible, where one recombinant biocatalyst can catalyse gas formation from exogenously supplied short-chain fatty acid precursors. This review explores current progress in bio-alkane gas production, and highlights the potential for implementation of scalable and sustainable commercial bioproduction hubs.
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Affiliation(s)
- Mohamed Amer
- EPSRC/BBSRC Future Biomanufacturing Research Hub, Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, BBSRC/EPSRC, The University of Manchester, Manchester, M1 7DN, UK
| | - Helen Toogood
- EPSRC/BBSRC Future Biomanufacturing Research Hub, Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, BBSRC/EPSRC, The University of Manchester, Manchester, M1 7DN, UK
| | - Nigel S Scrutton
- EPSRC/BBSRC Future Biomanufacturing Research Hub, Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, BBSRC/EPSRC, The University of Manchester, Manchester, M1 7DN, UK.
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3
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Crook N, Ferreiro A, Condiotte Z, Dantas G. Transcript Barcoding Illuminates the Expression Level of Synthetic Constructs in E. coli Nissle Residing in the Mammalian Gut. ACS Synth Biol 2020; 9:1010-1021. [PMID: 32324995 PMCID: PMC7293544 DOI: 10.1021/acssynbio.0c00040] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The development of robust engineered probiotic therapies demands accurate knowledge of genetic construct expression in the gut. However, the monetary and ethical costs of testing engineered strains in vertebrate hosts are incompatible with current high-throughput design-build-test cycles. To enable parallel measurement of multiple construct designs, we placed unique DNA barcodes in engineered transcripts and measured barcode abundances via sequencing. In standard curve experiments, the barcode sequences exhibited consistent relationships between input and measured abundances, which allowed us to use transcript barcoding to measure expression levels of 30 GFP-expressing strains of E. coli Nissle in parallel. Applying this technology in culture and in the mouse gut, we found that GFP expression in the gut could often be predicted from expression levels in culture, but several strains exhibited gut-specific expression. This work establishes the experimental design parameters and advantages of transcript barcoding to measure the performance of many engineered probiotic designs in mammalian hosts.
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Affiliation(s)
- Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Aura Ferreiro
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Zevin Condiotte
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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4
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Barsain BL, Yadav SK. Picrorhiza kurrooa Royle ex Benth., an Endangered Himalayan Elixir- Medicinal Importance and Exploration of Biotechnological Approaches in Picroside Production. CURRENT TRADITIONAL MEDICINE 2019. [DOI: 10.2174/2215083805666190625144322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although the history of P. kurrooa Royle ex Benth., popularly known as “Kutki
or Kadu” dates back to the Vedic era, it has only been about 69 years since research has focussed
on exploring its pharmacological properties. It is a small perennial medicinal herb
that belongs to the Scrophulariaceae family. Found primarily in the north-western alpine
Himalayan region at the altitudes of 3000-4300 meters (amsl), the plant has immense
therapeutic and medicinal properties. Uniquely gifted, the plant holds its reputation in the
modern system of medicine in the treatment of liver disorders. The species has earned an
endangered status lately due to various issues like unawareness on its conservation,
harvesting methods, and cultivation besides others. Therefore, various new scientific
methods are being developed for its propagation and conservation. This article provides an
overview of the therapeutic properties, various mode of propagation as well as the molecular
aspects of P. kurrooa. Also, the metabolic engineering strategies to modulate its secondary
metabolite picrosides are also discussed.
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Affiliation(s)
- Bharati Lalhal Barsain
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur-176061 (HP), India
| | - Sudesh Kumar Yadav
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur-176061 (HP), India
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5
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Bervoets I, Charlier D. Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology. FEMS Microbiol Rev 2019; 43:304-339. [PMID: 30721976 PMCID: PMC6524683 DOI: 10.1093/femsre/fuz001] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 01/21/2019] [Indexed: 12/15/2022] Open
Abstract
Gene expression occurs in two essential steps: transcription and translation. In bacteria, the two processes are tightly coupled in time and space, and highly regulated. Tight regulation of gene expression is crucial. It limits wasteful consumption of resources and energy, prevents accumulation of potentially growth inhibiting reaction intermediates, and sustains the fitness and potential virulence of the organism in a fluctuating, competitive and frequently stressful environment. Since the onset of studies on regulation of enzyme synthesis, numerous distinct regulatory mechanisms modulating transcription and/or translation have been discovered. Mostly, various regulatory mechanisms operating at different levels in the flow of genetic information are used in combination to control and modulate the expression of a single gene or operon. Here, we provide an extensive overview of the very diverse and versatile bacterial gene regulatory mechanisms with major emphasis on their combined occurrence, intricate intertwinement and versatility. Furthermore, we discuss the potential of well-characterized basal expression and regulatory elements in synthetic biology applications, where they may ensure orthogonal, predictable and tunable expression of (heterologous) target genes and pathways, aiming at a minimal burden for the host.
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Affiliation(s)
- Indra Bervoets
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Daniel Charlier
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
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6
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Gaudu P, Yamamoto Y, Jensen PR, Hammer K, Lechardeur D, Gruss A. Genetics of Lactococci. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0035-2018. [PMID: 31298208 PMCID: PMC10957224 DOI: 10.1128/microbiolspec.gpp3-0035-2018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Indexed: 11/20/2022] Open
Abstract
Lactococcus lactis is the best characterized species among the lactococci, and among the most consumed food-fermenting bacteria worldwide. Thanks to their importance in industrialized food production, lactococci are among the lead bacteria understood for fundamental metabolic pathways that dictate growth and survival properties. Interestingly, lactococci belong to the Streptococcaceae family, which includes food, commensal and virulent species. As basic metabolic pathways (e.g., respiration, metal homeostasis, nucleotide metabolism) are now understood to underlie virulence, processes elucidated in lactococci could be important for understanding pathogen fitness and synergy between bacteria. This chapter highlights major findings in lactococci and related bacteria, and covers five themes: distinguishing features of lactococci, metabolic capacities including the less known respiration metabolism in Streptococcaceae, factors and pathways modulating stress response and fitness, interbacterial dialogue via metabolites, and novel applications in health and biotechnology.
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Affiliation(s)
| | - Yuji Yamamoto
- Laboratory of Cellular Microbiology, School of Veterinary Medicine, Kitasato University, Towada, 034-8628, Aomori Japan
| | - Peter Ruhdal Jensen
- National Food Institute, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Karin Hammer
- DTU Bioengineering, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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7
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Davy AM, Kildegaard HF, Andersen MR. Cell Factory Engineering. Cell Syst 2019; 4:262-275. [PMID: 28334575 DOI: 10.1016/j.cels.2017.02.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 11/11/2016] [Accepted: 02/15/2017] [Indexed: 11/30/2022]
Abstract
Rational approaches to modifying cells to make molecules of interest are of substantial economic and scientific interest. Most of these efforts aim at the production of native metabolites, expression of heterologous biosynthetic pathways, or protein expression. Reviews of these topics have largely focused on individual strategies or cell types, but collectively they fall under the broad umbrella of a growing field known as cell factory engineering. Here we condense >130 reviews and key studies in the art into a meta-review of cell factory engineering. We identified 33 generic strategies in the field, all applicable to multiple types of cells and products, and proven successful in multiple major cell types. These apply to three major categories: production of native metabolites and/or bioactives, heterologous expression of biosynthetic pathways, and protein expression. This meta-review provides general strategy guides for the broad range of applications of rational engineering of cell factories.
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Affiliation(s)
- Anne Mathilde Davy
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Mikael Rørdam Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
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8
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Wang Y, Liu Q, Weng H, Shi Y, Chen J, Du G, Kang Z. Construction of Synthetic Promoters by Assembling the Sigma Factor Binding -35 and -10 Boxes. Biotechnol J 2018; 14:e1800298. [PMID: 30457214 DOI: 10.1002/biot.201800298] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 10/24/2018] [Indexed: 12/12/2022]
Abstract
Promoter is one of the key elements in regulating gene expression. Many natural or synthetic promoters have been modulated by their cis- or tans-regulatory elements to confer instant gene expression change in responding to designated stimuli. In addition, bacterial cells also engage different sigma factors to control the gene expression network at different growth phases or in response to the changing environment and external stresses. In this study, a set of promoters that assimilate the endogenous regulation of different sigma factors σ70 , σ38 , σ32 , and σ24 are synthesized. Promoters are designed to contain two or more kinds of interlocking sigma factor binding sites. The most competitive sigma factors will be automatically selected by the cell to take over the synthetic promoters during the cell growth course. Some of the synthetic promoters exhibit very strong strengths under different conditions, including stationary phase, low temperature, acidic pH, and high osmotic pressure. Comparing to the T7 promoter, synthetic promoter P21285 achieved higher yields of L-asparaginase and acid urease in Escherichia coli. The research not only expands the synthetic biology toolbox but also provide another strategy to design and construct synthetic promoters in prokaryotes.
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Affiliation(s)
- Yang Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Qingtao Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Huanjiao Weng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yanan Shi
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Zhen Kang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
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9
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Investigation of specific interactions between T7 promoter and T7 RNA polymerase by force spectroscopy using atomic force microscope. Biochem J 2018; 475:319-328. [DOI: 10.1042/bcj20170616] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 11/23/2017] [Accepted: 11/29/2017] [Indexed: 12/30/2022]
Abstract
The specific recognition and binding of promoter and RNA polymerase is the first step of transcription initiation in bacteria and largely determines transcription activity. Therefore, direct analysis of the interaction between promoter and RNA polymerase in vitro may be a new strategy for promoter characterization, to avoid interference due to the cell's biophysical condition and other regulatory elements. In the present study, the specific interaction between T7 promoter and T7 RNA polymerase was studied as a model system using force spectroscopy based on atomic force microscope (AFM). The specific interaction between T7 promoter and T7 RNA polymerase was verified by control experiments, and the rupture force in this system was measured as 307.2 ± 6.7 pN. The binding between T7 promoter mutants with various promoter activities and T7 RNA polymerase was analyzed. Interaction information including rupture force, rupture distance and binding percentage were obtained in vitro, and reporter gene expression regulated by these promoters was also measured according to a traditional promoter activity characterization method in vivo. Using correlation analysis, it was found that the promoter strength characterized by reporter gene expression was closely correlated with rupture force and the binding percentage by force spectroscopy. These results indicated that the analysis of the interaction between promoter and RNA polymerase using AFM-based force spectroscopy was an effective and valid approach for the quantitative characterization of promoters.
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10
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Portela RM, Vogl T, Kniely C, Fischer JE, Oliveira R, Glieder A. Synthetic Core Promoters as Universal Parts for Fine-Tuning Expression in Different Yeast Species. ACS Synth Biol 2017; 6:471-484. [PMID: 27973777 PMCID: PMC5359585 DOI: 10.1021/acssynbio.6b00178] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Indexed: 01/24/2023]
Abstract
Synthetic biology and metabolic engineering experiments frequently require the fine-tuning of gene expression to balance and optimize protein levels of regulators or metabolic enzymes. A key concept of synthetic biology is the development of modular parts that can be used in different contexts. Here, we have applied a computational multifactor design approach to generate de novo synthetic core promoters and 5' untranslated regions (UTRs) for yeast cells. In contrast to upstream cis-regulatory modules (CRMs), core promoters are typically not subject to specific regulation, making them ideal engineering targets for gene expression fine-tuning. 112 synthetic core promoter sequences were designed on the basis of the sequence/function relationship of natural core promoters, nucleosome occupancy and the presence of short motifs. The synthetic core promoters were fused to the Pichia pastoris AOX1 CRM, and the resulting activity spanned more than a 200-fold range (0.3% to 70.6% of the wild type AOX1 level). The top-ten synthetic core promoters with highest activity were fused to six additional CRMs (three in P. pastoris and three in Saccharomyces cerevisiae). Inducible CRM constructs showed significantly higher activity than constitutive CRMs, reaching up to 176% of natural core promoters. Comparing the activity of the same synthetic core promoters fused to different CRMs revealed high correlations only for CRMs within the same organism. These data suggest that modularity is maintained to some extent but only within the same organism. Due to the conserved role of eukaryotic core promoters, this rational design concept may be transferred to other organisms as a generic engineering tool.
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Affiliation(s)
- Rui M.
C. Portela
- REQUIMTE/LAQV,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Thomas Vogl
- Institute
for Molecular Biotechnology, NAWI Graz University
of Technology, Petersgasse 14/2, 8010 Graz, Austria
| | - Claudia Kniely
- Institute
for Molecular Biotechnology, NAWI Graz University
of Technology, Petersgasse 14/2, 8010 Graz, Austria
| | - Jasmin E. Fischer
- Institute
for Molecular Biotechnology, NAWI Graz University
of Technology, Petersgasse 14/2, 8010 Graz, Austria
| | - Rui Oliveira
- REQUIMTE/LAQV,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Anton Glieder
- Institute
for Molecular Biotechnology, NAWI Graz University
of Technology, Petersgasse 14/2, 8010 Graz, Austria
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11
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Zhou S, Du G, Kang Z, Li J, Chen J, Li H, Zhou J. The application of powerful promoters to enhance gene expression in industrial microorganisms. World J Microbiol Biotechnol 2017; 33:23. [DOI: 10.1007/s11274-016-2184-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 11/24/2016] [Indexed: 01/01/2023]
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12
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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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13
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Schreiber T, Tissier A. Libraries of Synthetic TALE-Activated Promoters: Methods and Applications. Methods Enzymol 2016; 576:361-78. [PMID: 27480693 DOI: 10.1016/bs.mie.2016.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The discovery of proteins with programmable DNA-binding specificities triggered a whole array of applications in synthetic biology, including genome editing, regulation of transcription, and epigenetic modifications. Among those, transcription activator-like effectors (TALEs) due to their natural function as transcription regulators, are especially well-suited for the development of orthogonal systems for the control of gene expression. We describe here the construction and testing of libraries of synthetic TALE-activated promoters which are under the control of a single TALE with a given DNA-binding specificity. These libraries consist of a fixed DNA-binding element for the TALE, a TATA box, and variable sequences of 19 bases upstream and 43 bases downstream of the DNA-binding element. These libraries were cloned using a Golden Gate cloning strategy making them usable as standard parts in a modular cloning system. The broad range of promoter activities detected and the versatility of these promoter libraries make them valuable tools for applications in the fine-tuning of expression in metabolic engineering projects or in the design and implementation of regulatory circuits.
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Affiliation(s)
- T Schreiber
- Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - A Tissier
- Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany.
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14
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Guan C, Cui W, Cheng J, Zhou L, Guo J, Hu X, Xiao G, Zhou Z. Construction and development of an auto-regulatory gene expression system in Bacillus subtilis. Microb Cell Fact 2015; 14:150. [PMID: 26392346 PMCID: PMC4578258 DOI: 10.1186/s12934-015-0341-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/12/2015] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Bacillus subtilis is an all-important Gram-positive bacterium of valuable biotechnological utility that has been widely used to over-produce industrially and pharmaceutically relevant proteins. There are a variety of expression systems in terms of types of transcriptional patterns, among which the auto-inducible and growth-phase-dependent promoters are gaining increasing favor due to their inducer-independent feature, allowing for the potential to industrially scale-up. To expand the applicability of the auto-inducible expression system, a novel auto-regulatory expression system coupled with cell density was constructed and developed in B. subtilis using the quorum-sensing related promoter srfA (PsrfA). RESULTS The promoter of the srf operon was used to construct an expression plasmid with the green fluorescent protein (GFP) downstream of PsrfA. The expression displayed a cell-density-dependent pattern in that GFP had a fairly low expression level at the early exponential stage and was highly expressed at the late exponential as well as the stationary stages. Moreover, the recombinant system had a similar expression pattern in wild-type B. subtilis 168, WB600, and WB800, as well as in B. subtilis 168 derivative strain 1681, with the complete deletion of PsrfA, indicating the excellent compatibility of this system. Noticeably, the expression strength of PsrfA was enhanced by optimizing the -10 and -35 core sequence by substituting both sequences with consensus sequences. Importantly, the expression pattern was successfully developed in an auto-regulatory cell-density coupling system by the simple addition of glucose in which GFP could not be strongly expressed until glucose was depleted, resulting in a greater amount of the GFP product and increased cell density. The expression system was eventually tested by the successful over-production of aminopeptidase to a desired level. CONCLUSION The auto-regulatory cell density coupling system that is mediated by PsrfA is a novel expression system that has an expression pattern that is split between cell-growth and over-expression, leading to an increase in cell density and elevating the overall expression levels of heterologously expressed proteins. The broad applicability of this system and inducer-free expression property in B. subtilis facilitate the industrial scale-up and medical applications for the over-production of a variety of desired proteins.
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Affiliation(s)
- Chengran Guan
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
| | - Wenjing Cui
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
| | - Jintao Cheng
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
| | - Li Zhou
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
| | - Junling Guo
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
| | - Xu Hu
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
| | - Guoping Xiao
- Wuxi Biortus Bioscience Co., Ltd, Wuxi, Jiangsu, 214122, China.
| | - Zhemin Zhou
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
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Bischof RH, Horejs J, Metz B, Gamauf C, Kubicek CP, Seiboth B. L-Methionine repressible promoters for tuneable gene expression in Trichoderma reesei. Microb Cell Fact 2015; 14:120. [PMID: 26271614 PMCID: PMC4536894 DOI: 10.1186/s12934-015-0308-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 07/30/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trichoderma reesei is the main producer of lignocellulolytic enzymes that are required for plant biomass hydrolysis in the biorefinery industry. Although the molecular toolbox for T. reesei is already well developed, repressible promoters for strain engineering and functional genomics studies are still lacking. One such promoter that is widely employed for yeasts is that of the L-methionine repressible MET3 gene, encoding ATP sulphurylase. RESULTS We show that the MET3 system can only be applied for T. reesei when the cellulase inducing carbon source lactose is used but not when wheat straw, a relevant lignocellulosic substrate for enzyme production, is employed. We therefore performed a transcriptomic screen for genes that are L-methionine repressible in a wheat straw culture. This analysis retrieved 50 differentially regulated genes of which 33 were downregulated. Among these, genes encoding transport proteins as well as iron containing DszA like monooxygenases and TauD like dioxygenases were strongly overrepresented. We show that the promoter region of one of these dioxygenases can be used for the strongly repressible expression of the Aspergillus niger sucA encoded extracellular invertase in T. reesei wheat straw cultures. This system is also portable to other carbon sources including D-glucose and glycerol as demonstrated by the repressible expression of the Escherichia coli lacZ encoded ß-galactosidase in T. reesei. CONCLUSION We describe a novel, versatile set of promoters for T. reesei that can be used to drive recombinant gene expression in wheat straw cultures at different expression strengths and in an L-methionine repressible manner. The dioxygenase promoter that we studied in detail is furthermore compatible with different carbon sources and therefore applicable for manipulating protein production as well as functional genomics with T. reesei.
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Affiliation(s)
- Robert H Bischof
- Austrian Centre of Industrial Biotechnology (ACIB) GmbH c/o Institute of Chemical Engineering, Technische Universität Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria.
| | - Jennifer Horejs
- Austrian Centre of Industrial Biotechnology (ACIB) GmbH c/o Institute of Chemical Engineering, Technische Universität Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria. .,Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Technische Universität Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria.
| | - Benjamin Metz
- Austrian Centre of Industrial Biotechnology (ACIB) GmbH c/o Institute of Chemical Engineering, Technische Universität Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria. .,Vogelbusch Biocommodities GmbH, Blechturmgasse 11, 1051, Vienna, Austria.
| | - Christian Gamauf
- Biotech and Renewables Center, Clariant GmbH, 81477, Munich, Germany.
| | - Christian P Kubicek
- Austrian Centre of Industrial Biotechnology (ACIB) GmbH c/o Institute of Chemical Engineering, Technische Universität Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria. .,Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Technische Universität Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria.
| | - Bernhard Seiboth
- Austrian Centre of Industrial Biotechnology (ACIB) GmbH c/o Institute of Chemical Engineering, Technische Universität Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria. .,Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Technische Universität Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria.
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16
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Yin S, Wang W, Wang X, Zhu Y, Jia X, Li S, Yuan F, Zhang Y, Yang K. Identification of a cluster-situated activator of oxytetracycline biosynthesis and manipulation of its expression for improved oxytetracycline production in Streptomyces rimosus. Microb Cell Fact 2015; 14:46. [PMID: 25886456 PMCID: PMC4393881 DOI: 10.1186/s12934-015-0231-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/25/2015] [Indexed: 11/10/2022] Open
Abstract
Background Oxytetracycline (OTC) is a broad-spectrum antibiotic commercially produced by Streptomyces rimosus. Despite its importance, little is known about the regulation of OTC biosynthesis, which hampered any effort to improve OTC production via engineering regulatory genes. Results A gene encoding a Streptomyces antibiotic regulatory protein (SARP) was discovered immediately adjacent to the otrB gene of oxy cluster in S. rimosus and designated otcR. Deletion and complementation of otcR abolished or restored OTC production, respectively, indicating that otcR encodes an essential activator of OTC biosynthesis. Then, the predicted consensus SARP-binding sequences were extracted from the promoter regions of oxy cluster. Transcriptional analysis in a heterologous GFP reporter system demonstrated that OtcR directly activated the transcription of five oxy promoters in E. coli, further mutational analysis of a SARP-binding sequence of oxyI promoter proved that OtcR directly interacted with the consensus repeats. Therefore, otcR was chosen as an engineering target, OTC production was significantly increased by overexpression of otcR as tandem copies each under the control of strong SF14 promoter. Conclusions A SARP activator, OtcR, was identified in oxy cluster of S. rimosus; it was shown to directly activate five promoters from oxy cluster. Overexpression of otcR at an appropriate level dramatically increased OTC production by 6.49 times compared to the parental strain, thus demonstrating the great potential of manipulating OtcR to improve the yield of OTC production. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0231-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shouliang Yin
- Department of Environmental and Biological Engineering, School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), D11 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China.
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China.
| | - Xuefeng Wang
- Shengxue Dacheng Pharmaceutical Co., Ltd, 50 Shengxue Road, Shijiazhuang, 051430, Hebei, People's Republic of China.
| | - Yaxin Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China.
| | - Xiaole Jia
- Shengxue Dacheng Pharmaceutical Co., Ltd, 50 Shengxue Road, Shijiazhuang, 051430, Hebei, People's Republic of China.
| | - Shanshan Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China.
| | - Fang Yuan
- Shengxue Dacheng Pharmaceutical Co., Ltd, 50 Shengxue Road, Shijiazhuang, 051430, Hebei, People's Republic of China.
| | - Yuxiu Zhang
- Department of Environmental and Biological Engineering, School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), D11 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China.
| | - Keqian Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China.
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17
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Gechev TS, Hille J, Woerdenbag HJ, Benina M, Mehterov N, Toneva V, Fernie AR, Mueller-Roeber B. Natural products from resurrection plants: Potential for medical applications. Biotechnol Adv 2014; 32:1091-101. [DOI: 10.1016/j.biotechadv.2014.03.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 03/10/2014] [Accepted: 03/11/2014] [Indexed: 01/25/2023]
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18
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Radeck J, Kraft K, Bartels J, Cikovic T, Dürr F, Emenegger J, Kelterborn S, Sauer C, Fritz G, Gebhard S, Mascher T. The Bacillus BioBrick Box: generation and evaluation of essential genetic building blocks for standardized work with Bacillus subtilis. J Biol Eng 2013; 7:29. [PMID: 24295448 PMCID: PMC4177231 DOI: 10.1186/1754-1611-7-29] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 11/12/2013] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Standardized and well-characterized genetic building blocks are a prerequisite for the convenient and reproducible assembly of novel genetic modules and devices. While numerous standardized parts exist for Escherichia coli, such tools are still missing for the Gram-positive model organism Bacillus subtilis. The goal of this study was to develop and thoroughly evaluate such a genetic toolbox. RESULTS We developed five BioBrick-compatible integrative B. subtilis vectors by deleting unnecessary parts and removing forbidden restriction sites to allow cloning in BioBrick (RFC10) standard. Three empty backbone vectors with compatible resistance markers and integration sites were generated, allowing the stable chromosomal integration and combination of up to three different devices in one strain. In addition, two integrative reporter vectors, based on the lacZ and luxABCDE cassettes, were BioBrick-adjusted, to enable β-galactosidase and luciferase reporter assays, respectively. Four constitutive and two inducible promoters were thoroughly characterized by quantitative, time-resolved measurements. Together, these promoters cover a range of more than three orders of magnitude in promoter strength, thereby allowing a fine-tuned adjustment of cellular protein amounts. Finally, the Bacillus BioBrick Box also provides five widely used epitope tags (FLAG, His10, cMyc, HA, StrepII), which can be translationally fused N- or C-terminally to any protein of choice. CONCLUSION Our genetic toolbox contains three compatible empty integration vectors, two reporter vectors and a set of six promoters, two of them inducible. Furthermore, five different epitope tags offer convenient protein handling and detection. All parts adhere to the BioBrick standard and hence enable standardized work with B. subtilis. We believe that our well-documented and carefully evaluated Bacillus BioBrick Box represents a very useful genetic tool kit, not only for the iGEM competition but any other BioBrick-based project in B. subtilis.
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Affiliation(s)
- Jara Radeck
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Korinna Kraft
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Julia Bartels
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Tamara Cikovic
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Franziska Dürr
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Jennifer Emenegger
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Simon Kelterborn
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Christopher Sauer
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany.,Present affiliation: Institute of Cell and Molecular Biosciences, Newcastle University, Centre for Bacterial Cell Biology, Richardson Road, NE2 4AX Newcastle upon Tyne, UK
| | - Georg Fritz
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany.,Ludwig-Maximilians-University Munich, Arnold Sommerfeld Center for Theoretical Physics, Theresienstr. 37, D-80333 München, Germany
| | - Susanne Gebhard
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Thorsten Mascher
- Department Biology I, AG Synthetic Microbiology, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
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Abstract
Well-characterized promoters are essential tools for metabolic engineering and synthetic biology. In Streptomyces coelicolor, the native kasOp is a temporally expressed promoter strictly controlled by two regulators, ScbR and ScbR2. In this work, first, kasOp was engineered to remove a common binding site of ScbR and ScbR2 upstream of its core region, thus generating a stronger promoter, kasOp3. Second, another ScbR binding site internal to the kasOp3 core promoter region was abolished by random mutation and screening of the mutant library to obtain the strongest promoter, kasOp* (where the asterisk is used to distinguish the engineered promoter from the native promoter). The activities of kasOp* were compared with those of two known strong promoters, ermEp* and SF14p, in three Streptomyces species. kasOp* showed the highest activity at the transcription and protein levels in all three hosts. Furthermore, relative to ermEp* and SF14p, kasOp* was shown to confer the highest actinorhodin production level when used to drive the expression of actII-ORF4 in S. coelicolor. Therefore, kasOp* is a simple and well-defined strong promoter useful for gene overexpression in streptomycetes.
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20
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Meng H, Wang J, Xiong Z, Xu F, Zhao G, Wang Y. Quantitative design of regulatory elements based on high-precision strength prediction using artificial neural network. PLoS One 2013; 8:e60288. [PMID: 23560087 PMCID: PMC3613377 DOI: 10.1371/journal.pone.0060288] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 02/25/2013] [Indexed: 01/31/2023] Open
Abstract
Accurate and controllable regulatory elements such as promoters and ribosome binding sites (RBSs) are indispensable tools to quantitatively regulate gene expression for rational pathway engineering. Therefore, de novo designing regulatory elements is brought back to the forefront of synthetic biology research. Here we developed a quantitative design method for regulatory elements based on strength prediction using artificial neural network (ANN). One hundred mutated Trc promoter & RBS sequences, which were finely characterized with a strength distribution from 0 to 3.559 (relative to the strength of the original sequence which was defined as 1), were used for model training and test. A precise strength prediction model, NET90_19_576, was finally constructed with high regression correlation coefficients of 0.98 for both model training and test. Sixteen artificial elements were in silico designed using this model. All of them were proved to have good consistency between the measured strength and our desired strength. The functional reliability of the designed elements was validated in two different genetic contexts. The designed parts were successfully utilized to improve the expression of BmK1 peptide toxin and fine-tune deoxy-xylulose phosphate pathway in Escherichia coli. Our results demonstrate that the methodology based on ANN model can de novo and quantitatively design regulatory elements with desired strengths, which are of great importance for synthetic biology applications.
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Affiliation(s)
- Hailin Meng
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jianfeng Wang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Zhiqiang Xiong
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Feng Xu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guoping Zhao
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yong Wang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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